gebhart/patrepeval huggingface dataset:
Nuclear Localization of the Nipah Virus W Protein Allows for Inhibition of both Virus- and Toll-Like Receptor 3-Triggered Signaling Pathways (2005)

The Nipah virus V and W proteins, which are encoded by the P gene via RNA editing, have a common N-terminal domain but unique C-terminal domains. They localize to the cytoplasm and nucleus, respectively, and have both been shown to function as inhibitors of JAK/STAT signaling. Here we report that V and W proteins also block virus activation of the beta interferon (IFN-beta) promoter and the IFN regulatory factor 3 (IRF3)-responsive IFN-stimulated gene 54 promoter. Surprisingly, only W protein shows strong inhibition of promoter activation in response to stimulation of Toll-like receptor 3 (TLR3) by extracellular double-stranded RNA. This activity is dependent on the nuclear localization of W protein. Within the unique C-terminal domain of W protein, we have identified a nuclear localization signal (NLS) that requires basic residues at positions 439, 440, and 442. This NLS is responsible for mediating the preferential interaction of W protein with karyopherin-alpha 3 and karyopherin-alpha 4. Nuclear localization of W protein therefore enables it to target both virus and TLR3 pathways, whereas the cytoplasmic V protein is restricted to inhibiting the virus pathway. We propose that this discrepancy is in part due to the V protein being less able to block signaling in response to the kinase, TBK-1, whereas both V and W can prevent promoter activation in response to IKKepsilon. We demonstrate that, when the TLR3 pathway is stimulated, the levels of phosphorylated IRF3 are reduced in the presence of W protein but not V protein, confirming the differential effects of these proteins and illustrating that W protein-mediated inhibition is due to a loss of active IRF3.
High-performance packet processing for ip route lookup and deep packet inspection (2011)

With the rapid growth of the user population and the traffic volume of the Internet in the past decade, the continuous improvement of network equipment becomes a solid necessity for today's and tomorrow's Internet. It is urgent to introduce enhanced architectures and algorithms to sustain future demands in terms of speed and scalability. In this thesis, we focus on two core network applications: (1) Internet Protocol (IP) route lookup and (2) Deep Packet Inspection (DPI) for Intrusion Detection and Prevention System (IDPS). We explore previous related work, define the problem, and state our motivation at the beginning of each chapter. We propose multiple novel algorithms, architectures, and data structures to improve throughput and scalability for these two applications. All proposed schemes are evaluated with software-based simulation and with hardware prototyping on Field Programmable Gate Arrays (FPGAs) and Dynamic Random Access Memory (DRAM) technology. 
To anticipate market demands, our target throughput for both applications is 100-Gbps and beyond. For a 100-Gbps link, 250 million packets for IP route lookup for the minimum packet length and 12.5 billion characters need to be processed in 1 second. In other words, there is only 4nsec to perform IP route lookup and 80psec to complete one character inspection in DPI. It has been a challenge to achieve this performance while maintaining excellent scalability and updatability. In this thesis, we propose solutions to overcome these challenges. In particular, we introduce a greater than 100-Gbps IP route look-up scheme with one FPGA and four DRAM chips, and 100-Gbps DPI with Regular Expression capability using pre-filtering technology.
An audio indexing system for election video material (2009)

In the 2008 presidential election race in the United States, the prospective candidates made extensive use of YouTube to post video material. We developed a scalable system that transcribes this material and makes the content searchable (by indexing the meta-data and transcripts of the videos) and allows the user to navigate through the video material based on content. The system is available as an iGoogle gadget <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> as well as a Labs product (labs.google.com/gaudi). Given the large exposure, special emphasis was put on the scalability and reliability of the system. This paper describes the design and implementation of this system.
Abstract 3771: Oncogenes and tumour-suppressors drive differential retinoblastoma evolution (2019)

Unlike any other tumour type, retinoblastomas can be driven by only two tumour-initiating events: bi-allelic loss of the tumour suppressor RB1 or amplification of the MYCN oncogene. These mutations drive morphologically indistinguishable tumours that arise at different ages, providing a unique model system to evaluate the influence of initiating mutation on tumour evolution. We performed high-resolution copy number analysis of 101 retinoblastoma and whole genome sequencing of 23. These data reveal that different initiating mutations cause probabilistic changes in somatic point and copy number mutations, but large changes in genomic rearrangements and mitochondrial number. Independent of the initiating mutation, retinoblastomas harbour multiple subclonal populations that preferentially accrue point mutations after subclonal diversification. These subclonal structures suggest caution when choosing chemotherapeutic strategies for primary treatment. Overall, initiating mutations influence evolutionary trajectory more than specific driver mutations: RB1- and MYCN-driven tumours harbour distinct mutational processes, sequences of mutation acquisition and patterns of subclonal diversification. These data show how tumour-initiating mutations drive clinical behaviour by subtly biasing multiple evolutionary processes. Validation in other tumour types is underway.Citation Format: Adriana Salcedo, John D. Watson, Hilary Racher, Diane Rushlow, Shadrielle Melijah G. Espiritu, Doroto H. Sendorek, Stephenie D. Prokopec, Donco Matveski, Fouad Yousif, Julie Livingstone, Brenda L. Gallie, Paul C. Boutros. Oncogenes and tumour-suppressors drive differential retinoblastoma evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3771.
Supplementary Movie from <i>In Vivo</i> Imaging of Methionine Aminopeptidase II for Prostate Cancer Risk Stratification (2023)

&lt;p&gt;Movie of super-resolution imaging of assembled probes in a single cell.&lt;/p&gt;
Abstract LB-165: Low TCR diversity (divpenia) is a new prognosis factor of overall survival in metastatic breast cancer (2011)

Abstract Rationale Lymphopenia (&amp;lt;1000 Lymphocytes/μl) or CD4+ T cell lymphopenia (&amp;lt;450/μl), detected before initiation of chemotherapy are predictive factors for toxicity and death in metastatic solid tumors (Borg et al 2004; Ray Coquard et al 2009). The goal of the present study was to further identify the characteristics of the T cells in these lymphopenic patients. TCR diversity was investigated and tested as predictive factor for overall survival (OS). Patients and methods The ImmunTraCkeR® assay (ImmunID, Grenoble France), which analyzes, through semi quantitative multiplex PCR, the V-D-J combinatorial diversity of TCR-beta chain (TRB), was used to investigate diversity of T cell repertoire on cryopreserved blood samples from a prospective cohort of untreated metastatic breast cancer patients (SEMTOF study)(n=66). Univariate and multivariate analysis of prognostic factors for OS were investigated in this series as well as in a validation series. Results A severe T cell Divpenia (T cell diversity below 33%) (average diversity for healthy people is 70%) was associated with median survival of 9 months vs 24 months for the remaining patients (logrank p.value=0.0047). In a multivariate analysis, including haemoglobin level, polynuclear neutrophil count and liver metastasis, divpenia (defined at 30% threshold defined by ROC curve analysis) was identified as an independent prognostic factor. The NDL® score (Numeration Diversity Lymphocytes representation) that combines lymphocytes numeration with TRB diversity, demonstrated that lympho-divpenia (T cell diversity below 33% and lymphopenia at 1Giga/L threshold) was associated with a poor prognosis in term of patients survival compared to patients with either a good numeration or good diversity or both good numeration and diversity (p.value=0.0202). Prognostic value of NDL® score was then evaluated on a prospective validation cohort of 33 patients (logrank p.value=0.002). Conclusion: Divpenia, and a combined parameter NDL are predictive factors for survival in metastatic breast cancer patients. An open clinical study (LYMPHOS1) will investigate divpenia and NDL® score in a larger prospective cohort of metastatic breast patients. Acknowledgments M.MANUEL is a CIFRE recipient. This work (Proof of Concept “LYMPHOS1”) was financially supported by CLARA (LYON, France) Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-165. doi:10.1158/1538-7445.AM2011-LB-165
Microwave-Synthesized Polysaccharide-Derived Carbon Dots as Therapeutic Cargoes and Toughening Agents for Elastomeric Gels (2020)

Fluorescent carbon dots (CDs) play a versatile role in materials science. Herein, we have developed alginate-derived nitrogen-doped CDs as a drug carrier and a toughening agent for hydrogels by a microwave-assisted method. In the first phase of work, we carried out covalent conjugation of the drug onto the CD surface for controlled delivery of drug molecules, and in the second phase of work, we demonstrated how CDs could act as a toughening agent as well as a viscosity modifier for poly(acrylic acid-<i>co</i>-methacrylamide) copolymer hydrogels. The hydrogels were evaluated by Fourier transformed infrared spectroscopy, X-ray photoelectron spectroscopy, and solid-state nuclear magnetic resonance. The hybrid hydrogels have been tested to be mechanically robust with extraordinary stretchability (∼1200% elongation at break), recoverable to the original position (low permanent set), tunable water uptake, and thixotropic character in dynamic stress. The crosslinked structure has been evaluated through void calculation revealing gradual densification of the network with increasing CD content. Exceptional gel strength (ratio of elastic modulus to loss modulus; <i>G</i>'/<i>G</i>″) has been achieved from analogous crosslinking made by CDs. The delayed network rupturing and superstretchability could make this material a good choice for soft biomaterials and soft robotics.
Hidden Markov tree modeling of complex wavelet transforms (2002)

Multiresolution signal and image models such as the hidden Markov tree aim to capture the statistical structure of smooth and singular (edgy) regions. Unfortunately, models based on the orthogonal wavelet transform suffer from shift-variance, making them less accurate and realistic. We extend the HMT modeling framework to the complex wavelet transform, which features near shift-invariance and improved angular resolution compared to the standard wavelet transform. The model is computationally efficient (with linear-time computation and processing algorithms) and applicable to general Bayesian inference problems as a prior density for the data. In a simple estimation experiment, the complex wavelet HMT model outperforms a number of high-performance denoising algorithms, including redundant wavelet thresholding (cycle spinning) and the redundant HMT.
Demonstration of an MgO based anti-fuse OTP design integrated with a fully functional STT-MRAM at the Mbit level (2015)

STT-MRAM technology has been attracting renewed attention since the embedability of a working STT-MRAM design has been demonstrated [1]. In this paper we expand on the versatility of STT-MRAM by demonstrating the conversion of a standard STT-MRAM cell to a One Time Programmable (OTP) anti-fuse cell. Both designs are integrated at the Mbit level on a single chip using the same magnetic stack, processing and CMOS cell design. A single BEOL mask change can convert an STT-MRAM device to an OTP design by simply reducing its size. The increased resistance yields larger voltage drop across the device, due to the voltage divider effect in the 1T-1MTJ cell and is sufficient to trigger reliable dielectric breakdown of the oxide tunnel barrier, effectively shorting the device. In this paper we demonstrate the seamless integration of an OTP based on STT-MRAM and 100% programming and reading yield at the Mbit level.
A global framework for architecture analysis in telecommunications (2004)

One currently observes a multiplication of actors and technologies involved in the provisioning of telecommunications services. To represent them and their relationships, to understand the stakes, many models have been designed, each one with its own application zone: business models, network management and architectures, etc. At the same time, the road towards next generation networks (NGN) needs to be carefully mastered. NGN are expected to support all kind of services, to provide generalized mobility with QoS guarantee and to be open with standardized interfaces and protocols. So one needs tools to deal consistently with this context complexity. This paper addresses a global framework for telecommunications architecture analysis, able to deal with the complexity of the domain. The framework is then illustrated by two applications: the first one presents a global QoS framework and the second one deals with the IP QoS issue.
Antitumour effects of PLC-γ1-(SH2)2-TAT fusion proteins on EGFR/c-erbB-2-positive breast cancer cells (2004)

Due to its pivotal role in the growth factor-mediated tumour cell migration, the adaptor protein phospholipase C-gamma1 (PLC-gamma1) is an appropriate target to block ultimately the spreading of EGFR/c-erbB-2-positive tumour cells, thereby minimising metastasis formation. Here, we present an approach to block PLC-gamma1 activity by using protein-based PLC-gamma1 inhibitors consisting of PLC-gamma1 SH2 domains, which were fused to the TAT-transduction domain to ensure a high protein transduction efficiency. Two proteins were generated containing one PLC-gamma1-SH2-domain (PS1-TAT) or two PLC-gamma1-SH2 domains (PS2-TAT). PS2-TAT treatment of the EGFR/c-erbB-2-positive cell line MDA-HER2 resulted in a reduction of the EGF-mediated PLC-gamma1 tyrosine phosphorylation of about 30%, concomitant with a complete abrogation of the EGF-driven calcium influx. In addition to this, long-term PS2-TAT treatment both reduces the EGF-mediated migration of about 75% combined with a markedly decreased time locomotion of single MDA-HER2 cells as well as decreases the proliferation of MDA-HER2 cells by about 50%. Due to its antitumoral capacity on EGFR/c-erbB-2-positive breast cancer cells, we conclude from our results that the protein-based PLC-gamma1 inhibitor PS2-TAT may be a means for novel adjuvant antitumour strategies to minimise metastasis formation because of the blockade of cell migration and proliferation.
Spin-induced nanomaterials for detection of chiral volatile organic compounds (2023)

The capacity to recognize chiral Volatile Organic Compounds (VOCs) is a noteworthy element in many areas, for example, chemistry, pharmacology, and ecological observing. This review centers around the recent advancements in the field of spin-based chiral recognition, with the potential to improve the detection and classification of chiral VOCs in wearable, convenient, low-power, and with least human contribution. It will present and discuss the utilization of chiral molecules and helical structures to impact the spin course of electrons going through them, offering another way for chiral recognition of VOCs. Different dimensionalities of nano materials and related hypothetical leaps forward will be presented and discussed, which could pave the way for smart and miniaturized chiral recognition devices. These devices would empower quicker and more precise location of chiral VOCs in different settings, making them advantageous for a scope of applications later on.
Nerve growth factor level in the prostatic fluid of patients with chronic prostatitis/chronic pelvic pain syndrome is correlated with symptom severity and response to treatment (2010)

• Nerve growth factor might contribute to the pathophysiology of CP/CPPS as changes in NGF level in EPS occurred in proportion to pain severity. Therefore, these results suggest that NGF could be used as a new biomarker to evaluate the symptoms of CP/CPPS and the effects of treatment.
Experiences building a communication-oriented JavaOS (2000)

Mobile code makes it easier to maintain, debug, update, and customize a system. Active networks are one of the more interesting applications of mobile code: code is injected into the nodes of a network to customize the network's functionality, such as routing, and to add new features, such as special-purpose congestion control and filtering algorithms. The challenge is to develop a communication-oriented platform for such systems. We refer to mobile code targeted at low-level, communication-oriented systems like active networks as liquid software, the key distinction being that liquid software is focused on the efficient transfer of data, not high-performance computation. To this end, we have designed and implemented Joust, which consists of a complete re-implementation of the Java virtual machine (including both the runtime system and a just-in-time compiler), running on the Scout operating system (a configurable, communication-oriented OS). The result is a configurable, high-performance platform for running liquid software. We present the results of implementing two different applications of liquid software on Joust, including a prototype architecture for active networks. Copyright © 2000 John Wiley & Sons, Ltd.
Effects on Rotavirus Cell Binding and Infection of Monomeric and Polymeric Peptides Containing α2β1 and αxβ2 Integrin Ligand Sequences (2004)

Integrin-using rotaviruses bind MA104 cell surface alpha2beta1 integrin via the Asp-Gly-Glu (DGE) sequence in virus spike protein VP4 and interact with alphaxbeta2 integrin during cell entry through outer capsid protein VP7. Infection is inhibited by the alpha2beta1 ligand Asp-Gly-Glu-Ala (DGEA) and the alphaxbeta2 ligand Gly-Pro-Arg-Pro (GPRP), and virus-alpha2beta1 binding is increased by alpha2beta1 activation. In this study, we analyzed the effects of monomers and polymers containing DGEA-, GPRP-, and DGEA-related peptides on rotavirus binding and infection in intestinal (Caco-2) and kidney (MA104) cells and virus binding to recombinant alpha2beta1. Blockade of rotavirus-cell binding and infection by peptides and anti-alpha2 antibody showed that Caco-2 cell entry is dependent on virus binding to alpha2beta1 and interaction with alphaxbeta2. At up to 0.5 mM, monomeric DGEA and DGAA inhibited binding to alpha2beta1 and infection. At higher concentrations, DGEA and DGAA showed a reduced ability to inhibit virus-cell binding and infection that depended on virus binding to alpha2beta1 but occurred without alteration in cell surface expression of alpha2, beta2, or alphavbeta3 integrin. This loss of DGEA activity was abolished by genistein treatment and so was dependent on tyrosine kinase signaling. It is proposed that this signaling activated existing cell surface alpha2beta1 to increase virus-cell attachment and entry. Polymeric peptides containing DGEA and GPRP or GPRP only were inhibitory to SA11 infection at approximately 10-fold lower concentrations than peptide monomers. As polymerization can improve peptide inhibition of virus-receptor interactions, this approach could be useful in the development of inhibitors of receptor recognition by other viruses.
On Capacity-Achieving Distributions for Complex AWGN Channels Under\n Nonlinear Power Constraints and their Applications to SWIPT (2017)

The capacity of a complex and discrete-time memoryless additive white\nGaussian noise (AWGN) channel under three constraints, namely, input average\npower, input amplitude and output delivered power is studied. The output\ndelivered power constraint is modelled as the average of linear combination of\neven moments of the channel input being larger than a threshold. It is shown\nthat the capacity of an AWGN channel under transmit average power and receiver\ndelivered power constraints is the same as the capacity of an AWGN channel\nunder an average power constraint. However, depending on the two constraints,\nthe capacity can be either achieved by a Gaussian distribution or arbitrarily\napproached by using time-sharing between a Gaussian distribution and On-Off\nKeying. As an application, a simultaneous wireless information and power\ntransfer (SWIPT) problem is studied, where an experimentally-validated\nnonlinear model of the harvester is used. It is shown that the delivered power\ndepends on higher order moments of the channel input. Two inner bounds, one\nbased on complex Gaussian inputs and the other based on further restricting the\ndelivered power are obtained for the Rate-Power (RP) region. For Gaussian\ninputs, the optimal inputs are zero mean and a tradeoff between transmitted\ninformation and delivered power is recognized by considering asymmetric power\nallocations between inphase and quadrature subchannels. Through numerical\nalgorithms, it is observed that input distributions (obtained by restricting\nthe delivered power) attain larger RP region compared to Gaussian input\ncounterparts.\n
EDF Length Dependence of Amplification Characteristics of Cladding Pumped 19-Core EDFA (2018)

We demonstrate a C-band cladding pumped 19-core EDFA. Optimum EDF length and output power of the EDFA agree with those of a cladding pumped 7-core EDFA. High output power is brought by sufficiently long EDF.
Ultraviolet laser induced domain inversion on chromium coated lithium niobate crystals (2014)

Direct UV laser writing on chromium coated lithium niobate (LiNbO&lt;sub&gt;3&lt;/sub&gt;) crystals is found to produce spontaneous domain inversion associated with the exposed UV laser tracks. Experimental evidence suggests that this effect is attributed to local out-diffusion of oxygen, reducing the LiNbO&lt;sub&gt;3&lt;/sub&gt; crystal surface due to the presence of chromium. The thin chromium film becomes hot and reactive after absorbing the UV laser radiation thus acting as an oxygen getter. This very efficient process enables the inversion of domains at lower intensities as compared to other direct laser based poling methods practically eliminating the deleterious surface damage induced by the direct absorption of the UV laser radiation by the crystal. Furthermore, the versatility of this domain fabrication method, is demonstrated by the production of inverted domain structures on Z-, Y- and 128° YX-cut substrates.
Refractive Micro‐Optics (2009)

This chapter contains sections titled: Micro-optics in Nature GRIN Lenses Surface-relief Micro-optics Micro-optics Arrays