gebhart/patrepeval huggingface dataset:
A Self-Steering Receiver Array Using Jointly Coupled Oscillators and Phased-Locked Loops (2014)

This paper presents an analog circuit scheme to steer phased-array receivers in the direction of an incoming signal. The proposed circuit technique utilizes a coupled-oscillator array along with a coupled-phased-locked loop to auto-align an N-element receive array towards the direction of the incident RF signal. A four-element receiver array is implemented in 45-nm CMOS SOI process and achieves auto-steering range of ±35° from broadside. A three-element version of the array demonstrates higher auto-steering angle covering ±70° range. The receiver also performs signal demodulation for the incident modulated RF signal, allowing high-data rate communication. A 60-Mbps 64-QAM modulated RF signal is demodulated with error-vector-magnitude (EVM) less than 4% across the steering angle range. The chip area is 3.45 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> including a pad frame with 30-mW/element power consumption. To the best of authors' knowledge, this is the first demonstration of an analog self-steering array in an integrated circuit.
A new chitinase-like xylanase inhibitor protein (XIP) from coffee (Coffea arabica) affects Soybean Asian rust (Phakopsora pachyrhizi) spore germination (2011)

Our data suggests that CaclXIP belongs to a class of naturally inactive chitinases that have evolved to act in plant cell defence as xylanase inhibitors. Its role on inhibiting germination of fungal spores makes it an eligible candidate gene for the control of Asian rust.
Nonlinear Estimation of Microbial and Enzyme Kinetic Parameters from Progress Curve Data (2001)

A computer program (BIOKINFIT) was developed to estimate microbial and enzyme kinetic parameters from progress curve data by nonlinear regression. BIOKINFIT overcomes the limitations associated with parameter estimation in nonlinear equations that are implicit in the dependent variable by numerically approximating the substrate concentration in the integrated kinetic expressions. The simplex method was used to minimize the error between experimentally observed and theoretically predicted substrate depletion data. The robustness of this approach was initially verified using synthetic substrate depletion data that were characterized by either simple or relative errors of known magnitude. Subsequently, previously published data from three different experiments including the pyruvate kinase reaction, 2-chlorophenol biodegradation, and glucose uptake by Penicillium chrysogenum were used to verify the utility of the present approach for kinetic parameter estimation. In all cases, experimental substrate depletion data were accurately described by the theoretical curves and kinetic parameter estimates obtained in this study using the simplex method were in close agreement with those reported previously. BIOKINFIT, available free of charge on request, offers a convenient and robust method of analyzing progress curve data in implicit kinetic expressions.
ChemInform Abstract: STEREOSELECTIVE SYNTHESIS OF CIS‐ AND TRANS‐2‐(3,4‐DIHYDROXYPHENYL)CYCLOBUTYLAMINE. CONFORMATIONALLY RESTRAINED ANALOGS OF DOPAMINE (1980)

Abstract Piperonal (I) kondensiert mit dem S‐Ylid (II) zum Cyclobutanon (IIIa), dessen Oxim (IIIb) zu den isomeren Aminen (IVa) (katalytisch über Pt) bzw. (IVb) (Na/Isopropanol) reduziert werden kann.
SEMAPLAN: combining planning with semantic matching to achieve web service composition (2006)

Composing existing Web services to deliver new functionality is a difficult problem as it involves resolving semantic, syntactic and structural differences among the interfaces of a large number of services. Unlike most planning problems, it can not be assumed that Web services are described using terms from a single domain theory. While service descriptions may be controlled to some extent in restricted settings (e.g., intra-enterprise integration), in Web-scale open integration, lack of common, formalized service descriptions prevent the direct application of standard planning methods. In this paper, we present a novel algorithm to compose Web services in the presence of semantic ambiguity by combining semantic matching and AI planning algorithms. Specifically, we use cues from domain-independent and domain-specific ontologies to compute an overall semantic similarity score between ambiguous terms. This semantic similarity score is used by AI planning algorithms to guide the searching process when composing services. Experimental results indicate that planning with semantic matching produces better results than planning or semantic matching alone. The solution is suitable for semi-automated composition tools or directory browsers.
Biomechanical response to acupuncture needling in humans (2001)

During acupuncture treatments, acupuncture needles are manipulated to elicit the characteristic "de qi" reaction widely viewed as essential to acupuncture's therapeutic effect. De qi has a biomechanical component, "needle grasp," which we have quantified by measuring the force necessary to pull an acupuncture needle out of the skin (pullout force) in 60 human subjects. We hypothesized that pullout force is greater with both bidirectional needle rotation (BI) and unidirectional rotation (UNI) than no rotation (NO). Acupuncture needles were inserted, manipulated, and pulled out by using a computer-controlled acupuncture needling instrument at eight acupuncture points and eight control points. We found 167 and 52% increases in mean pullout force with UNI and BI, respectively, compared with NO (repeated-measures ANOVA, P < 0.001). Pullout force was on average 18% greater at acupuncture points than at control points (P < 0.001). Needle grasp is therefore a measurable biomechanical phenomenon associated with acupuncture needle manipulation.
Oral delivery of peptides and proteins using lipid-based drug delivery systems (2012)

Lipid-based DDS are safe and suitable for oral delivery of peptides and proteins. Significant progress has been made in this area with several technologies on clinical trials. However, a better understanding of the mechanism of action in vivo is needed in order to improve the design and development of lipid-based DDS with the desired bioavailability and therapeutic profile.
Model‐Free and Model‐based Parameters Derived From CAIPIRINHA‐Dixon‐TWIST‐VIBE DCE‐MRI: Associations With Prognostic Factors and Molecular Subtypes of Invasive Ductal Breast Cancer (2022)

Stage 2.
Supplementary Table 4 from SMAD4 Loss in Colorectal Cancer Patients Correlates with Recurrence, Loss of Immune Infiltrate, and Chemoresistance (2023)

&lt;p&gt;Ordinal logistic regression analyses to assess the association of SMAD4 expression status with lymphocytic reaction patterns in validation cohort&lt;/p&gt;
P. aeruginosa augments irradiation injury via 15-lipoxygenase–catalyzed generation of 15-HpETE-PE and induction of theft-ferroptosis (2022)

Total body irradiation (TBI) targets sensitive bone marrow hematopoietic cells and gut epithelial cells, causing their death and inducing a state of immunodeficiency combined with intestinal dysbiosis and nonproductive immune responses. We found enhanced Pseudomonas aeruginosa (PAO1) colonization of the gut leading to host cell death and strikingly decreased survival of irradiated mice. The PAO1-driven pathogenic mechanism includes theft-ferroptosis realized via (a) curbing of the host antiferroptotic system, GSH/GPx4, and (b) employing bacterial 15-lipoxygenase to generate proferroptotic signal - 15-hydroperoxy-arachidonoyl-PE (15-HpETE-PE) - in the intestines of irradiated and PAO1-infected mice. Global redox phospholipidomics of the ileum revealed that lysophospholipids and oxidized phospholipids, particularly oxidized phosphatidylethanolamine (PEox), represented the major factors that contributed to the pathogenic changes induced by total body irradiation and infection by PAO1. A lipoxygenase inhibitor, baicalein, significantly attenuated animal lethality, PAO1 colonization, intestinal epithelial cell death, and generation of ferroptotic PEox signals. Opportunistic PAO1 mechanisms included stimulation of the antiinflammatory lipoxin A4, production and suppression of the proinflammatory hepoxilin A3, and leukotriene B4. Unearthing complex PAO1 pathogenic/virulence mechanisms, including effects on the host anti/proinflammatory responses, lipid metabolism, and ferroptotic cell death, points toward potentially new therapeutic and radiomitigative targets.
Impact of the optical routing on the transmission in transparent networks (2009)

We present an upgraded circulating loop to simply account for the actual impact of the different channels optical routings when assessing the transmission performance in the WDM transparent networks.
Rapid automatic assessment of microvascular density in sidestream dark field images (2011)

The purpose of this study was to develop a rapid and fully automatic method for the assessment of microvascular density and perfusion in sidestream dark field (SDF) images. We modified algorithms previously developed by our group for microvascular density assessment and introduced a new method for microvascular perfusion assessment. To validate the new algorithm for microvascular density assessment, we reanalyzed a selection of SDF video clips (n = 325) from a study in intensive care patients and compared the results to (semi-)manually found microvascular densities. The method for microvascular perfusion assessment (temporal SDF image contrast analysis, tSICA) was tested in several video simulations and in one high quality SDF video clip where the microcirculation was imaged before and during circulatory arrest in a cardiac surgery patient. We found that the new method for microvascular density assessment was very rapid (<30 s/clip) and correlated excellently with (semi-)manually measured microvascular density. The new method for microvascular perfusion assessment (tSICA) was shown to be limited by high cell densities and velocities, which severely impedes the applicability of this method in real SDF images. Hence, here we present a validated method for rapid and fully automatic assessment of microvascular density in SDF images. The new method was shown to be much faster than the conventional (semi-)manual method. Due to current SDF imaging hardware limitations, we were not able to automatically detect microvascular perfusion.
Toward a Universal μ-Agonist Template for Template-Based Alignment Modeling of Opioid Ligands (2019)

Opioid ligands are a large group of G-protein-coupled receptor ligands possessing high structural diversity, along with complicated structure-activity relationships (SARs). To better understand their structural correlations as well as the related SARs, we developed the innovative template-based alignment modeling in our recent studies on a variety of opioid ligands. As previously reported, this approach showed promise but also with limitations, which was mainly attributed to the small size of morphine as a template. With this study, we set out to construct an artificial μ-agonist template to overcome this limitation. The newly constructed template contained a largely extended scaffold, along with a few special μ-features relevant to the μ-selectivity of opioid ligands. As demonstrated in this paper, the new template showed significantly improved efficacy in facilitating the alignment modeling of a wide variety of opioid ligands. This report comprises of two main parts. Part 1 discusses the general construction process and the structural features as well as a few typical examples of the template applications and Part 2 focuses on the template refinement and validation.
Selective Isomerization of Hydrocarbon Chains on External Surfaces of Zeolite Crystals (1995)

A mechanism has been found that explains the distribution of products obtained in the isomerizations of long-chain alkanes on ZSM-22 and SAPO-11 catalysts so well that it should now be possible to tailor reactions for the synthesis of branched hydrocarbons. The reactions occur at the external surface of the catalyst according to a lock-and-key model (shown on the right); thus, the classical concept of shape-selective catalysis within micropores is substantially extended.
Vbeta-dependent stimulation of bovine and human T cells by host-specific staphylococcal enterotoxins (1997)

Staphylococcus aureus isolates from bovine and ovine species produce unique molecular variants of type C staphylococcal enterotoxin (SEC). The SEC animal variants have greater than 98% amino acid sequence identity with SEC1, a human-associated SEC. The two SEC animal variants have been designated SEC(bovine) and SEC(ovine) according to their corresponding host species. We showed previously that these toxins induce quantitatively different levels of T-cell stimulation in several animal species. The present study compared the abilities of these closely related host-specific SEC variants to stimulate Vbeta-bearing T cells from bovine and human donors. All three toxins expanded human T cells bearing T-cell receptor Vbeta elements (huVbeta) 3, 12, 13.2, 14, 15, 17, and 20. However, SEC1 resulted in greater expansion of hyVbeta12 than either SEC(bovine) or SEC(ovine). In addition, bovine T cells proliferate in a Vbeta-dependent manner in response to these superantigens (SAgs). All three toxins induced the proliferation of bovine T cells bearing the previously sequenced Vbeta element (boVbeta) from the bovine T-cell clone BTB13 (boVbetaBTB13). SEC1 and SEC(ovine) also were able to induce proliferation of bovine T cells bearing boVbetaBTB35, which SEC(bovine) failed to stimulate. The species-specific differences in T-cell proliferation exhibited by these closely related SEC variants may reflect the evolutionary adaptation of S. aureus, presumably to increase its host range by the manipulation of the immune system in a host-specific manner.
[Restless-leg syndrome--possible unrecognized cause for insomnia and irritability in children]. (2008)

Restless legs syndrome (RLS) has gradually been recognized as a cause for insomnia in adults, but there have been few reports about children with RLS in Japan. Here we described seven pediatric RLS patients. All of the parents of our patients had difficult times to make their children sleep due to irritability, restlessness, and demanding bedtime routines. All patients had asked their parents to rub their feet in bed, and it took more than half an hour to soothe them until they fell asleep. Their mothers had been exhausted from this night-time routine. However, they did not consider the routine abnormal, as it had been their habitual behavior since infancy. Some parents were too distressed or embarrassed to describe the symptoms of their child properly. Five patients had clear family history and none had obvious periodic leg movements during sleep. All patients showed low levels of ferritin and iron supplementation was effective in five cases. In the severest two cases, pramipexole, but not iron, was dramatically effective. Both patients started to show RLS symptoms in the early days of infancy, which may suggest more severe hereditary dopaminergic dysfunction. RLS does occur in childhood and pediatricians should bear it in mind as one of the differential diagnoses when seeing children who are irritated and/or having difficulty in initiating their sleep.
Evaluation of fully automated motion corrected first pass myocardial perfusion MRI with semi quantitative perfusion parameter maps in patients with ischemic heart disease (2012)

The purpose of the study is to evaluate a fully automated motion corrected first pass myocardial perfusion (FPMP) MRI with semi quantitative perfusion parameter maps in patients with suspected ischemic heart disease.
Real-time feature-based synthesis for live musical performance (2007)

A crucial set of decisions in digital musical instrument design deals with choosing mappings between parameters controlled by the performer and the synthesis algorithms that actually generate sound. Feature-based synthesis offers a way to parameterize audio synthesis in terms of the quantifiable perceptual characteristics, or features, the performer wishes the sound to take on. Techniques for accomplishing such mappings and enabling feature-based synthesis to be performed in real time are discussed. An example is given of how a real-time performance system might be designed to take advantage of feature-based synthesis's ability to provide perceptually meaningful control over a large number of synthesis parameters.
Assaying Surface Expression of Chemosensory Receptors in Heterologous Cells (2011)

The vivid world of odors is recognized by the sense of olfaction. Olfaction in mice is mediated by a repertoire of about 1200 G Protein Coupled Receptors (GPCRs) that are postulated to bind volatile odorant molecules and converting the extracellular signal into an intracellular signal by coupling with G protein Gαolf. Binding of the odorants to the receptors is thought to follow a combinatorial rule, that is, one odorant may bind several receptors and one receptor may bind several odorants to varying degrees. Biochemical, signaling and ligand binding studies have been conveniently carried out for most GPCRs using heterologous cells. However use of heterologous cells for study of odorant receptors, was precluded for a long time since on transfection they failed to export to the surface. Saito et al have demonstrated single membrane pass Receptor Transporting Protein (RTP) family chaperones show enhanced expression in the olfactory sensory neurons and act as chaperones to traffic odorant receptors to the surface in heterologous cells, when co transfected together. To carry out biochemical assays for receptors using heterologous cells, one must first determine if the receptor shows robust surface expression in the cell line. This can be assayed by overexpressing the receptors with the chaperone RTP1S followed by live cell staining to fluorescently label the extracellular domain or a tag in the extracellular domain exclusively. Here we demonstrate a protocol to carry out live cell staining that can be used to detect odorant receptors on the surface of HEK293T cells conveniently. In addition, it may also be used to assay for surface expression of other chemosensory receptors or GPCRs.
Acute and chronic tirasemtiv treatment improves in vivo and in vitro muscle performance in actin-based nemaline myopathy mice (2021)

Nemaline myopathy, a disease of the actin-based thin filament, is one of the most frequent congenital myopathies. To date, no specific therapy is available to treat muscle weakness in nemaline myopathy. We tested the ability of tirasemtiv, a fast skeletal troponin activator that targets the thin filament, to augment muscle force-both in vivo and in vitro-in a nemaline myopathy mouse model with a mutation (H40Y) in Acta1. In Acta1H40Y mice, treatment with tirasemtiv increased the force response of muscles to submaximal stimulation frequencies. This resulted in a reduced energetic cost of force generation, which increases the force production during a fatigue protocol. The inotropic effects of tirasemtiv were present in locomotor muscles and, albeit to a lesser extent, in respiratory muscles, and they persisted during chronic treatment, an important finding as respiratory failure is the main cause of death in patients with congenital myopathy. Finally, translational studies on permeabilized muscle fibers isolated from a biopsy of a patient with the ACTA1H40Y mutation revealed that at physiological Ca2+ concentrations, tirasemtiv increased force generation to values that were close to those generated in muscle fibers of healthy subjects. These findings indicate the therapeutic potential of fast skeletal muscle troponin activators to improve muscle function in nemaline myopathy due to the ACTA1H40Y mutation, and future studies should assess their merit for other forms of nemaline myopathy and for other congenital myopathies.
GaN laser diodes for quantum sensing, optical atomic clocks, and quantum computing (2022)

GaN laser diodes have the potential to be a key enabler for many quantum technologies, including quantum sensing, optical atomic clocks and ion-trap & neutral atom quantum computing, since the AlGaInN material system allows for laser diodes to be fabricated over a wide range of wavelengths from ultra-violet to visible, allowing the development of very high specification laser diode sources that are portable, robust and provide practical solutions that are otherwise unobtainable using more conventional laser sources. We report our latest results on a range of AlGaInN diode-lasers targeted to meet optical atomic clock and quantum gravity sensor applications. This includes the [5s2S1/2-5p2P1/2] cooling transition in strontium+ ion optical clocks at 422 nm, the [5s21S0-5p1P1] cooling transition in neutral strontium clocks at 461 nm and the [5s2s1/2 – 6p2P3/2] transition in rubidium at 420 nm.
4D X-ray CT for Evaluation of Progressive Damage Growth of Composites under Fatigue Loading (2023)

View Video Presentation: https://doi.org/10.2514/6.2023-0775.vid Due to the heterogeneous microstructures, fatigue damage growth mechanics of composites are complex and highly dependent on the type of loading mode and load sequencing. Unlike for metals where striation marks can be used for understanding the damage growth rates and mechanics, the final destructive failure mode of composites tends to overshadow damage initiation sites and propagation details. Damage initiation and propagation in composites typically occur from an internal defect/feature or from an area where there is a stress concentration (i.e., fastener hole or impact damage) and are not visible with standard nondestructive inspection (NDI) techniques until they are within the inspection threshold of the equipment or the inspection method, which is also a function of materials, geometry, and location of the defect/feature. Although standard NDI techniques such as ultrasonic testing (UT) and pulse thermography are adequate for detecting such defects, in-depth information related to manufacturing defects (including certain manufacturing features that could potentially be failure initiation or nucleation sites) is required to fully understand the structural capability (i.e., strength and durability) of composites. In addition to high-fidelity post-manufacturing inspections, detailed inspections are required to detect damage initiation and monitor damage propagation through the heterogeneous microstructures of composites. Therefore, a high-fidelity 3D inspection technique such as X-ray computed tomography is required to investigate the damage growth mechanics and interaction of multiple failure modes. Such detailed damage characteristics can then be used for development and validation of high-fidelity progressive damage growth analysis (PDA) techniques and life prediction tools. More importantly, the damage accumulation and growth in composites need to be fully characterized to aid in certification as well as establishing damage tolerance testing and analysis protocols.
Structural and functional characterization of the human immunodeficiency virus rev protein. (1989)

Expression of the human immunodeficiency virus (HIV) rev protein is required for expression of virus structural proteins. Site-directed mutagenesis was used to localize regions important for Rev function. We found that proteins with single amino acid substitution mutations concentrated within the amino termini and midportion of Rev were for the most part nonfunctional. Indirect immunofluorescence revealed that Rev was localized predominantly in the nucleolus. However, a deletion mutant that lacked the basic stretch of amino acids comprising residues Arg-Arg-Arg-Arg-Trp accumulated in the cytoplasm and was no longer functional. Consistent with this observation, a beta-galactosidase fusion protein containing this basic rich peptide at its amino termini was targeted to the nucleus. These observations indicate that the HIV rev protein has a distinct nuclear localization sequence and suggest that Rev-mediated regulation of gene expression involves nuclear events.