gebhart/patrepeval huggingface dataset:
The T box mechanism: tRNA as a regulatory molecule (2009)

The T box mechanism is widely used in Gram-positive bacteria to regulate expression of aminoacyl-tRNA synthetase genes and genes involved in amino acid biosynthesis and uptake. Binding of a specific uncharged tRNA to a riboswitch element in the nascent transcript causes a structural change in the transcript that promotes expression of the downstream coding sequence. In most cases, this occurs by stabilization of an antiterminator element that competes with formation of a terminator helix. Specific tRNA recognition by the nascent transcript results in increased expression of genes important for tRNA aminoacylation in response to decreased pools of charged tRNA.
Microbial metabolite p-cresol inhibits gut hormone expression and regulates small intestinal transit in mice (2023)

p-cresol is a metabolite produced by microbial metabolism of aromatic amino acid tyrosine. p-cresol and its conjugated forms, p-cresyl sulfate and p-cresyl glucuronide, are uremic toxins that correlate positively with chronic kidney disease and diabetes pathogenesis. However, how p-cresol affects gut hormones is unclear. Here, we expose immortalized GLUTag cells to increasing concentrations of p-cresol and found that p-cresol inhibited <i>Gcg</i> expression and reduced glucagon-like peptide-1 (GLP-1) secretion <i>in vitro</i>. In mice, administration of p-cresol in the drinking water for 2 weeks reduced the transcript levels of <i>Gcg</i> and other gut hormones in the colon; however, it did not affect either fasting or glucose-induced plasma GLP-1 levels. Furthermore, it did not affect glucose tolerance but promoted faster small intestinal transit in mice. Overall, our data suggest that microbial metabolite p-cresol suppresses transcript levels of gut hormones and regulates small intestinal transit in mice.
Initial phase control method for high-speed external modulation in optical minimum-shift keying format (2005)

We propose a high-speed external modulation method for optical minimum-shift keying (MSK), where initial phase control together with FSK modulation enables externally continuous-phase modulation with arbitrary frequency deviation. 10-Gb/s MSK modulation spectrum was experimentally obtained. (2 pages)
Polypeptide cleavages in the formation of poliovirus proteins. (1968)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Translating stem cell research to the clinic: a primer on translational considerations for your first stem cell protocol (2015)

Over the last two decades, a new therapeutic paradigm has emerged which has changed the way debilitating diseases may be treated in the future. Instead of using small-molecule drugs and devices to ameliorate the symptoms of disease, clinicians may harness the therapeutic power of cells to regenerate and cure diseases which currently represent a major unmet medical need. Advancements in the scientific knowledge of stem cell biology, along with highly encouraging preclinical proof-of-concept studies, in the last several years have served as a launch pad for testing such therapeutics in humans with life-threatening diseases. However, translating basic research findings into human therapy has not been straightforward and has presented many scientific, clinical, and regulatory challenges for scientists and clinicians. In this article, we provide a guidance framework for investigators for the design of early-phase clinical studies using stem cell-based therapeutics. Furthermore, important trial parameters and design features which must be considered before regulatory submission of such studies are highlighted.
Laboratory-based characterization of plutonium in soil particles using micro-XRF and 3D confocal XRF (2015)

Multiple laboratory-based techniques including confocal XRF, which provides 3D elemental maps, have been used to nondestructively detect and characterize Pu in contaminated soil particles.
EMFORCED: EM-Based Fingerprinting Framework for Remarked and Cloned Counterfeit IC Detection Using Machine Learning Classification (2019)

Electronics supply chain vulnerabilities have broadened in scope over the past two decades. With nearly all integrated circuit (IC) design companies relinquishing their fabrication, packaging, and test facilities, they are forced to rely upon companies from around the world to produce their ICs. This dependence leaves the electronics supply chain open to counterfeiting activities. In this article, we propose an electromagnetic (EM)-based fingerprinting framework, called EMFORCED, to detect remarked and cloned counterfeit ICs. Here, we demonstrate the benefits of using naturally occurring EM side channels to identify the IC design layout without decapsulating the chip under test. Enabling only the clock, Vdd, and ground pins allows us to generate a design-specific fingerprint that is dependent upon the physical parameters of the chip under test. EMFORCED leverages the EM emissions from the clock distribution network to create a holistic, design-level, fingerprint, including both temporal information and spatial information. We utilize the fingerprint information of functionally similar 8051-series microprocessors from three vendors and perform unsupervised (principal component analysis) and supervised (linear discriminant analysis) machine learning methods on all ICs to determine their intravendor and intervendor similarities. We acquired ICs from multiple dates and lot codes along with variants acquired from the gray market and analyzed them for authenticity using physical inspection and X-ray tomography. Statistical analysis and machine learning techniques are used to demonstrate the reference-free and reference-inclusive classification methods based on EMFORCED measurements. We demonstrate the classification accuracies of 99.46% and 100% for unsupervised and supervised approaches, respectively.
A semi-classical analysis of optical code division multiple access (2002)

The exact error rate has been derived for the noncoherent, optical matched-filter CDMA receiver, which decides for the data of a single user by comparing a photoelectron count to a threshold. The analysis is valid for arbitrary quantum efficiencies, binary signature sequences, random gain distributions, and dark currents, and it is broad in application. Single-user demodulation based on a conditionally compound-Poisson observation has been considered, focusing on the special case of prime codes, equal energies, and utility-gain photodetectors. It has been found that the approximation of perfect optical-to-electrical conversion yields poor estimates of the error rate and optimal threshold at moderate incident optical intensities and dark currents. Further, the combined approximation of perfect optical-to-electrical conversion and Gaussian-distributed MAI yields an underestimate of the optimal threshold and an error rate that is neither an upper nor a lower bound.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Balanced polarisation diversity receiver with built-in local laser diode (1992)

A new heterodyne receiver is demonstrated. The local laser diode (LD) was built-in and no fibre was used between the parts. The number of optical parts and assembly processes was reduced, and a better performance was achieved because there was no polarisation fluctuation of the local light. The effect of a mismatch in the beam profile is discussed.
Combination Strategy Based on Theoretical Aspects for Effective and Efficient Wireless Communications (2018)

In recent years, wireless communications systems, such as 5th generation (5G) mobile systems, have been developed as a complex combination of various elementary technologies. Therefore, it is important to consider how to effectively and efficiently combine these technologies from the viewpoint of network operation and system configuration. In this context, theoretical analysis is essential as a means of bridging the gap between different technologies. Moreover, finding common objectives among different technologies is expected to reduce computational cost. In this paper, the combination of multiuser MIMO (MU-MIMO) and user scheduling, such as resource allocation or user selection, are taken up as examples based on an awareness of the above issues. As for network operation, MU-MIMO resource allocation based on theoretical channel capacity considering the effect of time selective fading is introduced. Moreover, the efficient combination of MU-MIMO employing Tomlinson Harashima precoding (THP) and user selection using space orthogonality as a common measure is presented.
Mutants of Micromonospora viridifaciens sialidase have highly variable activities on natural and non-natural substrates (2015)

This study aimed to improve the hydrolase activity of the well-characterised bacterial sialidase from Micromonospora viridifaciens. The enzyme and its mutated versions were produced in Bacillus subtilis and secreted to the growth medium. Twenty amino acid positions in or near the active site were subjected to site-saturation mutagenesis and evaluated on the artificial sialidase substrate 2-O-(p-nitrophenyl)-α-d-N-acetylneuraminic acid and on the natural substrate casein glycomacropeptide. A considerably higher fraction of the mutants exhibited increased activity on the artificial substrate compared with the natural one, with the most proficient mutant showing a 13-fold improvement in kcat/Km. In contrast, no mutants displayed more than a 2-fold increase in activity on the natural substrate. To gain further insight into this important discrepancy, we analysed the stability of mutants using the PoPMuSiC software, a property that also correlates with the potential for introducing chemical variation, after validating the method with a set of experimental stability estimates. We found a significant correlation between improved hydrolase activity on the artificial substrate and reduced apparent stability. Together with the minor improvement on the natural substrate this shows an important difference between naturally evolved functionality and new laboratory functionality. Our results suggest that when engineering sialidases and potentially other proteins towards non-natural substrates that are not optimized by natural evolution, major changes in chemical properties are advantageous, and these changes tend to correlate with decreased stability, partly explaining commonly observed trade-offs between stability and proficiency.
How Frequency Injection Locking Can Train Oscillatory Neural Networks to Compute in Phase (2021)

Brain-inspired computing employs devices and architectures that emulate biological functions for more adaptive and energy-efficient systems. Oscillatory neural networks (ONNs) are an alternative approach in emulating biological functions of the human brain and are suitable for solving large and complex associative problems. In this work, we investigate the dynamics of coupled oscillators to implement such ONNs. By harnessing the complex dynamics of coupled oscillatory systems, we forge a novel computation model-information is encoded in the phase of oscillations. Coupled interconnected oscillators can exhibit various behaviors due to the strength of the coupling. In this article, we present a novel method based on subharmonic injection locking (SHIL) for controlling the oscillatory states of coupled oscillators that allow them to lock in frequency with distinct phase differences. Circuit-level simulation results indicate SHIL effectiveness and its applicability to large-scale oscillatory networks for pattern recognition.
Lattice Boltzmann Modeling of Micro-fluidic Devices (2002)

The results to date do indeed show that the lattice Boltzmann method accurately solves relevant, non-trivial flow problems. The parallelization of both the fluid and the mobile species in flow has enhanced this capability such that it is useful for solving relevant problems in a timely fashion. The initial studies of stationary or capture species revealed evidence of hydrodynamic screening between upstream and downstream particles. Numerical studies reveal that the critical length for which the test particle is hydrodynamically decoupled from upstream and downstream particles is on the order of 30 sphere radii. For mobile species, the LB capability was shown to be naturally suited for predicting the hydrodynamic lift phenomenon (inertial lift). A conversion factor was developed based on scaling arguments to include relevant forces generated by external fields. Using this conversion, an analytic solution for the Dielectrophoretic force was included into the LB capability which enabled the study of Dielectrophoretic particle capture. The Non-Newtonian enhancements have expanded the applicability of the LB capability to more physical systems. Specifically, with the bead-n-spring representation of macromolecules researchers will be able to study chain dynamics in micro-, physiological and Bio-MEMS environments. Furthermore, the ability to capture the shear thinning behavior, without any increase in computational time, positions this capability to be applied to a whole host of new problems involving biofluids.
Abstract 3316: Characterizing mechanisms of resistance to androgen deprivation in prostate cancer (2014)

Abstract Despite significant advances in the treatment of prostate cancer (PCa), this malignancy remains a leading cause of cancer death among men. PCa cells require androgen receptor (AR) signaling for their growth and survival. Androgen deprivation therapy (ADT) constitutes the main therapeutic option for patients with advanced PCa. However, the major cause of death in men with metastatic prostate cancer involves progression to castration-resistant prostate cancer (CRPC). Characterizing mechanisms of resistance to ADT could enable the development of more effective therapeutic strategies. To identify genes whose silencing drives resistance to ADT in androgen-sensitive PCa cells, we performed a systematic genome-wide suppressor RNAi screen in the androgen-sensitive LNCaP cells, using a 98,000-shRNA library, targeting approximately 16,000 human genes. After infection, cells were cultured in absence of androgens for several weeks. Cells showing the ability to proliferate upon androgen deprivation were harvested at different time points and shRNA sequences were identified and quantitated through nextgen sequencing. Hit genes were those with at least 2 shRNAs enriched &amp;gt;4 fold, and whose silencing exerted the most robust effects on cell proliferation. To validate the identified top-tier genes in vitro, we infected LNCaP cells with lentiviruses carrying shRNAs (2 shRNAs/candidate gene) targeting the top ∼30 candidate genes, in parallel with 15 negative control shRNAs. We monitored the ability of each shRNA to increase proliferation under androgen-deprived conditions, using cell viability assays. To determine whether any shRNAs drive castration resistance by reactivating the AR-signaling pathway, we analyzed the expression of known AR effector genes in the presence of candidate shRNAs and also tested their effect on cell proliferation in the presence of the direct AR antagonist MDV3100. In future, we will also validate candidate genes in vivo, using a LNCaP xenograft model. This study has identified several genes whose silencing may modulate resistance to ADT in prostate cancer. Additional functional studies should determine whether a subset of these may promote new therapeutic strategies for men with CRPC. Citation Format: Ginevra Botta, Judit Jane-Valbuena, Terence Wong, John Doench, Levi A. Garraway. Characterizing mechanisms of resistance to androgen deprivation in prostate cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3316. doi:10.1158/1538-7445.AM2014-3316
Designed Molecular Switches: Controlling the Conformation of Benzamido-diphenylacetylenes (2010)

With the goal of creating a molecular switch, the hydrogen-bonded diphenylacetylene structure has been modified such that an equilibrium now exists between two intramolecular H-bonded states. Through X-ray crystallography and (1)H NMR analysis it is shown that this equilibrium can be biased in a predictable manner by modulating the relative acidity of the amide NH's.
Super-resolution microscopy reveals structural diversity in molecular exchange among peptide amphiphile nanofibres (2016)

The dynamic behaviour of supramolecular systems is an important dimension of their potential functions. Here, we report on the use of stochastic optical reconstruction microscopy to study the molecular exchange of peptide amphiphile nanofibres, supramolecular systems known to have important biomedical functions. Solutions of nanofibres labelled with different dyes (Cy3 and Cy5) were mixed, and the distribution of dyes inserting into initially single-colour nanofibres was quantified using correlative image analysis. Our observations are consistent with an exchange mechanism involving monomers or small clusters of molecules inserting randomly into a fibre. Different exchange rates are observed within the same fibre, suggesting that local cohesive structures exist on the basis of β-sheet discontinuous domains. The results reported here show that peptide amphiphile supramolecular systems can be dynamic and that their intermolecular interactions affect exchange patterns. This information can be used to generate useful aggregate morphologies for improved biomedical function.
A design method of digital robust speed servo system considering output saturation (2000)

When a robust servo system having an integral element has a large error input, it often reveals windup phenomena caused by output saturation. It is very difficult for a strictly proper and high-order controller to avoid having windup phenomena caused by output saturation. This paper newly proposes the digital robust speed servo system with a complete algorithm for consideration of output saturation. The proposed algorithm completely considers the output saturation of a robust speed controller connected to a PI current controller in series. Moreover, this method can be applied to both a PI speed controller and an H∞ speed controller. The experimental results show that a robust speed servo system using the proposed algorithm has a good and stable response for a large step speed command. © 2000 Scripta Technica, Electr Eng Jpn, 132(3): 68–78, 2000
Ultrasonic Detection of a Plastic Hinge in Bolted Timber Connections (1995)

Connections between structural members are critical elements that typically govern the performance of structural systems; hence, techniques for monitoring the condition of connections are needed to provide early warning of structural damage. Plastic hinge formation in fasteners frequently occurs in timber connections when the yield capacity is exceeded. An innovative pulse echo testing technique was developed for detecting the formation of a plastic hinge in bolted timber connections and estimating the associated magnitude of connection displacement. A shift in overall signal centroid proved to be the best flTedictor of plastic hinge formation, with a coefficient of determination (R2) of 0.9. As the plastic hinge angle increased, the signal centroid shifted to the right since a higher proportion of pulse energy was forced to undergo multiple transverse wave reflections caused by the deformed geometry of the bolt. Because the determination of a shift in signal centroid requires the availability of prior test information for the initially undeformed fastener, an alternate linear relationship between echo amplitude ratios and plastic hinge formation was also proposed with an adjusted R2 of 0.87. This three parameter regression equation had the advantages of requiring no prior testing information and eliminating ambiguity in signal analysis associated with selection of echo start and end points. Plastic hinge formation was correlated with connection ductility, magnitude of connection overload and energy based measures of connection damage to assess residual connection capacity.
Valve-in-valve outcome: design impact of a pre-existing bioprosthesis on the hydrodynamics of an Edwards Sapien XT valve (2016)

The results of this study suggest that a surgical bioprosthesis with a large inner diameter and internally mounted leaflets improves the heamodynamics and potentially the durability of a valve-in-valve combination. These results should give the attending physicians critical information to consider when deciding on a bioprosthesis for younger patients.
Solid-Phase Synthesis of 2,3,5-Trisubstituted Indoles (2001)

2,3,5-Trisubstituted indoles are synthesized in three steps starting from resin-bound aniline 2. R1 is introduced by a palladium-mediated coupling of the aryl iodide with terminal alkynes followed by intramolecular cyclization to form the indole core. Acylation at C-3 with an acid chloride in the presence of AlCl(3) catalyst introduces R2. The indole C-5 position is then diversified either by Sonagashira or Suzuki couplings with the aryl bromide. Finally, indole N-1 can be modified by post-cleavage methylation. [reaction: see text]
Correlating Photoluminescence and Structural Properties of Uncapped and GaAs-Capped Epitaxial InGaAs Quantum Dots (2018)

The understanding of the correlation between structural and photoluminescence (PL) properties of self-assembled semiconductor quantum dots (QDs), particularly InGaAs QDs grown on (001) GaAs substrates, is crucial for both fundamental research and optoelectronic device applications. So far structural and PL properties have been probed from two different epitaxial layers, namely top-capped and buried layers respectively. Here, we report for the first time both structural and PL measurements from an uncapped layer of InGaAs QDs to correlate directly composition, strain and shape of QDs with the optical properties. Synchrotron X-ray scattering measurements show migration of In atom from the apex of QDs giving systematic reduction of height and enlargement of QDs base in the capping process. The optical transitions show systematic reduction in the energy of ground state and the first excited state transition lines with increase in capping but the energy of the second excited state line remain unchanged. We also found that the excitons are confined at the base region of these elliptically shaped QDs showing an interesting volume-dependent confinement energy scaling of 0.3 instead of 0.67 expected for spherical dots. The presented method will help us tuning the growth of QDs to achieve desired optical properties.