gebhart/patrepeval huggingface dataset:
<i>IRF5</i> Risk Polymorphisms Contribute to Interindividual Variance in Pattern Recognition Receptor-Mediated Cytokine Secretion in Human Monocyte-Derived Cells (2012)

Monocyte-derived cells display highly variable cytokine secretion upon pattern recognition receptor (PRR) stimulation across individuals; such variability likely affects interindividual inflammatory/autoimmune disease susceptibility. To define mechanisms for this heterogeneity, we examined PRR-induced monocyte-derived cell cytokine secretion from a large cohort of healthy individuals. Although cytokine secretion ranged widely among individuals, the magnitude of cytokine induction after individual nucleotide-binding oligomerization domain 2 (Nod2) and TLR2 stimulation (a cohort of 86 individuals) or stimulation of multiple TLRs (a cohort of 77 individuals), either alone or in combination with Nod2, was consistent intraindividually across these stimuli. Nod2 and TLRs signal through IFN regulatory factor 5 (IRF5), and common IRF5 polymorphisms confer risk for autoimmunity. We find that cells from rs2004640 IRF5 risk-associated allele carriers secrete increased cytokines upon individual or synergistic PRR stimulation in a gene dose- and ligand dose-dependent manner in both monocyte-derived dendritic cells and monocyte-derived macrophages. IRF5 expression knockdown in IRF5 risk allele carrier cells significantly decreases PRR-induced cytokines. Moreover, we find that IRF5 knockdown profoundly decreases Nod2-mediated MAPK and NF-κB pathway activation, whereas the PI3K and mammalian target of rapamycin pathways are not impaired. Finally, the IRF5 rs2004640 polymorphism is a major determinant of the variance (r(2) = 0.53) in Nod2-induced cytokine secretion by monocyte-derived cells from different individuals. We therefore show a profound contribution of a single gene to the variance in interindividual PRR-induced cytokines. The hyperresponsiveness of IRF5 disease-associated polymorphisms to a wide spectrum of microbial triggers has broad implications on global immunological responses, host defenses against pathogens, and inflammatory/autoimmune disease susceptibility.
Gastric mucosal blood flow measured by laser-Doppler velocimetry (1985)

To determine the feasibility of measuring gastric mucosal blood flow by laser-Doppler velocimetry (LDV), we utilized two LDV flowmeters to monitor blood flow in mucosa and serosa of chambered canine stomach. In isolated, nonautoregulating gastric segments vasodilated with isoproterenol, LDV mucosal and muscularis blood flows were both linearly related to total electromagnetic blood flow during step increases in perfusion pressure. To assess the depth of the LDV measurement, we recorded reactive hyperemia following arterial occlusion. Reactive hyperemia was frequently registered in the mucosa but rarely in muscularis. Placing a layer of nonperfused mucosa-submucosa between the probe and the perfused mucosa abolished the resting LDV mucosal flow signal and attenuated the recording of peak hyperemia by 85%. Furthermore, intra-arterial infusions of both adenosine and isoproterenol frequently increased LDV mucosal flow and decreased LDV muscularis flow, although total flow was consistently increased. These findings indicate that our LDV instruments yield linear, superficial measurements of gastric blood flow in either mucosa or muscularis. Although calibration in absolute units remains to be achieved, our results demonstrate that LDV is a practical means of studying the gastric mucosal microcirculation.
Whole-exome sequencing identifies rare, functional CFH variants in families with macular degeneration (2014)

We sequenced the whole exome of 35 cases and 7 controls from 9 age-related macular degeneration (AMD) families in whom known common genetic risk alleles could not explain their high disease burden and/or their early-onset advanced disease. Two families harbored novel rare mutations in CFH (R53C and D90G). R53C segregates perfectly with AMD in 11 cases (heterozygous) and 1 elderly control (reference allele) (LOD = 5.07, P = 6.7 × 10(-7)). In an independent cohort, 4 out of 1676 cases but none of the 745 examined controls or 4300 NHBLI Exome Sequencing Project (ESP) samples carried the R53C mutation (P = 0.0039). In another family of six siblings, D90G similarly segregated with AMD in five cases and one control (LOD = 1.22, P = 0.009). No other sample in our large cohort or the ESP had this mutation. Functional studies demonstrated that R53C decreased the ability of FH to perform decay accelerating activity. D90G exhibited a decrease in cofactor-mediated inactivation. Both of these changes would lead to a loss of regulatory activity, resulting in excessive alternative pathway activation. This study represents an initial application of the whole-exome strategy to families with early-onset AMD. It successfully identified high impact alleles leading to clearer functional insight into AMD etiopathogenesis.
Companion cognitive systems: A step towards human-level AI (2004)

We are developing Companion Cognitive Systems, a new kind of software that can be effectively treated as a collaborator. Aside from their potential utility, we believe this effort is important because it focuses on three key problems that must be solved to achieve human-level AI: Robust reasoning and learning, performance and longevity, and interactivity. We describe the ideas we are using to develop the first architecture for Companions: Analogical processing, grounded in cognitive science for reasoning and learning, a distributed agent architecture hosted on a cluster to achieve performance and longevity, and sketching and concept maps to provide interactivity.
Neutralizing Antibodies Isolated by a site-directed Screening have Potent Protection on SARS-CoV-2 Infection (2020)

Abstract Neutralizing antibody is one of the most effective interventions for acute pathogenic infection. Currently, over three million people have been identified for SARS-CoV-2 infection but SARS-CoV-2-specific vaccines and neutralizing antibodies are still lacking. SARS-CoV-2 infects host cells by interacting with angiotensin converting enzyme-2 (ACE2) via the S1 receptor-binding domain (RBD) of its surface spike glycoprotein. Therefore, blocking the interaction of SARS-CoV-2-RBD and ACE2 by antibody would cause a directly neutralizing effect against virus. In the current study, we selected the ACE2 interface of SARS-CoV-2-RBD as the targeting epitope for neutralizing antibody screening. We performed site-directed screening by phage display and finally obtained one IgG antibody (4A3) and several domain antibodies. Among them, 4A3 and three domain antibodies (4A12, 4D5, and 4A10) were identified to act as neutralizing antibodies due to their capabilities to block the interaction between SARS-CoV-2-RBD and ACE2-positive cells. The domain antibody 4A12 was predicted to have the best accessibility to all three ACE2-interfaces on the spike homotrimer. Pseudovirus and authentic SARS-CoV-2 neutralization assays showed that all four antibodies could potently protect host cells from virus infection. Overall, we isolated multiple formats of SARS-CoV-2-neutralizing antibodies via site-directed antibody screening, which could be promising candidate drugs for the prevention and treatment of COVID-19.
Distributed Control of Large-Scale Offshore Wind Farms (2009)

The control of wind turbine farms can be separated in two levels.The first level is the network operator giving a set point for active and reactive power for the whole farm.This project focuses on the next level of the wind farm control where the farm set point are distributed into single turbine set points.Currently, this is done in a basic manner where all turbines essentially are treated the same disregarding the present local wind field and turbine status.The aim with this project is to exploit information from all turbines in the control of individual turbines in the farm.This paper first discussed the above problem in more details.Then the five work packages included in the project are described.Finally preliminary work on the simulation model included in one of the work packages is presented.
Stem Cells from Human Fat as Cellular Delivery Vehicles in an Athymic Rat Posterolateral Spine Fusion Model (2008)

Adipose-derived stem cells show promise as gene transduction targets for inducing bone formation to enhance spinal fusion in biologically stringent environments.
Establishment and characterization of a murine hybridoma secreting monoclonal anti-DNA autoantibody. (1980)

Twenty-five clones of hybridoma cells secreting anti-DNA autoantibodies were isolated after fusions between plasmacytoma cells (P3-x 63 Ag 8.653) and spleen cells from nonimmunized autoimmune NZB/NZW F1 (B/W) mice. A monoclonal anti-DNA autoantibody was immunochemically analyzed.
Keyword query cleaning (2008)

Unlike traditional database queries, keyword queries do not adhere to predefined syntax and are often dirty with irrelevant words from natural languages. This makes accurate and efficient keyword query processing over databases a very challenging task. In this paper, we introduce the problem of query cleaning for keyword search queries in a database context and propose a set of effective and efficient solutions. Query cleaning involves semantic linkage and spelling corrections of database relevant query words, followed by segmentation of nearby query words such that each segment corresponds to a high quality data term. We define a quality metric of a keyword query, and propose a number of algorithms for cleaning keyword queries optimally. It is demonstrated that the basic optimal query cleaning problem can be solved using a dynamic programming algorithm. We further extend the basic algorithm to address incremental query cleaning and top- k optimal query cleaning. The incremental query cleaning is efficient and memory-bounded, hence is ideal for scenarios in which the keywords are streamed. The top- k query cleaning algorithm is guaranteed to return the best k cleaned keyword queries in ranked order. Extensive experiments are conducted on three real-life data sets, and the results confirm the effectiveness and efficiency of the proposed solutions.
Analysis of ovarian tumor pathology by Fourier Transform Infrared Spectroscopy (2010)

The measured spectroscopic features, which are the spectroscopic fingerprints of the tissues, provided the important differentiating information about the malignant and normal tissues. The findings of this study demonstrate the possible use of infrared spectroscopy in differentiating normal and malignant ovarian tissues.
Inverse halftoning algorithm using edge-based lookup table approach (2005)

The inverse halftoning algorithm is used to reconstruct a gray image from an input halftone image. Based on the recently published lookup table (LUT) technique, this paper presents a novel edge-based LUT method for inverse halftoning which improves the quality of the reconstructed gray image. The proposed method first uses the LUT-based inverse halftoning method as a preprocessing step to transform the given halftone image to a base gray image, and then the edges are extracted and classified from the base gray image. According to these classified edges, a novel edge-based LUT is built up to reconstruct the gray image. Based on a set of 30 real training images with both low-and high-frequency contents, experimental results demonstrated that the proposed method achieves a better image quality when compared to the currently published two methods, by Chang et al. and Meşe and Vaidyanathan.
3D dual-virtual-pinhole assisted single particle tracking microscopy (2014)

We propose a novel approach for high-speed, three-dimensional single particle tracking (SPT), which we refer to as dual-virtual-pinhole assisted single particle tracking microscopy (DVPaSPTM). DVPaSPTM system can obtain axial information of the sample without optical or mechanical depth scanning, so as to offer numbers of advantages including faster imaging, improved efficiency and a great reduction of photobleaching and phototoxicity. In addition, by the use of the dual-virtual-pinhole, the effect that the quantum yield exerts to the fluorescent signal can be eliminated, which makes the measurement independent of the surroundings and increases the accuracy of the result. DVPaSPTM system measures the intensity within different virtual pinholes of which the radii are given by the host computer. Axial information of fluorophores can be measured by the axial response curve through the ratio of intensity signals. We demonstrated the feasibility of the proposed method by a series of experiments. Results showed that the standard deviation of the axial measurement was 19.2 nm over a 2.5 μm range with 30 ms temporal resolution.
THERMOELECTRIC CONVERSION TO RECOVER HEAVY DUTY DIESEL EXHAUST ENERGY (1991)

Thermoelectric energy conversion has been evaluated as a method for utilizing a portion of the waste heat stream from a heavy duty diesel engine. The intent is to improve overall propulsion system efficiency and provide a reasonable payback to the user of a large truck. Several types of 14 V thermoelectric converters have been evaluated. These include liquid and air cooled versions operating in conjunction with the normal alternator powered electrical system of the truck. It appears feasible to design a convertor that can be installed in the exhaust system downstream of the turbocharger and operate over a full range of truck conditions (idle, city, cruise, uphill). The economic results of installing the converter depend upon a number of complex design tradeoffs. Using the cruise condition as the primary design point for a 1000 W thermoelectric convertor, its price is projected to be in the range of $0.65 to $0.85 per watt output. The use of advanced thermoelectric materials will enable improvements to be realized in both weight and size. (A) For the covering abstract of the proceedings see IRRD 853538.
Generalized expressions for characterizing a linear multiport circuit coupled with external fields (1994)

The outputs of a linear multiport circuit immersed in external fields are analyzed using the S-parameters in frequency and time domains. It is suggested that the matched output voltage is a proper and convenient parameter for characterizing the circuit coupled with external fields, since it can be measured easily in a higher frequency range than a few hundred megahertz. The output voltages of the circuit terminated with loads of arbitrary impedance are calculated from measured values of the matched output voltages, the S-parameters of the circuit, and the reflection coefficients of the loads. Related formulas are derived for the characterization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Automatic Building Extraction on High-Resolution Remote Sensing Imagery Using Deep Convolutional Encoder-Decoder With Spatial Pyramid Pooling (2019)

Automatic extraction of buildings from remote sensing imagery plays a significant role in many applications, such as urban planning and monitoring changes to land cover. Various building segmentation methods have been proposed for visible remote sensing images, especially state-of-the-art methods based on convolutional neural networks (CNNs). However, high-accuracy building segmentation from high-resolution remote sensing imagery is still a challenging task due to the potentially complex texture of buildings in general and image background. Repeated pooling and striding operations used in CNNs reduce feature resolution causing a loss of detailed information. To address this issue, we propose a light-weight deep learning model integrating spatial pyramid pooling with an encoder-decoder structure. The proposed model takes advantage of a spatial pyramid pooling module to capture and aggregate multi-scale contextual information and of the ability of encoder-decoder networks to restore losses of information. The proposed model is evaluated on two publicly available datasets; the Massachusetts roads and buildings dataset and the INRIA Aerial Image Labeling Dataset. The experimental results on these datasets show qualitative and quantitative improvement against established image segmentation models, including SegNet, FCN, U-Net, Tiramisu, and FRRN. For instance, compared to the standard U-Net, the overall accuracy gain is 1.0% (0.913 vs. 0.904) and 3.6% (0.909 vs. 0.877) with a maximal increase of 3.6% in model-training time on these two datasets. These results demonstrate that the proposed model has the potential to deliver automatic building segmentation from high-resolution remote sensing images at an accuracy that makes it a useful tool for practical application scenarios.
A Novel Omnidirectional Stereo Vision System with a Single Camera (2007)

Wide field of view is the most attractive feature of the omnidirectional vision. There exist two approaches to omnidirectional stereo imaging with a single camera. They use: (1) a double lobed mirror (Fiala & Basu, 2005)(Cabral et al., 2004), or (2) two mirrors (Jang et al., 2005). In this paper, a third approach is described using a mirror and a concave lens. By adjusting the position of the concave lens, it is possible to control the disparity between two stereo images and the accuracy of the 3D distance computation. Since the optical components adopted in the proposed system are commercially available, the proposed omnidirectional stereo imaging system is compact and cost-effective. Based on the simple optics composed of the reflection and the refraction on the convex mirror and the concave lens, an expression for the 3D distance is derived. The proposed method is versatile in the sense that it is also applicable to different types of convex mirrors, e.g., the parabolic mirror. The second approach (2) mentioned above involves a relatively lengthy baseline, and therefore a longer depth range than (1) and the approach proposed in this paper. Two simple ways of getting longer range of sight with (1) and the approach in this paper are to use a larger mirror or a camera with higher resolution.
Detecting Malicious URLs via a Keyword-Based Convolutional Gated-Recurrent-Unit Neural Network (2019)

With the continuous development of Web attacks, many web applications have been suffering from various forms of security threats and network attacks. The security detection of URLs has always been the focus of Web security. Many web application resources can be accessed by simply entering an URL or clicking a link in the browser. An attacker can construct various web attacks such as SQL, XSS, and information disclosure by embedding executable code or injecting malicious code into the URL. Therefore, it is necessary to improve the reliability and security of web applications by accurately detecting malicious URLs. This paper designs a convolutional gated-recurrent-unit (GRU) neural network for the detection of malicious URLs detection based on characters as text classification features. Considering that malicious keywords are unique to URLs, a feature representation method of URLs based on malicious keywords is proposed, and a GRU is used in place of the original pooling layer to perform feature acquisition on the time dimension, resulting in high-accuracy multicategory results. The experimental results show that our proposed neural network detection model is very suitable for high-precision classification tasks. Compared with other classification models, the model accuracy rate is above 99.6%. The use of deep learning to classify URLs to identify Web visitors' intentions has important theoretical and scientific values for Web security research, providing new ideas for intelligent security detection.
Real-Time Reverse Transcription-PCR Assay for Comprehensive Detection of Human Rhinoviruses (2007)

Human rhinoviruses (HRVs) are important contributors to respiratory disease, but their healthcare burden remains unclear, primarily because of the lack of sensitive, accurate, and convenient means of determining their causal role. To address this, we developed and clinically validated the sensitivity and specificity of a real-time reverse transcription-PCR (RT-PCR) assay targeting the viral 5' noncoding region defined by sequences obtained from all 100 currently recognized HRV prototype strains and 85 recently circulating field isolates. The assay successfully amplified all HRVs tested and could reproducibly detect 50 HRV RNA transcript copies, with a dynamic range of over 7 logs. In contrast, a quantified RNA transcript of human enterovirus 68 (HEV68) that showed the greatest sequence homology to the HRV primers and probe set was not detected below a concentration of 5 x 10(5) copies per reaction. Nucleic acid extracts of 111 coded respiratory specimens that were culture positive for HRV or HEV were tested with the HRV real-time RT-PCR assay and by two independent laboratories that used different in-house HRV/HEV RT-PCR assays. Eighty-seven HRV-culture-positive specimens were correctly identified by the real-time RT-PCR assay, and 4 of the 24 HEV-positive samples were positive for HRV. HRV-specific sequences subsequently were identified in these four specimens, suggesting HRV/HEV coinfection in these patients. The assay was successfully applied in an investigation of a coincidental outbreak of HRV respiratory illness among laboratory staff.
Merits of cellwise model-based OPC (2004)

One of the most compute intensive dataprep operations for 90nm PC level is the model-based optical proximity correction (MBOPC). The running time and output data size are growing unacceptably, particularly for ASICs and designs containing large macros built out of library cells (books). The reason for this growth is that the region-of-interest for MBOPC is approximately 600nm, which means that most library cells “see” interactions with adjacent books in the same row and also in adjacent rows.

In this paper, we investigate the merits of doing cellwise MBOPC. In its simplest form, the approach is to perform dataprep for each cell once per cell definition rather than once per placement. By inspection, this will reduce the computation time and output data size by a factor of P/D, where P is the number of book placements (100s to millions) and D is the number of book definitions. 
Our preliminary finding indicates that there is negligible difference between nominal CD for cellwise corrected cells and chipwise corrected cells. We will present our finding in terms of average CD and contact coverage, as well as runtime reduction.
Fuel efficiency and the physics of automobiles (1997)

Energy flows and energy efficiencies in the operation of a modern automobile are expressed in terms of simple algebraic approximations. One purpose is to make a car's energy use and the potential for reducing it accessible to non-specialists with technical backgrounds. The overall energy use depends on two factors, vehicle load and powertrain efficiency. The former depends on speed and acceleration and key vehicle characteristics such as mass. The latter depends on heat-engine thermodynamic efficiency, and engine and transmission frictions. The analysis applies to todays automobiles. Numerical values of important parameters are given so that the reader can make his or her own estimates. Various technologies to reduce the energy consumption of automobiles are discussed.
Micromachined thermal conductivity sensor for the liquid phase (2005)

Due to the small thermal masses and reduced conductivities, membrane-based micromachined thermal sensors offer features superior to those provided by comparable macroscopic measurement setups. Such a device is applied to determine the thermal transport properties of various liquids. By sinusoidally exciting a heater, that is placed on a membrane, and recording the resulting temperature at a specified distance, both the thermal conductivity and the diffusivity of the liquid can be determined by means of amplitude and phase measurements.