gebhart/patrepeval huggingface dataset:
Improved in vivo abdominal image quality using real-time estimation and correction of wavefront arrival time errors (2002)

The speed of sound varies with tissue type, yet commercial ultrasound imagers assume it is constant. Sound speed variation in abdominal fat and muscle layers is widely believed to be largely responsible for poor image contrast and resolution in some patients. The simplest model of the abdominal wall assumes that it adds a spatially varying time delay to the ultrasound wavefront. We describe an adaptive imaging system consisting of a GE LOGIQ 700 imager connected to a multi-processor computer. Arrival time errors for each beamforming channel, estimated by correlating each channel signal with the beamsum signal, are used to correct the imager's transmit and receive beamforming time delays at the image frame rate. A multi-row transducer provides two dimensional sampling of wavefront arrival time errors. After beamforming time delay correction, we observe significant improvement in abdominal images of healthy male volunteers, including increased contrast of blood vessels, increased brightness of liver tissue, and improved definition of the renal capsule and splenic boundary.
Azurin of Pathogenic Neisseria spp. Is Involved in Defense against Hydrogen Peroxide and Survival within Cervical Epithelial Cells (2005)

Laz, a lipid-modified azurin of the human pathogens Neisseria gonorrhoeae and Neisseria meningitidis, is involved in defense against oxidative stress and copper toxicity; laz mutant strains are hypersensitive to hydrogen peroxide and copper. The N. gonorrhoeae laz mutant also has decreased survival in an ex vivo primary human ectocervical epithelial assay.
22W Single-Frequency Vertical-External-Cavity Surface-Emitting Laser (2014)

We report on a single-frequency semiconductor disk laser which generates 22.1 W output power in continuous wave operation, at a wavelength of 1030 nm. The free-running linewidth is measured to be 3.2 MHz (apparatus limited).
Photoinduced Hydrogen Production by Direct Electron Transfer from Photosystem I Cross-Linked with Cytochrome c3to [NiFe]-Hydrogenase (2006)

The photosynthetic reaction center is an efficient molecular device for the conversion of light energy to chemical energy. In a previous study, we synthesized the hydrogenase/photosystem I (PSI) complex, in which Ralstonia hydrogenase was linked to the cytoplasmic side of Synechocystis PSI, to modify PSI so that it photoproduced molecular hydrogen (H2). In that study, hydrogenase was fused with a PSI subunit, PsaE, and the resulting hydrogenase-PsaE fusion protein was self-assembled with PsaE-free PSI to give the hydrogenase/PSI complex. Although the hydrogenase/PSI complex served as a direct light-to-H2 conversion system in vitro, the activity was totally suppressed by adding physiological PSI partners, ferredoxin (Fd) and ferredoxin-NADP+-reductase (FNR). In the present study, to establish an H2 photoproduction system in which the activity is not interrupted by Fd and FNR, position 40 of PsaE from Synechocystis sp. PCC6803, corresponding to the Fd-binding site on PSI, was selected and targeted for the cross-linking with cytochrome c3 (cytc3) from Desulfovibrio vulgaris. The covalent adduct of cytc3 and PsaE was stoichiometrically assembled with PsaE-free PSI to form the cytc3/PSI complex. The NADPH production by the cytc3/PSI complex coupled with Fd and FNR decreased to approximately 20% of the original activity, whereas the H2 production by the cytc3/PSI complex coupled with hydrogenase from Desulfovibrio vulgaris was enhanced 7-fold. Consequently, in the simultaneous presence of hydrogenase, Fd, and FNR, the light-driven H2 production by the hydrogenise/cytc3/PSI complex was observed (0.30 μmol H2/mg chlorophyll/h). These results suggest that the cytc3/PSI complex may produce H2in vivo.
The first activation study of a δ-carbonic anhydrase: TweCAδ from the diatom Thalassiosira weissflogii is effectively activated by amines and amino acids (2018)

The activation of the δ-class carbonic anhydrase (CAs, EC 4.2.1.1) from the diatom Thalassiosira weissflogii (TweCAδ) was investigated using a panel of natural and non-natural amino acids and amines. The most effective activator of TweCAδ was d-Tyr (K<sub>A</sub> of 51 nM), whereas several other amino acids and amines, such as L-His, L-Trp, d-Trp, dopamine and serotonin were submicromolar activators (K<sub>A</sub>s from 0.51 to 0.93 µM). The most ineffective activator of TweCAδ was 4-amino-l-Phe (18.9 µM), whereas d-His, l-/d-Phe, l-/d-DOPA, l-Tyr, histamine, some pyridyl-alkylamines, l-adrenaline and aminoethyl-piperazine/morpholine were moderately potent activators (K<sub>A</sub>s from 1.34 to 8.16 µM). For any δ-CA, there are no data on the crystal structure, homology modelling and the amino acid residues that are responsible for proton transfer to the active site are currently unknown making it challenging to provide a detailed rational for these findings. However, these data provide further evidence that this class of underexplored CA deserves more attention.
Exposure Invariance Test (2022)

<italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Images from cameras are usually provided in a non-linear form, often specific to a given camera manufacturer. However, tools are typically provided to convert to alternate useful forms that are independent of camera type. Of special usefulness is linear light. A linear light representation is implicitly proportional to the light seen by the camera. Exposure then becomes a multiplicative scale factor. Within the limits of the maximum exposure and noise floor, the image is inherently invariant with respect to exposure. This paper describes simple methods to verify this exposure invariance, thus providing a characterization of the useful working exposure range. The processing steps taken in making the linear representation are also implicitly verified</i> .
Programming Culture in the 2nd-Generation Attention Economy (2006)

In this paper, we consider how the relationship between content providers and content consumers is modified by configuration (especially in the case of end-user programming) and by measurement (especially in the case of audience statistics). This allows us to bring together social, economic and cultural concepts that sound as though they should be related, but seldom are: the kind of programming done to a computer as related to the kind done by a broadcaster, and the kind of attention measured by an economist as related to the kind measured by a psychologist. Author Keywords End-user configuration, audience measurement.
Poly(arylene ether)s with Low Refractive Indices: Poly(biphenylene oxide)s with Trifluoromethyl Pendant Groups via a Meta-Activated Nitro Displacement Reaction (2012)

High-molecular-weight poly(biphenylene oxide)s (PBPO) were prepared from AB-type monomers, 4′(3′)-hydroxy-4-nitro-2,6-bis(trifluoromethyl)biphenyl, through a meta-activated nitro displacement reaction. The displacement of nitro leaving group activated by the two trifluoromethyl groups at the meta-position produced high-molecular-weight polymers, which implies that nucleophilic aromatic substitution reaction of the nitro leaving group proceeded very effectively with two activating groups at the meta-position. The obtained polymers have weight-average molecular weight of 20 800–143 300 g/mol and molecular weight distribution of 1.68–2.85. While two homopolymers of 4′- or 3′-hydroxy-4-nitro-2,6-bis(trifluoromethyl)biphenyl, p-PBPO and m-PBPO, showed a semicrystalline morphology, copolymers of the two monomers were amorphous and dissolved in a wide range of organic solvents. The PBPOs possessed a high glass transition temperature (Tg) in the range of 169 to 208 °C depending on their structure and high thermal stability with 10% weight loss temperatures from 486 to 542 °C in nitrogen and from 465 to 516 °C in air. Moreover, PBPOs containing two trifluoromethyl groups showed low refractive indices in the range of 1.4979–1.5052 as well as low birefringence values of 0.0095–0.0148.
Alterations in the rostral ventromedial medulla after the selective ablation of μ-opioid receptor expressing neurons (2015)

The rostral ventromedial medulla (RVM) exerts both inhibitory and excitatory controls over nociceptive neurons in the spinal cord and medullary dorsal horn. Selective ablation of mu-opioid receptor (MOR)-expressing neurons in the RVM using saporin conjugated to the MOR agonist dermorphin-saporin (derm-sap) attenuates stress and injury-induced behavioral hypersensitivity, yet the effect of RVM derm-sap on the functional integrity of the descending inhibitory system and the properties of RVM neurons remain unknown. Three classes of RVM neurons (on-cells, off-cells, and neutral cells) have been described with distinct responses to noxious stimuli and MOR agonists. Using single unit recording in lightly anesthetized rats, RVM neurons were characterized after microinjections of derm-sap or saporin. Derm-sap treatment resulted in a reduction in on-cells and off-cells when compared to saporin controls (P < 0.05). The number of neutral cells remained unchanged. After derm-sap treatment, RVM microinjections of the glutamate receptor agonist homocysteic acid increased tail-flick latencies, whereas the MOR agonist DAMGO had no effect. Furthermore, electrical stimulation of the periaqueductal gray produced analgesia in both derm-sap and saporin controls with similar thresholds. Microinjection of kynurenic acid, a glutamate receptor antagonist, into the RVM disrupted periaqueductal gray stimulation-produced analgesia in both saporin-treated and derm-sap-treated rats. These results indicate that MOR-expressing neurons in the RVM are not required for analgesia produced by either direct or indirect activation of neurons in the RVM.
Modeling, Simulation and Comparison of Models for Wormhole Formation duringMatrix Stimulation of Carbonates (2002)

A new averaged/continuum model is presented for simulation of wormhole formation during matrix stimulation of carbonates. The model presented here differs from existing literature models in three fundamental aspects. First, we show that the dissolution process creates a Darcy velocity field with non-zero divergence. Second, we use two concentration variables to account for the local gradients at the pore level caused by the coupling between the flow, species diffusion and chemical reaction. Third, we account for both the asymptotic/diffusive and convective contributions to the local mass transfer coefficient between the fluid and solid. We argue that models that do not account for these effects do not retain the qualitative features of the reactive dissolution process and hence cannot be predictive. The averaged model developed here accounts for pore level physics by coupling the local pore scale phenomena to the macroscopic variables (Darcy velocity, pressure and reactant cup-mixing concentration) through the structure-property relationships (permeability-porosity, average pore size-porosity and interfacial area-porosity), and the dependence of the fluid-solid mass transfer coefficient and fluid phase dispersion coefficient on the evolving pore scale variables (average pore size and local Reynolds and Schmidt numbers).A preliminary analysis of the model is presented and the influence of various factors on flow channeling is examined using the new model. The model predictions are compared with the available laboratory data.
Sperm is epigenetically programmed to regulate gene transcription in embryos (2016)

For a long time, it has been assumed that the only role of sperm at fertilization is to introduce the male genome into the egg. Recently, ideas have emerged that the epigenetic state of the sperm nucleus could influence transcription in the embryo. However, conflicting reports have challenged the existence of epigenetic marks on sperm genes, and there are no functional tests supporting the role of sperm epigenetic marking on embryonic gene expression. Here, we show that sperm is epigenetically programmed to regulate embryonic gene expression. By comparing the development of sperm- and spermatid-derived frog embryos, we show that the programming of sperm for successful development relates to its ability to regulate transcription of a set of developmentally important genes. During spermatid maturation into sperm, these genes lose H3K4me2/3 and retain H3K27me3 marks. Experimental removal of these epigenetic marks at fertilization de-regulates gene expression in the resulting embryos in a paternal chromatin-dependent manner. This demonstrates that epigenetic instructions delivered by the sperm at fertilization are required for correct regulation of gene expression in the future embryos. The epigenetic mechanisms of developmental programming revealed here are likely to relate to the mechanisms involved in transgenerational transmission of acquired traits. Understanding how parental experience can influence development of the progeny has broad potential for improving human health.
Immunologic Responses of HIV-1–Infected Study Subjects to Immunization With a Mixture of Peptide Protein Derivative–V3 Loop Peptide Conjugates (1999)

Summary: V3 loop peptide sequences from several HIV-1 strains were covalently linked to purified protein derivative (PPD) of Mycobacterium tuberculosis. A mixture of PPD conjugates of V3 loop peptides from six different strains of HIV-1 induced a stronger antibody response than a single V3 peptide-conjugate administered to guinea pigs and humans. Sera from animals immunized with a PPD-six peptide-PPD conjugate neutralized multiple primary-isolate strains of HIV-1. Potent immune responses were noted only when animals were primed with bacillus Calmette-Guérin (BCG), PPD was covalently bound to the peptides, and PPD was used as the carrier protein. Based on these animal studies, an immunogen consisting of PPD-conjugated V3 loop peptides from five HIV-1 strains was tested in 7 HIV-1 seropositive PPD skin testpositive study subjects. Vaccinees exhibited over time a uniform increase in neutralizing antibodies for both laboratory adapted and primary isolates of HIV-1, including strains from multiple clades. In 3 patients with baseline viral loads between 8000 and 12,000 RNA copies/ml, the viral load declined in 2 patients to <400 copies/ml and in 1 patient to 1200 copies/ml without concurrent administration of highly active antiretroviral therapy (HAART).
Finding errors in components that exchange xml data (2007)

Two or more components (e.g., objects, modules, or programs) interoperate when they exchange data, such as XML data. Using Application Programming Interface (API) calls exported by XML parsers remains a primary mode of accessing and manipulating XML, and these API calls lead to various run-time errors in components that exchange XML data. Currently, no tool checks the source code of interoperating components for potential flaws caused by third-party API calls that lead to incorrect XML data exchanges and runtime errors, even when components are located within the same application
A technique for the recording of bioelectric potentials from free-flying insects (Lepidoptera: Heliconius erato) (1965)

The station
In Vivo and in Vitro Evaluation of Liquid Antacids (1973)

An in vivo test of the efficacy of liquid antacids given after a meal was shown to yield reproducible results. An average dose-response curve, obtained with the use of various doses of a single antacid, was different in subjects whose peak histamine response exceeded 25 mEq per hour and in those whose response was less than 16.6 mEq per hour. In individual subjects, however, the peak histamine response did not accurately predict the in vivo reduction in gastric acidity by antacid. Although the relative in vivo potency of equal volumes of four different antacids varied widely, this potency could be predicted with reasonable accuracy by means of an in vitro test, which showed the potency per milliliter of antacid to vary 17-fold among different commercial products. These experiments indicate that when antacids are prescribed, dosage should be determined by the milli-equivalents of neutralizing capacity rather than by an arbitrary volume or number of tablets of different antacids, that the variable responses of individual patients to antacids should be taken into account, and that the doses commonly used in the treatment of duodenal ulcer should be increased. (N Engl J Med 288:923–928, 1973)
Atomic transient recorder (2010)

In Bohr's model of the hydrogen atom, the electron takes about 150 attoseconds (1 as = 10(-18) s) to orbit around the proton, defining the characteristic timescale for dynamics in the electronic shell of atoms. Recording atomic transients in real time requires excitation and probing on this scale. The recent observation of single sub-femtosecond ( 1 fs = 10(-15) s) extreme ultraviolet (XUV) light pulses(1) has stimulated the extension of techniques of femtochemistry(2) into the attosecond regime(3,4). Here we demonstrate the generation and measurement of single 250-attosecond XUV pulses. We use these pulses to excite atoms, which in turn emit electrons. An intense, waveform-controlled, few cycle laser pulse(5) obtains 'tomographic images' of the time-momentum distribution of the ejected electrons. Tomographic images of primary ( photo) electrons yield accurate information of the duration and frequency sweep of the excitation pulse, whereas the same measurements on secondary ( Auger) electrons will provide insight into the relaxation dynamics of the electronic shell following excitation. With the current similar to750-nm laser probe and similar to100-eV excitation, our transient recorder is capable of resolving atomic electron dynamics within the Bohr orbit time.
Unconstrained and constrained motion control of a planar two‐link structurally flexible robotic manipulator (1994)

Abstract Unconstrained and constrained motion control of a planar two‐link structurally‐flexible robotic manipulator are considered in this study. The dynamic model is obtained by using the extended Hamilton's principle and the Galerkin criterion. A method is presented to obtain the linearized equations of motion in Cartesian space for use in designing the control system. The approach to solving the control problem is to use feedforward and feedback control torques. The feedforward torques maneuver the flexible manipulator along a nominal trajectory and the feedback torques minimize any deviations from the nominal trajectory. The feedforward and feedback torques are obtained by solving the inverse dynamics problem for the rigid manipulator and designing linear quadratic Gaussian with loop transfer recovery (LQG/LTR) compensators, respectively. The LQG/LTR design methodology is exploited to design a robust feedback control system that can handle modeling errors and sensor noise, and operate on Cartesian space trajectory errors. Computer simulated results are presented for an example planar, two‐link, structurally flexible robotic manipulator. © 1994 John Wiley &amp; Sons, Inc.
6F-4 Ultrasound Elastography for the Non-invasive Healing Follow-Up of Abdominal Aneurysms (2006)

In this paper, we propose to characterize the aneurysmal sac components and to follow the healing process after endovascular treatment of the aneurysm with a stent graft (SG). The study was performed on 11 dogs with bilateral aneurysms surgically created on iliac arteries. The healing process was evaluated on digital subtraction angiography, color Doppler display and ultrasound (US) elastography, 3 months after implantation of the SG. The elastography algorithms used are a 1D scaling factor approach, improved to avoid low signal-to-noise artifacts, and a 2D Lagrangian algorithm. Elastograms provided complementary information to other imaging modalities for healed cases (low pulsatility and aneurysmal sac filled with a solid thrombus), and for unhealed cases (endoleak in the sac associated with a high pulsatility), but unique findings were present when the aneurysm was incompletely healed. In conclusion, we found that ultrasound elastography is a good exam complementary to B-scan and Doppler to characterize aneurysms following endovascular repair
<title>Optimal processor allocation for sort-last compositing under BSP-tree ordering</title> (1999)

In this paper, we consider a parallel rendering model that exploits the fundamental distinction between rendering and compositing operations, by assigning processors from specialized pools for each of these operations. Our motivation is to support the parallelization of general scan-line rendering algorithms with minimal effort, basically by supporting a compositing back-end (i.e., a sort-last architecture) that is able to perform user-controlled image composition. Our computational model is based on organizing rendering as well as compositing processors on a BSP-tree, whose internal nodes we call the compositing tree. Many known rendering algorithms, such as volumetric ray casting and polygon rendering can be easily parallelized based on the structure of the BSP-tree. In such a framework, it is paramount to minimize the processing power devoted to compositing, by minimizing the number of processors allocated for composition as well as optimizing the individual compositing operations. In this paper, we address the problems related to the static allocation of processor resources to the compositing tree. In particular, we present an optimal algorithm to allocate compositing operations to compositing processors. We also present techniques to evaluate the compositing operations within each processor using minimum memory while promoting concurrency between computation and communication. We describe the implementation details and provide experimental evidence of the validity of our techniques in practice.
A Wireless Phase Shift Keying Transmitter with Q-Independent Phase Transition Time (2005)

Inductive coupling is a common way to wirelessly transmit data to medical implants. In such applications, the carrier frequency is often limited to tens of MHz which is able to well penetrate the skin. To achieve high data rate, the number of carrier cycles used to modulate each bit should be as small as possible. This usually requires lowering the quality factor (Q) of the data transmission network, resulting in increased power dissipation. This paper presents a novel data transmitter using phase shift keying which can modulate the phase of the carrier within two carrier cycles, independent of the Q of the network; thus low power dissipation can be achieved. The transmitter is designed by taking advantage of the multiplefrequency resonant network of class-E power amplifiers. Design guidelines for such a Q-independent phase modulator are provided. Simulations and experimental results demonstrate that the phase modulator functions as expected.