gebhart/patrepeval huggingface dataset:
Collision Imminent Steering at High Speed Using Nonlinear Model Predictive Control (2020)

Collision imminent steering is an automotive active safety feature designed to perform an aggressive lane change to avoid a forward collision in the event that the system determines there is insufficient distance to avoid a collision by braking alone.In this paper, a collision imminent steering system is developed using nonlinear model predictive control to perform a lane change at high speed in a highway environment. Two formulations are presented: one formulation to show the theoretical minimum lane change distance within which a safe lane change can be performed, and a second formulation to find the minimum aggressive maneuver for a given lane change distance. The nonlinear model predictive control formulation is posed as a constrained optimization problem, where solutions obey hard safety constraints of the highway environment. Constraint aggregation techniques are analyzed and introduced to monitor the peak tire slip throughout the maneuver. Numerical simulations of a typical luxury sedan in a highway setting show that minimum distance required to change lanes is about half the limit braking distance. Hence, there is a window of feasibility where the vehicle cannot avoid collision by braking alone, but can change lanes safely and maintain a safe trajectory throughout the maneuver. Additional simulations show that an active four wheel steering architecture improves performance over front only steering.
Development of a Live Attenuated Dengue Virus Vaccine Using Reverse Genetics (2006)

There are four serotypes of dengue (DEN1-DEN4) virus that are endemic in most areas of Southeast Asia, Central and South America, and other subtropical regions. The number of cases of severe disease associated with DEN virus infection is growing because of the continued spread of the mosquito vector, Aedes aegypti, which transmits the virus to humans. Infection with DEN virus can result in an asymptomatic infection, a febrile illness called dengue fever (DF), and the very severe disease called dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). Currently, a licensed vaccine is not available. However, a tetravalent vaccine is urgently needed to prevent DF and DHF/DSS, the latter of which occurs predominantly in partially immune individuals. A live attenuated, tetravalent DEN virus vaccine candidate has been generated using reverse genetics that is able to provide immunity to each of the four serotypes of DEN. Attenuation has been achieved by generating recombinant DEN (rDEN) viruses which are modified by deletion or, alternatively, by antigenic chimerization between two related DEN viruses using the following two strategies: 1) introduction of an attenuating 30 nucleotide deletion (Delta30) mutation into the 3' untranslated region of DEN1 and DEN4; and 2) replacement of structural proteins of the attenuated rDEN4Delta30 vaccine candidate with those from DEN2 or DEN3. Attenuation of the four monovalent vaccine candidates has been achieved for rhesus monkeys or humans and an immunogenic tetravalent vaccine candidate has been formulated. The level of attenuation of each dengue vaccine component can be increased, if needed, by introduction of additional attenuating mutations that have been well characterized.
Structural and genic characterization of stable genomic regions in breast cancer: Relevance to chemotherapy (2012)

Tumour genome analysis revealed 766 unstable (amplified and/or deleted) and 812 stable contiguous genomic regions. Replication analysis of an independent set of 171 breast tumours confirmed copy number stability of 1.3 Gb of the genome. We found that 5804 of these genes were dually stable. The composition of this gene set remained essentially unchanged (<2% reduction) after accounting for commonly mutated breast cancer genes found by sequencing and differential expression. The stable breast cancer genome is enriched for cellular metabolism, regulation of gene expression, DNA packaging (chromatin and nucleosome assembly), and regulation of apoptosis functions. Stable genes participating in multiple essential pathways were consistently found to be targets of chemotherapies. Preservation of stable, essential genes may be related to the effectiveness of certain chemotherapeutic agents that act on multiple gene products in this set.
Enzymatic Production of Chondroitin Oligosaccharides and Its Sulfate Derivatives (2022)

Chondroitin sulfate (CS) has a wide range of physiological functions and clinical applications. However, the biosynthesis of chondroitin oligosaccharides (o-CHs) and sulfate derivatives with specific length is always challenging. Herein, we report enzymatic strategies for producing homogeneous o-CHs and its sulfate derivatives from microbial sourced chondroitin. Chondroitin disaccharides, tetrasaccharides, hexasaccharides, octasaccharides, and decasaccharides with defined structure were produced by controllably depolymerizing microbial sourced chondroitin with an engineered chondroitinase ABC I. The highest conversion rates of the above corresponding o-CHs were 65.5%, 32.1%, 12.7%, 7.2%, and 16.3%, respectively. A new efficient enzymatic sulfation system that directly initiates from adenosine 5'-triphosphate (ATP) and sulfate was developed and improved the sulfation of chondroitin from 8.3% to 85.8% by optimizing the temperature, sulfate and ATP concentration. o-CHs decasaccharide, octasaccharide, hexasaccharide, tetrasaccharide and disaccharide were modified and the corresponding sulfate derivatives with one sulfate group were prepared. The enzymatic approaches constructed here for preparing o-CHs and its sulfate derivatives pave the way for the study of structure-activity relationship and applications.
SiC Device Junction Temperature Online Monitoring (2018)

This paper presents a SiC device junction temperature monitoring method. The device internal gate resistance has a consistent temperature dependence. With different junction temperature conditions, the equivalent gate loop impedance will be different and change the gate driver currents. Through proper signal processing, this gate loop current peak value can be captured and utilized as the junction temperature indicator. The concept and feasibility was verified through both simulation and experimental results.
Tipifarnib, a farnesyltransferase inhibitor, for metastatic urothelial carcinoma harboring HRAS mutations. (2020)

5086 Background: Tipifarnib is a farnesyltransferase inhibitor known to block RAS signaling and attenuate cancer cell proliferation. We tested the activity and safety of tipifarnib in patients with previously treated urothelial carcinoma (UC) carrying HRAS mutations. Methods: In a prospective phase II clinical trial, genetic screening was performed in 224 UC patients; those with missense HRAS mutations or STK11:rs2075606 received study treatment. Eligible patients received oral tipifarnib 900 mg twice daily on days 1–7 and 15–21 of 28-d treatment cycles. The primary endpoint was progression-free survival at 6 mo (PFS6). With two-stage design, at least 18 patients were required. Results: Among the 224 patients screened, we found 16 (7%) missense HRAS mutations (G13R, 7; Q61R, 4; G12S, 3; G12C, 2) and 104 (46%) STK11: rs2075606 carriers. In 21 patients enrolled, 14 and 7 patients had HRAS mutations and STK11:rs2075606, respectively. The most frequent adverse events included fatigue and hematologic toxicities. With a median follow-up of 28 months, 4 patients (19%) reached PFS6: 3 had missense HRAS mutations and one patient, enrolled as a STK11 carrier, had HRAS frameshift insertions at H27fs and H28fs rendering a nonsense HRAS mutation. Response rate was 24% (4 missense and one nonsense frameshift HRAS mutation); no response observed in UC patients with wild type HRAS tumors. Conclusions: Oral tipifarnib showed a manageable safety profile and encouraging anti-tumor efficacy against treatment-refractory UC containing HRAS mutations. Clinical trial information: NCT02535650 .
Grating-coupler based low-loss optical interlayer coupling (2011)

Optical interlayer couplers with 2.8dB insertion loss and 48nm bandwidth were designed and demonstrated in a commercial 130nm SOI CMOS process. 10Gb/s transmission through an interlayer-coupled link showed a power penalty of <;0.1dB.
Effect of the electrode particle shape in Li-ion battery on the mechanical degradation during charge–discharge cycling (2011)

The investigation addresses the effect of shape and aspect ratio, of typical electrode particles of Li-ion cell material, on the extent of fracture surface created due to intercalation-induced strain energy. Nodular, fibrous, and flaky-shaped particles were studied approximating them to sphere, cylinder, and disc geometries, respectively. Analytical expressions for stress distribution in slab and cylindrical-shaped particles were derived using thermal stress analogy. Such results are already available for spherical particles. Finite element study was carried out using COMSOL® Multiphysics package to complement the analytical work as well as for verification. The spatial and temporal variations of stresses and strain energy in the electrode particles of different shapes were established. Reportedly, solid electrolyte interphase formed on the fracture surface as well as the fracture-induced isolation of electrode material are the main causes of performance degradation and in this context, the intercalation-induced strain energy density becomes important. The sphericity of a particle, that is, the ratio of the surface area of a sphere to that of the particle of equal volume, was found to fittingly describe the effect of shape. The average strain energy density stored in a particle increases with the increasing sphericity. Therefore, fibrous and flaky-shaped particles are expected to have lower tendency for mechanical degradation than the nodular ones. The analysis is restricted only to the mechanics of mechanical degradation and not to the process or the chemistry point of view.
Fast generation of Fresnel holograms based on multirate filtering (2009)

One of the major problems in computer-generated holography is the high computation cost involved for the calculation of fringe patterns. Recently, the problem has been addressed by imposing a horizontal parallax only constraint whereby the process can be simplified to the computation of one-dimensional sublines, each representing a scan plane of the object scene. Subsequently the sublines can be expanded to a two-dimensional hologram through multiplication with a reference signal. Furthermore, economical hardware is available with which sublines can be generated in a computationally free manner with high throughput of approximately 100 M pixels/second. Apart from decreasing the computation loading, the sublines can be treated as intermediate data that can be compressed by simply downsampling the number of sublines. Despite these favorable features, the method is suitable only for the generation of white light (rainbow) holograms, and the resolution of the reconstructed image is inferior to the classical Fresnel hologram. We propose to generate holograms from one-dimensional sublines so that the above-mentioned problems can be alleviated. However, such an approach also leads to a substantial increase in computation loading. To overcome this problem we encapsulated the conversion of sublines to holograms as a multirate filtering process and implemented the latter by use of a fast Fourier transform. Evaluation reveals that, for holograms of moderate size, our method is capable of operating 40,000 times faster than the calculation of Fresnel holograms based on the precomputed table lookup method. Although there is no relative vertical parallax between object points at different distance planes, a global vertical parallax is preserved for the object scene as a whole and the reconstructed image can be observed easily.
Sphingosine Kinase 2 Inhibitors: Rigid Aliphatic Tail Derivatives Deliver Potent and Selective Analogues (2022)

Sphingosine 1-phosphate (S1P) is a pleiotropic signaling molecule that interacts with five native G-protein coupled receptors (S1P1-5) to regulate cell growth, survival, and proliferation. S1P has been implicated in a variety of pathologies including cancer, kidney fibrosis, and multiple sclerosis. As key mediators in the synthesis of S1P, sphingosine kinase (SphK) isoforms 1 and 2 have attracted attention as viable targets for pharmacologic intervention. In this report, we describe the design, synthesis, and biological evaluation of sphingosine kinase 2 (SphK2) inhibitors with a focus on systematically introducing rigid structures in the aliphatic lipid tail present in existing SphK2 inhibitors. Experimental as well as molecular modeling studies suggest that conformationally restricted "lipophilic tail" analogues bearing a bulky terminal moiety or an internal phenyl ring are useful to complement the "J"-shaped sphingosine binding pocket of SphK2. We identified <b>14c</b> (SLP9101555) as a potent SphK2 inhibitor (<i>K</i> <sub>i</sub> = 90 nM) with 200-fold selectivity over SphK1. Molecular docking studies indicated key interactions: the cyclohexyl ring binding in the cleft deep in the pocket, a trifluoromethyl group fitting in a small side cavity, and a hydrogen bond between the guanidino group and Asp308 (amino acid numbering refers to human SphK2 (isoform c) orthologue). <i>In vitro</i> studies using U937 human histiocytic lymphoma cells showed marked decreases in extracellular S1P levels in response to our SphK2 inhibitors. Administration of <b>14c</b> (dose: 5 mg/kg) to mice resulted in a sustained increase of circulating S1P levels, suggesting target engagement.
Vaccine testing of a recombinant activation‐associated secreted protein (ASP1) from <i>Ostertagia ostertagi</i> (2007)

Previous vaccination trials against the economically important cattle parasite Ostertagia ostertagi have indicated the protective capacity of activation-associated secreted proteins (ASPs). The further development of these antigens into a commercial vaccine will require their recombinant expression. The aim of the current study was to clone and express Oo-asp1 in a baculovirus expression system and to evaluate the protective capacity of the recombinant protein against an O. ostertagi challenge infection in cattle. The full coding sequence of Oo-asp1 was cloned in a baculovirus expression vector in frame with a carboxy-terminal Histidine tag and recombinant virus was used to infect an insect cell culture. Western blot analysis with anti-His and anti-Oo-ASP1 antibodies showed the production of recombinant Oo-ASP1. The cell pellet containing the recombinant was subsequently used to immunize seven calves three times intramuscularly with QuilA as adjuvant. Control animals were solely injected with the QuilA adjuvant. The challenge infection with O. ostertagi consisted of 30,000 L3 larvae per animal given over 30 days (1000 larvae/day, 5 days/week) and started the same day as the final immunization. Immunization with the recombinant Oo-ASP1 did not result in any level of protection against the challenge infection. There was no reduction in faecal egg output or in worm burdens. Moreover, Western blot analyses and ELISA indicated that, although the animals raised an antibody response against the recombinant Oo-ASP1, there was hardly a response against the native Oo-ASP1, suggesting that the baculovirus expressed recombinant was wrongly folded or lacked essential secondary modifications. Further analysis of the structure of the native ASPs and their glycosylations is being done.
Conformal VLC Receivers with Photodetector Arrays: Design, Analysis and Prototype (2019)

To enable visible light communication (VLC) for mobile receivers, we design and prototype a wide field-of-view (FOV) optical receiver with off-the-shelf components and in forms that are conformal to the receivers' surface. The VLC system uses high-efficiency optical transmitters with high brightness (7645 Lux in 1 m) low power (36 W) white LED panels which also provide proper lighting. To overcome the detrimental effects of the time-varying inter-symbol interference (ISI) due to the VLC receiver's high acceptance angle and vibration in its structure, we design and utilize an optimal multiple-symbol detection (MSD) algorithm. MSD attains remarkable improvements compared to the symbol-by-symbol detection but with exponential time cost. To decrease the MSD's computing demands, we then design an adaptive Decision Feedback Affine Projection Algorithm (DF-APA). DF-APA attains a notable further improvement with polynomial computation complexity which allows faster response to VLC channel dynamics. We, finally, test the system in presence of intense vibration in the receiver's body and show a 20 Mbps VLC link over 7 m distance.
Mobile services interworking for IMS and XML WebServices (2006)

An approach for interoperability between IMS and WebServices deployed within the IMS domain through the introduction of session management techniques for stateless WebServices based on existing SIP session management mechanisms is presented. The approach enables integration of WebServices applications into future telecommunications systems without the need for explicit usage of IMS/SIP protocols.
Characterizing ?3 opioid receptors with a selective monoclonal antibody (1996)

To help characterize kappa3 receptors and establish their relationship to traditional mu and delta receptors, we have generated a kappa3-selective monoclonal antibody. Monoclonal antibodies were raised against BE(2)-C cells, a human neuroblastoma cell line containing mu, kappa3, and delta opioid receptors. Of the 5,000 hybridoma cell lines screened, approximately 2,000 hybridomas tested positive against BE(2)-C membranes by ELISA, but only 98 of these were negative against a different neuroblastoma cell line lacking opioid receptors. Supernatants from one hybridoma, 8D8, inhibited up to 90% of 3H-NalBzoH (kappa3) binding without affecting 3H-DAMGO (mu) or 3H-naltrindole (delta) binding in BE(2)-C membranes. The selectivity of the antibody was further demonstrated by its blockade of the inhibition of cAMP accumulation in BE(2)-C cells by the kappa3 agonist NalBzoH but not the mu agonist morphine. Monoclonal antibody 8D8 (mAb8D8) also recognizes kappa3 receptors from mouse, rat, and calf brain. Administered intracerebroventricularly, mAb8D8 blocked kappa3 but not morphine (mu) analgesia in vivo. On Western blots, mAb8D8 recognized a protein with a molecular mass of approximately 70 kilodaltons in BE(2)-C. These studies demonstrate the selectivity of mAb8D8 for kappa3 receptors and provide additional support for the existence of this unique opioid receptor subtype.
Identification of intracellular carriers for the endocannabinoid anandamide (2009)

The endocannabinoid anandamide (arachidonoyl ethanolamide, AEA) is an uncharged neuromodulatory lipid that, similar to many neurotransmitters, is inactivated through its cellular uptake and subsequent catabolism. AEA is hydrolyzed by fatty acid amide hydrolase (FAAH), an enzyme localized on the endoplasmic reticulum. In contrast to most neuromodulators, the hydrophilic cytosol poses a diffusional barrier for the efficient delivery of AEA to its site of catabolism. Therefore, AEA likely traverses the cytosol with the assistance of an intracellular carrier that increases its solubility and rate of diffusion. To study this process, AEA uptake and hydrolysis were examined in COS-7 cells expressing FAAH restricted to the endoplasmic reticulum, mitochondria, or the Golgi apparatus. AEA hydrolysis was detectable at the earliest measurable time point (3 seconds), suggesting that COS-7 cells, normally devoid of an endocannabinoid system, possess an efficient cytosolic trafficking mechanism for AEA. Three fatty acid binding proteins (FABPs) known to be expressed in brain were examined as possible intracellular AEA carriers. AEA uptake and hydrolysis were significantly potentiated in N18TG2 neuroblastoma cells after overexpression of FABP5 or FABP7, but not FABP3. Similar results were observed in COS-7 cells stably expressing FAAH. Consistent with the roles of FABP as AEA carriers, administration of the competitive FABP ligand oleic acid or the selective non-lipid FABP inhibitor BMS309403 attenuated AEA uptake and hydrolysis by approximately 50% in N18TG2 and COS-7 cells. Taken together, FABPs represent the first proteins known to transport AEA from the plasma membrane to FAAH for inactivation and may therefore be novel pharmacological targets.
Semiochemical Production and Laboratory Behavior Response of the Brown Marmorated Stink Bug, Halyomorpha Halys (2015)

This information should lead to a better understanding of the biology, physiology, and chemical ecology of BMSB, which will help scientists and growers develop more efficient strategies based on natural products to manage BMSB population, therefore, reducing pesticide usage and protecting the crops from BMSB damage.
K-edge Coded Apertures for Compressive Spectral X-ray Tomography (2019)

Spectral computed tomography (SCT) is used to perform material characterization in 3D images, a feature that is not possible with conventional computed tomography (CT) systems. Currently, photon-counting detectors are used to obtain the energy binned images in SCT, however, these detectors are costly and the measured data have low signal to noise ratios. This paper presents a new approach for SCT which circumvents the limitations of current SCT systems. It combines conventional X-ray imaging systems with K-edge coded aperture masks. In this scheme, a particular filter pair is aligned with each X-ray beam in a multi-shot architecture, therefore obtaining compressive measurements in both the spectral and spatial domains. Then, the energy binned images are reconstructed using the alternating direction method of multipliers (ADMM) to solve a joint sparse and low-rank optimization problem that exploits the structure of the spectral data-cube. Simulations using coded fan-beam X-ray projections demonstrate the feasibility of the proposed approach.
Identification and Cloning of a β-Cell–Specific Zinc Transporter, ZnT-8, Localized Into Insulin Secretory Granules (2004)

SLC30A8, a novel member of the zinc transporter (ZnT) family, was identified by searching the human genomic and expressed sequence tag (EST) databases with the amino acid sequence of all known human ZnT. The protein (369 amino acids) predicted from this gene, ZnT-8, contains six transmembrane domains and a histidine-rich loop between transmembrane domains IV and V, like the other ZnT proteins. We demonstrated by RT-PCR on cDNA libraries and human tissue extracts that the ZnT-8 gene is solely transcribed in the pancreas, mainly in the islets of Langerhans. The gene, named SLC30A8, was cloned and sequenced. Confocal immunofluorescence analysis revealed that a ZnT-8-EGFP (enhanced green fluorescent protein) fusion product colocalized with insulin in the secretory pathway granules of the insulin-secreting INS-1 cells. Exposure of the ZnT-8-EGFP stably expressing HeLa cells to 75 μmol/l zinc caused an accumulation of zinc in intracellular vesicles compared with cells expressing EGFP alone. These results identified ZnT-8 as a ZnT specific to the pancreas and expressed in β-cells. Because ZnT-8 facilitates the accumulation of zinc from the cytoplasm into intracellular vesicles, ZnT-8 may be a major component for providing zinc to insulin maturation and/or storage processes in insulin-secreting pancreatic β-cells.