gebhart/patrepeval huggingface dataset:
Deoxyadenosine-deoxycytidine pairing in the d(C-G-C-G-A-A-T-T-C-A-C-G) duplex: conformation and dynamics at and adjacent to the dA.cntdot.dC mismatch site (1984)

Deoxyadenosine-deoxycytidine pairing at symmetrically related dA X dC mismatch sites in the d(C1-G2-C3-G4-A5-A6-T6-T5-C4-A3-C2-G1) self-complementary duplex (henceforth called 12-mer AC) has been investigated by proton and phosphorus NMR studies in aqueous solution. We demonstrate that base pairing is maintained on either side of the mismatch site in the 12-mer AC duplex at low temperature. The proton chemical shifts and NOE measurements rule out models in which the H-2 proton of adenosine at the mismatch site is stacked over adjacent dG X dC base pairs. A comparison of the hydrogen-exchange kinetics in the d(C-G-C-G-A-A-T-T-C-G-C-G) duplex (henceforth called 12-mer) with standard dG X dC base pairs at position 3 from either end with the 12-mer AC duplex, which contains dA X dC mismatches at these positions, demonstrates kinetic destabilization at dG X dC base pair 4 adjacent to the mismatch site and at dA X dT base pairs 5 and 6 far from this site. This contrasts with previous hydrogen-exchange studies on the 12-mer GT and 12-mer GA duplexes where the kinetic destabilization was localized to base pair 4, which is adjacent to the mispairing site. The melting temperature of the 12-mer AC duplex in 0.1 M phosphate is approximately 30 degrees C lower than the corresponding value for the 12-mer duplex.(ABSTRACT TRUNCATED AT 250 WORDS)
Decay Reactions of Aryldiazenyl Radicals in Solution (1987)

Abstract The decay processes of aryldiazenyl radicals were studied by using a time-resolved ESR method. The first order rate constants of decomposition were determined at −117–−48 °C in cyclopropane solutions in the presence or absence of olefins. Aryldiazenyl radicals were relatively persistent and the k1 of phenyldiazenyl-d5 at −96 °C in cyclopropane was 34 s−1. The k1 of 20 aryldiazenyl radicals at −96 °C afforded a ρ value of +1.53 (r=0.91) in a Hammett plot. Activation energies ranged from 46.2 to 25.2 kJ mol−1 and the frequency factors, log A, from 13.2 to 8.2 s−1. The second-order decay rates were measured at the initial period of the decay process at lower temperatures, in a batch system (cyclopropane) and in a flow system (isohexane). The rate constant of phenyldiazenyl-d5 in cyclopropane was 9.2·10−5 M−1 s−1 at −93 °C and the Arrhenius parameters were Ea=23.5 kJ mol−1 and logA=12.77 M−1 s−1, respectively.
OXAZAHYDROBORATE IONS (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOXAZAHYDROBORATE IONSRobert A. Wiesboeck, Anthony R. Pitochelli, and M. Frederick HawthorneCite this: J. Am. Chem. Soc. 1961, 83, 19, 4108–4109Publication Date (Print):October 1, 1961Publication History Published online1 May 2002Published inissue 1 October 1961https://doi.org/10.1021/ja01480a047RIGHTS & PERMISSIONSArticle Views31Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (259 KB) Get e-Alerts Get e-Alerts
Conformational Changes in Conantokin-G Induced upon Binding of Calcium and Magnesium as Revealed by NMR Structural Analysis (1998)

The apo- and metal-bound solution conformations of synthetic conantokin-G (con-G, G1Egamma gammaL5Q gamma NQgamma 10LIRgamma K15SN-CONH2, gamma = gamma-carboxyglutamic acid), an antagonist of N-methyl-D-aspartate receptor-derived neuronal ion channels, have been examined by one- and two-dimensional 1H NMR at neutral pH. A complete structure for the Mg2+-loaded peptide was defined by use of distance geometry calculations and was found to exist as an alpha-helix that spans the entire peptide. The alpha-helical nature of Mg2+/con-G was also supported by the small values (<5.5 Hz) of the 3JHNalpha coupling constants measured for amino acid residues 3-5, 8, 9, and 11-16, and the small values (<4 ppb/K) of the temperature coefficients observed for the alphaNH protons of residues 5-17. This conformation contrasted with that obtained for apo-con-G, which was nearly structureless in solution. Docking of Mg2+ into con-G was accomplished by use of the genetic algorithm/molecular dynamics simulation method, employing the NMR-derived Mg2+-loaded structure for initial coordinates in the midpoint calculations. For the 3 Mg2+/con-G model, it was found that binding of one Mg2+ ion is stabilized by oxygen atoms from three gamma-carboxylates of Gla3, Gla4, and Gla7; another Mg2+ is coordinated by two oxygen atoms, one from each of the gamma-carboxylates of Gla7; and a third metal ion through three donor oxygen atoms of gamma-carboxylates from Gla10 and Gla14. As shown from direct metal binding measurements to mutant con-G peptides, these latter two Gla residues probably stabilized the tightest binding Mg2+ ion. Circular dichroism studies of these same peptide variants demonstrated that all Gla residues contribute to the adoption of the Mg2+-dependent alpha-helical conformation in con-G. The data obtained in this investigation provide a molecular basis for the large conformational alteration observed in apo-con-G as a result of divalent cation binding and allow assessment of the roles of individual Gla residues in defining certain of the structure-function properties of con-G.
Bridges from hospitals to the laboratory: genetic portraits of methicillin-resistant<i>Staphylococcus aureus</i>clones (2004)

Methicillin-resistant Staphylococcus aureus (MRSA) emerged in the early 1960's after the acquisition of the methicillin resistance gene mecA, which is carried by the staphylococcal cassette chromosome mec (SCCmec). MRSA seemed to have arisen by multiple introductions of SCCmec into successful methicillin-susceptible S. aureus (MSSA) lineages. MRSA is one of the most common agents of nosocomial infections worldwide increasing the cost and mortality compared to MSSA infections. Little by little, MRSA has acquired resistance to all antibiotics available in clinical practice, which complicates treatment. This situation was further aggravated by the recent reports of vanA-mediated vancomycin-resistant S. aureus. As a reaction to the emergence and spread of multidrug-resistant MRSA worldwide, international surveillance systems such as the CEM/NET initiative have been created. The characterization of over 3000 MRSA isolates from different regions of the world evidenced the existence of only a few epidemic clones spread worldwide, namely the Iberian, Brazilian, Hungarian, New York/Japan, Pediatric and EMRSA-16 clones. It was found that in surveillance or evolutionary studies strains should be characterized by a combination of different typing methods, namely pulsed-field gel electrophoresis, multi-locus sequence typing and SCCmec typing. In recent years, community-acquired MRSA (CA-MRSA) has become a growing public health concern. However, although many authors reported the emergence of CA-MRSA isolates, a standard definition has not been created and the prevalence of MRSA among persons without risk factors seems to remain very low. CA-MRSA has distinct properties compared to epidemic nosocomial clones and its origin is still unclear. Certain authors suggest there is MRSA transmission from the hospital setting to the community, namely transfer of nosocomial MRSA minor clones or sporadic isolates showing a high degree of similarity with CA-MRSA; others believe CA-MRSA strains represent new acquisitions of SCCmec DNA in susceptible backgrounds. Many questions concerning this extraordinarily versatile and threatening pathogen remain unanswered, needing future investigation
Large-area, scalable fabrication of conical TiN/GST/TiN nanoarray for low-power phase change memory (2011)

We demonstrate the fabrication and phase change memory performance of a conical TiN/Ge2Sb2Te5 (GST)/TiN nanoarray prepared viablock copolymer lithography and straightforward two-step etching. The created 30 nm scale phase change memory cell (aerial array density: ∼207 Gbit inch−2) showed a threshold switching voltage of 1.1 V, a value compatible to conventional phase change memory cells. More significantly, the cell could be amorphized by a reset pulse of 1.8 V height and 100 ns width, where the reset current was 100 μA. Such a low reset current, presumably caused by nanoscale small cell dimension, is greatly beneficial for low power consumption device operation. Reversibly, the set operation was accomplished by crystallization with a set pulse of 1.2 V height, 100 ns width, and 100 ns trailing. This work provides a significant step for low power consumption and ultra-high density storage based on phase change materials.
On the regulation of cold‐labile cytosolic and of mitochondrial acetyl‐CoA hydrolase in rat liver (1985)

The discovery of a cold-labile cytosolic acetyl-CoA hydrolase of high activity in rat liver by Prass et al. [(1980) J. Biol. Chem. 255, 5215-5223] has questioned the importance of mitochondrial acetyl-CoA hydrolase for the formation of free acetate [Grigat et al. (1979) Biochem. J. 177, 71-79] under physiological conditions. Therefore this problem has been reevaluated by comparing various properties of the two enzymes. Cold-labile cytosolic acetyl-CoA hydrolase bands with an apparent Mr of 68000 during SDS/polyacrylamide gel electrophoresis, while the native enzyme elutes in two peaks with apparent Mr of 136000 and 245000 during gel chromatography in the presence of 2 mM ATP. The mitochondrial enzyme elutes under the same conditions with an apparent Mr of 157000. Under conditions where the cold-labile enzyme binds strongly to DEAE-Bio-Gel and ATP-agarose, the mitochondrial enzyme remains unbound. The cold-labile enzyme can be activated 14-fold by ATP, half-maximal activation occurring already at 40 microM ATP. AdoPP[NH]P, AdoPP[CH2]P and GTP have a similar though weaker effect. ADP as well as GDP can completely inhibit the cold-labile enzyme with 50% inhibition occurring for both nucleotides at about 1.45 microM. The binding of ATP and ADP is competitive. Acetyl phosphate and pyrophosphate have no effect on the activity of the cold-labile enzyme. The mitochondrial acetyl-CoA hydrolase is not affected by these nucleotides. CoASH is a strong product inhibitor (approximately equal to 80% inhibition at 40 microM CoASH) of the cold-labile enzyme, but only a weak inhibitor of the mitochondrial enzyme. Under in vivo conditions the activity of the cold-labile cytosolic acetyl-CoA hydrolase can be no more than 7% of the activity calculated for mitochondrial acetyl-CoA hydrolase under the same conditions. Accordingly the mitochondrial enzyme seems to be mainly responsible for the formation of free acetate by the intact liver, especially in view of the fact that the substrate specificity of the mitochondrial enzyme is much higher (activity ratios acetyl-CoA/butyryl-CoA 4.99 and 1.16 for the mitochondrial and the cold-labile enzyme respectively). Alloxan diabetes neither increased the activity of the cold-labile enzyme nor that of the mitochondrial enzyme. No experimental support has been found yet for the hypothesis that the acetyl-CoA hydrolase activity of the cold-labile enzyme represents the side-activity of an acetyl-transferase.
Effect of H2O adsorption on electron transport in a carbon nanotube (2002)

We have studied the adsorption of H2O molecules on a single-wall carbon nanotube (NT) using first-principles gradient-corrected density-functional theory. Subsequently, Green’s function-based Landauer–Büttiker multichannel formalism within a tight-binding model is used to calculate the electron transport, and our results suggest that H2O molecules adsorbed on the NT surface reduce the electronic conduction in the tube in agreement with recent experimental measurements. The decrease of conductance with water adsorption is explained on the basis of charge transfer between the adsorbate and the NT.
Myoclonus Associated with the Use of Gabapentin (2000)

GBP-associated myoclonus appears to be relatively frequent. It is usually mild and can easily be overlooked. Discontinuation of therapy is not necessary in most cases.
Improving on the Range Rule of Thumb (2012)

In manufacturing it is useful to have a quick estimate of the standard deviation. This is often done with the range rule of thumb: σ ~ (sample range)/4. This rule works well when the data comes from a normal distribution and the sample size is around 30, but fails miserably for other distributions and sample sizes. Through the use of Monte Carlo simulations we suggest new rules of thumb for the normal distribution, uniform distribution, and exponential distribution which are dependent on sample size. We then seek to verify these empirical results theoretically.
Measurement of Near Surface Residual Stresses Using Electric Discharge Wire Machining (1994)

In previous work it has been shown that near surface residual stresses may be deduced from surface strains produced by making a cut of progressively increasing depth. The process of electric discharge wire machining (EDWM), by providing very narrow cuts, greatly improves the ability of the method to resolve a stress gradient near the surface. However, the EDWM process may also introduce residual stresses. In the present work a model for estimating the influence of EDWM is presented, and a procedure for eliminating its effect on residual stress measurement is developed. Experimental results validate the theoretical approach.
Chlamydial CT441 Is a PDZ Domain-Containing Tail-Specific Protease That Interferes with the NF-κB Pathway of Immune Response (2007)

Chlamydia species are bacterial pathogens that affect over 140 million individuals worldwide. Ocular infection by Chlamydia trachomatis is the leading cause of preventable blindness, and urogenital tract infection by Chlamydia causes sexually transmitted disease. As obligate intracellular organisms, Chlamydia species have evolved mechanisms to evade the host immune system, including the degradation of the transcription factors regulatory factor X5 and upstream stimulation factor 1, which are required for the expression of major histocompatibility complex molecules I and II by CPAF and cleavage of p65 of the NF-kappaB pathway by the encoded CT441 protein. Here, we report the characterization of CT441 as a tail-specific protease. CT441 contains a PDZ domain of protein-protein interactions and a Ser/Lys dyad catalytic unit. Mutation at either Ser455 or Lys481 in the active site ablated CT441 activity of p65 cleavage. In addition, we found that the production of CT441 Tsp, which was detected at the middle and late stages of an infection, correlated with p65 cleavage activity. In addition to high homology, human and mouse p65 proteins also contain an identical C-terminal tail of 22 amino acid (aa) residues. However, only human p65 was susceptible to cleavage. Using molecular biology approaches, we mapped the p65 cleavage site(s) to a region that differs from that of mouse p65 by 6 aa residues. Additionally, the substitution of T352 with a proline inhibited p65 cleavage. Together, the study demonstrates that CT441 is a tail-specific protease that is capable of interfering with the NF-kappaB pathway of host antimicrobial and inflammatory responses.
Design and construction of a cable-controlled, parallel link manipulator (1984)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1984.
Estimating fracture trace intensity, density, and mean length using circular scan lines and windows (2002)

Fracture characterization protocols that reduce sampling bias are likely to yield higher quality input for exploration and development decisions when dealing with naturally fractured reservoirs. A new set of estimators for fracture density, intensity, and mean trace length corrects for sampling biases and provides a useful integrated description for bulk aspects of a fracture network. These estimators are based on counts of intersections between fracture traces and circular scan lines and of trace terminations in circular windows. Application to synthetic fracture patterns with known parameters validates the use of the new estimators, which are then applied to natural fault trace maps from seismic volumes and joint trace maps from rock pavements. The new estimators are distribution independent and eliminate the effects of orientation, censoring, and length biases, which limit the effectiveness of other sampling techniques. Estimator accuracy improves as sample size increases, particularly for larger circles that exceed a fracture-defined block size. Estimator accuracy for mean trace length improves when the sample exceeds threshold count values for fracture terminations based on guidance from the analysis of similar synthetic patterns. These new estimators also provide both inputs and independent checks of predictions for fracture-generator programs used to model fracture populations in a rock volume.
Signal Processing by Parametric Interactions in Delay-Line Devices (1973)

A new type of signal-processing device which employs the parametric interaction between surface or volume acoustic waves passing in opposite directions through an acoustic delay line is described. These devices are capable of giving the real-time convolution of two modulated signals, and the time inversion of an arbitrary signal. As one signal acts as the reference for the other, a virtually infinite range of electronically variable signal-processing functions, such as recognition of digital codes, pulse compression of an FM chirp, and the realization of a fast Fourier transform, is possible. Early devices which employed the nonlinearity of the acoustic medium tended to give outputs of the order of 60 dB less than the input signal. Recent developments, in which a semiconductor placed near the piezoelectric medium interacts with the acoustic wave, have yielded results where the loss from input to output is of the order of 30 dB.
Application of Machine Learning in Wireless Networks: Key Techniques and Open Issues (2018)

As a key technique for enabling artificial intelligence, machine learning (ML) is capable of solving complex problems without explicit programming. Motivated by its successful applications to many practical tasks like image recognition, both industry and the research community have advocated the applications of ML in wireless communication. This paper comprehensively surveys the recent advances of the applications of ML in wireless communication, which are classified as: resource management in the MAC layer, networking and mobility management in the network layer, and localization in the application layer. The applications in resource management further include power control, spectrum management, backhaul management, cache management, beamformer design and computation resource management, while ML based networking focuses on the applications in clustering, base station switching control, user association and routing. Moreover, literatures in each aspect is organized according to the adopted ML techniques. In addition, several conditions for applying ML to wireless communication are identified to help readers decide whether to use ML and which kind of ML techniques to use, and traditional approaches are also summarized together with their performance comparison with ML based approaches, based on which the motivations of surveyed literatures to adopt ML are clarified. Given the extensiveness of the research area, challenges and unresolved issues are presented to facilitate future studies, where ML based network slicing, infrastructure update to support ML based paradigms, open data sets and platforms for researchers, theoretical guidance for ML implementation and so on are discussed.
Deaths from Norovirus among the Elderly, England and Wales (2008)

The number of deaths in England and Wales associated with gastrointestinal pathogens, norovirus in particular, in persons >or=65 years was estimated for 2001-2006. Regression analysis was used to model monthly counts of gastrointestinal pathogens in fecal samples from infected patients against monthly counts of deaths from infectious and noninfectious intestinal diseases. Data came from the Office of National Statistics (death registrations from local registrars) and from the Health Protection Agency (laboratory results). Model results suggest that 20% (13.3%-26.8%) of deaths in persons >or=65 years of age caused by infectious intestinal disease other than Clostridium difficile were associated with norovirus infection in this period and that 13% (7.5%-18.5%) of deaths caused by noninfectious intestinal disease were associated with norovirus. An estimated 80 deaths each year in this age group may be associated with norovirus infection.
Distributed detection with multiple sensors I. Fundamentals (1997)

In this paper basic results on distributed detection are reviewed. In particular we consider the parallel and the serial architectures in some detail and discuss the decision rules obtained from their optimization based an the Neyman-Pearson (NP) criterion and the Bayes formulation. For conditionally independent sensor observations, the optimality of the likelihood ratio test (LRT) at the sensors is established. General comments on several important issues are made including the computational complexity of obtaining the optimal solutions the design of detection networks with more general topologies, and applications to different areas.