gebhart/patrepeval huggingface dataset:
Novel near-infrared Raman spectroscopy of biological fluids (2002)

Raman spectroscopy sensitivity in medical applications, is limited by the fact that most biological samples. are strongly fluorescent in the visible, which makes the much weaker Raman signals at the same wavelengths nearly impossible to detect. Our group is working to combine rapid wavelength modulation, which is important for overcoming drift noise, with multichannel wavelength detection, which is essential for high-throughput Raman spectroscopy systems. One essential component of our system is a wavelength-tunable diode laser. Early applications of this work have focused upon the detection of hemoglobin, myoglobin, and creatinine in urine samples. Urine fluoresces enough at 830 nm excitation that the Raman peaks of these chemicals are nearly invisible in a conventionally-obtained Raman spectrum.
Aminoacyl‐tRNA‐Synthetasen als Zielenzyme für eine rationale Arzneimittelentwicklung (1981)

Abstract Das „maßgeschneiderte”︁ Arzneimittel ist ein alter Traum seit Paracelsus′ : „Dosis sola facit venenum”︁. Ein ideales Pharmakon sollte den pathologischen Vorgang oder den parasitären Organismus maximal inhibieren und dabei den menschlichen Körper minimal schädigen. Um dieses Ziel zu erreichen, muß man versuchen, metabolische Unterschiede zwischen dem pathologischen bzw. parasitären und dem normalen menschlichen Stoffwechsel gezielt auszunutzen. Dies erscheint heute aufgrund der vertieften Kenntnisse enzymatischer Vorgänge ein möglicher, sogar vielversprechender Weg. Das Pharmakon sollte dabei an einem zentral wichtigen Prozeß eingreifen. Ein solcher Prozeß ist die Proteinbiosynthese, bei der die erforderliche Genauigkeit im Zusammenbau der Makromoleküle durch den Vorgang des „Korrekturlesens”︁ erreicht wird. Es zeigt sich, daß dieser Mechanismus je nach Spezies verschieden verläuft.
AND/R: Advanced neutron diffractometer/reflectometer for investigation of thin films and multilayers for the life sciences (2006)

An elastic neutron scattering instrument, the advanced neutron diffractometer/reflectometer (AND/R), has recently been commissioned at the National Institute of Standards and Technology Center for Neutron Research. The AND/R is the centerpiece of the Cold Neutrons for Biology and Technology partnership, which is dedicated to the structural characterization of thin films and multilayers of biological interest. The instrument is capable of measuring both specular and nonspecular reflectivity, as well as crystalline or semicrystalline diffraction at wave-vector transfers up to approximately 2.20 Å(-1). A detailed description of this flexible instrument and its performance characteristics in various operating modes are given.
Identity and Reference (1978)

Identity and Reference Get access STEPHEN READ STEPHEN READ UNIVERSITY OF ST. ANDREWS Search for other works by this author on: Oxford Academic Google Scholar Mind, Volume LXXXVII, Issue 4, 1978, Pages 533–552, https://doi.org/10.1093/mind/LXXXVII.4.533 Published: 01 January 1978
Consideration for Affects of an XOR in a Random Number Generator Using Ring Oscillators (2021)

A cloud service to offer entropy has been paid much attention to. As one of the entropy sources, a physical random number generator is used as a true random number generator, relying on its irreproducibility. This paper focuses on a physical random number generator using a field-programmable gate array as an entropy source by employing ring oscillator circuits as a representative true random number generator. This paper investigates the effects of an XOR gate in the oscillation circuit by observing the output signal period. It aims to reveal the relationship between inputs and the output through the XOR gate in the target generator. The authors conduct two experiments to consider the relevance. It is confirmed that combining two ring oscillators with an XOR gate increases the complexity of the output cycle. In addition, verification using state transitions showed that the probability of the state transitions was evenly distributed by increasing the number of ring oscillator circuits.
Approximating Clustering Coefficient and Transitivity (2005)

Since its introduction in the year 1998 by Watts and Strogatz, the clustering-coefficient has become a frequently used tool for analyzing graphs. In 2002 the transitivity was proposed by Newman, Strogatz and Watts as an alternative to the clustering-coefficient. However, as we illustrate by several examples both parameters may differ vastly. On the other hand, an extension of the definitions to weighted versions provides the formal relation between them. As many networks considered in complex systems are huge, the efficient computation of such network parameters is crucial. Several algorithms with polynomial running time can be derived from results known in graph theory. The main contribution of this work is a new fast approximation algorithm for the weighted clustering-coefficient which also gives very efficient approximation algorithms for the clustering-coefficient and the transitivity. We namely present an algorithm with running time in $O(1)$ for the clustering-coefficient, respectively with running time in $O(n)$ for the transitivity. By an experimental study we demonstrate the performance of the proposed algorithms on real-world data as well as on generated graphs. These results also support the assumption that normally the values of clustering-coefficient and transitivity differ considerably.
Spontaneous and Continuous Cyclooxygenase-2-Dependent Prostaglandin E2 Production by Stromal Cells in the Murine Small Intestine Lamina Propria: Directing the Tone of the Intestinal Immune Response (2001)

The mechanisms allowing the gastrointestinal immune system to avoid an inappropriate inflammatory response to nonpathogenic luminal Ags are poorly understood. We have previously described a role for cyclooxygenase (COX)-2-dependent arachidonic acid metabolites produced by the murine small intestine lamina propria in controlling the immune response to a dietary Ag. To better understand the role of COX-2-dependent arachidonic acid metabolites produced by the lamina propria, we examined the pattern of expression and the cellular source of COX-2 and COX-2-dependent PGE(2). We now demonstrate that non-bone marrow-derived lamina propria stromal cells have basal COX-2 expression and that COX-2-dependent PGE(2) production by these cells is spontaneous and continuous. The other mucosal and nonmucosal lymphoid compartments examined do not share this phenotype. In contrast to the majority of descriptions of COX-2 expression, COX-2 expression by lamina propria stromal cells is not dependent upon exogenous stimuli, including adhesion, LPS signaling via Toll-like receptor 4, or the proinflammatory cytokines TNF-alpha, IFN-gamma, and IL-1 beta. These findings, in conjunction with the known immunomodulatory capacities of PGs, suggest that COX-2 expression by the small intestine lamina propria is a basal state contributing to the hyporesponsiveness of the intestinal immune response.
Genetic determinants of statin intolerance (2007)

These preliminary pharmacogenetic results, if confirmed, are consistent with the idea that statin intolerance which is manifested primarily through muscle symptoms is associated with genomic variation in COQ2 and thus perhaps with the CoQ10 pathway.
MSIsensor: microsatellite instability detection using paired tumor-normal sequence data (2013)

https://github.com/ding-lab/msisensor
[Dynamic changes and significance of antithrombin and fibrinolytic function in advanced lung cancer patients during chemotherapy]. (2007)

Chemotherapy may enhance the prethrombotic state in advanced lung cancer patients. Dynamic observation of antithrombin and fibrinolytic function during chemotherapy might be useful for preventing pulmonary hemorrhage and pulmonary infarct and estimating prognosis of those patients.
Multi-rate detection for the IS-95 CDMA forward traffic channels (2002)

The IS-95 direct sequence code division multiple access (DS-CDMA) system has become a US digital cellular standard. In the forward traffic channels (from the base station to the mobiles), the speech encoder rate can vary, depending on the speech activity in the transmitter. At the receiver, the decoder does not know which one of the speech encoder rate the transmitter used. This paper focuses on the IS-95 system that uses the 8 kbps speech encoder and describes an algorithm to determine the encoder rate used for the transmitted sequence, with high confidence, so that the appropriate Viterbi decoder can be applied only once and not four times. This can reduce the overall decoder complexity and increase the throughput by a factor of two. It can also reduce the power consumption in the decoder.
Synthesis and Activation of Asparagine in Asparagine Auxotrophs of <i>Saccharomyces cerevisiae</i> (1979)

l ‐Asparagine synthesis in Saccharomyces cerevisiae is performed by a glutamine‐dependent asparagine synthetase of the type found in higher organisms. Auxotrophy for asparagine has been obtained in two classes of mutants. In class I, asparagine synthetase activity is cancelled. These mutants combinetwo mutations, asnA − and asnB − . Neither asnA − nor asnB − mutation alone. leads to total auxotrophy. Partial auxotrophy as well as a strong decrease in enzyme activity result from asnA − mutation. No change is detectable in cells with the asnB − mutation alone. This, and Jones' report [ J. Bacteriol. 134 , 200–207 (1978)] of auxotrophy resulting from the combination of two mutations, are strong supports for asparagine synthesis being an unusual biosynthetic operation. In class II, auxotrophy results from a single mutation which leads to a modification of the efficiency of the asparaginyl‐tRNA synthetase ( asnRS − mutation). This auxotrophy is cancelled if asparaginase I activity (the only one present in ∑ 1278b wild type) is cancelled by casnI − mutation. This latter mutation allows an increase in the asparagine pool which is able to compensate for the asparaginyl‐tRNA synthetase partial defect of the asnRS − mutant.
Spot-size converter integrated semiconductor optical amplifiers for optical gate applications (1999)

A spot-size converter integrated semiconductor optical amplifier (SSC-SOA) was developed as a gate element in an optical switch matrix for photonic switching applications. By a selective metal-organic vapor phase epitaxy technique, a bulk InGaAsP stripe, including an active region and thickness tapered SSCs, was grown. Wavelength composition of the stripe, strain on the stripe, and electrode coverage above the SSC region were optimized. As a result, gate operation for fiber-to-fiber gain of 0 dB was achieved at a low injection current of 30 mA, and the polarization dependence of the gain was eliminated as well.
Virtual synchronous generator: Laboratory scale results and field demonstration (2009)

This paper describes an approach to demonstrate the operation of virtual synchronous generators (VSG) in practical distribution systems. After an extensive simulation phase at laboratory scale, the field demonstration is planned at two sites located in the Netherlands and in Romania, for small VSGs of 10 times 5 kW and one large VSG of 100 kW respectively.
Improved V3 genotyping with duplicate PCR amplification for determining HIV-1 tropism (2011)

The genotypic determination of HIV-1 tropism can be improved by duplicate amplifications and sequencing the pooled PCR products. This is a good compromise between improved sensitivity and reasonable cost for the genotype-based determination of tropism.
Optical Summation of RF Signals (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We present two concepts dedicated to the optical summation of RF signals for radar applications. The first technique relies on a photodiode simultaneously illuminated on its top and back sides. We experimentally demonstrate the summation of two signals covering the whole 25-GHz photodiode bandwidth with amplitude and phase errors below <formula formulatype="inline"> <tex>${\pm}{\hbox {1 dB}}$</tex></formula> and <formula formulatype="inline"> <tex>${\pm {\hbox {4}}}^{\circ}$</tex></formula>, respectively. The heterodyne beating noise, which occurs in this type of summation device, is also discussed. The second technique is based on a traveling-wave detector array. We experimentally demonstrates the summation of four signals in the whole 25-GHz photodiodes bandwidth. However, the “summation bandwidth” is limited to 10 GHz due to amplitude and phase errors. </para>
Inhibition of elongation factor 1-dependent aminoacyl-tRNA binding to ribosomes by Shiga-like toxin I (VT1) from<i>Escherichia coli</i>O157:H7 and by Shiga toxin (1987)

A Vero toxin (VT1 or Shiga-like toxin I) from <it>Escherichia coli</it> O157:H7 was found to inactivate 60S ribosomal subunits of rabbit reticulocyte resulting in the inhibition of protein synthesis. The mode of inhibition of both VT1 and Shiga toxin was similar and involved the blocking of elongation-1-dependent binding of aminoacyl-tRNA of ribosomes. Non-enzymatic binding of aminoacyl-tRNA to ribosomes, peptide bond formation and translocation were not inhibited by either VT1 or Shiga toxin.
Characterization and Comparison of the CO<sub>2</sub> Absorption Performance into Single and Blended Alkanolamines in a Packed Column (2004)

The performance of carbon dioxide (CO2) absorption into aqueous solutions of single and blended alkanolamines was evaluated experimentally in a bench-scale absorber packed with high-efficiency packings. The absorption experiments were conducted under atmospheric pressure, using a feed gas mixture containing 10% CO2 and 90% nitrogen. Monoethanolamine (MEA), diethanolamine (DEA), diisopropanolamine (DIPA), methyldiethanolamine (MDEA), 2-amino-2-methyl-1-propanol (AMP), and their mixtures including MEA−MDEA, DEA−MDEA, MEA−AMP, and DEA−AMP were tested in this work. The absorption performance was presented in terms of the CO2 removal efficiency, absorber height requirement, effective interfacial area for mass transfer, and overall mass-transfer coefficient (KGae). Comparison of the absorption performance between the tested alkanolamines was made over ranges of operating conditions to establish the correlation between single- and blended-alkanolamine systems.
Biocatalysis with Unnatural Amino Acids: Enzymology Meets Xenobiology (2017)

The goal of xenobiology is to design biological systems endowed with unusual biochemical functions, whereas enzymology concerns the study of enzymes, the workhorses of biocatalysis. Biocatalysis employs enzymes and organisms to perform useful biotransformations in synthetic chemistry and biotechnology. During the past few years, the effects of incorporating noncanonical amino acids (ncAAs) into enzymes with potential applications in biocatalysis have been increasingly investigated. In this Review, we provide an overview of the effects of new chemical functionalities that have been introduced into proteins to improve various facets of enzymatic catalysis. We also discuss future research avenues that will complement unnatural mutagenesis with standard protein engineering to produce novel and versatile biocatalysts with applications in synthetic organic chemistry and biotechnology.
Computational Mapping of the Conformational Transitions in Agonist Selective Pathways of a G-Protein Coupled Receptor (2010)

The active state conformation of a G-protein coupled receptor (GPCR) is influenced by the chemical structure and the efficacy of the bound ligand. Insight into the active state conformation as well as the activation pathway for ligands with different efficacies is critical in designing functionally specific drugs for GPCRs. Starting from the crystal structure of the beta2-adrenergic receptor, we have used coarse grain computational methods to understand the modulation of the potential energy landscape of the receptor by two full agonists, two partial agonists, and an inverse agonist. Our coarse grain method involves a systematic conformational spanning of the receptor transmembrane helices followed by an energy minimization and ligand redocking in each sampled conformation. We have derived the activation pathways for several agonists and partial agonists, using a Monte Carlo algorithm, and these are in agreement with fluorescence spectroscopy measurements. The calculated pathways for the full agonists start with an energy downhill step leading to a stable intermediate followed by a barrier crossing leading to the active state. We find that the barrier crossing involves breaking of an interhelical hydrogen bond between helix5 and helix6, and polarization of the binding site residues by water facilitates the barrier crossing. The uphill step in the partial agonist salbutamol induced activation is distinct from full agonist norepinephrine, and originates from steric hindrance with the aromatic residues on helix6. Virtual ligand screening with the salbutamol-stabilized conformation shows enrichment of noncatechol agonists over the norepinephrine-stabilized conformation. Our computational method provides an unprecedented opportunity to derive hypotheses for experiments and also understand activation mechanisms in GPCRs.
Enhanced Raman sensitivity using an actively stabilized external resonator (2001)

An enhancement up to 250-fold in laser Raman signals for real-time gas analysis has been achieved within an actively stabilized external resonator (ASER), whose length is actively matched to the single-frequency excitation laser using the Pound–Drever technique. With the Raman cell present, enhancements up to 50-fold are achieved, and the resulting detection limit for hydrogen in ambient-pressure gas mixtures is about ten parts-per-million in a 1 min analysis period at unity signal-to-noise ratio. Based upon the recent development of a fiber-pumped Nd:YVO4 laser with single-frequency output exceeding 5 W at 532 nm, this highly sensitive instrument is applied to detection of tritiated gases, wherein the compactness and low heat of this laser head permit placing the entire optical system, including laser head, charge coupled Raman detector, and ASER, within the glove box necessary for secondary containment of tritium, thereby accomplishing a robust, highly sensitive Raman analytical system for hazardous substances.
Role of activated protein C and its receptor in inhibition of tumor metastasis (2009)

Engagement of endothelial protein C receptor (EPCR) by activated protein C (aPC) decreases expression of endothelial adhesion molecules implicated in tumor-endothelium interactions. We examined the role of the aPC/EPCR pathway on tumor migration and metastasis. In vitro, B16-F10 melanoma cells showed decreased adhesion to and transmigration through endothelium treated with recombinant human aPC (rhaPC). In murine B16-F10 metastasis models, transgenic EPCR overexpressing (Tie2-EPCR) mice exhibited marked reductions in liver (50%) and lung (92%) metastases compared with wild-type (WT) animals. Intravital imaging showed reduced B16-F10 entrapment within livers of Tie2-EPCR compared with WT mice. A similar reduction was observed in WT mice treated with rhaPC. Strikingly, rhaPC treatment resulted in a 44% reduction in lung metastases. This was associated with decreased lung P-selectin and TNF-alpha mRNA levels. These findings support an important role for the aPC/EPCR pathway in reducing metastasis via inhibition of tumor cell adhesion and transmigration.
Short Block-Length Codes for Ultra-Reliable Low Latency Communications (2018)

This article reviews state of the art channel coding techniques for URLLC. The stringent requirements of URLLC services, such as ultrahigh reliability and low latency, have made it the most challenging feature of 5G of mobile networks. The problem is even more challenging for services beyond the 5G promise, such as tele-surgery and factory automation, which require latencies less than 1ms and packet error rates as low as 10-9. This article provides an overview of channel coding techniques for URLLC and compares them in terms of performance and complexity. Several important research directions are identified and discussed in more detail.
The prevalence of nosocomial infection in intensive care units in Europe. Results of the European Prevalence of Infection in Intensive Care (EPIC) Study. EPIC International Advisory Committee (1995)

<h3>Objective.</h3> —To determine the prevalence of intensive care unit (ICU)—acquired infections and the risk factors for these infections, identify the predominant infecting organisms, and evaluate the relationship between ICU-acquired infection and mortality. <h3>Design.</h3> —A 1-day point-prevalence study. <h3>Setting.</h3> —Intensive care units in 17 countries in Western Europe, excluding coronary care units and pediatric and special care infant units. <h3>Patients.</h3> —All patients (>10 years of age) occupying an ICU bed over a 24-hour period. A total of 1417 ICUs provided 10 038 patient case reports. <h3>Main Outcome Measures.</h3> —Rates of ICU-acquired infection, prescription of antimicrobials, resistance patterns of microbiological isolates, and potential risk factors for ICU-acquired infection and death. <h3>Results.</h3> —A total of 4501 patients (44.8%) were infected, and 2064 (20.6%) had ICU-acquired infection. Pneumonia (46.9%), lower respiratory tract infection (17.8%), urinary tract infection (17.6%), and bloodstream infection (12%) were the most frequent types of ICU infection reported. Most frequently reported microorganisms were Enterobacteriaceae (34.4%),<i>Staphylococcus aureus</i>(30.1%; [60% resistant to methicillin]),<i>Pseudomonas aeruginosa</i>(28.7%), coagulase-negative staphylococci (19.1%), and fungi (17.1%). Seven risk factors for ICU-acquired infection were identified: increasing length of ICU stay (>48 hours), mechanical ventilation, diagnosis of trauma, central venous, pulmonary artery, and urinary catheterization, and stress ulcer prophylaxis. ICU-acquired pneumonia (odds ratio [OR], 1.91; 95% confidence interval [CI], 1.6 to 2.29), clinical sepsis (OR, 3.50; 95% CI, 1.71 to 7.18), and bloodstream infection (OR, 1.73; 95% CI, 1.25 to 2.41) increased the risk of ICU death. <h3>Conclusions.</h3> —ICU-acquired infection is common and often associated with microbiological isolates of resistant organisms. The potential effects on outcome emphasize the importance of specific measures for infection control in critically ill patients. (<i>JAMA</i>. 1995;274:639-644)
Electrosleep—A Clinical Trial (1970)

Electrosleep is a technique of psychiatric treatment that has been undergoing development in the USSR for approximately 20 years, with a great flurry of interest in the past five years. The authors report briefly on a clinical evaluation of electrosleep in the United States to alert other investigators in this country to a new area of possible interest.
On Approximate Speculative Lock Elision (2017)

Each synchronization point represents a point of serialization, and thereby can easily hurt parallel scalability. As demonstrated by recent studies, approximating, i.e., relaxing synchronization by eliminating a subset of synchronization points spatio-temporally can help improve parallel scalability, as long as approximation incurred violations of basic execution semantics remain predictable and controllable. Even if the divergence from fully-synchronized execution renders lower computation accuracy ratherthan catastrophic program termination, for approximation to be viable, the accuracy loss must be bounded. In this paper, we assess the viability of approximate synchronization using Speculative Lock Elision (SLE), which was adopted by hardware transactional memory implementations from industry, as a baseline for comparison. Specifically, we investigate the efficacy of exploiting semantic and temporal characteristics of critical sections in preventing excessive loss in computation accuracy, and devise a light-weight, proof-of-concept Approximate Speculative Lock Elision (ASLE) implementation, which exploits existing hardware support for SLE.