gebhart/patrepeval huggingface dataset:
Mechanism of substrate inactivation of Escherichia coli S-adenosylmethionine decarboxylase (1987)

S-Adenosylmethionine decarboxylase, a pyruvoyl-containing decarboxylase, is inactivated in a time-dependent process under turnover conditions. The inactivation is dependent on the presence of both substrate and Mg2+, which is also required for enzyme activity. The rate of inactivation is dependent on the concentration of substrate and appears to be saturable. Inactivation by [methionyl-3,4-14C]-adenosylmethionine results in stoichiometric labeling of the protein. In contrast, when either S-[methyl-3H]adenosylmethionine or [8-14C]adenosylmethionine is used, there is virtually no incorporation of radioactivity. Automated Edman degradation of the alpha (pyruvoyl-containing) subunit reveals that substrate inactivation results in the conversion of the pyruvoyl group to an alanyl residue. These data suggest a mechanism of inactivation which involves the transamination of the nascent product to the pyruvoyl group, followed by the elimination of methylthioadenosine and the generation of a 2-propenal equivalent which could undergo a Michael addition to the enzyme. This is the first evidence for a transamination mechanism for substrate inactivation of a pyruvoyl enzyme.
Molecular microbial analysis of Bifidobacterium isolates from different environments by the species-specific amplified ribosomal DNA restriction analysis (ARDRA) (2001)

One hundred and six isolates of the genus Bifidobacterium, isolated from different environments (mainly gastrointestinal), were identified and classified taxonomically to species level by amplified ribosomal DNA restriction analysis. Two restriction endonucleases (Sau3AI and BamHI) were chosen for aligning the 16S rRNA sequences of 16 bifidobacterial species retrieved from various databases, to obtain species-specific restriction patterns. A rapid and accurate identification scheme was obtained by comparing the resulting 16S rDNA digestion profiles of 16 Bifidobacterium type-strains and 90 strains of various origins. All of the investigated strains were previously confirmed at the species level as belonging to the genus Bifidobacterium by fluorescence in-situ hybridisation and by polymerase chain reaction amplification with genus- and species-specific primers. The present work demonstrates that species-specific detection of Bifidobacterium adolescentis, Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium catenulatum, Bifidobacterium coryneforme, Bifidobacterium cuniculi, Bifidobacterium dentium, Bifidobacterium infantis, Bifidobacterium lactis, Bifidobacterium longum, Bifidobacterium suis, Bifidobacterium magnum, Bifidobacterium pseudolongum, Bifidobacterium pseudocatenulatum and Bifidobacterium pullorum present in different micro-ecological environments (e.g. gastrointestinal tract) can be accomplished in a reliable, rapid and accurate manner, circumventing the recognised deficiencies of traditional identification techniques.
Investigations on hessian-free optimization for cross-entropy training of deep neural networks (2013)

Context-dependent deep neural network HMMs have been shown to achieve recognition accuracy superior to Gaussian mixture models in a number of recent works. Typically, neural networks are optimized with stochastic gradient descent. On large datasets, stochastic gradient descent improves quickly during the beginning of the optimization. But since it does not make use of second order information, its asymptotic convergence behavior is slow. In regions with pathological curvature, stochastic gradient descent may almost stagnate and thereby falsely indicate convergence. Another drawback of stochastic gradient descent is that it can only be parallelized within minibatches. The Hessian-free algorithm is a second order batch optimization algorithm that does not suffer from these problems. In a recent work, Hessian-free optimization has been applied to a training of deep neural networks according to a sequence criterion. In that work, improvements in accuracy and training time have been reported. In this paper, we analyze the properties of the Hessian-free optimization algorithm and investigate whether it is suited for cross-entropy training of deep neural networks as well.
Performance of a DSP based phase-shifted PWM controlled, zero-voltage-switching direct-current regulated magnet power supply (2006)

In this paper, a power supply being used for powering quadrupole magnets of a 2.5 GeV synchrotron machine is discussed. Main focus is on the implementation of a digital control of the power supply using a digital signal processor (DSP), TMS320F2812 from TI. The control system is designed to regulate the magnet current against the variations of line-voltage, load-impedance and other parameters. The power circuit consists of an AC-DC converter followed by a DC-DC converter based on zero-voltage-switched (ZVS) high frequency inverter driven by phase-shifted pulses. The paper describes the power circuit, digital implementation of various control-loops, computer simulation and design of control loops, and finally, the simulation results along with the results achieved from the actual system.
Establishing quasi-steady state operations of microphysiological systems (MPS) using tissue-specific metabolic dependencies (2018)

Microphysiological systems (MPS), consisting of tissue constructs, biomaterials, and culture media, aim to recapitulate relevant organ functions in vitro. MPS components are housed in fluidic hardware with operational protocols, such as periodic complete media replacement. Such batch-like operations provide relevant nutrients and remove waste products but also reset cell-secreted mediators (e.g. cytokines, hormones) and potentially limit exposure to drugs (and metabolites). While each component plays an essential role for tissue functionality, MPS-specific nutrient needs are not yet well-characterized nor utilized to operate MPSs at more physiologically-relevant conditions. MPS-specific nutrient needs for gut (immortalized cancer cells), liver (human primary hepatocytes) and cardiac (iPSC-derived cardiomyocytes) MPSs were experimentally quantified. In a long-term study of the gut MPS (10 days), this knowledge was used to design operational protocols to maintain glucose and lactate at desired levels. This quasi-steady state operation was experimentally validated by monitoring glucose and lactate as well as MPS functionality. In a theoretical study, nutrient needs of an integrated multi-MPS platform (gut, liver, cardiac MPSs) were computationally simulated to identify long-term quasi-steady state operations. This integrative experimental and computational approach demonstrates the utilization of quantitative multi-scale characterization of MPSs and incorporating MPS-specific information to establish more physiologically-relevant experimental operations.
G-106 The pro- and anti-inflammatory effector functions of IgG (2016)

Immunoglobulin G (IgG) antibodies play an important role in the defense against pathogenic microorganisms but are also responsible for tissue destruction and inflammation during autoimmune diseases such as rheumatoid arthritis and SLE. Paradoxically pooled IgG preparations from thousands of donors (IVIg) are also an efficient treatment to suppress several autoimmune diseases and chronic inflammation. Research over the last years has highlighted the role of the sugar domain attached to the IgG Fc-fragment as a molecular switch, which can enhance or block the pro- and anti-inflammatory effector functions of the antibody molecule. Of note, altered IgG glycosylation patterns, containing low levels of terminal galactose and sialic acid residues, have been associated with active autoimmune disease in RA, SLE, and Crohns disease, for example. As sialylated IgG glycovariants have been suggested to be responsible for the anti-inflammatory activity of IVIg, one possible mechanism of IVIg therapy may be to replenish this active anti-inflammatory and immunomodulatory IgG glycovariant, thereby re-establishing immune homeostasis. The aim of this presentation is to summarize our current knowledge about the molecular and cellular mechanisms involved in the pro- and anti- inflammatory activities of IgG and how we can use novel humanized mouse models to translate the findings obtained in inbred mouse models to the human immune system.
Homology among tet determinants in conjugative elements of streptococci (1981)

A mutation to tetracycline sensitivity in a resistant strain of Streptococcus pneumoniae was shown by several criteria to be due to a point mutation in the conjugative omega (cat-tet) element found in the chromosomes of strains derived from BM6001, a clinical strain resistant to tetracycline and chloramphenicol. Strains carrying the mutation were transformed back to tetracycline resistance with the high efficiency of a point marker by donor deoxyribonucleic acids from its ancestral strain and from nine other clinical isolates of pneumococcus and by deoxyribonucleic acids from group D Streptococcus faecalis and group B Streptococcus agalactiae strains that also carry conjugative tet elements in their chromosomes. It was not transformed to resistance by tet plasmid deoxyribonucleic acids from either gram-negative or gram-positive species, except for one that carried transposon Tn916, the conjugative tet element present in the chromosomes of some S. faecalis strains. The results showed that the tet determinants in conjugative elements of several streptococcal species share a high degree of deoxyribonucleic acid sequence homology and suggested that they differ from other tet genes.
<title>Analysis of kinetic rate modeling of thermal damage in laser-irradiated tissue</title> (1991)

Theoretical modeling of the thermal and optical processes involved in the interaction of laser light with tissue has progressed both qualitatively and quantitatively as a tool for understanding laser coagulation and ablation. Optimal procedure and dosimetry prescription for laser irradiation of tissue in various applications requires a knowledge of the thermal damage process in tissue and its dynamic behavior. Previous work in the area of thermal damage modeling date back to the work of Henriques (1947) on pig skin. Agah et al. (1987) have evaluated damage coefficients for human vascular tissue. Interesting work on quantitative histology is in progress by Thomsen et al. (1989) in which thermal damage coefficients are correlated to birefringent microscopic observations. A study of the dynamics of thermal damage and ablation indicate the presence and variation of damage in different tissues even before the onset of the ablative process (Rastegar, et al. 1988). In the present study, using a kinetic rate model for thermal damage, the behavior of the damage model has been analyzed to determine sensitivities of tissue parameters, effects of temperature dependence, and possibility of predictions based on isotherm propagation.
Recent progress in understanding the persistent luminescence in SrAl<sub>2</sub>O<sub>4</sub>:Eu,Dy (2019)

Ever since the discovery of SrAl 2 O 4 :Eu,Dy persistent afterglow material, that can intensively glow up to 20 h, the mechanism of long-lasting luminescence has been a popular area of research. The research is focused on discovering the mechanism of persistent luminescence in order to prolong the duration and intensity of afterglow in a controlled way. Although most researchers agree on the general things, there are still many unclarities and ambiguities to discuss upon. This review paper briefly sketches in the highlights of past research on the luminescence mechanism in SrAl 2 O 4 :Eu,Dy, mainly focusing on the research conducted in the past decade dedicated to clearing these ambiguities. This paper provides an overview of the latest persistent luminescence mechanisms offered by researchers.
Si-doped GaN∕AlN quantum dot superlattices for optoelectronics at telecommunication wavelengths (2006)

We report on the controlled growth by molecular beam epitaxy of 20-period Si-doped GaN∕AlN quantum dot (QD) superlattices, in order to tailor their intraband absorption within the 1.3–1.55μm telecommunication spectral range. The QD size can be tuned by modifying the amount of GaN in the QDs, the growth temperature, or the growth interruption time (Ostwald ripening). By adjusting the growth conditions, QDs with height (diameter) within the range of 1–1.5nm (10–40nm), and density between 1011 and 1012cm−2 can be synthesized, fully strained on the AlN pseudosubstrate. To populate the first electronic level, silicon can be incorporated into the QDs without significant perturbation of the QD morphology. All the samples exhibit strong p-polarized intraband absorption at room temperature. The broadening of the absorption peak remains below 150meV and can be as small as ∼80meV. This absorption line is attributed to transition from the s ground level of the QD to the first excited level along the growth axis, pz. The peak energies of both photoluminescence emission and intraband absorption are consistent with the QD structural characteristics, and with their evolution by changing the growth conditions. Tuning of the intraband absorption from 0.740eV (1.68μm)to0.896eV (1.38μm) is demonstrated. Finally, we show that the AlN buffer layer can be replaced by a conductive AlxGa1−xN (x=0.35 and 0.6) ternary alloy without significant modification of the intraband properties of the QD stack.
Powder Explosion Inhibitor Prepared from Waste Incinerator Slag: Applied to Explosion Suppression of Oil Shale Dust Explosion (2022)

In this paper, a method for waste incineration slag is proposed. An incineration acidification alkalization modification was carried out based on the characteristics of the oxides (SiO2, CaO, Al2O3, Fe2O3, and MgO) of waste incineration slag. With modified slag as the carrier and NaHCO3 as the supporter, a slag-based composite powder explosion inhibitor was prepared with the solvent-crystallization wet coating (WCSC), ball milling dry coating (DCBM), and air impact dry coating (DCAI) methods. The advantages and disadvantages of the three methods were compared and analyzed. Explosion suppression experiments on oil shale dust were carried out, and the explosion suppression mechanism was described. The explosion suppression process of the modified slag–NaHCO3 composite powder explosion inhibitor for oil shale dust was found to involve a synergy of physical and chemical inhibition. This explosion suppression mechanism indicates three requirements for the preparation and application of industrial solid waste-based composite powder explosion inhibitors. The feasibility of preparing composite powder explosion inhibitors from waste incinerator slag was discussed from the experimental point of view and its explosion suppression performance on oil shale dust was studied with the intention of providing a new form of resource utilization for waste incinerator slag.
Robust control for a two-axis gimbaled sensor system with multivariable feedback systems (2010)

A dynamic model for the stabilisation loop of a two-axis gimbaled sensor system is formulated and system parameters have been identified by practical experiments. The validity of the dynamic model is illustrated by the experimental and simulation result. The Lead-proportional-integral (PI) controller design using a loop-shaping method based on the frequency response for the stabilisation loop of the sensor system is realised. This practical design approach has been proven to be simple and robust in actual application. The robust H∞ controller design approach combining model matching and mixed sensitivity problem to improve the command following and disturbance rejection performance in the presence of external disturbances and model uncertainties is implemented, which is designed within the framework of the standard H∞ optimisation problem by combining a conventional mixed sensitivity and model matching problem with robust stability. The experimental and simulation results show that the both two proposed controllers satisfy all desired requirements for the stabilisation loop associated with the gain crossover frequency, the gain and phase margin and the body-motion decoupling performance. It is shown through performance comparison and analysis that the proposed H∞ controller is preferable to the proposed Lead-PI controller in terms of system stability, the disturbance rejection rate and because of its fast time response characteristics. However, it is clear that the two proposed controller design procedures for the robust control of the stabilisation loop of a two-axis gimbaled sensor system can be very effective in practical applications in terms of both stability and disturbance rejection.
Field Programmable Analog Arrays for Conditioning Ultrasonic Sensors (2007)

This paper proposes the use of field programmable analog arrays (FPAAs) as adaptive conditioning blocks for ultrasonic sensors. The uncertainty achievable through this technique, in fact, results very sensitive to the measurement conditions, due to the attenuation affecting the echo during its propagation. Indeed, FPAAs emulate analog circuits whose characteristics have to be dynamically tuned according to different operating conditions. Actually, the signal provided by the ultrasonic sensor is properly processed in order to improve the overall measurement accuracy. In this paper, the prototype of a distance meter based on time-of-flight (TOF) measurement is presented in order to evidence the advantages gained by FPAA features in processing the sensor output to compensate echo attenuation and distortion versus target distance. The prototype working is supervised by a digital signal controller (DSC) whose tasks are: 1) driving the ultrasonic transducer; 2) performing the echo acquisition; 3) tuning on the fly the FPAA features; 4) evaluating the TOF; 5) measuring the target distance; and 6) delivering the final result to the end user. This paper is completed by the results achieved in a number of experimental tests allowing interesting considerations to be drawn. In particular, the experiments confirm the prototype reliability and effectiveness also with ultrasonic echoes characterized by very low signal-to-noise ratios.
Optical and electrical hybrid flexible printed circuit boards with unique photo-defined polymer waveguide layers (2010)

Optical and electrical hybrid flexible printed circuit boards with unique photo-defined polymer waveguide layers have been investigated. The photo-defined waveguides are made by simple pattering process, known as "Photo-addressing". In the process, only ultraviolet irradiation through a photo mask over photosensitive dry film is carried out to form entire waveguide patterns, and any additional steps like etching or developing are not required. We are now giving high priority to further process development how to integrate them with conventional flexible printed circuit boards, and gathering data of basic characteristics, properties and reliabilities of those kinds of hybrid product.
p53 over‐expression identifies a subset of nodal peripheral T‐cell lymphomas with a distinctive biological profile and poor clinical outcome (2001)

Peripheral T-cell lymphomas (PTCL) are usually characterized by aggressive clinical behaviour and poor clinical outcome, but their biological background has not been extensively investigated to date, due to their low incidence, about 10% of all non-Hodgkin's lymphoma cases in Western countries, and also to the paucity of specific molecular-genetic abnormalities. Neverthless, there is increasing biological and clinical evidence that primary nodal PTCL should be considered separately from extra-nodal cases, but little is known about biological factors of possible clinical and prognostic impact. This immunohistochemical study has analysed the expression of p53, Mdm2, p21WAF1, BCL-2 and p-glycoprotein (MDR-1 gene product) in a series of 45 cases of nodal peripheral T-cell lymphomas (PTCL) with ‘high-grade’ histology. The immunohistochemical findings were then correlated with proliferative activity and clinical outcome. p53 was over-expressed in 13 cases (28.9%). p53 positive cases showed significantly higher proliferative activity (p<0.01), more frequent expression of Bcl-2 (p<0.01) and less frequent expression of p21WAF1 than p53 negative cases. Mdm2 and p-glycoprotein were expressed in 4/13 (30.8%) and 8/13 (61.5%) p53 positive cases respectively, and in none (0%) of the p53 negative cases (p<0.01). Analysis of the survival curves showed that p53 positive cases were associated with a significantly poorer clinical outcome than p53 negative cases, in terms of both overall survival (p=0.0032) and event-free survival (p=0.0004). Furthermore, multivariate analysis showed that p53 expression was the most important independent prognostic variable. These findings indicate that p53 over-expression identifies a subset of nodal PTCL cases with a distinctive biological profile (higher proliferative activity, less frequent expression of p21WAF1 and more frequent expression of Bcl-2, Mdm2 and p-glycoprotein than p53 negative cases) and poor clinical outcome. The immunohistochemical analysis of p53 expression is a simple, rapid and low-cost method which may provide information of potential clinical and prognostic value in nodal peripheral T-cell lymphomas. Copyright © 2001 John Wiley & Sons, Ltd.
Intrinsic defect in B cells of patients with hyper-immunoglobulin M syndrome (1995)

We challenge the theory that the CD40-CD40 ligand is the only explanation for X-linked immunodeficiency in patients with hyper-immunoglobulin M (IgM) syndrome (HIGM1), and we demonstrate an intrinsic defect in the patients' B cells. Patients with HIGM1 have a defective CD40 ligand on their activated T-helper cells; therefore, they cannot receive signals for isotype switching when the cells are activated by T cell-dependent antigens. We activated mononuclear cells from three patients with HIGM1 and from three healthy blood donors with T cell-independent mitogens and studied their proliferative responses and Ig secretion. Normal murine plasma membrane fragments were implanted into peripheral blood mononuclear cells, and the cells were activated with Staphylococcus aureus Cowan I, pokeweed mitogen, and lipopolysaccharide. This implantation significantly augmented the proliferative responses to the mitogens in two patients. However, it augmented IGM secretion in response to B-cell mitogens in only one patient. No IgG or IgA response could be detected in the implanted mononuclear cells that originated from patients with HIGM1, unlike implanted mononuclear cells from healthy donors, which responded by IgM, IgG, and IgA antibody secretion following their stimulation with B-cell mitogens. The data suggest that the B cells of patients with HIGM1 possess an additional defect which prevents Ig isotype switching in response to T cell-independent mitogens. This defect is not located in the membrane receptors or within the membrane enzymes.