gebhart/patrepeval huggingface dataset:
Disturbed Communication between Actin- and Nucleotide-binding Sites in a Myosin II with Truncated 50/20-kDa Junction (1999)

The kinetic and functional consequences of deleting nine residues from an actin-binding surface loop (loop 2) were examined to investigate the role of this region in myosin function. The nucleotide binding properties of myosin were not altered by the deletion. However, the deletion affected actin binding and the communication between the actin- and nucleotide-binding sites. The affinity of M765NL for actin (644 nM) was approximately 100-fold lower than that of wild-type construct M765 (5.8 nM). Despite this reduction in affinity, actin binding weakened the affinity of ADP for the motor to a similar extent for both mutant and wild-type constructs. The addition of 0.5 microM actin decreased ADP affinity from 0.6 to 34 microM for M765NL and from 1.6 to 39 microM for M765. In contrast, communication between the actin- and nucleotide-binding sites appears disturbed in regard to phosphate release: thus, basal ATPase activity for M765NL (0.19 s-1) was 3-fold larger than for M765 (0.06 s-1), and the stimulation of ATPase activity by actin was 5-fold lower for M765NL. These results indicate different paths of communication between the actin- and nucleotide-binding sites, in regard to ADP and Pi release, and they confirm that loop 2 is involved in high affinity actin binding.
Analytics and Motion Planning of a Novel Four-Wheel Vehicle With Expanding Wheels (2002)

This paper describes analytics and experiments on a novel 4-wheel vehicle. The vehicle has back wheel drive and steering in addition to wheels that can expand and change radius. The motivation for this design is to attain added navigation capability by expanding the wheels according to the requirements of the terrain. In this paper, we discuss the motion of the vehicle on a flat floor. The steering angle is kept at zero so that the vehicle has a planar motion. The contact point of the wheel with the ground is assumed to be directly underneath the center of the wheel and has no slip. The rolling constraints are nonholonomic, i.e., are non-integrable. The rate constraints are written in an input-affine drift-less control system. The structure of this drift-less control system allows to determine the differentially flat outputs of the system. Motion planning of the vehicle between two configurations is achieved through planning of these differentially flat outputs. These trajectories are then used to determine a feedback controller. A dynamic simulation is performed using MATLAB. The motions are currently being implemented on the physical hardware using a dSPACE control system.
A linear DNA encoding the SARS-CoV-2 receptor binding domain elicits potent immune response and neutralizing antibodies in domestic cats (2023)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of the COVID-19 pandemic, has been shown to infect a wide range of animal species, especially mammals, and besides human-to-human transmission, human-to-animal transmission has also been observed in some wild animals and pets, especially in cats. It has been demonstrated that cats are permissive to COVID-19 and are susceptible to airborne infections. Given the high transmissibility potential of SARS-CoV-2 to different host species and the close contact between humans and animals, it is crucial to find mechanisms to prevent the transmission chain and reduce the risk of spillover to susceptible species. Here, we show results from a clinical trial conducted in domestic cats to assess safety and immunogenicity of a linear DNA (linDNA) vaccine encoding the receptor-binding domain (RBD) from SARS-CoV-2 (Lin-COVID-eVax). Lin-COVID-eVax proved to be safe, with no significant adverse events, and was able to elicit both RBD-specific antibodies and T cells. Also, the linDNA vaccine induced neutralizing antibody titers against ancestral SARS-CoV-2 virus and its variants. These findings demonstrate the safety and immunogenicity of a genetic vaccine against COVID-19 administered to cats and strongly support the development of vaccines for preventing viral spread in susceptible species, especially those in close contact with humans.
A high efficiency 3.3 kW loosely-coupled wireless power transfer system without magnetic material (2015)

This paper proposes a loosely-coupled wireless power transfer (WPT) system without magnetic material, which has 95.0% dc-to-dc efficiency working at 1MHz and 3.3kW output power. The coil size is 320mm×320mm, and the coupling coefficient k is 14.0% at 150mm air-gap distance. The magnetic material is removed to increase system switching frequency to MHz level and eliminate the magnetic losses. Power loss models of the circuit components are presented to calculate the total losses and the system efficiency. It shows that, through designing the circuit parameters to minimize the power losses, the maximum achievable efficiency can be higher than 95% even at a coupling coefficient of 10%. This paper provides the guideline for high-frequency and high efficiency WPT system design.
Generation of osteoclasts from isolated hematopoietic progenitor cells (1989)

A variety of studies have shown that osteoclasts originate from bone marrow, but their exact progenitors and differentiation pathway remain unclear. The treatment of mice with a high dose of 5-fluorouracil (5-FU) results in an enrichment for primitive hematopoietic progenitors; using this procedure, we prepared a new class of murine hematopoietic colonies that had very high secondary plating efficiencies in vitro. When spleen cells from mice pretreated in vivo with 5-FU were cultured in the presence of methylcellulose medium containing recombinant interleukin-3 (rIL-3), small colonies consisting of blast cells with little sign of differentiation developed on day 7 of culture. We lifted these blast colonies, pooled them, and replated them as secondary methylcellulose cultures in the presence of rIL-3 and erythropoietin. Approximately 60% of the cells formed colonies comprising various combinations of neutrophils, macrophages, eosinophils, mast cells, megakaryocytes, and erythroblasts. We replated such blast cells into microtiter wells and cultured them in the presence of rIL-3 (100 U/mL) or recombinant granulocyte-macrophage colony stimulating factor (GM-CSF) (100 U/mL) plus 1.25(OH)2D3 (10(-7) mol/L). Multinucleated cells appeared from day 14 of culture and approximately 100 giant cells per well were scored on day 21 of culture. Parathyroid hormone (1 U/mL) also induced the multinucleated cell formation. May-Grunwald-Giemsa staining revealed the large cells containing many nuclei in their cytoplasm, which is characteristic of bone-resorbing cells or osteoclasts. These cells showed a tartrate-resistant acid phosphatase (TRAP) activity. Calcitonin caused a striking shape change in these cells and suppressed the formation of multinucleated cells. Moreover, electron microscopy shows that these cells were able to resorb fetal calvariae. In the presence of r granulocyte-colony stimulating factor, r macrophage-colony stimulating factor, or r interleukin-6 plus 1.25(OH)2D3, formation of TRAP-positive multinucleated cells was lower compared with the support of rIL-3 or rGM-CSF. Mature macrophages collected from colonies did not form the multinucleated cells as described above, even in the presence of rIL-3 and 1.25(OH)2D3. Moreover, to exclude the possibility that osteoclasts generated from non-blast cells, we performed a cloning experiment from one isolated blast cell and demonstrated that single cells differentiate into osteoclasts or macrophages in the presence of rIL-3 with or without 1.25(OH)2D3. This system will provide a useful model for further analysis of osteoclast formation in vitro.
Chronic toxicity of copper and ammonia to juvenile freshwater mussels (unionidae) (2007)

The objectives of the present study were to develop methods for conducting chronic toxicity tests with juvenile mussels under flow-through conditions and to determine the chronic toxicity of copper and ammonia to juvenile mussels using these methods. In two feeding tests, two-month-old fatmucket (Lampsilis siliquoidea) and rainbow mussel (Villosa iris) were fed various live algae or nonviable algal mixture for 28 d. The algal mixture was the best food resulting in high survival (>or=90%) and growth. Multiple copper and ammonia toxicity tests were conducted for 28 d starting with two-month-old mussels. Six toxicity tests using the algal mixture were successfully completed with a control survival of 88 to 100%. Among copper tests with rainbow mussel, fatmucket, and oyster mussel (Epioblasma capsaeformis), chronic value ([ChV], geometric mean of the no-observed-effect concentration and the lowest-observed-effect concentration) ranged from 8.5 to 9.8 microg Cu/L for survival and from 4.6 to 8.5 microg Cu/L for growth. Among ammonia tests with rainbow mussel, fatmucket, and wavy-rayed lampmussel (L. fasciola), the ChV ranged from 0.37 to 1.2 mg total ammonia N/L for survival and from 0.37 to 0.67 mg N/L for growth. These ChVs were below the U.S. Environmental Protection Agency 1996 chronic water quality criterion (WQC) for copper (15 microg/L; hardness 170 mg/L) and 1999 WQC for total ammonia (1.26 mg N/L; pH 8.2 and 20 degrees C). Results indicate that toxicity tests with two-month-old mussels can be conducted for 28 d with >80% control survival; growth was frequently a more sensitive endpoint compared to survival; and the 1996 chronic WQC for copper and the 1999 chronic WQC for total ammonia might not be adequately protective of the mussel species tested. However, a recently revised 2007 chronic WQC for copper based on the biotic ligand model may be more protective in the water tested.
Simulation of the Viscous Sintering of Two Particles (1990)

The viscous sintering of two initially spherical particles is modeled as creeping flow in response to surface tension. The governing equations are solved using the finite‐element method. The condensed results of this simulation, the center‐to‐center approach velocity, and the rate of change of contact area were presented earlier. Some details of the flow field during sintering and the evolution of the neck geometry in the early stages of sintering are presented here. Important numerical issues are detailed.
TE LSP Crossing Topology-Transparent Zones (2019)

A topology-transparent zone is virtualized as the edges of the zone
fully connected. This document presents the procedures for the
establishment of Traffic Engineering (TE) LSPs crossing Topology-
Transparent Zones.
Resnet-based quality evaluation of image mosaic and training data balance (2021)

Many image Mosaic algorithms have been pro-posed in recent decades, we also need the algorithm to evaluate the quality of image stitching. This paper verifies the possibility of image mosaic quality evaluation based on neural network. Experiment results show it is effective and has the strong scalability on different data sets. Furthermore, the influence of training data balance and the network deep of ResNet are analyzed. Ten times amount data will reduce the mean error from 2 to 1. Balance data set can reduce the mean error significantly. The deeper ResNet34 is better than ResNet18 which can train faster but needs more memory space.
Highly efficient organic p–i–n photovoltaic cells based on tetraphenyldibenzoperiflanthene and fullerene C70 (2012)

In this work, tetraphenyldibenzoperiflanthene (DBP) and fullerene C70 were used to construct organic photovoltaic cells. A power conversion efficiency of 5.19% was obtained by inserting a blend layer of DBP and C70 between the two neat layers, i.e. the so-called p–i–n structure, while the bilayer cell has an efficiency of 3.56%. The significant enhancement in photocurrent was mainly ascribed to absorption of the blend film. Interestingly optical characterization revealed that DBP molecules in the blend film showed a preferable orientation parallel to the substrate surface, suggesting that anisotropic properties can be realized in vacuum deposited donor–acceptor blend films for efficient light harvesting. Photoresponse of the p–i–n cells extended into the spectral range longer than band-edge absorption of the two materials, which is clearly associated with formation of charge transfer states between the DBP donor and C70 acceptor. On the other hand, the charge transfer states cause increase of saturation current of the diodes, and thus decrease of open circuit voltage. Our results indicate that the controversial effects of such charge transfer states should be considered in organic solar cells with respect to material selection and device design.
Synthesis of Conformationally Restricted Cyclic Hexadepsipeptidesvia Direct Amide Cyclization (2000)

Ring closure by direct amide cyclization was used in the synthesis of 19-membered cyclic depsipeptides 27 (Schemes 1 and 3). The linear hexapeptide precursors 4, containing the β-hydroxy acid 3-hydroxy-2-phenylpropanoic acid (Tro), and five α-amino acids of the type Aib, Gly, and Pro, were prepared according to Scheme 2. The α,α-disubstituted α-amino acid Aib was incorporated into the peptide chain via the azirine/oxazolone method, and Gly and Pro were introduced by using the TBTU/HOBt coupling method. The cyclic depsipeptides 27a – 27f were obtained in reasonable-to-excellent yields (Scheme 3 and Table 1).
Comparing Aurora A and Aurora B as molecular targets for growth inhibition of pancreatic cancer cells (2006)

To address the increased need to understand the similarities and differences in targeting Aurora A or Aurora B for the treatment of cancer, we systematically evaluated the relative importance of Aurora A and/or Aurora B as molecular targets using antisense oligonucleotides. It was found that perturbations in Aurora A and Aurora B signaling result in growth arrest and apoptosis preferentially in cancer cells. The biological fingerprints of Aurora A and Aurora B inhibition were compared and contrasted in efforts to identify the superior therapeutic target. Due to the different biological responses, we conclude that each Aurora kinase should be treated as autonomous drug targets, which can be targeted independently or in combination. We observed no advantages to targeting both kinases simultaneously and feel that an Aurora A-targeted therapy may have some beneficial consequences over an Aurora B-targeted therapy, such as mitotic arrest and the rapid induction of apoptosis.
RNAi prodrugs decrease elevated mRNA levels of Polo‐like kinase 1 in ex vivo cultured primary cells from pediatric acute myeloid leukemia patients (2021)

Polo-like kinase 1 (Plk1) is an important regulator of the cell cycle and it is frequently overexpressed in cancer cells. Several small molecule inhibitors have been developed to target Plk1 and some of them have reached clinical trials in adults with acute myeloid leukemia (AML). Pediatric AML patients have a poor prognosis and survivors suffer from long-term side effects. As adult AML cells have an elevated expression of Plk1, AML is a disease candidate for Plk1 inhibition. However, the relative success of clinical trials have been hampered by adverse reactions. Herein, PLK1-targeting RNA interference (RNAi) prodrugs that enter cells without a transfection reagent are used to target PLK1 selectively in primary cells from pediatric AML patients. We show that PLK1 and PLK4 mRNA expression are significantly higher in pediatric AML patients when compared to healthy donors and that PLK1 is downregulated by on average 50% using RNAi prodrugs without a significant effect on other PLK family members. In addition, the RNAi prodrug-induced decrease in PLK1 can be used to potentiate the effect of cytarabine. In summary, PLK1-targeting RNAi prodrugs can decrease the elevated levels of PLK1 in primary cells from pediatric AML patients and sensitize pediatric AML cells to chemotherapeutics.
Regulation of Transfer Functions by the imp Locus of the Streptomyces coelicolor Plasmidogenic Element SLP1 (1999)

SLP1(int) is a 17.2-kb genetic element that normally is integrated site specifically into the chromosome of Streptomyces coelicolor A3(2). The imp operon within SLP1(int) represses replication of both chromosomally integrated and extrachromosomal SLP1. During mating with S. lividans, SLP1(int) can excise, delete part of imp, and form a family of autonomously replicating conjugative plasmids. Earlier work has shown that impA and impC gene products act in concert to control plasmid maintenance and regulate their own transcription. Here we report that these imp genes act also on a second promoter, P(opimp) (promoter opposite imp), located adjacent to, and initiating transcription divergent from, imp to regulate loci involved in the intramycelial transfer of SLP1 plasmids. spdB1 and spdB2, two overlapping genes immediately 3' to P(opimp) and directly regulated by imp, are shown by Tn5 mutagenesis to control transfer-associated growth inhibition (i.e., pocking). Additional genes resembling transfer genes of other Streptomyces spp. plasmids and required for SLP1 transfer and/or postconjugal intramycelial spread are located more distally to P(opimp). Expression of impA and impC in an otherwise competent recipient strain prevented SLP1-mediated gene transfer of chromosomal and plasmid genes but not plasmid-independent chromosome-mobilizing activity, suggesting that information transduced to recipients after the formation of mating pairs affects imp activity. Taken together with earlier evidence that the imp operon regulates SLP1 DNA replication, the results reported here implicate imp in the overall regulation of functions related to the extrachromosomal state of SLP1.
Phenotypic Assessment and the Discovery of Topiramate (2016)

The role of phenotypic assessment in drug discovery is discussed, along with the discovery and development of TOPAMAX (topiramate), a billion-dollar molecule for the treatment of epilepsy and migraine.
Analysis and Design of A New Micro Jerk Sensor with Viscous Coupling (2003)

A new method for jerk detection (derivative of acceleration) is proposed. By using a 2 degrees of freedom (DOF) model with viscous coupling, we measure jerk directly as a position change in mass without differential circuit. Analysis by numerical formulas show the principle of the proposed jerk detection and simulation results show suitable parameters such as viscosity, mass ratio, and spring coefficient ratio for jerk detection. We also propose a micro jerk sensor based on the micro electro mechanical system (MEMS). Results of analysis show that the microstructure is suitable for the proposed viscous coupling.
Gate-Recessed InAlN/GaN HEMTs on SiC Substrate With Al[subscript 2]O[subscript 3] Passivation (2009)

We studied submicrometer (L[subscript G] = 0.15-0.25 Ã Â¿m) gate-recessed InAlN/AlN/GaN high-electron mobility transistors (HEMTs) on SiC substrates with 25-nm Al[subscript 2]O[subscript 3] passivation. The combination of a low-damage gate-recess technology and the low sheet resistance of the InAlN/AlN/GaN structure resulted in HEMTs with a maximum dc output current density of I[subscript DS,max] = 1.5 A/mm and a record peak extrinsic transconductance of g[subscript m,ext] = 675 mS/mm. The thin Al[subscript 2]O[subscript 3] passivation improved the sheet resistance and the transconductance of these devices by 15% and 25%, respectively, at the same time that it effectively suppressed current collapse.
A Dual-Mode Bluetooth Transceiver with a Two-Point-Modulated Polar-Loop Transmitter and a Frequency-Offset-Compensated Receiver (2007)

An entire dual-mode transceiver capable of both the conventional GFSK-modulated Bluetooth and the Medium-Rate π/4-DQPSK-modulated Bluetooth has been investigated and reported. The transmitter introduces a novel two-point-modulated polar-loop technique without the global feedback to realize reduced power consumption, small chip area and also high modulation accuracy. The receiver shares all the circuits for both operating modes except the demodulators and also features a newly-proposed cancellation technique of the carrier-frequency offset. The transceiver has been confirmed by system or circuit simulations to meet all the dual-mode Bluetooth specifications. The simulation results show that the transmitting power can be larger than 10dBm while achieving the total power efficiency above 30% and also RMS DEVM of 0.050. It was also confirmed by simulation that the receiver is expected to attain the sensitivity of -85dBm in both modes while satisfying the image-rejection and the blocker-suppression specifications. The proposed transceiver will provide a low-cost, low-power single-chip RF-IC solution for the next-generation Bluetooth communication.
Carotenoid cleavage dioxygenases and their apocarotenoid products in plants (2009)

Carotenoid cleavage dioxygenases (CCDs) catalyze the cleavage of carotenoids in various organisms. In Arabidopsis, the CCD enzyme family consists of nine members, which are further divided into two subfamilies: five 9-cis epoxycarotenoid dioxygenases (NCEDs) and four CCDs. The NCEDs are involved in the biosynthesis of the plant hormone abscisic acid (ABA). CCDs are only distantly related to the NCEDs, and their substrate specificities and activities differ from those of the NCEDs. Recent evidence indicates that apocarotenoids produced by the action of CCDs play various roles in the growth and development of plants; these apocarotenoids include a novel plant hormone that controls shoot branching and pollinator attractants produced in reproductive organs. This review focuses on enzymes belonging to the CCD subfamily; their enzymatic activities and the functions of their apocarotenoid products are discussed.
Benzo[4,5]thieno[2,3-b]pyridine derivatives as host materials for high efficiency green and blue phosphorescent organic light-emitting diodes (2013)

Benzo[4,5]thieno[2,3-b]pyridine (BTP) was newly developed as an electron deficient moiety for high triplet energy materials and two BTP derivatives with the BTP and carbazole groups were synthesized as high triplet energy bipolar host materials. The BTP derivatives were effective as the host materials for green and blue phosphorescent organic light-emitting diodes and a high quantum efficiency above 20% was achieved both in green and blue devices.
Retinal blood flow in response to an intravitreal injection of ranibizumab for neovascular age‐related macular degeneration (2011)

Intravitreal ranibizumab treatment for NV-AMD induces a reduction in arteriolar diameter, velocity, and blood flow in patients who have received <1.50 mg of ranibizumab.
Dynamic Finite Element Analysis of a Piezoelectric Bimorph Beam Deflector With Consideration of Hysteresis Effect (2003)

This study is devoted to propose a method of finite element technique to account for the hysteresis effect of a piezoelectric bimorph beam deflector. To this end, the constitutive equations of a general piezoelectric material are first modified to include the hysteresis effect by adding a polarization term in one of constitutive equations. Based on these modified constitutive equations and employment of Preisach model for hysteresis, the governing equations of the bimorph beam are derived through the utilization of Hamilton’s principle and calculus of variation. In addition, according to the common physical rules, boundary, transition and continuous conditions are next formulated to complement the governing equations. Simulations are finally conducted to show the effectiveness of the proposed modeling technique and decipher the dynamic behavior of the piezoelectric beam with consideration of hysteresis effect.