gebhart/patrepeval huggingface dataset:
Presence of Bovine Viral Diarrhoea Virus in Lymphoid Cell Populations of Persistently Infected Cattle (1993)

Cattle infected in utero with bovine viral diarrhoea virus (BVDV) often develop a lifelong persistent infection (PI). During this PI, BVDV infects many cell types including peripheral blood mononuclear cells (PBMNC). To define the lymphoid cell populations in which BVDV persists PBMNC subpopulations were separated using monoclonal antibodies to cell surface markers. Separated cells were analysed by a sensitive PCR assay for BVDV, in conjunction with flow cytometry to identify antigen-containing cells and with viral infectivity assays. The results indicate that BVDV establishes a productive PI in monocytes and T cells bearing the marker BoCD4, BoCD8 or gamma-delta T cell receptor. BVDV was not detected in B cells as a productive nor a latent infection.
Optimum Reaction Conditions for the Synthesis of Macromonomers Via the High‐Temperature Polymerization of Acrylates (2009)

Abstract Macromonomers are valuable synthetic building blocks: They can be copolymerized with low molecular weight monomers to generate brush‐like structures or serve as conjugation substrates in pericylic, metathesis, and thiolene reactions. Based on earlier reports on the facile high temperature formation of macromonomers from acrylates, a complex kinetic model is developed which accounts for the key reactions constituting the macromonomer formation process. On the basis of the kinetic model, the important rate coefficients governing acrylate polymerization (e.g., β ‐scission and termination rate coefficients of midchain radicals, backbiting and intramolecular chain transfer rate coefficients) as well as the reaction conditions (e.g., initial monomer concentration, reaction temperature, radical flux) are systematically varied and their influence on the synthetic success is critically evaluated. The systematic coefficient variation reveals that there exist optimum reaction conditions under which the high temperature macromonomers formation may be conducted with maximum success. The present study provides a concise summary of these conditions. magnified image
Endothelin‐1, nitric oxide, and glutamate in the normal and glaucomatous dog eye (2007)

Endothelin-1 and nitric oxide increased in aqueous humor and vitreous of dogs with spontaneous glaucoma while the changes in glutamate varied.
A Cognitive scheme for Radio Admission Control in LTE systems (2012)

In order to provide QoS requirements in high speed future communication networks, such as LTE, the operator has to provide a Radio Admission Control algorithm which will guarantee the QoS of different service types (e.g. voice, data, video, ftp) while maximizing radio resource utilization. In this paper we propose a Cognitive Radio Admission Control Scheme based on a Multilayer Feed-forward Neural Network. According to our scheme, the eNodeB performs Radio Admission Control using a cognitive engine that learns from the past experience how the admission of a new session would affect the QoS of all sessions in the future. We implemented our Radio Admission Control Scheme using a LTE-EPC simulator. Since our scheme is based on learning from the past experience, we expect that it will be able to satisfy QoS requirements, in a variety of realistic scenarios, which can not be accounted for in analytical models.
Ligand-Induced Dynamics of Neurotrophin Receptors Investigated by Single-Molecule Imaging Approaches (2015)

Neurotrophins are secreted proteins that regulate neuronal development and survival, as well as maintenance and plasticity of the adult nervous system. The biological activity of neurotrophins stems from their binding to two membrane receptor types, the tropomyosin receptor kinase and the p75 neurotrophin receptors (NRs). The intracellular signalling cascades thereby activated have been extensively investigated. Nevertheless, a comprehensive description of the ligand-induced nanoscale details of NRs dynamics and interactions spanning from the initial lateral movements triggered at the plasma membrane to the internalization and transport processes is still missing. Recent advances in high spatio-temporal resolution imaging techniques have yielded new insight on the dynamics of NRs upon ligand binding. Here we discuss requirements, potential and practical implementation of these novel approaches for the study of neurotrophin trafficking and signalling, in the framework of current knowledge available also for other ligand-receptor systems. We shall especially highlight the correlation between the receptor dynamics activated by different neurotrophins and the respective signalling outcome, as recently revealed by single-molecule tracking of NRs in living neuronal cells.
Dynamic feedback (1997)

This paper presents dynamic feedback, a technique that enables computations to adapt dynamically to different execution environments. A compiler that uses dynamic feedback produces several different versions of the same source code; each version uses a different optimization policy. The generated code alternately performs sampling phases and production phases. Each sampling phase measures the overhead of each version in the current environment. Each production phase uses the version with the least overhead in the previous sampling phase. The computation periodically resamples to adjust dynamically to changes in the environment.We have implemented dynamic feedback in the context of a parallelizing compiler for object-based programs. The generated code uses dynamic feedback to automatically choose the best synchronization optimization policy. Our experimental results show that the synchronization optimization policy has a significant impact on the overall performance of the computation, that the best policy varies from program to program, that the compiler is unable to statically choose the best policy, and that dynamic feedback enables the generated code to exhibit performance that is comparable to that of code that has been manually tuned to use the best policy. We have also performed a theoretical analysis which provides, under certain assumptions, a guaranteed optimality bound for dynamic feedback relative to a hypothetical (and unrealizable) optimal algorithm that uses the best policy at every point during the execution.
Communicating Diagnostic Uncertainty at Emergency Department Discharge: A Simulation-Based Mastery Learning Randomized Trial (2022)

The Uncertainty Communication Education Module significantly increased mastery in communicating diagnostic uncertainty at the first postintervention test among emergency physicians in standardized patient encounters. Further work should assess the impact of clinical implementation of these communication skills.
A critical assessment of methods of correcting for drift from the yield surface in elasto‐plastic finite element analysis (1985)

Abstract The analysis of elasto‐plastic boundary value problems using the finite element method involves many discretizations. These lead to the problem of yield surface drift in which the stress state predicted at the end of an elasto‐plastic increment of loading does not lie on the current yield surface. As such discrepancies are comulative it is important to ensure that the stresses are corrected back to the yield surface during each increment of loading. In this paper five methods of accounting for this drift are examined. These involve correcting the stresses by projecting back along the plastic flow, the total strain increment and the accumulated effective stress direction. In addition a ‘correct’, method which accounts for the changes in elastic strains which accompany any stress correction is considered. This method is theoretically more sound than the other approximate approaches. All five methods have been used in finite element analyses of the stress changes that occur adjacent to a single pile installed in a uniform deposit of soil on pile loading. The soil was assumed to be normally consolidated and was modelled using a form of modified Cam Clay. Comparison of these results with an analysis, in which yield surface drift was negligible indicated that only the ‘correct’ method and the method involving projecting back along the plastic flow direction give accurate predictions. Substantiai errors occur if the other methods of correcting for yield surface drift are employed. It is recommended that the ‘correct’ method be adopted for finite element calculations.
Vagus Nerve Stimulation in Ischemic Stroke: Old Wine in a New Bottle (2014)

Vagus nerve stimulation (VNS) is currently Food and Drug Administration-approved for treatment of both medically refractory partial-onset seizures and severe, recurrent refractory depression, which has failed to respond to medical interventions. Because of its ability to regulate mechanisms well-studied in neuroscience, such as norepinephrine and serotonin release, the vagus nerve may play an important role in regulating cerebral blood flow, edema, inflammation, glutamate excitotoxicity, and neurotrophic processes. There is strong evidence that these same processes are important in stroke pathophysiology. We reviewed the literature for the role of VNS in improving ischemic stroke outcomes by performing a systematic search for publications in Medline (1966-2014) with keywords "VNS AND stroke" in subject headings and key words with no language restrictions. Of the 73 publications retrieved, we identified 7 studies from 3 different research groups that met our final inclusion criteria of research studies addressing the role of VNS in ischemic stroke. Results from these studies suggest that VNS has promising efficacy in reducing stroke volume and attenuating neurological deficits in ischemic stroke models. Given the lack of success in Phase III trials for stroke neuroprotection, it is important to develop new therapies targeting different neuroprotective pathways. Further studies of the possible role of VNS, through normally physiologically active mechanisms, in ischemic stroke therapeutics should be conducted in both animal models and clinical studies. In addition, recent advent of a non-invasive, transcutaneous VNS could provide the potential for easier clinical translation.
Robust Semantic Template Matching Using a Superpixel Region Binary Descriptor (2019)

Almost all conventional template-matching methods employ low-level image features to measure the similarity between a template image and a scene image using similarity measures such as pixel intensity and pixel gradient. Although these methods have been widely used in many applications, they cannot simultaneously address all types of robustness challenges. In this study, with the goal of simultaneously addressing the various challenges, we present a robust semantic template-matching approach (RSTM). Inspired by the local binary descriptor, we propose a novel superpixel region binary descriptor (SRBD) to construct a multilevel semantic fusion feature vector for RSTM. SRBD uses a new kernel-distance-based simple linear iterative clustering (KD-SLIC) method to extract the stable superpixels from the template image; Then, based on the average intensity difference between each superpixel region and its neighbors, the dominant gradient orientation of each superpixel can be obtained, and the semantic features of each superpixel can be described as the dominant orientation difference vector, which is coded as the rotation-invariant SRBD. In the off-line matching phase, the fusion semantic feature vector of RSTM combines the multilevel SRBD features with different numbers of superpixels. In the online matching phase, to cope with rotation invariance, a marginal probability model is proposed and applied to locate the positions of template images in the scene image. Moreover, to accelerate computation, an image pyramid is employed. We conduct a series of experiments on a large dataset randomly selected from the MS COCO dataset to fully analyze the robustness of this approach. The experimental results show that RSTM simultaneously addresses rotation changes, scale changes, noise, occlusions, blur, nonlinear illumination changes and deformation with high time efficiency while also outperforming previous stateof- the-art template-matching methods.
Supplementary Table 2 from Maximizing the Efficacy of MAPK-Targeted Treatment in <i>PTEN</i><sup>LOF</sup><i>/BRAF</i><sup>MUT</sup> Melanoma through PI3K and IGF1R Inhibition (2023)

&lt;p&gt;PI3Kβi (rac-KIN-193) treatment induces the interaction of p85 with a panel of proteins in &lt;i&gt;PTEN&lt;sup&gt;LOF&lt;/sup&gt;&lt;/i&gt;/&lt;i&gt;BRAF&lt;sup&gt;MUT&lt;/sup&gt;&lt;/i&gt; melanoma. RVH-421 were treated with DMSO or 1μM PI3Kβi for 2h. Lysates were subjected to immunoprecipitation using an antibody targeting p85. Proteins in the range of 75 to 250 kDa were identified by LC-MS as described. Total spectra counts were used as a measure for protein quantity. The table summarizes the proteins enriched upon PI3Kβi treatment in the p85 precipitate. A spectral count ratio of 4 (log&lt;sub&gt;2&lt;/sub&gt; (PI3Kβi /DMSO) &gt; 2) was taken as an arbitrary cutoff for significant enrichment.&lt;/p&gt;
Piecewise 2D autoregression for predictive image coding (2002)

We propose an on-line piecewise two-dimensional autoregression algorithm (P2AR) for modeling and coding of images. The algorithm assumes no stationarity of the source. The resulting P2AR predictor can be loosely considered as a universal parametric image model in the sense that no prior knowledge about the image are assumed. The predictor parameters are causal and dynamically adapted to the source, hence suits one-pass image coding with no side information. The good fit of the model to a variety of images is demonstrated by its superior performance when being used in lossless image coding. We reduced the bit rate of the benchmark lossless image codec CALIC by three percent averaging over the JPEG set of test images, simply by replacing the context-sensitive, non-linear GAP predictor of CALIC with the P2AR predictor. The performance margin gets much larger when the source is highly nonstationary. In order to make on-line 2D autoregression computationally feasible, we developed a novel and efficient algorithm for computing and updating covariances of regression variables on a pixel-by-pixel basis. This algorithm can also be applied in image segmentation, texture classification, and other image analysis tasks that require heavy computations of second order statistics.
Simple method for integrating DFB laser and silicon photonics platform (2015)

A simple and practical method for integrating a DFB laser and a silicon photonics platform without additional optical components such as lenses and an isolator is proposed. Optical-coupling and feedback-tolerance characteristics are experimentally measured.
Accumulation of Pb and Zn in Gametophytes and Sporophytes of the Moss Funaria hygrometrica(Funariales) (2001)

Accumulation of lead and zinc was studied in the moss Funaria hygrometrica Hedw. collected from mine tailings. Heavy metal accumulation in gametophytes and sporophytes was quantified by graphite furnace atomic absorption spectrometry (GFAAS) and inductively coupled plasma-atomic emission spectrometry (ICP-AES). Pb and Zn accumulation in the placental zone was analysed by x-ray scanning electron microscopy (SEM) and transmission electron microscopy (TEM) microanalysis. Spectrometry showed that while moss gametophytes accumulated considerable concentrations of heavy metals, sporophytes accumulated only small concentrations of metals. X-ray SEM and TEM showed that the two metals accumulated in placental transfer cells on both the gametophytic and sporophytic sides. To investigate the uptake pattern for both metals under controlled conditions, F. hygrometrica plants collected from a non-polluted site were treated in the laboratory with separate solutions of Pb and Zn at two concentrations (10 −2 and 10 −4 M ) for 24 or 168 h. Metal accumulation was analysed separately in gametophytes and sporophytes using GFAAS and ICP–AES. Each generation had a different accumulation quotient for both metals, and gametophytes accumulated significantly more metal than sporophytes. Concentrations of Zn in sporophytes were always higher than concentrations of Pb. The findings are discussed in relation to the role performed by the gametophyte and the placenta in the accumulation and sequestration of Pb and Zn. Copyright 2001 Annals of Botany Company
On the security of Angle of Arrival estimation (2016)

Angle of Arrival (AoA) estimation has found its way to a wide range of applications. Much attention has been paid to study different techniques for AoA estimation and its applications for jamming suppression, however, security vulnerability issues of AoA estimation itself under hostile activity have not been paid the same attention. In this paper, the problem of AoA estimation in Rician flat fading channel under jamming condition is investigated. We consider the scenario in which a receiver with multiple antenna is trying to estimate the AoA of the specular line of sight (LOS) component of signal received from a given single antenna transmitter using a predefined training sequence. A jammer equipped with multiple antennas is trying to interrupt the AoA estimation phase by sending an arbitrary signal. We derive the optimal jammer and receiver strategies in various scenarios based on the knowledge of the opponent strategies and the available information about the communication channel. In all scenarios, we derive the optimal jammer signal design as well as its optimal power allocation policy. The results show the optimality of the training based Maximum Likelihood (ML) AoA estimator in case of randomly generated jamming signal. We also show that, the optimal jammer strategy is to emit a signal identical to the predefined training sequence turning the estimation process into a highest power competition scenario in which the detected AoA is the one for the transmitting entity of higher power. The obtained results are supported by the provided computer simulation.
Inhibitory activity of interleukin B on the suppressor T cell hybrid T2D4. (1987)

Interleukin B (IL-B), a product of unstimulated B cells, is defined by its ability to selectively prevent the differentiation of suppressor T lymphocytes from precursors into effectors. The present study was undertaken to determine whether IL-B could also be active in modulating the activity of the T cell hybrid T2D4, which produces immunoglobulin-binding suppressor factors. T2D4 cells can be selectively induced by incubation with various isotypes of antibody to express isotype-specific Fc receptors and to release soluble factors that suppress production of the corresponding isotype. The data presented here demonstrate that IL-B is greatly effective in inhibiting T2D4 activities. Either pretreatment with IL-B or continuous exposure to IL-B prevents isotype activation of T2D4. As a result, T2D4 cells do not express isotype receptors and do not produce detectable amounts of isotype-specific suppressor factors. This IL-B regulatory activity on T2D4 is temperature dependent and is inhibited by cytochalasin B. These findings provide new insights on the mechanism by which IL-B enhances antibody responses, and they offer a conceptual framework for analyzing IL-B activity on suppressor T cells.
Suppression of mitogen‐induced peripheral B cell differentiation by soluble Fcγ receptors released from lymphocytes (1980)

Soluble receptors for FcIgG released from unstimulated human peripheral blood lymphocytes were isolated by affinity chromatography on Sepharose 4B-IgG. This material was shown to interfere with the differentiation of peripheral blood B cells into Ig-secreting cells in cultures stimulated with pokeweek or Nocardia opaca extracts. Neither cell viability nor [3H]thymidine incorporation were altered, but the number of Ig-containing cells and that of Ig-secreting cells were decreased. These effects were dose-related. They were found to be associated with Fc IgG-binding soluble material, since absorption on Sepharose 4B-IgG but not on pepsin-digested F(ab')2 fragments removed the inhibitory activity. This suppressor factor, released by unstimulated lymphocytes, may represent a human analogue of murine immunoglobulin-binding factor (IBF) produced by alloactivated T cells.
Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease (2020)

Abstract Congenital Heart Disease (CHD) affects approximately 7-9 children per 1000 live births. Numerous genetic studies have established a role for rare genomic variants at the copy number variation (CNV) and single nucleotide variant level. In particular, the role of de novo mutations (DNM) has been highlighted in syndromic and non-syndromic CHD. To identify novel haploinsufficient CHD disease genes we performed an integrative analysis of CNVs and DNMs identified in probands with CHD including cases with sporadic thoracic aortic aneurysm (TAA). We assembled CNV data from 7,958 cases and 14,082 controls and performed a gene-wise analysis of the burden of rare genomic deletions in cases versus controls. In addition, we performed mutation rate testing for DNMs identified in 2,489 parent-offspring trios. Our combined analysis revealed 21 genes which were significantly affected by rare genomic deletions and/or constrained non-synonymous de novo mutations in probands. Fourteen of these genes have previously been associated with CHD while the remaining genes ( FEZ1, MYO16, ARID1B, NALCN, WAC, KDM5B and WHSC1 ) have only been associated in singletons and small cases series, or show new associations with CHD. In addition, a systems level analysis revealed shared contribution of CNV deletions and DNMs in CHD probands, affecting protein-protein interaction networks involved in Notch signaling pathway, heart morphogenesis, DNA repair and cilia/centrosome function. Taken together, this approach highlights the importance of re-analyzing existing datasets to strengthen disease association and identify novel disease genes.
Superoxide, H2O2, and iron are required for TNF-α-induced MCP-1 gene expression in endothelial cells: role of Rac1 and NADPH oxidase (2004)

Reactive oxygen species (ROS) play an important but not yet fully defined role in the expression of inflammatory genes such as monocyte chemoattractant protein (MCP)-1. We used complementary molecular and biochemical approaches to explore the roles of specific ROS and their molecular linkage to inflammatory signaling in endothelial cells. Adenovirus-mediated expression of superoxide dismutase and catalase inhibited TNF-alpha-induced MCP-1 gene expression, suggesting important roles of superoxide (O(2)(-).) and H(2)O(2) in MCP-1 gene activation. In addition, the iron chelator 1,2-dimethyl-3-hydroxypyridin-4-one and the hydroxyl radical scavengers dimethylthiourea and dimethyl sulfoxide inhibited TNF-alpha-induced MCP-1 expression, suggesting important roles of iron and hydroxyl radicals in inflammatory signal activation. In contrast, scavenging of peroxynitrite with 5,10,15,20-tetrakis-(4-sulfonatophenyl)prophyrinato iron (III) chloride had no effect on TNF-alpha-induced MCP-1 expression. Inhibition of NADPH oxidase, the major oxidase responsible for O(2)(-). generation, with diphenylene iodonium suppressed TNF-alpha-induced MCP-1 mRNA accumulation. Rac1 is an upstream signaling molecule for the activation of NADPH oxidase and O(2)(-). generation. Expression of dominant negative N17Rac1 by adenovirus suppressed TNF-alpha-induced MCP-1 mRNA levels and MCP-1 protein secretion. Expression of N17Rac1 inhibited TNF-alpha-induced MCP-1 and NF-kappaB transcriptional activity. These data suggest that ROS such as superoxide and H(2)O(2) derived from Rac1-activated NADPH oxidase mediate TNF-alpha-induced MCP-1 expression in endothelial cells.