gebhart/patrepeval huggingface dataset:
Molecular interactions of a replication initiator protein, RepA, with the replication origin of the enterococcal plasmid p703/5. (2007)

We previously identified the origin of replication of p703/5, a small cryptic plasmid from the KBL703 strain of Enterococcus faecalis. The origin of replication contains putative regulatory cis-elements required for replication and a replication initiator (RepA) gene. The replicon of p703/5 is similar in its structural organization to theta-type plasmids, and RepA is homologous to a family of Rep proteins identified in several plasmids from Gram-positive bacteria. Here, we report molecular interactions between RepA and the replication origin of p703/5. DNase I footprinting using recombinant RepA together with electrophoretic mobility shift assays confirmed the binding of RepA to the replication origin of p703/5 via iterons and an inverted repeat. We also demonstrated the formation of RepA dimers and the different binding of RepA to the iteron and the inverted repeat using gel filtration chromatographic analysis, a chemical crosslinking assay, and electrophoretic mobility shift assays in the presence of guanidine hydrochloride. Our results suggest that RepA plays a regulatory role in the replication of the enterococcal plasmid p703/5 via mechanisms similar to those of typical iteron-carrying theta-type plasmids.
Improving Spiking Dynamical Networks: Accurate Delays, Higher-Order Synapses, and Time Cells (2017)

Researchers building spiking neural networks face the challenge of improving the biological plausibility of their model networks while maintaining the ability to quantitatively characterize network behavior. In this work, we extend the theory behind the neural engineering framework (NEF), a method of building spiking dynamical networks, to permit the use of a broad class of synapse models while maintaining prescribed dynamics up to a given order. This theory improves our understanding of how low-level synaptic properties alter the accuracy of high-level computations in spiking dynamical networks. For completeness, we provide characterizations for both continuous-time (i.e., analog) and discrete-time (i.e., digital) simulations. We demonstrate the utility of these extensions by mapping an optimal delay line onto various spiking dynamical networks using higher-order models of the synapse. We show that these networks nonlinearly encode rolling windows of input history, using a scale invariant representation, with accuracy depending on the frequency content of the input signal. Finally, we reveal that these methods provide a novel explanation of time cell responses during a delay task, which have been observed throughout hippocampus, striatum, and cortex.
Taste Receptors in the Gastrointestinal Tract. I. Bitter taste receptors and α-gustducin in the mammalian gut (2006)

Molecular sensing by gastrointestinal (GI) cells plays a critical role in the control of multiple fundamental functions in digestion and also initiates hormonal and/or neural pathways leading to the regulation of caloric intake, pancreatic insulin secretion, and metabolism. Molecular sensing in the GI tract is also responsible for the detection of ingested harmful drugs and toxins, thereby initiating responses critical for survival. The initial recognition events and mechanism(s) involved remain incompletely understood. The notion to be discussed in this article is that there are important similarities between the chemosensory machinery elucidated in specialized neuroepithelial taste receptor cells of the lingual epithelium and the molecular transducers localized recently in enteroendocrine open GI cells that sense the chemical composition of the luminal contents of the gut.
Immunologic constant of rejection signature is prognostic in soft-tissue sarcoma and refines the CINSARC signature (2022)

ICR signature is independently associated with postoperative MFS in early-stage STS, independently from other prognostic features, including CINSARC. We built a robust prognostic clinicogenomic model integrating ICR, CINSARC, and pathological type, and suggested differential vulnerability of each prognostic group to different systemic therapies.
In Vitro Effects of Low Concentrations of Penicillin and Sulfadiazine on Streptococcus mutans (1976)

Investigations were conducted to determine the in vitro effects of low levels of penicillin and sulfadiazine on the growth, plaque formation, and agglutination of Streptococcus mutans and on the synthesis and activity of enzymes synthesizing extracellular polymers. The concentrations tested were equivalent to those expected in the saliva of subjects receiving oral therapy with the agents. Penicillin at 0.5 ng/ml and sulfadiazine at 1 mug/ml substantially inhibited in vitro plaque formation. At these concentrations, sulfadiazine but not penicillin also inhibited growth of the organism. Neither antimicrobial agent affected the agglutination of S. mutans with dextran or the synthesis or activity of enzymes synthesizing extracellular polymers. The effect of sulfadiazine on plaque formation was attributed, at least in part, to the inhibitory action of that agent on S. mutans growth.
Imaging Brain Collaterals (2017)

Leptomeningeal collaterals provide the primary source of perfusion to ischemic brain tissue following the onset of acute ischemic stroke and are becoming an important imaging biomarker for stroke therapy triage. Collateral circulation is predictive of infarct growth, end infarct volume, and response to endovascular therapy. The strength of the collateral circulation varies among patients and is partially dependent on genetic and modifiable risk factors. Collateral circulation may be assessed by standard angiographic techniques, including digital subtraction angiography, computed tomography and magnetic resonance (MR) angiography, as well as a growing array of advanced MR techniques including arterial spin labeling and dynamic MR angiography. Simple scoring systems are used to estimate the relative strength of the collateral circulation for a given patient, although there are some discrepancies in the predictive value of these systems. In this review, we discuss methods and techniques for determining the robustness of the collateral circulation and the role of the collateral circulation in acute ischemic stroke assessment and triage.
Chromatic-dispersion-insensitive DGD monitoring by adding a frequency-shifted carrier along the orthogonal polarization state (2004)

We demonstrate accurate DGD monitoring by adding a frequency-shifted carrier along the orthogonal polarization state and extracting the regenerated RF power near the bit-rate frequency. This monitoring signal is insensitive to chromatic dispersion.
Synthesis and Properties of Dinuclear Copper(II) Complexes Containing Dinucleating Ligands with Imidazole Nitrogen and Two Exogenous Bridging Ligands (1994)

Abstract Dinuclear copper(II) complexes, [Cu2(nR)X2] (ClO4)2 (X = N3−, NCS−, and OAc−) have been synthesized and characterized, where nR = N,N,N′,N′-tetrakis[(1-methyl-2-benzimidazolyl)methyl]-1,3-diaminopropane (3Me), N,N,N′,N′-tetrakis[(1-ethyl-2-benzimidazolyl)methyl]-1,3-diaminopropane (3Et), N,N,N′,N′-tetrakis[(1-methyl-2-benzimidazolyl)methyl]-1,4-diaminobutane (4Me), and N,N,N′,N′-tetrakis[(1-ethyl-2-benzimidazolyl)methyl]-1,4-diaminobutane (4Et). Although a weak antiferromagnetic interactions were found for [Cu2(3Me)(NCS)2](ClO4)2·3H2O (coupling constant J = −2.1 cm−1, H = −2JS1·S2) and [Cu2(3Me)(OAc)2](ClO4)2·H2O (J = −2.0 cm−1), no exchange interaction has been observed to 4.2 K for [Cu2(3Me)(N3)2](ClO4)2·H2O. The Electrochemistry of these complexes in N,N-dimethylformamide showed two electron reductions at +210 — −30 mV vs. Ag–AgCl (Cu2+–Cu2+ → Cu+–Cu+).
Nobody Knows Where the Blues Come From: Lyrics and History. Edited by Robert Springer. Jackson: University Press of Mississippi, 2006. vi + 303 + v pp. ISBN 1-57806-797-9 (2009)

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Electrodeposition of platinum-iridium alloy nanowires for hermetic packaging of microelectronics (2012)

An electrodeposition technique was applied for fabrication of dense platinum-iridium alloy nanowires as interconnect structures in hermetic microelectronic packaging to be used in implantable devices. Vertically aligned arrays of platinum-iridium alloy nanowires with controllable length and a diameter of about 200 nm were fabricated using a cyclic potential technique from a novel electrodeposition bath in nanoporous aluminum oxide templates. Ti/Au thin films were sputter deposited on one side of the alumina membranes to form a base material for electrodeposition. Scanning Electron Microscopy (SEM) and Energy Dispersive Spectroscopy (EDS) were used to characterize the morphology and the chemical composition of the nanowires, respectively. SEM micrographs revealed that the electrodeposited nanowires have dense and compact structures. EDS analysis showed a 60:40% platinum-iridium nanowire composition. Deposition rates were estimated by determining nanowire length as a function of deposition time. High Resolution Transmission Electron Microscopy (HRTEM) images revealed that the nanowires have a nanocrystalline structure with grain sizes ranging from 3 nm to 5 nm. Helium leak tests performed using a helium leak detector showed leak rates as low as 1 × 10(-11) mbar L s(-1) indicating that dense nanowires were electrodeposited inside the nanoporous membranes. Comparison of electrical measurements on platinum and platinum-iridium nanowires revealed that platinum-iridium nanowires have improved electrical conductivity.
Compacting Garbage Collection can be Fast and Simple (1996)

Copying garbage collectors are now standard for the memory-management subsystems of functional and object-oriented programming languages. Compacting garbage collection has correspondingly fallen out of favor. We revitalize the case for compaction by demonstrating that a simple compacting collector, extended with the generational garbage collection heuristic, exhibits performance as effectively as or better than a well-designed generational copying collector on real programs running in real environments. The observation that compaction preserves allocation order across collections leads to a new generalization of the generational heuristic that reduces the movement of long-lived objects. We measure the effect of substituting our compacting generational collector for a copying collector in Standard ML of New Jersey.
Walking Away from Myasthenia Gravis (P02.208) (2013)

OBJECTIVE: We test the hypothesis that 3-month exercise program for MG will improve fitness, ventilatory capacity, and function, and reduce fatigue.
Selective etherification of β-citronellene catalyzed by zeolite beta (2015)

A continuous flow, liquid phase, heterogeneous catalytic process for chemoselective etherification of β-citronellene monoterpene using the zeolite beta catalyst.
Ternary organic solar cells with small voltage losses (Conference Presentation) (2018)

The voltage loss in organic photovoltaics (OPVs) is defined as the difference between the open circuit voltage and the voltage offset between the lowest unoccupied molecular orbital (LUMO) of the acceptor and the highest occupied MO (HOMO) of the donor forming the charge dissociating heterojunction. Widely employed fullerene acceptors show significant voltage losses, approaching 0.8 V, thereby reducing the potential efficiencies of OPVs. In this work, we show that ternary blends of two non-fullerene acceptors with a polymer donor are effective in significantly reducing the voltage losses in near-infrared (NIR) OPVs. A narrow energy gap non-fullerene acceptor, FIDC, sharing similar HOMO energies with the acceptor BT-CIC [1], (absorption up to 1000 nm) is blended with the polymer PCE-10. The power conversion efficiency (PCE) of the ternary cell is increased from 10.7% in a BT-CIC:PCE-10 binary cell to 12.6% in the BT-CIC:FIDC:PCE-10 ternary cell. Further, the short-circuit current density is increased from 22.3 mA cm-2 to 25.5 mA cm-2. Importantly, the ternary cell decreased the voltage loss from 0.61 to 0.54 V. The ternary devices showed larger open circuit voltage of 0.70V than either the analogous BT-CIC (0.69 V) or FIDC (0.66 V) binary devices [2,3]. This work points to a simple means for increasing the materials available for spanning the visible and NIR spectra in very high efficiency, low loss OPVs. 1. Li, Y.; Lin, J.-D.; Che, X.; Qu, Y.; Liu, F.; Liao, L.-S.; Forrest, S. R. J. Am. Chem. Soc. 2017, 139, 17114. 2. Ameri, T.; Khoram, P.; Min, J.; Brabec, C. J. Adv. Mater. 2013, 25, 4245. 3. Fu, H.; Wang, Z.; Sun, Y. Solar RRL 2018, 2, 1700158.
Atomistic simulations of heat transport in real-scale silicon nanowire devices (2012)

Utilizing atomistic lattice dynamics and scattering theory, we study thermal transport in nanodevices made of 10 nm thick silicon nanowires, from 10 to 100 nm long, sandwiched between two bulk reservoirs. We find that thermal transport in devices differs significantly from that of suspended extended nanowires, due to phonon scattering at the contact interfaces. We show that thermal conductance and the phonon transport regime can be tuned from ballistic to diffusive by varying the surface roughness of the nanowires and their length. In devices containing short crystalline wires, phonon tunneling occurs and enhances the conductance beyond that of single contacts.
A Comparison of Time Delay in Three Continuous Glucose Monitors for Adolescents and Adults (2017)

There are differences in the estimated PG to CGMG time delays between CGM devices in the same subjects. The delay between PG and CGMG is smaller for adolescents than for adults. The PG-to-CGMG time delay is influenced by both instrument and host factors.
Acoustic Startle Evokes Bilaterally Synchronous Oscillatory EMG Activity in the Healthy Human (2003)

Despite animal evidence that the reticulospinal system is of major importance to movement, this motor pathway has remained relatively inaccessible to experimentation in the human. Consequently, little is known about its function in health and disease. Here, we use the acoustic startle response to demonstrate that one type of reticulospinal activity in the human is associated with a characteristic pattern of bilateral synchronization between motor units. Surface electromyography (EMG) was recorded from upper limb muscles in 15 healthy subjects during the reflex startle to unexpected acoustic stimulation, voluntary movements mimicking the startle and during sustained voluntary tonic contraction. Frequency analysis demonstrated autospectral peaks at approximately 14 Hz in deltoid and biceps muscles only during the startle reflex. Similarly, coherence spectra of the EMG recorded between homologous proximal upper limb muscles demonstrated a peak centered approximately 12-16 Hz during reflex startles. Coherence in the 10- to 20-Hz band was significantly greater in the startle reflex than during voluntary sham startles or voluntary tonic contraction for deltoid, but not first dorsal interosseous, muscles. The coherence at 10-20 Hz between EMGs from homologous muscles represents a potential surrogate measure of reticulospinal activity that may be useful in determining the contribution of the reticulospinal system to different types of movement in health and disease.
Cosmogenic radionuclides in precipitation (1994)

A combination of three-hundred and fifty event and sub-event ($\sim$3 mm resolution) ground level precipitation samples were collected near West Lafayette, IN. They included most of the significant precipitation events occurring between April 18, 1992 and August 31, 1993. The cosmogenic radionuclide ($\rm\sp7Be(t\sb{1/2} = 53 d),\ \sp{10}Be(t\sb{1/2} = 1.5\ My),\ and\ \sp{36}Cl(t\sb{1/2} = 0.3\ My)),\ anion\ (Cl\sp-,\ NO\sb3\sp-,\ SO\sb4\sp{2-}),\ and\ cation\ (Na\sp+,\ K\sp+,\ Mg\sp{2+},\ and\ Ca\sp{2+})$ concentrations were measured in selected samples. Accelerator mass spectrometry was used to determine the $\rm\sp{10}Be\ and\ \sp{36}Cl$ content. We used these data along with other standard meteorological data bases to investigate relationships between the cosmogenic radionuclides in mid-latitude wet deposition and storm type, air mass history, and season. Understanding the circumstances that lead to local variations in the ratio of $\rm\sp{10}Be\ to\ \sp{36}Cl$ should aid other investigators in unlocking information stored in form of this ratio in the ice sheets, and thereby gain a better understanding of paleoclimates. In addition, the source functions for these radionuclides and how they vary with differing meteorological conditions are needed for ground water ($\rm\sp{36}Cl)$ and erosion rate ($\rm\sp{10}Be)$ studies. A departure from the $\rm\sp{10}Be/\sp{36}Cl$ ratio of 40 predicted by Lal et al. 1967 is seen. Using a new semiempirical cross section formula, we estimated the production ratio to be $\sim$9. Our mean $\rm\sp{10}Be/\sp{36}Cl$ ratio is 11.4 and typically varies from 4 to 40. We see a higher mean $\rm\sp{10}Be/\sp{36}Cl$ ratio in stratiform precipitation (14), and a lower mean ratio in convective precipitation (9.7). The estimated $\rm\sp{10}Be$ flux from re-suspended soil is 10% of the total $\rm\sp{10}Be$ flux.
Near-field recording with 266 nm laser for disc mastering process (2003)

We developed a near-field recording process with a 266 nm blue-violet laser and an objective lens of 1.35 NA. A two-stage servo with air suspension and PZT control sufficiently constrained the gap fluctuation between the supersphere solid immersion lens (SIL) and the glassmaster. As a result, the expected small size of the pit pattern was obtained. We expect that this breakthrough will be refined much more and improve the density of optical recording.
Etoposide Prevents Apoptosis in Mouse Liver With D–Galactosamine/Lipopolysaccharide–Induced Fulminant Hepatic Failure Resulting in Reduction of Lethality (2001)

D-Galactosamine (GalN)/lipopolysaccharide (LPS)-induced liver injury is an experimental model of fulminant hepatic failure in which tumor necrosis factor alpha (TNF-alpha) plays a pivotal role. We examined the effects of etoposide on GalN/LPS-induced fulminant hepatic failure. Mice were given an intraperitoneal dose of GalN (800 microg/g body weight)/LPS (100 ng/g body weight) with and without intraperitoneal etoposide (10 microg/g body weight) treatment. Liver injury was assessed biochemically and histologically. TNF-alpha levels in the serum, and apoptosis of hepatocytes and CPP32/caspase-3 in the liver, were determined. GalN/LPS treatment caused lethal liver injury in 87% of animals (13 of 15). The effect was associated with significant increases in TNF-alpha and alanine transaminase (ALT) levels in serum, the number of apoptotic hepatocytes, CPP32/caspase-3 activity, and TNF receptor 1 (TNFR1) mRNA expression in the liver. Etoposide (10 microg/g body weight) was given 3 times (at 50, 26, and 4 hours before GalN/LPS administration). Treatment of GalN/LPS-treated mice with etoposide reduced apoptosis of hepatocytes, resulting in reduction of lethality (13% [2 of 15]), while another topoisomerase II inhibitor, IRCF-193, showed no significant effect. The antilethal effect of etoposide was also confirmed in GalN/TNF-alpha-induced fulminant hepatic failure. Etoposide treatment reduced CPP32/caspase-3 activity in the liver, although it did not alter the serum TNF-alpha levels or hepatic TNFR1 mRNA expressions. In addition, etoposide treatment enhanced the mRNA and protein expression of Bcl-xL, an antiapoptotic molecule in the liver. The present findings suggest that etoposide prevents endotoxin-induced lethal liver injury by up-regulation of Bcl-xL, and that etoposide could be useful for the treatment of TNF-alpha-mediated liver diseases.
Timing Jitter Distribution and Power Spectral Density of a Second-Order Bang–Bang Digital PLL With Transport Delay Using Fokker–Planck Equations (2018)

In this paper, a second-order bang-bang digital phase-locked loop (BBPLL) with dominant random walk phase noise and transport delay is analyzed using Fokker-Plank equations. Explicit closed-form expressions are derived for the timing error probability distribution function, jitter variance, and power spectral density (psd). For the type-II BBPLL considered in this paper, the timing error distribution is shown to be Laplacian and not Gaussian distributed as previously assumed, while the derived psd is Lorentzian, which is consistent with earlier works. The analytical solutions are valid as long as the continuous-time approximation of the BBPLL dynamics is accurate as is the case for typical operating loop bandwidths. The accuracy of the derived expressions is validated via simulation.
Glycine Reuptake Inhibition as a New Therapeutic Approach in Schizophrenia: Focus on the Glycine Transporter 1 (GlyT1) (2012)

Primary negative symptoms (affective flattening or blunting, alogia, avolition) are prominent in approximately 20% of individuals suffering from schizophrenia. These symptoms are particularly associated with impaired functional outcome and poor prognosis. This is in part due to the lack of specific and effective treatments despite the development and use of the second generation antipsychotics. There is increasing evidence that suggests that combined dysfunction of the dopamine and glutamate neurotransmitter systems may underlie some of the key clinical and pathophysiological features of schizophrenia. Specifically, hypofunction of the N-methyl-D-aspartate receptor (NMDAR) at critical circuits within the brain appears to be an important mechanism. Thus, it would be anticipated that modulation of NMDAR function by increasing the availability of the glutamate co-agonist, glycine, within the synaptic cleft may provide a new therapeutic strategy for the management of schizophrenia. However, the direct glycine receptor agonists such as glycine and D-cycloserine (d-4-amino-3-isoxazolidinone) have demonstrated limited efficacy in studies to date. One of the most promising approaches for enhancing NMDAR function involves modification of the activity of the high affinity glycine transporter 1 (GlyT1). Numerous compounds have been synthesized, with the early compounds being substituted glycine derivatives such as sarcosine (N-methylglycine) and Org 24598. More recent developments have focused on the non-amino acid derivatives Org 25935 (cis-N-methyl-N-(6-methoxy-1- phenyl-1,2,3,4-tetrahydronaphthalen-2-ylmethyl)amino-methylcarboxylic acid hydrochloride) and bitopertin (RG 1678). Of the molecules being investigated currently, a proof-of-concept, double-blind study of bitopertin has yielded encouraging findings, with a significant decrease in negative symptoms and no major tolerability or toxicity issues. Further studies are needed to confirm these findings and to explore the potential application of these therapies in different clinical situations in order to achieve greatest effect on negative symptoms. In addition, there is still much to be learned about this class of agents in terms of other potential domains of efficacy such as positive symptoms or cognition as well as long-term safety.