gebhart/patrepeval huggingface dataset:
Solvent extraction of fatty acids from natural oils with liquid water at elevated temperatures and pressures (1990)

The use of liquid water at elevated temperatures and pressures as an extractive solvent for separating mixtures of compounds which occur in natural oils has been studied. A southern pine tall oil and a distillate from the deodorization of soybean oil were extracted with liquid water at temperatures from 298 to 312°C and pressures between 103 and 121 bar. Results indicate that water can be used to extract fatty and resin acids from crude tall oil to obtain a product with a high acid content that produces less pitch during distillation. The process can also be used to extract fatty acids from vegetable oil deodorizer distillate.
Mapping of receptor binding sites on IL-1 β by reconstruction of IL-1ra-like domains (1995)

Upon structure comparison between IL-1 beta and its antagonist IL-1ra, single or multiple residues along the IL-1 beta sequence were replaced with the corresponding amino acids present in the IL-1ra protein, in the attempt to identify sites important for receptor binding and for biologic activity on the two molecules. Ten of fifteen mutant proteins had activity comparable to that of wild-type IL-1 beta in three different biologic assays and in receptor binding, indicating that the introduced changes did not influence the functional structure of the protein. Conversely, three mutants (SMIL-9: 127/263 R/T-->W/Y; SMIL-10: 125/127/263/265 T/R/T/Q-->R/W/Y/E; SMIL-15:222/227 I/E-->S/S) showed an increased binding capacity for IL-1RI, not paralleled by increased agonist activity, indicating that the introduced IL-1ra residues could be involved in the nonagonist IL-1RI binding site. On the other hand, two mutants showed diminished binding capacity with concomitant decrease in biologic activity. Both mutants (SMIL-1, five substitutions in the loop 202-214; and SMIL-3, total replacement of the loop 164-173 with the IL-1ra stretch 52-55) included substitutions of residues allegedly important for agonist binding to IL-1RI. Mutant SMIL-3 showed the most profound reduction in binding capacity for IL-1RI (CDw121a) and a more than 1,000-fold reduced biologic activity both in vitro and in vivo, but it retained full capacity of binding to IL-1RII (CDw121b) and acted as a selective antagonist of IL-1RII. From these results the following conclusions can be drawn. IL-1 beta binds to IL-1RI and to IL-1RII through different sites, and the loop 164-173 appears as one of the areas involved in the selective interaction with IL-1RI. Agonist (IL-1 beta) and nonagonist (IL-1ra) binding to IL-1RI occur through distinct sites, with loops 164-173 and 202-214 of IL-1 beta identified as two of the sites selectively involved in agonist binding to the activating receptor.
Automatic Network Slicing for Multi-Mode Internet of Underwater Things (MM-IoUT) (2022)

In recent years, many underwater communication applications have been proposed and tested, leading to the Internet of underwater things (IoUT) concept. In the IoUT, sensors may be deployed individually on sea surface and seabed as well as in water at different depths. They also may be integrated into underwater items such as fish, plants, autonomous underwater vehicles (AUVs), remotely operated underwater vehicles (ROVs), and divers. Depending on the application, different connectivity requirements must be satisfied such as data rate, latency, and reliability. However, the underwater communication channels pose a significant challenge to meet these requirements. To accommodate various applications with different service level agreements (SLAs), a multimode (acoustic, optical, and magnetic induction (MI)) communication system is proposed to take advantage of the modes' complementary features. Furthermore, an automatic network slicing (ANS) solution is proposed to provide globally optimized resource management, enhanced quality of service (QoS), simplified network operation, reduced deployment cost, and functional isolation of services. Taking the channel characteristics of the acoustic, optical, and MI communication modes into consideration, an optimization problem is formulated and solved for multimode IoUT (MM-IoUT) to enable admission control, routing, and dynamic resource allocation based on the different SLAs. Numerical analysis is conducted to verify the proposed solution and evaluate its performance.
Adaptive asymmetric linearization of radio over fiber links for wireless access (2002)

The biggest concern in the use of radio-over-fiber (ROF) links in wireless access is their limited dynamic range due to nonlinear distortion (NLD). In this paper, a higher order adaptive filter based nonlinearity compensation scheme is proposed. Pre-compensation is done for the downlink while post-compensation is done for the uplink to result in asymmetry with respect to complexity. This centralized signal processing is attractive in that it keeps the remote unit simple. Accurate measurements of ROF link parameters are not required with this approach because the filters are adapted from the distortion of the input/output base band signal. This technique also facilitates fast tracking of modifications and drifts in the link characteristics. Measurements and simulation results show that gradually saturating amplitude nonlinearity can be adequately linearized with some backoff from the clipping limit. A 42% backoff is required for pre-compensation to protect the laser while only a 16.7% backoff is required for post-compensation. Phase pre-compensation is accomplished with a higher accuracy than phase post-compensation.
Uncertainty-aware circuit optimization (2002)

Almost by definition, well-tuned digital circuits have a large number of equally critical paths, which form a so-called "wall" in the slack histogram. However, by the time the design has been through manufacturing, many uncertainties cause these carefully aligned delays to spread out. Inaccuracies in parasitic predictions, clock slew, model-to-hardware correlation, static timing assumptions and manufacturing variations all cause the performance to vary from prediction. Simple statistical principles tell us that the variation of the limiting slack is larger when the height of the wall is greater.Although the wall may be the optimum solution if the static timing predictions were perfect, in the presence of uncertainty in timing and manufacturing, it may no longer be the best choice. The application of formal mathematical optimization in transistor sizing increases the height of the wall, thus exacerbating the problem. There is also a practical matter that schematic restructuring downstream in the design methodology is easier to conceive when there are fewer equally critical paths. This paper describes a method that gives formal mathematical optimizers the incentive to avoid the wall of equally critical paths, while giving up as little as possible in nominal performance. Surprisingly, such a formulation reduces the degeneracy of the optimization problem and can render the optimizer more effective. This "uncertainty-aware" mode has been implemented and applied to several high-performance microprocessor macros. Numerical results are included.
Triplet management in organic light emitting diodes and lasers (2012)

By doping a molecule with low triplet energy in the active regions of organic light emitting diodes and lasers, we demonstrate suppressed triplet-induced losses, thus overcoming a significant obstacle to electrically pumped organic lasers.
Photopolarimetric measurement of the Mueller matrix by Fourier analysis of a single detected signal (1978)

All 16 elements of the Mueller matrix of an optical system (sample) can be encoded onto, hence can be retrieved from, a single detected signal using a class of photopolarimeters with modulated polarizing and analyzing optics. The general theory of operation of such polarimeters is presented. We also propose a specific new photopolarimeter whose polarizing and analyzing optics are modulated by synchronously rotating two quarter-wave retarders at angular speeds ω and 5ω. When the light flux leaving such polarimeter is linearly detected, a periodic signal J=a0+∑n=112(an cos nωft+bn sin nωft) is generated, with fundamental frequency ωf = 2ω. From the Fourier amplitudes a0, an, bn, to be measured by performing a discrete Fourier transform (DFT) of the signal ℐ, the 16 elements of the Mueller matrix are simply determined.
Differentiation of human pluripotent stem cells to brain microvascular endothelial cell-like cells suitable to study immune cell interactions (2021)

We describe the extended endothelial cell culture method (EECM) for the differentiation of human pluripotent stem cells (hPSCs) into brain microvascular endothelial cell (BMEC)-like cells. EECM-BMEC-like cells resemble primary human BMECs in morphology, molecular junctional architecture, and diffusion barrier characteristics. A mature immune phenotype with proper endothelial adhesion molecule expression makes this model distinct from any other hPSC-derived <i>in vitro</i> blood-brain barrier (BBB) model and suitable to study immune cell migration across the BBB in a disease relevant and personalized fashion. For complete details on the use and execution of this protocol, please refer to Lian et al. (2014), Nishihara et al. (2020a).
Photoelectrochemical etching of p-type GaN heterostructures (2009)

We have developed a method for photoelectrochemical etching of p-type semiconductors, including GaN, that relies on the built-in bandbending already inherent to optical devices. Electron-hole pairs are generated by filtered light in a buried small bandgap layer, and a pn junction separates the charge. Electrons are sent into the n-type layer, where they are extracted, and holes to the surface, where they participate in etching reactions. This technique is rapid and inexpensive, and it requires no applied bias or elevated temperatures. This technique has widespread applications to GaN optical devices where ion-damage-free etching or wide tunability of etch parameters is desired.
Separation of metallic single‐walled carbon nanotubes using various amines (2010)

Abstract Separation of metallic single‐walled carbon nanotubes (m‐SWNTs) using various amines in different concentrations was investigated. The SWNTs dispersions were characterized with Vis–NIR and Raman spectrometers. The proportion of m‐SWNTs toward semiconducting SWNTs increased with an increase of concentration of amines. SWNTs thin films were prepared from the SWNTs dispersion. The sheet resistance of SWNTs films decreased with an increase of proportion of m‐SWNTs.
Structure of the N-terminal domain of a type B1 G protein-coupled receptor in complex with a peptide ligand (2007)

The corticotropin releasing factor (CRF) family of ligands and their receptors coordinate endocrine, behavioral, autonomic, and metabolic responses to stress and play additional roles within the cardiovascular, gastrointestinal, and other systems. The actions of CRF and the related urocortins are mediated by activation of two receptors, CRF-R1 and CRF-R2, belonging to the B1 family of G protein-coupled receptors. The short-consensus-repeat fold (SCR) within the first extracellular domain (ECD1) of the CRF receptor(s) comprises the major ligand binding site and serves to dock a peptide ligand via its C-terminal segment, thus positioning the N-terminal segment to interact with the receptor's juxtamembrane domains to activate the receptor. Here we present the 3D NMR structure of ECD1 of CRF-R2beta in complex with astressin, a peptide antagonist. In the structure of the complex the C-terminal segment of astressin forms an amphipathic helix, whose entire hydrophobic face interacts with the short-consensus-repeat motif, covering a large intermolecular interface. In addition, the complex is characterized by intermolecular hydrogen bonds and a salt bridge. These interactions are quantitatively weighted by an analysis of the effects on the full-length receptor affinities using an Ala scan of CRF. These structural studies identify the major determinants for CRF ligand specificity and selectivity and support a two-step model for receptor activation. Furthermore, because of a proposed conservation of the fold for both the ECD1s and ligands, this structure can serve as a model for ligand recognition for the entire B1 receptor family.
Bracing the human body with supernumerary Robotic Limbs for physical assistance and load reduction (2014)

A new approach to physically assisting the human with a wearable robot is presented. Supernumerary Robotic Limbs (SRLs) attached to the human waist support the body efficiently when the human is taking fatiguing postures, e.g. hunching over, squatting, or reaching the ceiling. Unlike a leg exoskeleton, where powered joints are attached to the human joints and are constrained to move together with the human limb, the SRL can take an arbitrary posture to maximize the load bearing efficiency. Taking a near-singular configuration, the SRL can bear a large load with small power consumption. First, the “bracing” strategy for supporting the human body is described, followed by a mathematical analysis of the load bearing efficiency. The optimal SRL posture and joint torques are then obtained in order to minimize the human load. Numerical and experimental results using a prototype of the SRL demonstrate the effectiveness of the method.
Elliptical cavity resonators for dual-mode narrowband filters (2002)

A novel cavity resonator with elliptical cross-section is proposed in order to realize dual-mode narrowband filters without tuning and coupling elements. No discontinuities are required inside the cavities hence significantly enhancing the unloaded Q, the ability to operate with higher power levels, and the ease of manufacturing. Dual-mode coupling is generated by the step discontinuity between the input rectangular waveguide and an inclined elliptical waveguide; a rigorous full-wave electromagnetic model for this discontinuity has been developed. Proper choice of the ellipticity and of the inclination angle allows us to obtain the desired coupling and tuning actions. Representative prototypes of elliptical cavities exhibiting various degrees of coupling have been carefully measured; the favorable comparison between experimental and theoretical results proves the accuracy of the model and its applicability for narrowband X/Ku band filters.
A recursive all-lag reference-code correlator for generating odd correlations (2002)

An all-lag reference-code correlator generates an all-lag even- or odd-correlation vector at a rate equal to the rate of incoming data samples. Direct implementation of an all-lag reference-code correlator requires N parallel correlators, and the resultant degree of complexity is of the order N/sup 2/, where N is the length of the reference code. In a previous paper, a recursive form for generating all-lag even correlations was derived. In this paper, we derive the recursive form for generating all-lag odd correlations. It is shown that the corresponding correlator can be implemented with a complexity approximately equal to that of a single parallel correlator. That is, the degree of complexity of the proposed recursive all-lag reference-code correlator is of the order N. Thus, substantial reduction in the implementation complexity is achieved.
Studying the impact of hardware prefetching and bandwidth partitioning in chip-multiprocessors (2011)

Modern high performance microprocessors widely employ hardware prefetching technique to hide long memory access latency. While very useful, hardware prefetching tends to aggravate the bandwidth wall, a problem where system performance is increasingly limited by the availability of the off-chip pin bandwidth in Chip Multi-Processors (CMPs).In this paper, we propose an analytical model-based study to investigate how hardware prefetching and memory bandwidth partitioning impact CMP system performance and how they interact. The model includes a composite prefetching metric that can help determine under which conditions prefetching can improve system performance, a bandwidth partitioning model that takes into account prefetching effects, and a derivation of the weighted speedup optimum bandwidth partition sizes for different cores. Through model-driven case studies, we find several interesting observations that can be valuable for future CMP system design and optimization. We also explore simulation-based empirical evaluation to validate the observations and show that maximum system performance can be achieved by selective prefetching, guided by the composite prefetching metric, coupled with dynamic bandwidth partitioning.
A Non-Tumorigenic Human Liver Epithelial Cell Culture Model for Chemical and Biological Carcinogenesis Investigations (1991)

A new medium has been formulated that will support in vitro replication of normal human liver epithelial cells for 4 passages (12 population doublings). The replicating cells uniformly contain keratin 18, but keratin 19 is not detectable. In addition, albumin remains discernable in many of the cells throughout their culture life-span. The SV40 large T-antigen gene has been introduced into the genome of cells from six cultures that were initiated from both adult and neonatal donors. The life spans of two of these are indefinite whereas, the others have extended population doubling potentials. The transformed cells have near-normal karyotypes and, initially, they express cytokeratin 18, albumin, and cytochromes. With continued passaging, however, they became positive also for cytokeratin 19 and loose expression of most hepato-specific proteins. However, when incubated as roller cultures, the cells re-acquire the ability to metabolize benzo[a]pyrene, aflatoxin B1, and dimethylnitrosamine to electrophilic derivatives that form carcinogen-DNA adducts. Further, when co-cultured with fibroblasts or on extracted basement membrane material, the cells synthesize albumin and acute phase proteins.Therefore, by using appropriate culture conditions, the “immortalized” human liver epithelial cells may serve as a useful model for chemical and biological carcinogenesis studies.
Accelerated phase contrast MRI using hybrid one‐ and two‐sided flow encodings only (HOTFEO) (2018)

The aim of this work was to develop and evaluate a fast phase contrast magnetic resonance imaging (PC-MRI) technique with hybrid one- and two-sided flow encodings only (HOTFEO) for accurate blood flow and velocity measurements of three-directional velocity encoding PC-MRI. Four-dimensional (4D) PC-MRI acquires flow-compensated (FC) and three-directional flow-encoded (FE) echoes in an interleaved fashion. We hypothesize that the blood flow velocity direction (not magnitude) has minimal change between two consecutive cardiac phases. This assumption provides a velocity direction constraint that can achieve 4/3-fold acceleration using three-directional FE data to calculate FC data instead of acquiring them. The HOTFEO acquisition pattern can address the ill-conditioned constraint and improve the calculation accuracy. HOTFEO was evaluated in healthy volunteers and compared with conventional two-dimensional (2D) and 4D flow imaging techniques with FC and three-directional FE acquisitions (FC/3FE). Compared with FC/3FE, Bland-Altman tests showed that the 4/3-fold accelerated HOTFEO technique resulted in relatively small bias error for total volumetric flow (0.89% for prospective 2D data, -1.19% for retrospective 4D data and -3.40% for prospective 4D data) and maximum peak velocity (0.50% for prospective 2D data, -0.17% for retrospective 4D data and -2.00% for prospective 4D data) measurements in common carotid arteries. HOTFEO can accelerate three-directional velocity encoding PC-MRI whilst maintaining the measurement accuracy of the total volumetric flow and maximum peak velocity.
Scalable On-Chip Interconnect Topologies (2008)

Driven by continuing scaling of Moore’s law, chip multiprocessors and systems-on-a-chip are expected to grow the core count from dozens today to hundreds in the near future. Cost and performance scalability of on-chip interconnect topologies is critical to meeting these demands. In this work, we seek to develop a better understanding of how network topologies scale with regard to cost and performance considering the advantages and limitations afforded on a die. Our contributions are three-fold. First, we introduce a taxonomy for on-chip interconnect topologies. Second, we propose a new topology, called Multidrop Express Channels (MECS), that uses a one-to-many communication model to provide a high degree of connectivity in a bandwidth-efficient manner. And third, using a combination of analytical- and simulation-based studies, we show that MECS can provide considerable latency and throughput advantages over previously proposed topologies in a cost-competitive manner.
Efficacy of an HSV-1 Neuro-Attenuated Vaccine in Mice Is Reduced by Preventing Viral DNA Replication (2022)

We previously isolated an HSV-1 mutant, KOS-NA, that contains two non-synonymous mutations in UL39. One of the mutations, resulting in an R950H amino acid substitution in ICP6, renders KOS-NA severely neuro-attenuated and significantly reduces HSV-1 latency. Vaccination of mice with KOS-NA prior to corneal challenge provides significant protection against HSV-1-mediated eye diseases even at a very low immunizing dose, indicating its utility as a vaccine scaffold. Because KOS-NA contains a neuro-attenuating mutation in a single gene, we sought to improve its safety by deleting a portion of the UL29 gene whose protein product, ICP8, is essential for viral DNA replication. Whereas KOS-NA reduced replication of HSV-1 challenge virus in the corneal epithelium and protected mice against blepharitis and keratitis induced by the challenge virus, KOS-NA/8- and an ICP8- virus were significantly less efficacious except at higher doses. Our results suggest that the capacity to replicate, even at significantly reduced levels compared with wild-type HSV-1, may be an important feature of an effective vaccine. Means to improve safety of attenuated viruses as vaccines without compromising efficacy should be sought.
Beneficiation of Chipped and Shredded Woody Biomass (2012)

Forest Concepts, with funding from USDA NIFA SBIR program, developed methods and equipment to reprocess low-value dirty forest chips, tree service chips, and hog fuel into high value clean wood fiber and other valuable fractions. Traditional clean sources of mill residuals (sawdust, shavings, and chips) are declining rapidly due to improved sawmilling efficiencies and a general decline in the number of sawmills in operation. Thus, competition for low-cost clean fiber is intense. A USDA NIFA SBIR supported beneficiation project sought to increase the clean fiber supply by tapping low grade, often inexpensive or negative cost raw materials. To validate the SBIR funded engineering science work, our engineers designed and built a set of demonstration-scale (one ton per hour) machines that can be mixed and matched to clean low grade woody biomass to meet nearly any ash or bark content specification. Results of validation tests demonstrate the performance of innovative methods for cleaning high-ash land clearing debris.