gebhart/patrepeval huggingface dataset:
Selective inhibitors of the osteoblast proteasome stimulate bone formation in vivo and in vitro (2003)

We have found that the ubiquitin-proteasome pathway exerts exquisite control of osteoblast differentiation and bone formation in vitro and in vivo in rodents. Structurally different inhibitors that bind to specific catalytic β subunits of the 20S proteasome stimulated bone formation in bone organ cultures in concentrations as low as 10 nM. When administered systemically to mice, the proteasome inhibitors epoxomicin and proteasome inhibitor–1 increased bone volume and bone formation rates over 70% after only 5 days of treatment. Since the ubiquitin-proteasome pathway has been shown to modulate expression of the Drosophila homologue of the bone morphogenetic protein-2 and -4 (BMP-2 and BMP-4) genes, we examined the effects of noggin, an endogenous inhibitor of BMP-2 and BMP-4 on bone formation stimulated by these compounds and found that it was abrogated. These compounds increased BMP-2 but not BMP-4 or BMP-6 mRNA expression in osteoblastic cells, suggesting that BMP-2 was responsible for the observed bone formation that was inhibited by noggin. We show proteasome inhibitors regulate BMP-2 gene expression at least in part through inhibiting the proteolytic processing of Gli3 protein. Our results suggest that the ubiquitin-proteasome machinery regulates osteoblast differentiation and bone formation and that inhibition of specific components of this system may be useful therapeutically in common diseases of bone loss.
Bioengineered Tooth Buds Exhibit Features of Natural Tooth Buds (2018)

Tooth loss is a significant health issue currently affecting millions of people worldwide. Artificial dental implants, the current gold standard tooth replacement therapy, do not exhibit many properties of natural teeth and can be associated with complications leading to implant failure. Here we propose bioengineered tooth buds as a superior alternative tooth replacement therapy. We describe improved methods to create highly cellularized bioengineered tooth bud constructs that formed hallmark features that resemble natural tooth buds such as the dental epithelial stem cell niche, enamel knot signaling centers, transient amplifying cells, and mineralized dental tissue formation. These constructs were composed of postnatal dental cells encapsulated within a hydrogel material that were implanted subcutaneously into immunocompromised rats. To our knowledge, this is the first report describing the use of postnatal dental cells to create bioengineered tooth buds that exhibit evidence of these features of natural tooth development. We propose future bioengineered tooth buds as a promising, clinically relevant tooth replacement therapy.
Photonic choke-joints for dual-polarization waveguides (2010)

Summary form only given: Two photonic choke joint (PCJ) structures for dual-polarization waveguides have been investigated. Structures with Cartesian and Archimedean tiling were implemented to provide a low-loss non-contacting surface at a waveguide interface while preserving the signal polarizations. The optimal dimensions for each tiling configuration have been determined. For each of these schemes the experimental results for structures with a finite tiling provide near ideal transmission and reflection performance over the full waveguide band.
Standoff Detection of Trace Molecules by Remote High Gain Backward Lasing in Air (2016)

Abstract : This research explored the potential for backward lasing from natural constituents in air with the objective of developing revolutionary methods for standoff detection of trace gases. Backward lasing enables far-field monitoring through modulation methods. The approach utilizes the very high gain available from multiphoton pumping of atomic species, which can be created by the dissociation of molecules in air. Lasing has been demonstrated from oxygen, nitrogen and water vapor. In each of these cases the lasing is achieved by two photon pumping of the atomic fragments, leading to high gain backward lasing from oxygen, nitrogen, and hydrogen atoms. The research has demonstrated that predissociation significantly enhances the efficiency, and in the cases of nitrogen and water vapor it is essential. Backward lasing from two simultaneously pumped, closely separated regions in the air provides a method for the reduction of pulse to pulse fluctuations. Further reduction in pulse to pulse fluctuations will be possible if the dissociate step is eliminated by using argon, which requires three photon pumping. Backward lasing from argon in air has been achieved, but at argon concentrations of 10 . Future work is expected to reduce this threshold to the 1 natural concentration of argon in air.
Planar Ultrawideband Modular Antenna (PUMA) arrays scalable to mm-waves (2013)

A new class of Planar Ultrawideband Modular Antenna (PUMA) arrays, the PUMAv3, is introduced. PUMAv3 is scalable to mm-wave frequencies (≈50 GHz) and improves bandwidth by 50% without the use of a matching network or external baluns. The enabling technical innovations include a new feeding mechanism that relies on capacitively loaded shorting vias and an alteration on the superstrate loading scheme. Infinite array full-wave simulations of a dual-polarized PUMAv3 suggest 10.6-47.6 GHz (4.5:1) operation with good VSWR levels out to θ = 45°, high port isolation and low cross-polarization.
HIV-Specific Antibody Responses in HIV-Infected Patients: From a Monoclonal to a Polyclonal View (2015)

HIV infections represent a major global health threat, affecting more than 35 million individuals worldwide. High infection rates and problems associated with lifelong antiretroviral treatment emphasize the need for the development of prophylactic and therapeutic immune intervention strategies. It is conceivable that insights for the design of new immunogens capable of eliciting protective immune responses may come from the analysis of HIV-specific antibody responses in infected patients. Using sophisticated technologies, several monoclonal neutralizing antibodies were isolated from HIV-infected individuals. However, the majority of polyclonal antibody responses found in infected patients are nonneutralizing. Comprehensive analyses of the molecular targets of HIV-specific antibody responses identified that during natural infection antibodies are mainly misdirected towards gp120 epitopes outside of the CD4-binding site and against regions and proteins that are not exposed on the surface of the virus. We therefore argue that vaccines aiming to induce protective responses should include engineered immunogens, which are capable of focusing the immune response towards protective epitopes.
Automated system for measuring polarization-dependent loss (1994)

Polarization-dependent loss (PDL) is the maximum difference in transmission with respect to polarization state. Many optical components, such as isolators and couplers, exhibit PDL. In a previous paper a manual PDL-measurement method using a three-paddle polarization controller and an erbium-doped fiber depolarizer was presented.1 In that approach any error in the measurement results in lower-than-actual PDL values. In this work we present a new approach that uses the Mueller-matrix description of the device under test (DUT) to measure the PDL. In addition, this method determines the polarization states that produce maximum and minimum transmission. With this information, the range of the insertion loss as a function of polarization state can be obtained.
Acoustic modeling of subword units for large vocabulary speaker independent speech recognition (1989)

The field of large vocabulary, continuous speech recognition has advanced to the point where there are several systems capable of attaining between 90 and 95% word accuracy for speaker independent recognition of a 1000 word vocabulary, spoken fluently for a task with a perplexity (average word branching factor) of about 60. There are several factors which account for the high performance achieved by these systems, including the use of hidden Markov models (HMM) for acoustic modeling, the use of context dependent sub-word units, the representation of between-word phonemic variation, and the use of corrective training techniques to emphasize differences between acoustically similar words in the vocabulary. In this paper we describe one of the large vocabulary speech recognition systems which is being developed at AT&T Bell Laboratories, and discuss the methods used to provide high word recognition accuracy. In particular, we focus on the techniques used to obtain acoustic models of the sub-word units (both context independent and context dependent units), and discuss the resulting system performance as a function of the type of acoustic modeling used.
TArgeted Motion Estimation and Reduction (TAMER): Data Consistency Based Motion Mitigation for MRI Using a Reduced Model Joint Optimization (2018)

We introduce a data consistency based retrospective motion correction method, TArgeted Motion Estimation and Reduction (TAMER), to correct for patient motion in Magnetic Resonance Imaging (MRI). Specifically, a motion free image and motion trajectory are jointly estimated by minimizing the data consistency error of a SENSE forward model including rigid-body subject motion. In order to efficiently solve this large non-linear optimization problem, we employ reduced modeling in the parallel imaging formulation by assessing only a subset of target voxels at each step of the motion search. With this strategy we are able to effectively capture the tight coupling between the image voxel values and motion parameters. We demonstrate in simulations TAMER's ability to find similar search directions compared to a full model, with an average error of 22%, vs. 73% error when using previously proposed alternating methods. The reduced model decreased the computation time fold compared to a full image volume evaluation. In phantom experiments, our method successfully mitigates both translation and rotation artifacts, reducing image RMSE compared to a motion-free gold standard from 21% to 14% in a translating phantom, and from 17% to 10% in a rotating phantom. Qualitative image improvements are seen in human imaging of moving subjects compared to conventional reconstruction. Finally, we compare in vivo image results of our method to the state-of-the-art.
Construction of a high-NFOM multiphoton microscope with large-angle resonant raster scanning (2022)

A resonant-scanning multiphoton optical microscope (MPM) with a millimeter-scale field-of-view (FOV) often encounters a poor Nyquist figure-of-merit (NFOM), leading to an aliasing effect owing to limited effective voxel-sampling rate. In this protocol, we provide a design guideline to enable high-NFOM MPM imaging while simultaneously securing a large FOV/digital-resolution ratio and a fast resonant raster-scanning speed. We further provide a free version of our custom acquisition software to assist with a smooth and easy construction process. For complete details on the use and execution of this protocol, please refer to Borah et al. (2021).
HERO: Hierarchical energy optimization for data center networks (2012)

With the rapid growth of data center networks in providing a myriad of services and applications to store, access, and process data, the power consumption of data center networks has become critically important and must be efficiently managed. In this paper, we discuss the power optimization of data center networks in a hierarchical perspective. We establish a two-level power optimization model to reduce the power consumption of data center networks by switching off network switches and links while still guaranteeing full connectivity and maximum link utilization. After having shown that the addressed problem falls in the class of capacity constraint multi-commodity flow problems, we design several simple heuristic algorithms to solve the problem. Our simulations show that hierarchical energy optimization can effectively save power consumption in data center networks.
One Step Radiosynthesis of 6-[<sup>18</sup>F]Fluoronicotinic Acid 2,3,5,6-Tetrafluorophenyl Ester ([<sup>18</sup>F]F-Py-TFP): A New Prosthetic Group for Efficient Labeling of Biomolecules with Fluorine-18 (2010)

The labeling of biomolecules for positron emission tomography (PET) with no-carrier-added fluorine-18 is almost exclusively accomplished using prosthetic groups in a two step procedure. The inherent complexity of the process renders full automation a challenge and leads to protracted synthesis times. Here we describe a new (18)F-labeled prosthetic group based on nicotinic acid tetrafluorophenyl ester. Reaction of [(18)F]fluoride at 40 degrees C with the trimethylammonium precursor afforded 6-[(18)F]fluoronicotinic acid tetrafluorophenyl ester ([(18)F]F-Py-TFP) directly in 60-70% yield. [(18)F]F-Py-TFP was conveniently purified by Sep-Pak cartridge prior to incubation with a peptide containing the RGD sequence. The desired conjugate was formed rapidly and in good yields. An in vitro receptor-binding assay for the integrin alpha(v)beta(3) was established to explore competition with peptide and peptidomimetic prepared from F-Py-TFP with (125)I-echistatin. The nonradioactive conjugates were found to possess high binding affinities with calculated K(i) values in the low nanomolar range.
Assembly and Photonic Properties of Superparamagnetic Colloids in Complex Magnetic Fields (2011)

Interparticle magnetic dipole force has been found to drive the formation of dynamic superparamagnetic colloidal particle chains that can lead to the creation of photonic nanostructures with rapidly and reversibly tunable structural colors in the visible and near-infrared spectrum. Although most studies on magnetic assembly utilize simple permanent magnets or electromagnets, magnetic fields, in principle, can be more complex, allowing the localized modulation of assembly and subsequent creation of complex superstructures. To explore the potential applications of a magnetically tunable photonic system, we study the assembly of magnetic colloidal particles in the complex magnetic field produced by a nonideal linear Halbach array. We demonstrate that a horizontal magnetic field sandwiched between two vertical fields would allow one to change the orientation of the particle chains, producing a high contrast in color patterns. A phase transition of Fe(3)O(4)@SiO(2) particles from linear particle chains to three-dimensional crystals is found to be determined by the interplay of the magnetic dipole force and packing force, as well as the strong electrostatic force. While a color pattern with tunable structures and diffractions can be instantly created when the particles are assembled in the form of linear chains in the regions with vertical fields, the large field gradient in the horizontal orientation may destabilize the chain structures and produces a pattern of 3D crystals that compliments that of initial chain assemblies. Our study not only demonstrates the great potential of magnetically responsive photonic structures in the visual graphic applications such as signage and security documents but also points out the potential challenge in pattern stability when the particle assemblies are subjected to complex magnetic fields that often involve large field gradients.
A miniaturized UWB bi-planar yagi-like antenna (2017)

A novel Ultra-wideband (UWB) Yagi-like antenna is proposed targeting the 5 GHz WLAN bands. The bi-planar design relies on the technique of using a half loop ring on each side of the substrate which provides a miniaturization of 45%, a minimum measured -10 dB percent bandwidth of 43.3%, and a high gain of 6.43 dBi. The total board size of the miniaturized model is 50 × 40 × 0.76 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . The proposed Yagi-like antenna has directional radiation characteristics with a very high front-to-back ratio (FBR) of more than 19 dB using a small ground plane size of 11×40 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , and directivity of around 7 dB using a single director element. The efficiency of the antenna is 92%.
Decimation-enhanced finite alphabet iterative decoders for LDPC codes on the BSC (2011)

Finite alphabet iterative decoders (FAID) with multilevel messages that can surpass BP in the error floor region for LDPC codes on the BSC were previously proposed in [1]. In this paper, we propose decimation-enhanced decoders. The technique of decimation which is incorporated into the message update rule, involves fixing certain bits of the code to a particular value. Under appropriately chosen rules, decimation can significantly reduce the number of iterations required to correct a fixed number of errors, while maintaining the good performance of the original decoder in the error floor region. At the same time, the algorithm is much more amenable to analysis. We shall provide a simple decimation scheme for a particularly good 7-level FAID for column-weight three codes on the BSC, that helps to correct a fixed number of errors in fewer iterations, and provide insights into the analysis of the decoder. We shall also examine the conditions under which the decimation-enhanced 7-level FAID performs at least as good as the 7-level FAID.
A reconfigurable processor architecture and software development environment for embedded systems (2004)

Flexibility, high computing power and low energy consumption are strong guidelines when designing new generation embedded processors. Traditional architectures are no longer suitable to provide a good compromise among these contradictory implementation requirements. In this paper we present a new reconfigurable processor that tightly couples a VLIW architecture with a configurable unit implementing an additional configurable pipeline. A software development environment is also introduced providing a user-friendly tool for application development and performance simulation. Finally, we show that the HW/SW reconfigurable platform proposed achieves dramatic improvement in both speed and energy consumption on signal processing computation kernels.
Performance analysis of closed-loop transmit diversity in the presence of feedback errors (2003)

Transmit diversity techniques have received a lot of attention recently, and open-loop and closed-loop downlink transmit diversity modes for two transmit antennas have been included in 3GPP WCDMA release 4. System capacity can be increased from that of open-loop modes if the transmitter is equipped with additional side information of the downlink channel. In a frequency division duplex system, this means that the receiver has to provide the information through a feedback mechanism. We study the performance loss caused by feedback errors using the bit error probability as a performance measure. It is shown that the asymptotic diversity of closed-loop schemes is reduced to one in the presence of feedback errors, i.e., the performance is similar to a single transmit antenna system with some SNR gain. The proof is given in a very general manner and it is valid for a large variety of feedback schemes. Two example schemes, selection and cophasing algorithms, are discussed in more detail to verify the results.
Minimax Design of Nonlinear Phase FIR Filters with Optimality Certificates (2016)

The Parks-McClellan algorithm provides an efficient method for designing a linear phase FIR filter with a pre-specified weight function on the approximation error. For the given filter order and the specified weight function, the filter designed with this algorithm will have the unique optimal frequency response that approximates a desired filter response as certified by the alternation theorem. In this paper, a nonlinear phase FIR filter design algorithm is provided that allows the specification of a piecewise constant weight function on the approximation error in an analogous manner to linear phase FIR filters. For the given filter order and weight function, the resulting filter will provably have the unique optimal magnitude response that approximates a desired filter response, where the certification of optimality is given and is also based on the alternations that the weighted error function exhibits. Furthermore, the method is applicable to designing filters with both real- and complex-valued coefficients, which in turn determines the number of required alternations.
Fast Parallel Computation Of Manipulator Inverse Dynamics (1991)

Method for fast parallel computation of inverse dynamics problem, essential for real-time dynamic control and simulation of robot manipulators, undergoing development. Enables exploitation of high degree of parallelism and, achievement of significant computational efficiency, while minimizing various communication and synchronization overheads as well as complexity of required computer architecture. Universal real-time robotic controller and simulator (URRCS) consists of internal host processor and several SIMD processors with ring topology. Architecture modular and expandable: more SIMD processors added to match size of problem. Operate asynchronously and in MIMD fashion.
N-Linked Glycosylation Status of Classical Swine Fever Virus Strain Brescia E2 Glycoprotein Influences Virulence in Swine (2006)

E2 is one of the three envelope glycoproteins of classical swine fever virus (CSFV). Previous studies indicate that E2 is involved in several functions, including virus attachment and entry to target cells, production of antibodies, induction of protective immune response in swine, and virulence. Here, we have investigated the role of E2 glycosylation of the highly virulent CSFV strain Brescia in infection of the natural host. Seven putative glycosylation sites in E2 were modified by site-directed mutagenesis of a CSFV Brescia infectious clone (BICv). A panel of virus mutants was obtained and used to investigate whether the removal of putative glycosylation sites in the E2 glycoprotein would affect viral virulence/pathogenesis in swine. We observed that rescue of viable virus was completely impaired by removal of all putative glycosylation sites in E2 but restored when mutation N185A reverted to wild-type asparagine produced viable virus that was attenuated in swine. Single mutations of each of the E2 glycosylation sites showed that amino acid N116 (N1v virus) was responsible for BICv attenuation. N1v efficiently protected swine from challenge with virulent BICv at 3 and 28 days postinfection, suggesting that glycosylation of E2 could be modified for development of classical swine fever live attenuated vaccines.