gebhart/patrepeval huggingface dataset:
All-optical integrated atomic clock (2010)

We describe a novel architecture for realization of a miniature all-optical atomic clock. We show theoretically that a hyperparametric oscillator based on a whispering gallery mode resonator can be used as a miniature frequency divider for the clock. Such a frequency divider allows for transferring the long term frequency stability from the optical frequency domain to the RF frequency domain. We present some details for the clock that utilizes the thermally stable isoclinic point of the inhomogeneously broadened D <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> line of <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">87</sup> Rb for frequency stabilization, and report on progress towards its experimental realization.
Functional In Vivo Delivery of Multiplexed Anti-HIV-1 siRNAs via a Chemically Synthesized Aptamer With a Sticky Bridge (2012)

One of the most formidable impediments to clinical translation of RNA interference (RNAi) is safe and effective delivery of the siRNAs to the desired target tissue at therapeutic doses. We previously described in vivo cell type-specific delivery of anti-HIV small-interfering RNAs (siRNAs) through covalent conjugation to an anti-gp120 aptamer. In order to improve the utility of aptamers as siRNA delivery vehicles, we chemically synthesized the gp120 aptamer with a 3' 7-carbon linker (7C3), which in turn is attached to a 16-nucleotide 2' OMe/2' Fl GC-rich bridge sequence. This bridge facilitates the noncovalent binding and interchange of various siRNAs with the same aptamer. We show here that this aptamer-bridge-construct complexed with three different Dicer substrate siRNAs (DsiRNAs) results in effective delivery of the cocktail of DsiRNAs in vivo, resulting in knockdown of target mRNAs and potent inhibition of HIV-1 replication. Following cessation of the aptamer-siRNA cocktail treatment, HIV levels rebounded facilitating a follow-up treatment with the aptamer cocktail of DsiRNAs. This follow-up injection resulted in complete suppression of HIV-1 viral loads that extended several weeks beyond the final injection. Collectively, these data demonstrate a facile, targeted approach for combinatorial delivery of antiviral and host DsiRNAs for HIV-1 therapy in vivo.
Contrast-enhanced ultrasound imaging with high CTR and improved resolution by bubble-echo based deconvolution (2015)

In microvascular perfusion imaging by contrastenhanced ultrasound (CEUS), inhibiting the strong tissue backscattering to enhance contrast-to-tissue ratio (CTR) and improving the imaging resolution to distinguish small vessels are two critical aspects. CTR has been greatly enhanced based on the strong nonlinear responses of contrast microbubbles under ultrasound insonation. However, the resolution of CEUS image is still limited by the finite bandwidth of the imaging system. In this paper, a peculiar bubble-echo based deconvolution (BED) was proposed based on a modified convolution model for CEUS to improve both CTR and resolution. A novel bubble-echo based PSF was constructed using the modified Herring equation, where bubble-echo referred to the theoretical backscattered echo from a single bubble under the insonification. Deconvolution was implemented axially using regularized inverse Wiener filtering. The efficiency of the proposed BED was verified by combining with fundamental imaging, second harmonic imaging and pulse inversion technique. Meanwhile, as comparisons, the approved cepstrum based deconvolution (CEPD) and pulse inversion bubble-wavelet imaging (PIWI) were also performed. In vivo rabbit kidney perfusion experiments were carried out to evaluate the above methods from CTR, time-intensity-curve and resolution. BED performed better than CEPD and PIWI in enhancing CTR, and had a higher resolution than PIWI. All results indicate that BED provides new CEUS methods with higher CTR and good resolution, which has important significance to microvascular perfusion evaluation in deep tissue.
A Defined Tuberculosis Vaccine Candidate Boosts BCG and Protects Against Multidrug-Resistant <i>Mycobacterium tuberculosis</i> (2010)

Despite the widespread use of the childhood vaccine against tuberculosis (TB), Mycobacterium bovis bacillus Calmette-Guérin (BCG), the disease remains a serious global health problem. A successful vaccine against TB that replaces or boosts BCG would include antigens that induce or recall the appropriate T cell responses. Four Mycobacterium tuberculosis (Mtb) antigens--including members of the virulence factor families PE/PPE and EsX or antigens associated with latency--were produced as a single recombinant fusion protein (ID93). When administered together with the adjuvant GLA-SE, a stable oil-in-water nanoemulsion, the fusion protein was immunogenic in mice, guinea pigs, and cynomolgus monkeys. In mice, this fusion protein-adjuvant combination induced polyfunctional CD4 T helper 1 cell responses characterized by antigen-specific interferon-γ, tumor necrosis factor, and interleukin-2, as well as a reduction in the number of bacteria in the lungs of animals after they were subsequently infected with virulent or multidrug-resistant Mtb strains. Furthermore, boosting BCG-vaccinated guinea pigs with fusion peptide-adjuvant resulted in reduced pathology and fewer bacilli, and prevented the death of animals challenged with virulent Mtb. Finally, the fusion protein elicited polyfunctional effector CD4 and CD8 T cell responses in BCG-vaccinated or Mtb-exposed human peripheral blood mononuclear cells. This study establishes that the protein subunit vaccine consisting of the fusion protein and adjuvant protects against TB and drug-resistant TB in animals and is a candidate for boosting the protective efficacy of the childhood BCG vaccine in humans.
Lactoferrin in health and disease. (2007)

Lactoferrin, an iron-binding glycoprotein, can be regarded as a cell-secreted mediator that bridges innate and adaptive immune function by regulating target cell response. It is a major pleiotropic mediator that directly assists in the development of T-helper cell polarization. The aim of this minireview is to provide a summary of the most recent work presented at the Lactoferrin Minisymposium at the University of Texas, Health Science Center at Houston, Texas, USA, regarding role of lactoferrin in maintaining immune homeostasis. The data presented here lay emphasis on the significance of lactoferrin in the resolution or progression of the immune responses, thus giving lactoferrin bookend properties in controlling the initial reactions to infectious assault, trauma, and injury. These findings may be critically important in the development of therapeutically relevant protocols.
Utilizing combinations of molecular targeted agents to sensitize tumor cells to EGFR inhibitors (2008)

EGFR inhibitors have achieved clinical antitumor activity as single agents. The specific inhibition of EGFR and associated pathways provides a mechanism for efficacious inhibition of tumor cell growth while minimizing toxicities often associated with chemotherapeutic drugs. The challenge of using targeted cancer drugs as single agents is the potential for de novo or acquired resistance due to established or adapted alternate signal transduction pathways. In this chapter, we will describe how cancer drug combinations with EGFR inhibitors can be rationally identified by utilizing our understanding of the molecular mechanism and related biomarkers of EGFR inhibitor sensitivity. Such combinations may ultimately provide better efficacy and reduced toxicity for patients.
Unique Antibody Responses to Malondialdehyde-Acetaldehyde (MAA)-Protein Adducts Predict Coronary Artery Disease (2014)

Malondialdehyde-acetaldehyde adducts (MAA) have been implicated in atherosclerosis. The purpose of this study was to investigate the role of MAA in atherosclerotic disease. Serum samples from controls (n = 82) and patients with; non-obstructive coronary artery disease (CAD), (n = 40), acute myocardial infarction (AMI) (n = 42), or coronary artery bypass graft (CABG) surgery due to obstructive multi-vessel CAD (n = 72), were collected and tested for antibody isotypes to MAA-modifed human serum albumin (MAA-HSA). CAD patients had elevated relative levels of IgG and IgA anti-MAA, compared to control patients (p<0.001). AMI patients had a significantly increased relative levels of circulating IgG anti-MAA-HSA antibodies as compared to stable angina (p<0.03) or CABG patients (p<0.003). CABG patients had significantly increased relative levels of circulating IgA anti-MAA-HSA antibodies as compared to non-obstructive CAD (p<0.001) and AMI patients (p<0.001). Additionally, MAA-modified proteins were detected in the tissue of human AMI lesions. In conclusion, the IgM, IgG and IgA anti-MAA-HSA antibody isotypes are differentially and significantly associated with non-obstructive CAD, AMI, or obstructive multi-vessel CAD and may serve as biomarkers of atherosclerotic disease.
ChemInform Abstract: Synthesis and Pharmacological Studies of (2‐Aminoethyl)‐6‐benzoxazolinones. (1986)

Abstract Die im Titel genannten Verbindungen (III) werden aus den Bromethylbenzoxazolinonen (II) hergestellt, welche reduktiv aus den entsprechenden Bromacetylverbindungen (I) erhalten werden.
Surface-enhanced Raman scattering nanodomes fabricated by nanoreplica molding (2010)

We demonstrate a surface-enhanced Raman scattering substrate consisting of a closely spaced metal nanodome array fabricated on flexible plastic film. We used a low cost, large area replica molding process to produce a 2-dimensional periodic array of cylinders that is subsequently overcoated with SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> and silver thin films to form dome-shaped structures. Finite element modeling was used to investigate the electromagnetic field distribution of the nanodome array structure and the effect of the nanodome separation distance on the electromagnetic field enhancement. The SERS enhancement from the nanodome array substrates was experimentally verified using rhodamine 6G as the analyte. With a separation distance of 17 nm achieved between adjacent domes using a process that is precisely controlled during thin film deposition, a reproducible SERS enhancement factor of 1.37 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> was demonstrated. The nanoreplica molding process presented in this work allows for simple, low cost, high-throughput fabrication of uniform nanoscale SERS substrates over large surface areas without the requirement for high resolution lithography or defect-free deposition of spherical microparticle monolayer templates.
Human microbiome aging clocks based on deep learning and tandem of permutation feature importance and accumulated local effects (2018)

The human gut microbiome is a complex ecosystem that both affects and is affected by its host status. Previous analyses of gut microflora revealed associations between specific microbes and host health and disease status, genotype and diet. Here, we developed a method of predicting the biological age of the host based on the microbiological profiles of gut microbiota using a curated dataset of 1,165 healthy individuals (1,663 microbiome samples). Our predictive model, a human microbiome clock, has an architecture of a deep neural network and achieves the accuracy of 3.94 years mean absolute error in cross-validation. The performance of the deep microbiome clock was also evaluated on several additional populations. We further introduce a platform for biological interpretation of individual microbial features used in age models, which relies on permutation feature importance and accumulated local effects. This approach has allowed us to define two lists of 95 intestinal biomarkers of human aging. We further show that this list can be reduced to 39 taxa that convey the most information on their host's aging. Overall, we show that (a) microbiological profiles can be used to predict human age; and (b) microbial features selected by models are age-related.
Detection and analysis of cartilage degeneration by spatially resolved streaming potentials (2002)

Cartilage molecular changes in osteoarthritis are most commonly related to the degradation and loss of proteoglycan and collagen fibrils of the extracellular matrix, which directly influence tissue stiffness and compression-generated streaming potentials. In this study, we evaluated the potential of a new technique, spatially resolved mapping of streaming potentials, to non-destructively indicate cartilage health or degeneration. Matched pairs of bovine cartilage/bone explant disks were cultured for 11 days in a serum free medium with and without interleukin-lalpha (IL-1alpha). The electromechanical properties (static stiffness, dynamic stiffness and streaming potentials) of cartilage disks were measured during unconfined compression using a mechanical tester coupled with a linear array of eight 50 microm diameter platinum-iridium microelectrodes. After 11 days of culture, the proteoglycan content of IL-1alpha treated disks was significantly reduced and the denatured and cleaved collagen content was increased compared to control disks. These biochemical alterations were concomitant with the reductions in the amplitudes of the static stiffness, the dynamic stiffness and the streaming potential profile as well as changes in the shape of the streaming potential profile. We found that spatial mapping of streaming potentials presents several advantages for the development of a clinical instrument to evaluate the degeneration of articular cartilage.
New Chemical Reaction Process of a Bi<sub>2</sub>Te<sub>2.7</sub>Se<sub>0.3</sub> Nanomaterial for Feasible Optimization in Transport Properties Resulting in Predominant n-Type Thermoelectric Performance (2016)

Various chemical reaction processes have been adopted to synthesize Bi2Te3 thermoelectric nanomaterials for achieving remarkably low thermal conductivities, but chemical contaminations were usually pointed out as flaws, severely deteriorating electrical conductivities. We devised a novel water-based chemical reaction process for a Bi2Te2.7Se0.3 nanocompound in which the possibility for chemical contaminations was reduced. We successfully synthesized a small and highly distributed Bi2Te2.7Se0.3 nanocompound with high purity and adequately packed it via a spark plasma sintering process to produce a nanobulk structure. The resulting nanobulk specimen exhibited a physical density as high as the theoretical one with highly distributed nanograins; thus, we were able to obtain remarkably high electrical conductivity while maintaining thermal conductivity as low as possible. The synergistic effect was greatly induced between the transport properties; thus, the highest reported figure of merit value was achieved for n-type Bi2Te3 in the bulk phase.
An AMTEC vapor-vapor, series connected cell (1992)

The alkali metal thermal‐to‐electric converter (AMTEC) converts heat energy to electrical energy with efficiencies up to 3 to 4 times the state of the art static converters. However, the high current, low voltage output of a single module requires difficult series connecting of cells, and several life limiting concerns may reduce the achievable efficiency. A concept is proposed that incorporates internal series connecting of cells and sodium supply as a vapor without condensation. This concept overcomes many of the long term materials concerns in liquid anode systems and results in a module with about the same power density, but at a higher voltage and lower current. The vapor‐vapor AMTEC concept is described and its performance predicted for typical AMTEC operating conditions.
Layered wireless video multicast using directional relays (2008)

In this paper, we explore the use of directional antennas in relay transmission to improve the performance of video multicast with omni-directional relays in infrastructure- based wireless networks. We describe the system setup with directional relays and determine the user partition along with transmission time scheduling that can optimize a multicast performance criterion. We demonstrate that directional relays significantly improve the multicast system performance compared to omni-directional relays. Furthermore, it also provides larger coverage area.
Model-based optimal attitude and positioning control of small-scale unmanned helicopter (2005)

In this paper, we propose a model-based control system design for autonomous flight and guidance control of a small-scale unmanned helicopter. Small-scale unmanned helicopters have been studied by way of fuzzy and neural network theory, but control that is not based on a model fails to yield good stabilization performance. For this reason, we design a mathematical model and a model-based controller for a small-scale unmanned helicopter system. In order to realize a fully autonomous small-scale unmanned helicopter, we have designed a MIMO attitude controller and a trajectory controller equipped with a Kalman filter-based LQI for a small-scale unmanned helicopter. The design of the trajectory controller takes into consideration the characteristics of attitude closed-loop dynamics. Simulations and experiments have shown that the proposed scheme for attitude control and position control is very useful.
Clinical blood flow measurements using diffraction-grating transducers (2002)

Changing the phase or frequency of the signal driving a diffraction-grating transducer produces beams at known, multiple angles; these multiple angle beams can be used to make angle-independent Doppler measurements. This paper addresses three questions in developing a diffraction-grating instrument for measuring blood flow: how efficient and broadband can these transducers be, how close can such transducers be placed to blood vessels, and can the Doppler spectrum shape be used to determine the velocity profile.
The cell surface leucine-rich repeat receptor for <i>At</i> Pep1, an endogenous peptide elicitor in <i>Arabidopsis</i> , is functional in transgenic tobacco cells (2006)

AtPep1 is a 23-aa endogenous peptide elicitor from Arabidopsis leaves that signals the activation of components of the innate immune response against pathogens. Here, we report the isolation of an AtPep1 receptor from the surface of Arabidopsis suspension-cultured cells. An (125)I-labeled AtPep1 analog interacted with suspension-cultured Arabidopsis with a K(d) of 0.25 nM, and an (125)I-labeled azido-Cys-AtPep1 photoaffinity analog specifically labeled a membrane-associated protein of approximately 170 kDa. The labeled protein was purified to homogeneity, and its tryptic peptides were identified as gene At1g73080, which encodes a leucine-rich repeat receptor kinase, here called PEPR1. Verification of the binding protein as the receptor for AtPep1 was established by demonstrating the loss of function of microsomal membranes of two SALK insertional mutants and by a gain in function of the alkalinization response to AtPep1 by tobacco suspension-cultured cells expressing the At1g73080 transgene. Synthetic homologs of AtPep1, deduced from the C termini of six known paralogs of PROPEP1, were biologically active and were competitors of the interaction of an AtPep1 radiolabeled analog with the receptor. The data are consistent with a role for PEPR1 as the receptor for AtPep1 to amplify innate immunity in response to pathogen attacks.
[Effect of vitronectin on the healing of rabbit corneal epithelial damage]. (1990)

Vitronectin is one of the major cell-adhesive glycoproteins in mammalian plasma. We investigated the effect of topically applied vitronectin on the healing of rabbit corneal epithelial damage. Vitronectin was purified from rabbit serum by heparin-Sepharose affinity chromatography and autoclaved at 121 degrees C for 20 min after adjusting the concentration to 0.2 mg/ml with saline. Rabbit corneal epithelium was abraded with ethanol and a laser blade in the central portion of the cornea which had been demarcated with a 6.5 mm trephine. Vitronectin eye drops were instilled into the right eye, and sterile saline drops into the left eye as control. The dimensions of the circular epithelial defect were measured at various times after wounding. The area of epithelial damage of vitronectin-treated eyes was smaller than that of control eyes at 2hr-12hr after abrasion (p less than 0.01). These results suggested that topically applied vitronectin might accelerate the corneal epithelial wound healing at an early stage. Vitronectin can be considered as a candidate for treatment of corneal epithelial damage.
Registration of 34 Sorghum Germplasm Lines Resistant to Acetolactate Synthase–Inhibitor Herbicides (2011)

Sorghum [ Sorghum bicolor (L.) Moench] germplasm lines designated KS201 through KS234 (Reg. No. GP‐684, PI 659520 to Reg. No. GP‐717, PI 659553) were developed and released by the Kansas Agricultural Experiment Station, Manhattan, KS in 2007. The donor of the herbicide resistance gene, Tailwind, was crossed to adapted‐seed and pollinator‐parent lines. The progenies were treated with the target herbicide, and resistant individuals were repeatedly backcrossed to the adapted parents. Backcrossing was performed until the undesirable wild characteristics from the donor parent were eliminated. Lines KS201 through KS218 are R lines and restore fertility in A1 cytoplasm system; lines KS219 through KS234 are B lines and do not restore fertility in A1 cytoplasm. All lines possess a unique genetic resistance to acetolactate synthase (ALS)–inhibitor herbicide families and are useful breeding materials for the development of commercial hybrids with ALS resistance. The lines are all of combine‐harvester height and reach 50% flowering 60 to 82 d after planting at Manhattan, KS. A majority of the lines are pigmented plant types and have variable grain color and seed sizes within the range common to existing public inbreds.
Peer Assisted Streaming of Scalable Video via Optimized Distributed Caching (2009)

In this paper, we propose a method for peer assisted on demand delivery of scalable video using an optimal, distributed caching algorithm for cache constrained peers. We assume that there are one or more content delivery servers that are provisioned to support delivery of the base layer for all of the peers, and the enhancement layer is only supported for a fraction of peers. It has been shown that in such an application, peer assisted content distribution improves the delivery of the content. In this paper, we use peer assisted delivery of the enhancement layer and show that in a cache constrained video-on-demand environment, availability of the cached content becomes a bottleneck. By using peer arrival rates and supply-demand analysis of the peers, we propose better caching policies at each peer. One proposed policy (referred to as "static optimal") optimizes the utility of the currently available caching opportunities. The other proposed policy (referred to as "dynamic programming" solution) on the other hand performs utility optimization by further considering the future caching opportunities during the streaming operation. Experimental results show that the proposed methods allow more peers to access the enhancement layer; hence, more peers experience improved video quality compared to traditional caching methods.