gebhart/patrepeval huggingface dataset:
Involvement of p130Cas and p105HEF1, a Novel Cas-like Docking Protein, in a Cytoskeleton-dependent Signaling Pathway Initiated by Ligation of Integrin or Antigen Receptor on Human B Cells (1997)

The Crk-associated substrate p130(Cas) (Cas) and the recently described human enhancer of filamentation 1 (HEF1) are two proteins with similar structure (64% amino acid homology), which are thought to act as "docking" molecules in intracellular signaling cascades. Both proteins contain an N-terminal Src homology (SH), three domain and a cluster of SH2 binding motifs. Here we show that ligation of either beta1 integrin or B cell antigen receptor (BCR) on human tonsillar B cells and B cell lines promoted tyrosine phosphorylation of HEF1. In contrast, Cas tyrosine phosphorylation was observed in certain B cell lines but not in tonsillar B cells, indicating a more general role for HEF1 in B cell signaling. Interestingly, pretreatment of tonsillar B cells with cytochalasin B dramatically reduced both integrin- and BCR-induced HEF1 phosphorylation, suggesting that some component of the BCR-mediated signaling pathway is closely linked with a cytoskeletal reorganization. Both HEF1 and Cas were found to complex with the related adhesion focal tyrosine kinase (RAFTK), and when tyrosine phosphorylated, with the adapter molecule CrkL. In addition, the two molecules were detected in p53/56(Lyn) immunoprecipitates, and Lyn kinase was found to specifically bind the C-terminal proline-rich sequence of Cas in an in vitro binding assay. These associations implicate HEF1 and Cas as important components in a cytoskeleton-linked signaling pathway initiated by ligation of beta1 integrin or BCR on human B cells.
GAN-based Super-Resolution and Segmentation of Retinal Layers in Optical coherence tomography Scans (2022)

In this paper, we design a Generative Adversarial Network (GAN)-based solution for super-resolution and segmentation of optical coherence tomography (OCT) scans of the retinal layers. OCT has been identified as a non-invasive and inexpensive modality of imaging to discover potential biomarkers for the diagnosis and progress determination of neurodegenerative diseases, such as Alzheimer's Disease (AD). Current hypotheses presume the thickness of the retinal layers, which are analyzable within OCT scans, can be effective biomarkers. As a logical first step, this work concentrates on the challenging task of retinal layer segmentation and also super-resolution for higher clarity and accuracy. We propose a GAN-based segmentation model and evaluate incorporating popular networks, namely, U-Net and ResNet, in the GAN architecture with additional blocks of transposed convolution and sub-pixel convolution for the task of upscaling OCT images from low to high resolution by a factor of four. We also incorporate the Dice loss as an additional reconstruction loss term to improve the performance of this joint optimization task. Our best model configuration empirically achieved the Dice coefficient of 0.867 and mIOU of 0.765.
Method and apparatus for ensuring a uniform temperature profile in ribbon fiber lasers and amplifiers (2023)

A uniform temperature profile is provided across the width of the core of a ribbon fiber laser or amplifier by the use of insulating elements at the core edges and a spatially variable gain in the fiber core. High average power ribbon fibers, enable a variety of applications such as practical laser cutting and beam combining.
Applications of Ionic Liquids in Chemical Science (2018)

The ionic liquids are very important solvents in chemical science. These are termed as melts, designer solvents, electrolytes, ionic glasses, fused salts, ionic fluid, and green solvents. The ionic liquids are being used in the different research and industrial areas of chemical science. The most important applications of the ionic liquids in the chemical science include extraction, separation, electro-analysis and spectroscopic studies. This chapter describes the utility of the ionic liquids in the chemical science. Besides, the efforts were made to highlight the toxicity and future of the ionic liquids.
Establishment of a pig influenza challenge model for evaluation of monoclonal antibody delivery platforms (2020)

Abstract Monoclonal antibodies are a possible adjunct to vaccination and drugs in treatment of influenza virus infection. However questions remain whether small animal models accurately predict efficacy in humans. We have established the pig, a large natural host animal for influenza, with many physiological similarities to humans, as a robust model for testing monoclonal antibodies. We show that a strongly neutralizing monoclonal antibody (2-12C) against the hemagglutinin head administered prophylactically at 15 mg/kg reduced viral load and lung pathology after pandemic H1N1 influenza challenge. A lower dose of 1 mg/kg of 2-12C or a DNA plasmid encoded version of 2-12C, reduced pathology and viral load in the lungs, but not viral shedding in nasal swabs. We propose that the pig influenza model will be useful for testing candidate monoclonal antibodies and emerging delivery platforms prior to human trials.
Discovering optimal targets for adoptive T-cell immunotherapy of leukemia (P4346) (2013)

Abstract The main barrier in allogeneic hematopoietic cell transplantation is the risk of developing graft-versus-host disease. This can be prevented by the injection of CD8 T cells targeted to leukemia associated antigens (LAAs) or minor histocompatibility antigens (MiHAs). Several studies in humans have established the value of LAAs and MiHAs as target for immunotherapy on solid tumors and leukemia, respectively. Importantly, their therapeutic efficacy has never been assessed on a per antigen basis. Thus, our goal is to directly compare the therapeutic efficacy of T-cells targeted to LAAs or MiHAs expressed on EL4 cells. We selected 4 MiHAs and 4 LAAs and confirmed their immunogenicity by in vitro cytotoxicity assays. We evaluated the anti-leukemic activity of antigen-specific CD8 T cells in vivo. Notably, mice immunized against MiHAs showed enhanced survival compared to mice immunized against LAAs. We found that decreased survival of EL4 bearing mice cannot be explained by weaker MHC I/Peptide interactions. Interestingly, we showed that T cells specific for 4 LAAs and 1 MiHA are undetectable by flow cytometry and that the abundance of tetramer positive cells correlates strongly with survival of EL4 bearing mice. We propose that CD8 T cells, mainly targeted to LAAs, bind weakly to their MHC I/Peptide complexes, leading to decreased immunogenicity. We believe that the insights gained from our studies will serve as guide for selecting the best antigens for future clinical trials.
Seminal plasma activates cyclooxygenase-2 and prostaglandin E2 receptor expression and signalling in cervical adenocarcinoma cells (2002)

Enhanced cyclooxygenase (COX) expression and prostaglandin E2 (PGE2) synthesis are regarded as promoters of neoplastic cell proliferation and angiogenesis. Expression of COX-2 and synthesis of PGE2 are up-regulated in cervical carcinomas. In sexually active women, growth and invasiveness of neoplastic cervical epithelial cells may be also under the direct influence of PGE2 present in seminal plasma. The aims of this study were to investigate the effect of seminal plasma and PGE2 on the expression of COX-2 and expression and signalling of the PGE2 receptor subtypes (EP1-EP4) in HeLa (cervical adenocarcinoma) cells. Treatment of HeLa cells with seminal plasma or PGE2 resulted in up-regulation of COX-2 expression (P < 0.05). In addition, seminal plasma induced the mRNA expression of EP1, EP2 and EP4 receptors, whilst PGE2 treatment of HeLa cells induced the expression of the EP4 receptor (P < 0.05). This was coincident with a rapid accumulation of adenosine 3',5'-cyclic monophosphate (cAMP) in HeLa cells stimulated with seminal plasma or PGE2, which was greater in seminal plasma stimulated cells compared with PGE2 stimulated cells (P < 0.05). Subsequently, we investigated whether the effect of seminal plasma on cAMP signalling in HeLa cells was mediated via the cAMP-linked EP2/EP4 receptors. Stimulation of HeLa cells with seminal plasma or PGE2 resulted in an augmented cAMP accumulation in cells transfected with the EP2 or EP4 receptor cDNA compared with control transfected cells (P < 0.05). These data suggest that, in sexually active women, seminal plasma may play a role in modulating neoplastic cell function and cervical tumorigenesis.
Protocol Coding through Reordering of User Resources: Applications and Capacity Results (2010)

While there are continuous efforts to introduce new communication systems and standards, it is legitimate to ask the question: how can one send additional bits by minimally changing the systems that are already operating? This is of a significant practical interest, since it has a potential to generate additional value of the systems through, for example, introduction of new devices and only a software update of the access points or base stations, without incurring additional cost for infrastructure hardware installation. The place to look for such an opportunity is the communication protocol and we use the term *protocol coding* to refer to strategies for sending information by using the degrees of freedom available when one needs to decide the actions taken by a particular communication protocol. In this paper we consider protocol coding that gives a rise to *secondary communication channels*, defined by combinatorial ordering of the user resources (packets, channels) in a primary (legacy) communication system. We introduce communication models that enable us to compute the capacity of such secondary channels under suitable restrictions imposed by the primary systems. We first show the relation to the capacity of channels with causal channel state information at the transmitter (CSIT), originally considered by Shannon. By using the specific communication setup, we develop an alternative framework for achieving the capacity and we discuss coding strategies that need to be used over the secondary channels. We also discuss some practical features of the secondary channels and their applications that add value to the existing wireless systems.
The A0 inversion model of program paging behavior (1976)

When the parameters of a simple stochastic model of the memory referencing behavior of computer programs are carefully selected, the model is able to mimic the paging behavior of a set of actual programs. The mimicry is successful using several different page replacement algorithms and a wide range of real memory sizes in a virtual memory environment. The model is based on the independent reference model with a new procedure for determining the page reference probabilities, the parameters of the model. We call the result the A0 inversion independent reference model. Since the fault rate (or miss ratio) is one aspect of program behavior that the model is able to capture for many different memory sizes, the model should be especially useful for evaluating multilevel memory organizations based on newly emerging memory technologies.
Quantitative imaging of murine osteoarthritic cartilage by phase‐contrast micro–computed tomography (2012)

We established an imaging technology that comprehensively assessed and quantified the 2-dimensional and 3-dimensional changes of articular cartilage. Application of this technology will facilitate the rapid and high-throughput assessment of genetic and therapeutic models of OA in mice.
Unusual condensation-ring closure reaction [forming cyclopropyl sulfoxides] (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUnusual condensation-ring closure reaction [forming cyclopropyl sulfoxides]Abraham Nudelman and Donald J. CramCite this: J. Org. Chem. 1969, 34, 11, 3659–3661Publication Date (Print):November 1, 1969Publication History Published online1 May 2002Published inissue 1 November 1969https://pubs.acs.org/doi/10.1021/jo01263a109https://doi.org/10.1021/jo01263a109research-articleACS PublicationsRequest reuse permissionsArticle Views49Altmetric-Citations5LEARN 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
Active Lysogeny in Listeria Monocytogenes Is a Bacteria-Phage Adaptive Response in the Mammalian Environment (2020)

Some Listeria monocytogenes (Lm) strains harbor a prophage within the comK gene, which renders it inactive. During Lm infection of macrophage cells, the prophage turns into a molecular switch, promoting comK gene expression and therefore Lm intracellular growth. During this process, the prophage does not produce infective phages or cause bacterial lysis, suggesting it has acquired an adaptive behavior suited to the pathogenic lifestyle of its host. In this study, we demonstrate that this non-classical phage behavior, named active lysogeny, relies on a transcriptional response that is specific to the intracellular niche. While the prophage undergoes lytic induction, the process is arrested midway, preventing the transcription of the late genes. Further, we demonstrate key phage factors, such as LlgA transcription regulator and a DNA replicase, that support the phage adaptive behavior. This study provides molecular insights into the adaptation of phages to their pathogenic hosts, uncovering unusual cooperative interactions.
TCP over Satellite Hybrid Networks: A Survey (2002)

Satellite is going to play an important role in the global information infrastructure. Satellite canprovide direct to home Internet service (i.e. DirecPC from Hughes Network System) and it can alsoserve as traffic trunk in the middle of the network. About 98 percent of the Internet traffic is TCPtraffic. TCP works well in the terrestrial fiber network. However, in the satellite hybrid networks,because of the long propagation delay, large bandwidth-delay product, high bit error rate anddownstream/upstream bandwidth asymmetry, TCP performance degrades dramatically. This paperaddresses the problems of TCP in satellite data networks and reviews the proposed solutions in theliterature. For each solution, the advantages and disadvantages are pointed out. In addition,extensive simulations have been done for the proxy based scheme currently used in the industry tofind out how and to what extent the enhancements, such as connection splitting, window scalingand selective acknowledgement, benefit the TCP throughput.
Chiral N‐Heterocyclic Carbene/Pyridine Ligands for the Iridium‐Catalyzed Asymmetric Hydrogenation of Olefins (2013)

Swapping N,P for C,N: Iridium complexes of bidentate pyridine-based C,N ligands with an N-heterocylic carbene (NHC) unit proved to be efficient and highly enantioselective hydrogenation catalysts. As a result of the lower acidity of iridium hydride intermediates produced from NHC-based complexes, these catalysts are much better suited than analogous N,P-ligand complexes for the hydrogenation of acid-sensitive substrates.
Specific heats of hydrogen, deuterium, and neon in porous Vycor glass (1983)

The specific heats of hydrogen, deuterium, and neon in porous Vycor glass have been measured. The freezing and melting temperatures have been determined, and a lower limit has been placed on the values of the liquid-solid surface energy.
Toward Pediatric T Lymphoblastic Lymphoma Stratification Based on Minimal Disseminated Disease and NOTCH1/FBXW7 Status (2021)

While outcome for pediatric T lymphoblastic lymphoma (T-LL) has improved with acute leukemia-type therapy, survival after relapse remains rare. Few prognostic markers have been identified: <i>NOTCH1</i> and/or <i>FBXW7</i> (<i>N/F</i>) mutations identify good prognosis T-LL and high-level minimal disseminated disease (MDD) is reported to be of poor prognosis. We evaluated MDD and/or MRD status by 8-color flow cytometry and/or digital droplet PCR in 82 pediatric T-LL treated according to the EURO-LB02 prednisone reference arm. Both techniques gave identical results for values ≥0.1%, allowing compilation. Unlike historical studies, an MDD threshold of 1% had no prognostic significance. The 54% (42/78) of patients with MDD ≥0.1% had a relatively favorable outcome (5-y overall survival [OS] 97.6% versus 80.6%, <i>P</i> = 0.015, 5-y event-free-survival [EFS] 95.2% versus 80.6%, <i>P</i> = 0.049). MDD lower than 0.1% had no impact in <i>N/F</i> mutated T-LL, but identified the <i>N/F</i> germline patient with a high risk of relapse. Combining oncogenetic and MDD status identified 86% of patients (n = 49) with an excellent outcome and 14% of <i>N/F</i> germline/MDD <0.1% patients (n = 8) with poor prognosis (5y-OS 95.9% versus 37.5%, <i>P</i> < 0.001; 5y-EFS 93.9% versus 37.5%, <i>P</i> < 0.001). If confirmed by prospective studies, MDD and <i>N/F</i> mutational status would allow identification of a subset of patients who merit consideration for alternative front-line treatment.
Randomised, double-blind, placebo-controlled pilot trial of omeprazole in idiopathic pulmonary fibrosis (2019)

A large randomised controlled trial of PPIs for cough in IPF appears feasible and justified but should address barriers to randomisation and incorporate safety assessments in relation to respiratory infection and changes in lung function.
BiS-KM: Enabling Any-Precision K-Means on FPGAs (2020)

K-Means is a popular clustering algorithm widely used and extensively studied in the literature. In this paper we explore the challenges and opportunities in using low precision input in conjunction with a standard K-Means algorithm as a way to improve the memory bandwidth utilization on hardware accelerators. Low precision input through quantization has become a standard technique in machine learning to reduce computational costs and memory traffic. When applied in FPGAs, several issues need to be addressed. First and foremost is the overhead of storing the data at different precision levels since, depending on the training objective, different levels of precision might be needed. Second, the FPGA design needs to accommodate varying precision without requiring reconfiguration. To address these concerns, we propose Bit-Serial K-Means (BiS-KM), a combination of a hybrid memory layout supporting data retrieval at any level of precision, a novel FPGA design based on bit-serial arithmetic, and a modified K-Means algorithm tailored to FPGAs. We have tested BiS-KM with various data sets and compared our design with a state-of-the-art FPGA accelerator. BiS-KM achieves an almost linear speedup as precision decreases, providing a more effective way to perform K-Means on FPGAs.
A 1.4-million-element CCD image sensor (1987)

A 2/3" format 1.4 megapixel full-frame CCD image sensor with a cell size of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6.8×6.8μ</tex> m, that achieves a quantum efficiency of 50% at 550nm, will be disclosed. Output-amplifier noise is 15rms electrons. Amplifier uses buried channel LDD NMOSFETs. Input-referred sensitivity is 15μV/electron over a 71MHz bandwidth. Device has been fabricated using a two-phase, two-level polysilicon process.
Detoxification of the Lipid Peroxidation Aldehyde, 4-Hydroxynonenal, by Apple Phloretin In Vitro and in Mice (2023)

4-Hydroxy-2-nonenal (4-HNE) is a secondary cytotoxic product generated from lipid peroxidation of polyunsaturated fatty acids (PUFAs). The accumulation of 4-HNE can covalently modify biomolecules, such as DNA and proteins, leading to various pathological conditions. Apple phloretin has been shown to be able to trap 4-HNE <i>in vitro</i>, but the trapping mechanisms of 4-HNE by phloretin are not fully understood. Moreover, whether the <i>in vitro</i> trapping efficacy of phloretin toward 4-HNE could be transferred into <i>in vivo</i> environments has never been investigated. In the present study, we observed the formation of 4-HNE conjugates of phloretin increased as phloretin decreased during the <i>in vitro</i> incubation. We then purified and characterized three mono-4-HNE-conjugates of phloretin using NMR and LC-MS/MS techniques. We thereafter demonstrated that apple phloretin could scavenge <i>in vivo</i> 4-HNE via the formation of at least three mono-4-HNE-conjugates of phloretin in a dose-dependent manner in mice after oral administration of three doses of phloretin (25, 100, and 400 mg/kg). The findings from this study pave the way to understanding how dihydrochalcones could act as effective scavengers of 4-HNE by working as sacrificial nucleophiles <i>in vivo</i>, thereby preventing or reducing the risk of 4-HNE-associated chronic diseases.
Bayesian Optimization for Stack-up Design (2019)

Black-box function optimization is a challenging problem worldwide. Bayesian Optimization is a powerful method used to handle the optimization of functions, which are usually too costly for evaluation. Non-convex black-box function optimization arises in many applied problems. One example of such kind of problems is the PCB stack-up design. With its various covariance functions and different values of hyper-parameters Bayesian Optimization is applied for five-dimensional stack-up design optimization. The results obtained using the Bayesian Optimization are compared with results of other methods.
Function of the Golgi-located phosphate transporter PHT4;6 is critical for senescence-associated processes in Arabidopsis (2016)

The phosphate transporter PHT4;6 locates to the trans-Golgi compartment, and its impaired activity causes altered intracellular phosphate compartmentation, leading to low cytosolic Pi levels, a blockage of Golgi-related processes such as protein glycosylation and hemicellulose biosynthesis, and a dwarf phenotype. However, it was unclear whether altered Pi homeostasis in pht4;6 mutants causes further cellular problems, typically associated with limited phosphate availability. Here we report that pht4;6 mutants exhibit a markedly increased disposition to induce dark-induced senescence. In control experiments, in which pht4;6 mutants and wild-type plants developed similarly, we confirmed that accelerated dark-induced senescence in mutants is not a 'pleiotropic' process associated with the dwarf phenotype. In fact, accelerated dark-induced senescence in pht4;6 mutants correlates strongly with increased levels of toxic NH4 (+) and higher sensitivity to ammonium, which probably contribute to the inability of pht4;6 mutants to recover from dark treatment. Experiments with modified levels of either salicylic acid (SA) or trans-zeatin (tZ) demonstrate that altered concentrations of these compounds in pht4;6 plants act as major cellular mediators for dark-induced senescence. This conclusion gained further support from the notion that the expression of the pht4;6 gene is, in contrast to genes coding for major phosphate importers, substantially induced by tZ. Taken together, our findings point to a critical function of PHT4;6 to control cellular phosphate levels, in particular the cytosolic Pi availability, required to energize plant primary metabolism for proper plant development. Phosphate and its allocation mediated by PHT4;6 is critical to prevent onset of dark-induced senescence.