gebhart/patrepeval huggingface dataset:
Annealing networks and fractal landscapes (2002)

The conventional explanation for the poor scaling of Hopfield and Tank networks is that they have difficulty in balancing the tradeoff between the path length and the legality components of the energy function. An experiment is described which suggests that the conventional explanation is either wrong, or, at best, incomplete. An alternative explanation is proposed, i.e., that these networks might scale better if their dynamics effectively implemented a divide-and-conquer strategy, if they recursively decomposed the problem into smaller independent subproblems. An annealing network can do so if the energy landscape has a self-similar quasi-fractal structure. It is the author's belief that this proposition applies to both discrete and analog networks. His proposition is supported by describing his work in finding low-cost solutions for traveling salesman problems. The implications for two other optimization problems (graph bisection and coloring) are considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Horizontal transfer and evolution of wall teichoic acid gene cassettes in Bacillus subtilis (2021)

<b>Background:</b> Wall teichoic acid (WTA) genes are essential for production of cell walls in gram-positive bacteria and necessary for survival and variability in the cassette has led to recent antibiotic resistance acquisition in pathogenic bacteria. <b>Methods:</b> Using a pan-genome approach, we examined the evolutionary history of WTA genes in <i>Bacillus subtilis</i> ssp. <i>subtilis</i>. <b>Results:</b> Our analysis reveals an interesting pattern of evolution from the type-strain WTA gene cassette possibly resulting from horizontal acquisition from organisms with similar gene sequences. The WTA cassettes have a high level of variation which may be due to one or more independent horizontal transfer events during the evolution of <i>Bacillus subtilis</i> ssp. <i>subtilis</i>. This swapping of entire WTA cassettes and smaller regions within the WTA cassettes is an unusual feature in the evolution of the <i>Bacillus subtilis</i> genome and highlights the importance of horizontal transfer of gene cassettes through homologous recombination within <i>B. subtilis</i> or other bacterial species. <b>Conclusions:</b> Reduced sequence conservation of these WTA cassettes may indicate a modified function like the previously documented WTA ribitol/glycerol variation. An improved understanding of high-frequency recombination of gene cassettes has ramifications for synthetic biology and the use of <i>B. subtilis</i> in industry.
A Novel Method for Inducing Nerve Growth via Modulation of Host Resting Potential: Gap Junction-Mediated and Serotonergic Signaling Mechanisms (2014)

A major goal of regenerative medicine is to restore the function of damaged or missing organs through the implantation of bioengineered or donor-derived components. It is necessary to understand the signals and cues necessary for implanted structures to innervate the host, as organs devoid of neural connections provide little benefit to the patient. While developmental studies have identified neuronal pathfinding molecules required for proper patterning during embryogenesis, strategies to initiate innervation in structures transplanted at later times or alternate locations remain limited. Recent work has identified membrane resting potential of nerves as a key regulator of growth cone extension or arrest. Here, we identify a novel role of bioelectricity in the generation of axon guidance cues, showing that neurons read the electric topography of surrounding cells, and demonstrate these cues can be leveraged to initiate sensory organ transplant innervation. Grafts of fluorescently labeled embryological eye primordia were used to produce ectopic eyes in Xenopus laevis tadpoles. Depolarization of host tissues through anion channel activation or other means led to a striking hyperinnervation of the body by these ectopic eyes. A screen of possible transduction mechanisms identified serotonergic signaling to be essential for hyperinnervation to occur, and our molecular data suggest a possible model of bioelectrical control of the distribution of neurotransmitters that guides nerve growth. Together, these results identify the molecular components of bioelectrical signaling among cells that regulates axon guidance, and suggest novel biomedical and bioengineering strategies for triggering neuronal outgrowth using ion channel drugs already approved for human use.
Study on the Evaluation of Mine Environmental Sustainable Development Based on Fuzzy Petri Nets (2018)

To evaluate the sustainable development of mine environment, fuzzy Petri nets and variable weight theory were introduced into the study of sustainable development of mine ecological environment. Based on the self-purification and repair functions of the environmental system, a fault tree model of mine environmental pollution was constructed, and the fault tree model was transformed into a mine pollution model based on fuzzy Petri nets. Finally, an inference algorithm and evaluation method based on the fuzzy Petri net model were described. It provides a theoretical basis for the sustainable development evaluation of the mine environment.
Phase I Clinical Trial of Systemically Administered TUSC2(FUS1)-Nanoparticles Mediating Functional Gene Transfer in Humans (2012)

ClinicalTrials.gov NCT00059605.
Oxidic Aerogels (2002)

The prelims comprise: Introduction to Aerogels Aerogel Preparation Oxidic Aerogels
Multi-step control of muscle diversity by Hox proteins in the Drosophila embryo (2010)

Hox transcription factors control many aspects of animal morphogenetic diversity. The segmental pattern of Drosophila larval muscles shows stereotyped variations along the anteroposterior body axis. Each muscle is seeded by a founder cell and the properties specific to each muscle reflect the expression by each founder cell of a specific combination of 'identity' transcription factors. Founder cells originate from asymmetric division of progenitor cells specified at fixed positions. Using the dorsal DA3 muscle lineage as a paradigm, we show here that Hox proteins play a decisive role in establishing the pattern of Drosophila muscles by controlling the expression of identity transcription factors, such as Nautilus and Collier (Col), at the progenitor stage. High-resolution analysis, using newly designed intron-containing reporter genes to detect primary transcripts, shows that the progenitor stage is the key step at which segment-specific information carried by Hox proteins is superimposed on intrasegmental positional information. Differential control of col transcription by the Antennapedia and Ultrabithorax/Abdominal-A paralogs is mediated by separate cis-regulatory modules (CRMs). Hox proteins also control the segment-specific number of myoblasts allocated to the DA3 muscle. We conclude that Hox proteins both regulate and contribute to the combinatorial code of transcription factors that specify muscle identity and act at several steps during the muscle-specification process to generate muscle diversity.
A systematic review of convalescent plasma treatment for COVID19 (2020)

ABSTRACT Background Transfusion of convalescent immune plasma (CP) is commonly used in epidemics. Several articles now describe clinical report data of CP for treatment of SARS-CoV-2-induced COVID-19 disease. Methods A systematic literature review was conducted using the NCBI curated COVID-19 related open-resource literature database LitCovid to identify studies using CP as treatment for COVID-19 patients. We retrieved and curated all COVID-19 related patient and treatment characteristics from previously reported studies. A Poisson model was developed to evaluate the association between age of the patients, older age being the most common risk factor for COVID-19 mortality, and recovery time since CP treatment using data extracted from the literature. Results From 18,293 identified COVID-19 related articles, we included ten studies reporting results of CP treatment for COVID-19 from a total of 61 patients. Decreased symptoms of severe COVID-19 and clearance of SARS-CoV-2 RNA were the most direct observations. We found that patients over the age of sixty who received CP treatment for COVID-19 had a significantly prolonged recovery estimated by viral clearance (from 10 to 29 days since first dose of CP) compared to younger patients, who recovered from the infection in less than a week after receiving CP treatment. Conclusions Limited published results on plasma transfusion treatment for COVID-19 disease with concomitant treatments suggest that CP therapy for COVID-19 is well tolerated and effective. First randomized clinical trial results, however, revealed no improvements in recovery time for elderly patients with severe COVID-19 between standard treatment alone and added with convalescent plasma. Accordingly, we argue that older patients may need a significantly longer time for recovery. Further randomized clinical trial data for COVID-19 with rigorous ethical standards is urgently needed.
LTE Relay Architecture and Its Upper Layer Solutions (2010)

The relay technology is an essential piece of LTE-Advanced in its pursuit of cost effective capacity enhancement and coverage extension. Simple RF repeaters have been widely used in cellular technologies to offer coverage extension. However, they cannot distinguish desired signals from interference and noise and are unable to operate with sophisticated mechanisms, such as power control, beam-forming, and adaptive modulating/coding. As a result, simple RF repeaters do not provide capacity enhancement nor do they reach the capacity potential of extended coverage areas. The use of more sophisticated relay in cellular technologies is relatively new. With its great benefits in QoS differentiation, capacity enhancement, and coverage extension, the development of LTE relay technology faces challenges in providing backward compatibility, minimizing complexity, providing sufficient QoS differentiation, reducing over the air overhead, and ensuring security. This paper addresses these challenges with solutions in the aspect of relay architecture and upper layer designs.
Downhole Upgrading of Orinoco Basin Extra-Heavy Crude Oil Using Hydrogen Donors under Steam Injection Conditions. Effect of the Presence of Iron Nanocatalysts (2015)

An extra-heavy crude oil underground upgrading concept and laboratory experiments are presented which involve the addition of a hydrogen donor (tetralin) to an Orinoco Basin extra-heavy crude oil under steam injection conditions (280–315 °C and residence times of at least 24-h). Three iron-containing nanocatalysts (20 nm, 60 nm and 90 nm) were used and the results showed increases of up to 8° in API gravity, 26% desulfurization and 27% reduction in the asphaltene content of the upgraded product in comparison to the control reaction using inert sand. The iron nanocatalysts were characterized by SEM, XPS, EDAX, and Mössbauer spectroscopy before and after the upgrading reactions. The results indicated the presence of hematite (Fe2O3) as the predominant iron phase. The data showed that the catalysts were deactivating by particle sintering (~20% increase in particle size) and also by carbon deposition. Probable mechanisms of reactions are proposed.
Towards the assessment of biomechanical interfaces: Topography of hidden objects obtained with THz holography (2017)

We report on the first steps towards THz imaging of biomechanical interfaces. A THz digital holography setup in reflection is used with synthetic aperture techniques to reconstruct the profile of a fingertip replica with a lateral resolution of 200 μm and a depth resolution of 20 μm. A method for the reconstruction of the profile of a sample hidden behind a THz-transparent material is also proposed. Experimental proof is provided by retrieving the bent profile of a metallic resolution target behind a Teflon plate.
Whole body detection and imaging of nitric oxide generation in mice following cardiopulmonary arrest: Detection of intrinsic nitrosoheme complexes (2001)

Ischemic tissues generate nitric oxide (NO) by direct reduction of tissue nitrite under the acidic conditions that occur during ischemia. In view of the important implications of this enzyme-independent mechanism of NO generation on the pathogenesis and treatment of tissue injury, the NO formation in mice subjected to cardiopulmonary arrest was measured and imaged. Real-time measurement of NO generation was performed by detection of naturally generated NO-heme complexes in tissues using L-band electron paramagnetic resonance (EPR) spectroscopy. To distinguish NO generated from nitrite, animals were labeled with isotopically enriched (15)N-nitrite. Mice were infused with nitrite (70 mg/kg, intravenous), cardiopulmonary arrest induced by an overdose of phenobarbital, and transferred to the EPR resonator. Measurements of NO generation were performed on the intact animal at the levels of the head, thorax, and abdomen. At the end of 3 hr, major organs were isolated and analyzed for their NO signal. The NO complexes were found to have maximum levels in lung, heart, and liver. Three-dimensional spatial mapping of the NO complex in the intact animal subjected to cardiopulmonary arrest was performed using EPR imaging techniques. The images also confirmed the maximum formation in the lungs, heart, and liver. The present data reveal that mice subjected to cardiopulmonary arrest generate large amounts of NO, which is nitrite mediated. The observed signal was largely due to heme-bound NO, which accounted for the high concentrations found in these organs. This increased NO formation during cardiopulmonary arrest could contribute to the difficulty of resuscitation after long periods of arrest. Magn Reson Med 45:700-707, 2001.
A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains (2008)

Cyclic nucleotides (cAMP and cGMP) regulate multiple intracellular processes and are thus of a great general interest for molecular and structural biologists. To study the allosteric mechanism of different cyclic nucleotide binding (CNB) domains, we compared cAMP-bound and cAMP-free structures (PKA, Epac, and two ionic channels) using a new bioinformatics method: local spatial pattern alignment. Our analysis highlights four major conserved structural motifs: 1) the phosphate binding cassette (PBC), which binds the cAMP ribose-phosphate, 2) the "hinge," a flexible helix, which contacts the PBC, 3) the beta(2,3) loop, which provides precise positioning of an invariant arginine from the PBC, and 4) a conserved structural element consisting of an N-terminal helix, an eight residue loop and the A-helix (N3A-motif). The PBC and the hinge were included in the previously reported allosteric model, whereas the definition of the beta(2,3) loop and the N3A-motif as conserved elements is novel. The N3A-motif is found in all cis-regulated CNB domains, and we present a model for an allosteric mechanism in these domains. Catabolite gene activator protein (CAP) represents a trans-regulated CNB domain family: it does not contain the N3A-motif, and its long range allosteric interactions are substantially different from the cis-regulated CNB domains.
A novel method for assessment of airway opening pressure without the need for low-flow insufflation (2023)

Determination of P<sub>cond</sub> during constant-flow assist control ventilation may permit to easily and safely detect and measure AOP.
Prostacyclin effects on the blood pressure responses to norepinephrine in rats treated with aspirin or indomethacin. (1980)

The atherosclerotic condition is associated with a reduction of PGI2 synthesis; moreover, in the presence of elevated serum cholesterol levels, pressor responses to norepinephrine are potentiated. In order to verify if a complete inhibition of PGI2 production affects the vascular reactivity, it was assayed two cycloxygenase inhibitors (lysine acetylsalicylate and indomethacin) in rats. The two drugs significantly potentiated the blood pressure responses to norepinephrine, and completely inhibited PGI2-like substances production by arterial rings. The prostacyclin infusion (15 ng/kg/min, i.v.) completely reversed such potentiation, without any major modification in the basal blood pressure values. These results show that PGI2 production is responsible for vascular tone modulation and may partially explain the altered vascular reactivity in the atherosclerotic condition.
Stereoselective Syntheses of Tetrahydrolipstatin and of an Analogue, Potent Pancreatic‐Lipase Inhibitors Containing a β‐Lactone Moiety (1987)

Abstract Tetrahydrolipstatin ( 1 ) and itsanalogue 2 are representatives of a new class of pancreatic‐lipase inhibtors. Two stereoselective synthetic approaches are described.
The Application of Proteomic Techniques to Fungal Protein Identification and Quantification (2007)

The number of sequenced genomes has increased rapidly in the last few years, supporting a revolution in bioinformatics that has been leveraged by scientists seeking to analyze the proteomes of numerous biological systems. The primary technique employed for the identification of peptides and proteins from biological sources is mass spectrometry (MS). This analytical process is usually in the form of whole-protein analysis (termed "top-down" proteomics) or analysis of enzymatically produced peptides (known as the "bottom-up" approach). This article will focus primarily on the more common bottom-up proteomics to include topics such as sample preparation, separation strategies, MS instrumentation, data analysis, and techniques for protein quantification. Strategies for preparation of samples for proteomic analysis, as well as tools for protein and peptide separation will be discussed. A general description of common MS instruments along with tandem mass spectrometry (MS/MS) will be given. Different methodologies of sample ionization including matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) will be discussed. Data analysis methods including database search algorithms and tools for protein sequence analysis will be introduced. We will also discuss experimental strategies for MS protein quantification using stable isotope labeling techniques and fluorescent labeling. We will introduce several fungal proteomic studies to illustrate the use of these methods. This article will allow investigators to gain a working knowledge of proteomics along with some strengths and weaknesses associated with the techniques presented.
Competitive adsorption of amylopectin and amylose on cationic nanoparticles: a study on the aggregation mechanism (2016)

In this study we investigate the interactions between cationic nanoparticles and anionic starch, where the starch was composed of 20 wt% of amylose, a linear polymer, and 80 wt% of amylopectin, a branched polymer. The mechanism of aggregation was investigated by scattering techniques. It was found that the cationic particles formed large aggregates with the starch as a result of selective adsorption of the amylopectin. Amylose did not participate significantly in the aggregate formation even when the charge ratio of starch to particles was <1. For starch to particle ratio >1 stabilization was recovered mostly due to the large hindrance brought about by the highly branched amylopectin. This results in a shift of the stabilization mechanism from electrostatic to electrosteric. The internal structure of the aggregates was composed of primary particles with starch coils adsorbed on the surface. This information supports the proposed aggregation mechanism, which is based on adsorption of the negatively charged starch in patches on the positively charged nanoparticles causing attractive interaction between the particles.
Characterization of the elicitor structure of potexviruses triggering the Rx-mediated resistance in crop species (2009)

National audience
Analytical Spectroscopy Using Modular Systems (2003)

This article describes the development of three analytical spectroscopy experiments that compare the determination of salicylic acid (SA) content in aspirin tablets. The experiments are based on UV–vis, fluorescence, and Raman spectroscopies and utilize modular spectroscopic components. Students assemble their own instruments, optimize them with respect to signal-to-noise, generate calibration curves, determine the SA content in retail aspirin tablets, and assign features in the respective spectra to functional groups within the active material. Using this approach in the discovery-based setting, the students gain invaluable insight into method-specific parameters, such as instrumental components, sample preparation, and analytical capability. In addition, the students learn the fundamentals of fiber optics and signal processing using the low-cost CCD based spectroscopic components.
On-chip image rejection in a low-if cmos receiver (2006)

An adaptive image-reject mixer is realized in a 0.18μm CMOS technology. The circuit achieves high image-rejection ratios without off-chip filters in applications such as TV tuners. Test results show a 54dB image-rejection ratio in a low-IF receiver. The circuit consumes 75mW from a 1.8V supply and occupies 2.25mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> including pads
Polymorphism in Crystalline Cinchomeronic Acid (2006)

The structural relationship between the two crystal forms of cinchomeronic acid (CA 3,4-dicarboxypyridine) has been investigated by single crystal X-ray diffraction, IR and Raman spectroscopy and solid state NMR spectroscopy, showing that the two polymorphs form a monotropic system, with the orthorhombic form I being the thermodynamically stable form, while the monoclinic form II is unstable. In both forms CA crystallizes as a zwitterion and decomposes before melting. The crystal structure and spectroscopic analysis indicate that the difference in stability can be ascribed to the strength of the hydrogen-bonding patterns established by the protonated N-atom and the carboxylic/carboxylate O-atoms.
Magnetic Bead-Based Chemiluminescent Metal Immunoassay with a Colloidal Gold Label (2005)

A novel, sensitive chemiluminescent (CL) immunoassay has been developed by taking advantage of a magnetic separation/mixing process and the amplification feature of colloidal gold label. First, the sandwich-type complex is formed in this protocol by the primary antibody immobilized on the surface of magnetic beads, the antigen in the sample, and the second antibody labeled with colloidal gold. Second, a large number of Au3+ ions from each gold particle anchored on the surface of magnetic beads are released after oxidative gold metal dissolution and then quantitatively determined by a simple and sensitive Au3+-catalyzed luminol CL reaction. Third, this protocol is evaluated for a noncompetitive immunoassay of a human immunoglobulin G, and a concentration as low as 3.1 x 10(-12) M is determined, which is competitive with colloidal gold-based anodic stripping voltammetry (ASV), colorimetric ELISA, or immunoassays based on fluorescent europium chelate labels. The high performance of this protocol is related to the sensitive CL determination of Au3+ ion (detection limit of 2 x 10(-10) M), which is 25 times higher than that by ASV at a single-use carbon-based screen-printed electrode. From the analytical chemistry point of view, this protocol will be quite promising for numerous applications in immunoassay and DNA hybridization.