gebhart/patrepeval huggingface dataset:
Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination (2018)

Clinical trial registration: The trial was registered with ClinicalTrials.gov with Identifier NCT01537185; the results are available from https://clinicaltrials.gov/ct2/show/results/NCT01537185.
Rheological and Dispersing Properties of Calcite-Goethite Mixed Aqueous Suspension (1976)

Based on flow and sedimentation measurements, rheological and dispersing properties of calcite-goethite mixed suspensions were evaluated and their mutual correlation was discussed. By applying Casson's equation to the results of flow measurements, two parameters, as and αβ, were calculated, whereas from sedimentation experiments the median diameter and the sedimentation volume were obtained and taken as the criteria of dispersity. These four parameters varied themselves parallel to each other with varying mixing composition of two solid components, total solid content being kept constant, and they showed maxima at the volume fraction of goethite approximately equal to 0.8. The parameter αβ was found to serve as a practical and yet well defined measure of interparticle forces in liquid media, even for a mixed suspension where heteroflocculation predominantly takes place.
Molecular Optimization by Capturing Chemist’s Intuition Using Deep Neural Networks (2020)

A main challenge in drug discovery is finding molecules with a desirable balance of multiple properties. Here, we focus on the task of molecular optimization, where the goal is to optimize a given starting molecule towards desirable properties. This task can be framed as a machine translation problem in natural language processing, where in our case, a molecule is translated into a molecule with optimized properties based on the SMILES representation. Typically, chemists would use their intuition to suggest chemical transformations for the starting molecule being optimized. A widely used strategy is the concept of matched molecular pairs where two molecules differ by a single transformation. We seek to capture the chemist's intuition from matched molecular pairs using machine translation models. Specifically, the sequence-to-sequence model with attention mechanism, and the Transformer model are employed to generate molecules with desirable properties. As a proof of concept, three ADMET properties are optimized simultaneously: logD, solubility, and clearance, which are important properties of a drug. Since desirable properties often vary from project to project, the user-specified desirable property changes are incorporated into the input as an additional condition together with the starting molecules being optimized. Thus, the models can be guided to generate molecules satisfying the desirable properties. Additionally, we compare the two machine translation models based on the SMILES representation, with a graph-to-graph translation model HierG2G, which has shown the state-of-the-art performance in molecular optimization. Our results show that the Transformer can generate more molecules with desirable properties by making small modifications to the given starting molecules, which can be intuitive to chemists. A further enrichment of diverse molecules can be achieved by using an ensemble of models.
Management of Multilevel, Multiclient Cache Hierarchies with Application Hints (2011)

Multilevel caching, common in many storage configurations, introduces new challenges to traditional cache management: data must be kept in the appropriate cache and replication avoided across the various cache levels. Additional challenges are introduced when the lower levels of the hierarchy are shared by multiple clients. Sharing can have both positive and negative effects. While data fetched by one client can be used by another client without incurring additional delays, clients competing for cache buffers can evict each other’s blocks and interfere with exclusive caching schemes. We present a global noncentralized, dynamic and informed management policy for multiple levels of cache, accessed by multiple clients. Our algorithm, MC 2 , combines local, per client management with a global, system-wide scheme, to emphasize the positive effects of sharing and reduce the negative ones. Our local management scheme, Karma , uses readily available information about the client’s future access profile to save the most valuable blocks, and to choose the best replacement policy for them. The global scheme uses the same information to divide the shared cache space between clients, and to manage this space. Exclusive caching is maintained for nonshared data and is disabled when sharing is identified. Previous studies have partially addressed these challenges through minor changes to the storage interface. We show that all these challenges can in fact be addressed by combining minor interface changes with smart allocation and replacement policies. We show the superiority of our approach through comparison to existing solutions, including LRU, ARC, MultiQ, LRU-SP, and Demote, as well as a lower bound on optimal I/O response times. Our simulation results demonstrate better cache performance than all other solutions and up to 87% better performance than LRU on representative workloads.
Simplified approach to assessing intravenous flow characteristics in the therapeutic infusion range (1988)

It is shown that the pressure-flow (P-F) relationship in intravenous infusion systems can be simply described by the flow parameters R/sub L/ (linear-resistance) and F/sub E/ (flow nonlinearity). The relative-pressure error due to nonlinear flow is found to be insignificant in the flow range used for therapeutic intravenous infusion therapy (F<or=300 ml/h); a linear P-F model would therefore suffice. At higher flows such as 999 ml/h and in the fluid resuscitation range, the nonlinear contribution to the P-F relationship becomes significant.<<ETX>>
Printed electronics and additive packaging for microwave applications (2017)

There is growing interest in adopting additive technologies for the production of RF/microwave electronics. In addition to the ability for rapid prototyping, printed electronics can offer the manufacturing of electronics in nontraditional form factors-flexible, lightweight, conformable or wearable. Developing printed electronics for the RF/microwave/wireless domain is particularly challenging since the requisite materials, fabrication technologies (i.e., printing), device characterization and design methodolgies require higher performance than low frequency applications. In addition to use in DoD systems (e.g., radars, communications) this printing technology can be applied to commercial applications such as IoT and 5G telecommunication products and may benefit from expoiting additive technologies in microelectronic packaging.
Brain Erythropoietin Receptor Expression in Alzheimer Disease and Mild Cognitive Impairment (2007)

Cellular mechanisms conferring neuroprotection in the brains of patients with Alzheimer disease (AD) remain incompletely understood. Erythropoietin (Epo) and the erythropoietin receptor (EpoR) are expressed in neural tissues and protect against oxidative and other stressors in various models of brain injury and disease. Our objective in this study was to determine whether EpoR is upregulated in the brains of persons with sporadic AD and mild cognitive impairment (MCI). Postmortem hippocampus and temporal cortex from subjects with AD, MCI, and no cognitive impairment (NCI) were procured from the Religious Orders Study. Total immunoreactive EpoR protein was determined by Western blotting. Astrocytes expressing immunoreactive EpoR were quantified in 4 temporal and 6 hippocampal regions, and correlated with clinical, neuropsychologic, and neuropathologic indices. Total immunoreactive EpoR protein was markedly increased in AD and MCI temporal cortex versus NCI tissues. Composite measures of glial EpoR expression in temporal cortex layers I to IV were significantly greater in the MCI group compared with the NCI and AD groups. Hippocampal EpoR scores were increased in persons with MCI and AD relative to those with NCI. There was substantial subregional heterogeneity in disease-related EpoR expression patterns in AD and MCI temporal cortex and hippocampus. There was no association of EpoR-positive astrocytes with summary measures of global cognition or AD pathology. We conclude that upregulation of EpoR in temporal cortical and hippocampal astrocytes is an early, potentially neuroprotective, event in the pathogenesis of sporadic AD.
High-Frequency Injection-Based Stator Flux Linkage and Torque Estimation for DB-DTFC Implementation on IPMSMs Considering Cross-Saturation Effects (2014)

Deadbeat-direct torque and flux control (DB-DTFC) is a direct torque control method that provides the fastest possible torque control, low ripple, easily integrated dynamic loss minimization control, and one control law that uses the inherent volt-second source properties of power electronics to enable operation over all operating conditions, including voltage limits. DB-DTFC is a model-based discrete time controller that relies on precise machine parameter, flux, and torque estimation to provide fast dynamic torque control. In this paper, a new method for high-frequency injection (HFI)-based self- and mutual incremental inductance estimation is proposed and evaluated in both simulations and experiments. In this new method, the estimated incremental inductances including cross-coupling inductance due to cross saturation are curve fitted offline and then used to calculate the apparent inductances. With the apparent inductances, the stator resistance and permanent-magnet flux linkage are estimated using recursive least squares method online. The stator flux linkage observer using the identified machine parameters yields improved stator flux linkage estimates that enable precise torque calculation. Experimental evaluation of the HFI-based flux estimates on torque estimation and control accuracy is performed at an interior permanent-magnet synchronous machine drive test bench with a torque transducer mounted.
A silicon-based flexible tactile sensor for ubiquitous robot companion applications (2006)

We present the fabrication process and characteristics of a 3-axes flexible tactile sensor available for normal and shear mode fabricated using Si micromachining and packaging technologies. The fabrication processes for the 3 axes flexible tactile sensor were classified in the fabrication of sensor chips and their packaging on the flexible PCB. The variation rate of resistance was about 2.1%/N and 0.5%/N in applying normal and shear force, respectively. Because this tactile sensor can measure the variations of resistance of the semiconductor strain gauge for normal and shear force, it can be used to sense touch, pressure, hardness, and slip.
Parthenolide, an anti-inflammatory NFκB inhibitor, stimulates platelet production and blunts platelet activation (87.17) (2010)

Abstract Platelets play a significant role in hemostasis, and are critically involved in common medical complications including thrombocytopenia, ischemia, and atherosclerosis. Platelets can also directly induce inflammation and influence immune cells by releasing inflammatory mediators such as CD40 Ligand, TGF-β, PGE2, IL-1β, and MIP-1α. Despite these recent findings, platelet signaling pathways remain unclear and are under current investigation. Recently, our lab identified the presence of NFκB transcription factors in platelets. Because platelets are anucleate, we hypothesize an alternative role for NFκB in platelet function. To further study the role of NFκB in platelets, we tested the effects of an NFκB inhibitor, Parthenolide, on human platelets and Meg-01 cells, a human megakaryoblastic cell line. Parthenolide is an extract of the Feverfew plant used in herbal therapies to dampen inflammation. We found that Parthenolide directly influenced human platelets by diminishing clot retraction and spreading. In addition, we found that Parthenolide increased platelet production, increased heme oxygenase-1 (up to 2000-fold), and increased glutathione levels over time (p=0.02) in Meg-01 cells. These data suggest that the anti-inflammatory properties of Parthenolide may be partially due to its ability to suppress platelet activation and up-regulate anti-oxidant pathways.
Epigenomic analysis of bronchial epithelial cells in smokers at risk of developing lung cancer (2007)

A91 Background: DNA methylation abnormalities are both very early events in cancer development and very widespread events in advanced neoplastic disease. Due to the early nature of DNA methylation disturbance, it also has applications as a biomarker in serum, sputum, and biopsies. However, analysis of epigenetic events has been limited by technique throughput and by sample material requirement, thus limiting this approach to the analysis of only a few genes. The ability to analyze many loci from minute starting materials in the small airways of the lung would greatly facilitate the use of DNA methylation as both a discovery tool and as a biological marker.  >Objective: The objective of the current study is to improve current technologies and adapt them to the investigation of exfoliated bronchial epithelial cells collected by bronchoscopy. With the new techniques, we will monitor the effect of steroid treatment on the epigenome of bronchial cells.  >Methods: Patients were treated for 4 weeks with inhaled steroid. Exfoliated bronchial cells were collected during bronchoscopy from airways ≤ 2mm in diameter both before and after treatment. Nucleic acids (DNA/RNA) were extracted by standard biochemical means. DNA methylation profiles were generated for the epithelial cells using a whole genome tiling path (WGTP) array by methylation dependent immunoprecipitation (MeDIP) array CGH. In MeDIP, immunoprecipitation with anti-5’-methylcytosine isolates methylated DNA fragments. The methylated fragments and input DNA (without immunoprecipitation) from the same sample are differentially labeled with Cyanine-3 and Cyanine-5 respectively, and competitively co-hybridized to the genomic array. Dye ratios at individual spots on the array are mapped to their genomic location, and are used to infer methylation status. This approach generates a DNA methylation map spanning the entire genome.  >Results: Our results indicate that whole genome DNA methylation profiles can be produced reliably from airway epithelial cells. We have reduced the material requirement to only 1μg of genomic DNA, without requiring subsequent sample amplification. Analysis of DNA methylation profiles before and after treatment with steroid identified 17 regions of DNA hypermethylation and 16 regions of DNA hypomethylation corresponding to steroid treatment that were present in a minimum of 50% (5/10) of patients analyzed.  >Conclusion: We have demonstrated that MeDIP aCGH is a valuable tool for the analysis of DNA methylation profiles in the small airways of the lung. This suggests the potential of using this technique for genome-wide assessment of methylation changes in lung diseases.
Low-Noise Amplifier Design Considerations For Use in Antenna Arrays (2015)

This work analyzes the implications of noise coupling in arrays of antennas on the design of low-noise amplifiers (LNAs). To select LNA design parameters in a manner familiar to LNA designers, the effective noise temperatures T <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</sup> of LNAs are presented. The effect of beamformer coefficients and antenna coupling on T <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</sup> is analyzed in a manner similar to a stand-alone LNA analysis. This leads to the proposed LNA design strategy of selecting LNA Γ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">opt</sub> near the reflection coefficient of antenna ports and selecting the largest practical |S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> | with a proper phase. This strategy is based on the assumption that the antenna array may be used for various beamforming and nonbeamforming applications, unknown at the time of the design. Numerical simulations of a 38- and 41-element antenna arrays show that a global search of LNA S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> and Γ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">opt</sub> , which result in the minimum average beam-equivalent receiver noise temperature T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rec</sub> , finds nearly identical results to the proposed LNA design strategy. For a 41-element array with high antenna coupling at low frequencies, the proposed method shows as much as 80% improvement in the T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rec</sub> over conventional LNA design strategies that do not account for the intended use of the amplifier in an array.
Digital Rights Management for Consumer Devices (2006)

This chapter focuses on the technical aspects of specific content protection schemes. The ongoing digital revolution has presented both a threat and a promise to the entertainment industry. Digital technologies promise inexpensive consumer devices, convenient distribution and duplication, and flexible new business models. In the late 1980s, the consumer electronics industry had developed a new technology called Digital Audio Tape. Broadcast encryption brings with it several desirable properties, not the least of which is that it needs substantially less device overhead than public key cryptography. The consumer promise of the personal digital domain is enticing. Freed from having to count copies, consumers could make unlimited copies for backup and for the convenience of playback at various places and times. The Serial Copy Management System is the heart of simplicity. Two bits in a header are used to encode three states: “copy freely,” “copy once,” or “copy never.” The Content Scrambling System works by assigning each device manufacturer a single key.
Micro orifice based cell pairing and fusion on microfluidic chip (2009)

Micro orifice assisted cell fusion assures high-yield fusion without compromising the cell viability. This paper examines feasibility of a cell pairing method compatible with micro orifice based cell fusion to create large number of viable fusants for studying post-fusion cell behavior. We fabricated a microfluidic chip which contained a chamber and a partition. The partition divided the chamber into two compartments and it had a number of embedded micro orifices. The voltage applied to the electrodes located at each compartment generated electric field distribution concentrating in each micro orifice. Cells introduced into each compartment moved towards micro orifice by manipulation of hydrostatic pressure. Dielectrophoretic force trapped the cells in micro orifice and established cell to cell contact through orifice. By applying a pulse, cell fusion was initiated to form a neck between cells. The neck passing through orifice resulted in immobilization of the fused cell pair. Unfused cells washed away. Then, the chip was loaded to a microscope stage incubator for time lapse imaging of the immobilized fusants. The viable fusants were successfully generated by fusion of mouse fibroblast cells. Time lapse observation of the five fusants showed that fused cell pairs were released from micro orifice and became one body. Fusants which reached to cell division phase divided into three daughter cells. We conclude that the presented method of cell pairing and fusion is suitable for high-yield generation of viable fusants and studying of post-fusion phenomena.
Active Neutron Interrogation to Detect Shielded Fissionable Material (2009)

Portable electronic neutron generators (ENGs) may be used to interrogate suspicious items to detect, characterize, and quantify the presence fissionable material based upon the measurement of prompt and/or delayed emissions of neutrons and/or photons resulting from fission. The small size (<0.2 m3), light weight (<12 kg), and low power consumption (<50 W) of modern ENGs makes them ideally suited for use in field situations, incorporated into systems carried by 2-3 individuals under rugged conditions. At Idaho National Laboratory we are investigating techniques and portable equipment for performing active neutron interrogation of moderate sized objects less than ~2-4 m3 to detect shielded fissionable material. Our research in this area relies upon the use of pulsed deuterium-tritium ENGs and the measurement of die-away prompt fission neutrons and other neutron signatures in-between neutron pulses from the ENG and after the ENG is turned off.
In vitro effects of the active metabolite of leflunomide, A77 1726, on feline herpesvirus–1 (2007)

Leflunomide may be an alternative to current calcineurin-based immunosuppressive protocols used in feline organ transplantation because of its antiherpesviral activity.
Dual-Source Computed Tomography (2007)

Scanning with 83 milliseconds temporal resolution improved image quality of coronary plaque at higher heart frequencies.
Operation Characteristics of A6 Relativistic Magnetron Using Single-Stepped Cavities With Axial Extraction (2014)

We report the performance of an A6 relativistic magnetron with single-stepped cavities output. Particle-in-cell simulation shows the electronic efficiency of an A6 relativistic magnetron with an anode block made of six single-stepped cavities can be up to 78% with an output power of one gigawatt for an applied voltage of 400 kV. When the A6 relativistic magnetron with axial extraction using six single-stepped cavities is applied with a voltage of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="TeX">\(V \sim 400~{\rm kV}\pm 50\) </tex-math></inline-formula> kV the electronic efficiency can be as high as 60%, while the output power can be as high as 1 GW. And, when a 10-ns voltage pulse of 400 kV is applied on this magnetrons with diffraction output using single-stepped cavities, the output power pulse can be as high 1.2 GW. The results in this paper will provide a reference for choosing a cavity that is easily manufactured, so that a physical experiment is more feasible.
Facilitating Video Access by Visualizing Automatic Analysis. (1999)

ABSTRACT When reviewing collections of video such as recorded meetings or presentations, users are often interested only in an overview or short segments of these documents. We present techniques that use automatic feature analysis, such as slide detection and applause detection, to help locate the desired video and to navigate to regions of interest within it. We built a web-based interface that graphically presents information about the contents of each video in a collection such as its keyframes and the distribution of a particular feature over time. A media player is tightly integrated with the web interface. It supports navigation within a selected file by visualizing confidence scores for the presence of features and by using them as index points. We conducted a user study to refine the usability of these tools.