gebhart/patrepeval huggingface dataset:
Click chemistry and Oligonucleotides: How a simple reaction can do so much (2008)

Copper catalyzed Alkyne Azide 1,3-dipolar cycloaddition (CuAAC) "click reaction" was applied for the construction of oligonucleotide conjugates, circular objects and phosphodiester glyco-clusters. To this end, several strategies were developed to introduce either alkyne or azide functions into an oligonucleotide.
Evaluation of the cobas Cdiff Test for Detection of Toxigenic Clostridium difficile in Stool Samples (2017)

Nucleic acid amplification tests (NAATs) are reliable tools for the detection of toxigenic <i>Clostridium difficile</i> from unformed (liquid or soft) stool samples. The objective of this study was to evaluate performance of the cobas Cdiff test on the cobas 4800 system using prospectively collected stool specimens from patients suspected of having <i>C. difficile</i> infection (CDI). The performance of the cobas Cdiff test was compared to the results of combined direct and broth-enriched toxigenic culture methods in a large, multicenter clinical trial. Additional discrepancy analysis was performed by using the Xpert <i>C. difficile</i> Epi test. Sample storage was evaluated by using contrived and fresh samples before and after storage at -20°C. Testing was performed on samples from 683 subjects (306 males and 377 females); 113 (16.5%) of 683 subjects were positive for toxigenic <i>C. difficile</i> by direct toxigenic culture, and 141 of 682 subjects were positive by using the combined direct and enriched toxigenic culture method (reference method), for a prevalence rate of 20.7%. The sensitivity and specificity of the cobas Cdiff test compared to the combined direct and enriched culture method were 92.9% (131/141; 95% confidence interval [CI], 87.4% to 96.1%) and 98.7% (534/541; 95% CI, 97.4% to 99.4%), respectively. Discrepancy analysis using results for retested samples from a second NAAT (Xpert C. difficile/Epi test; Cepheid, Sunnyvale, CA) found no false-negative and 4 false-positive cobas Cdiff test results. There was no difference in positive and negative results in comparisons of fresh and stored samples. These results support the use of the cobas Cdiff test as a robust aid in the diagnosis of CDI.
Downlink scheduling in CDMA data networks (1999)

Massachusetts Ins tit ut e of
Status, Challenges and Perspectives of Mainstream Nitritation-Anammox for Wastewater Treatment (2018)

The nitritation-anammox process is an efficient and cost-effective approach for biological nitrogen removal, but its application in treating mainstream wastewater remains a great challenge. Mainstream nitritation-anammox processes could create opportunities for achieving energy self-sufficient or energy-generating wastewater treatment plants. Significant advancements have been achieved via pilot- and full-scale trials to overcome the major obstacles under mainstream conditions, such as repression of nitrite-oxidizing bacteria, limiting the overgrowth of denitrifiers, and effective selection and retention of ammonia-oxidizing bacteria and anammox bacteria. This review paper intends to provide a detailed update of research progress on mainstream nitritation-anammox processes, discuss metabolic interactions, and examine major challenges and possible solutions towards the future development of mainstream nitritation-anammox.
Chiral fiber gratings: perspectives and challenges for sensing applications (2007)

Chiral fiber gratings are produced in a microforming process in which optical fibers with noncircular or nonconcentric cores are twisted as they pass though a miniature oven. Periodic glass structures as stable as the glass material itself are produced with helical pitch that ranges from under a micron to hundreds of microns. The geometry of the fiber cross section determines the symmetry of the resulting structure which in turn determines its polarization selectivity. Single helix structures are polarization insensitive while double helix gratings interact only with a single optical polarization. Both single and double helix gratings may act as a fiber long period grating, coupling the core and cladding modes. The coupling is manifested in a series of narrow dips in the transmission spectrum. The dip position is sensitive to fiber elongation, twist and temperature, and to the refractive index of the surrounding medium. The suitability of chiral gratings for sensing pressure, temperature and liquid levels is investigated. Polarization insensitive single helix silica glass gratings display excellent stability up to temperatures of 600°C, while a pressure sensor with dynamic range of nearly 40 dB is demonstrated in polarization selective double helix gratings.
EndoS2 is a unique and conserved enzyme of serotype M49 group A <i>Streptococcus</i> that hydrolyses N-linked glycans on IgG and α1-acid glycoprotein (2013)

Many bacteria have evolved ways to interact with glycosylation functions of the immune system of their hosts. Streptococcus pyogenes [GAS (group A Streptococcus)] secretes the enzyme EndoS that cleaves glycans on human IgG and impairs the effector functions of the antibody. The ndoS gene, encoding EndoS, has, until now, been thought to be conserved throughout the serotypes. However, in the present study, we identify EndoS2, an endoglycosidase in serotype M49 GAS strains. We characterized EndoS2 and the corresponding ndoS2 gene using sequencing, bioinformatics, phylogenetic analysis, recombinant expression and LC-MS analysis of glycosidic activity. This revealed that EndoS2 is present exclusively, and highly conserved, in serotype M49 of GAS and is only 37% identical with EndoS. EndoS2 showed endo-β-N-acetylglucosaminidase activity on all N-linked glycans of IgG and on biantennary and sialylated glycans of AGP (α1-acid glycoprotein). The enzyme was found to act only on native IgG and AGP and to be specific for free biantennary glycans with or without terminal sialylation. GAS M49 expression of EndoS2 was monitored in relation to carbohydrates present in the culture medium and was linked to the presence of sucrose. We conclude that EndoS2 is a unique endoglycosidase in serotype M49 and differs from EndoS of other GAS strains by targeting both IgG and AGP. EndoS2 expands the repertoire of GAS effectors that modify key glycosylated molecules of host defence.
SHAPE AND COLOR FEATURES FOR OBJECT RECOGNITION SEARCH (2009)

A bio-inspired shape feature of an object of interest emulates the integration of the saccadic eye movement and horizontal layer in vertebrate retina for object recognition search where a single object can be used one at a time. The optimal computational model for shape-extraction-based principal component analysis (PCA) was also developed to reduce processing time and enable the real-time adaptive system capability. A color feature of the object is employed as color segmentation to empower the shape feature recognition to solve the object recognition in the heterogeneous environment where a single technique - shape or color - may expose its difficulties. To enable the effective system, an adaptive architecture and autonomous mechanism were developed to recognize and adapt the shape and color feature of the moving object. The bio-inspired object recognition based on bio-inspired shape and color can be effective to recognize a person of interest in the heterogeneous environment where the single technique exposed its difficulties to perform effective recognition. Moreover, this work also demonstrates the mechanism and architecture of the autonomous adaptive system to enable the realistic system for the practical use in the future.
Electrostatic Propulsion Using C60 Molecules (1993)

Report proposes use of C60 as propellant material in electrostatic propulsion system of spacecraft. C60, C70, and similar molecules, have recently been found to have characteristics proving advantageous in electrostatic propulsion. Report discusses these characteristics and proposes experiments to determine feasibility of concept.
Discovery of a novel class of AKT pleckstrin homology domain inhibitors (2008)

AKT, a phospholipid-binding serine/threonine kinase, is a key component of the phosphoinositide 3-kinase cell survival signaling pathway that is aberrantly activated in many human cancers. Many attempts have been made to inhibit AKT; however, selectivity remains to be achieved. We have developed a novel strategy to inhibit AKT by targeting the pleckstrin homology (PH) domain. Using in silico library screening and interactive molecular docking, we have identified a novel class of non-lipid-based compounds that bind selectively to the PH domain of AKT, with "in silico" calculated K(D) values ranging from 0.8 to 3.0 micromol/L. In order to determine the selectivity of these compounds for AKT, we used surface plasmon resonance to measure the binding characteristics of the compounds to the PH domains of AKT1, insulin receptor substrate-1, and 3-phosphoinositide-dependent protein kinase 1. There was excellent correlation between predicted in silico and measured in vitro K(D)s for binding to the PH domain of AKT, which were in the range 0.4 to 3.6 micromol/L. Some of the compounds exhibited PH domain-binding selectivity for AKT compared with insulin receptor substrate-1 and 3-phosphoinositide-dependent protein kinase 1. The compounds also inhibited AKT in cells, induced apoptosis, and inhibited cancer cell proliferation. In vivo, the lead compound failed to achieve the blood concentrations required to inhibit AKT in cells, most likely due to rapid metabolism and elimination, and did not show antitumor activity. These results show that these compounds are the first small molecules selectively targeting the PH domain of AKT.
Splash: Simulation optimization in complex systems of systems (2012)

Decision-makers increasingly need to bring together multiple models across a broad range of disciplines to guide investment and policy decisions around highly complex issues such as population health and safety. We discuss the use of the Smarter Planet Platform for Analysis Simulation of Health (Splash) for cross-disciplinary modeling, simulation, sensitivity analysis, and optimization in the setting of complex systems of systems. Splash is a prototype system that allows combination of existing heterogeneous simulation models and datasets to create composite simulation models of complex systems. Splash, built on a combination of data-integration, workflow management, and simulation technologies, facilitates loose coupling of models via data exchange. We describe the various components of Splash, with an emphasis on the experiment-management component. This latter component uses user-supplied metadata about models and datasets to provide, via an interactive GUI, a unified view over all of the parameters in all of the component models that make up a composite model, a mechanism for selecting the factors to vary, and a means for allowing users to easily specify experimental designs for the selected factors. The experiment manager also provides a mechanism for systematically varying the inputs to the composite models. We show how the experiment manager can be used to implement some simple stochastic-optimization functionality by implementing the Rinott procedure for selecting the best system. We also implement a sensitivity-analysis method based on a fractional-factorial experimental design. We demonstrate this technology via a composite model comprising a financial-rate model and a healthcare payer model.
3D Crosspoint Memory as a Parallel Architecture for Computing Network Reachability (2018)

A novel in-memory computing design that can compute single-source reachability and transitive closure of graphs is introduced. The proposed design leverages the parallel flow of information in three-dimensional crosspoint memories and can be implemented using memories with two layers of 1-diode 1-resistor (1D1R) interconnects. Our logic-in-memory designs mitigate the infamous memory-processor bottleneck characteristic of John von Neumann architectures and have runtime complexities of O(n) and O(n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) using O(n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) memory cells for the single-source reachability and transitive closure problems, respectively, where n is the number of nodes in the graph. This work builds upon preliminary results presented in [1].
Regenerative Electroless Etching of Silicon (2016)

Regenerative electroless etching (ReEtching), described herein for the first time, is a method of producing nanostructured semiconductors in which an oxidant (Ox<sub>1</sub> ) is used as a catalytic agent to facilitate the reaction between a semiconductor and a second oxidant (Ox<sub>2</sub> ) that would be unreactive in the primary reaction. Ox<sub>2</sub> is used to regenerate Ox<sub>1</sub> , which is capable of initiating etching by injecting holes into the semiconductor valence band. Therefore, the extent of reaction is controlled by the amount of Ox<sub>2</sub> added, and the rate of reaction is controlled by the injection rate of Ox<sub>2</sub> . This general strategy is demonstrated specifically for the production of highly luminescent, nanocrystalline porous Si from the reaction of V<sub>2</sub> O<sub>5</sub> in HF(aq) as Ox<sub>1</sub> and H<sub>2</sub> O<sub>2</sub> (aq) as Ox<sub>2</sub> with Si powder and wafers.
Enhancement of the activity of the antibiotic laidlomycin by acylation and the 13C NMR spectra of laidlomycin and its esters. (1982)

Selective monoacylation of the antibiotic laidlomycin at C-26 has led to derivatives that display enhanced activity toward favorably altering rumen fermentation and preventing avian coccidiosis. Diacylated derivatives (C-7, C-26) were found to be inactive. The structures of these compounds were determined by 13C NMR spectroscopy.
Neuroprotective Diterpenes from the Fruiting Body of <i>Antrodia </i><i>c</i><i>amphorata</i> (2006)

Three new compounds, 19-hydroxylabda-8(17)-en-16,15-olide (1), 3beta,19-dihydroxylabda-8(17),11E-dien-16,15-olide (2), and 13-epi-3beta,19-dihydroxylabda-8(17),11E-dien-16,15-olide (3), together with four known compounds, 19-hydroxylabda-8(17),13-dien-16,15-olide (4), 14-deoxy-11,12-didehydroandrographolide (5), 14-deoxyandrographolide, and pinusolidic acid, were isolated from the fruiting bodies of Antrodia camphorata. The structures of compounds 1-3 were elucidated by the analysis of their spectroscopic data. The in vitro neuroprotective activity of all compounds was evaluated, and compounds 1-5 protected neurons from Abeta damage by 39.2, 35.0, 36.7, 30.6, and 27.0%, respectively, at concentrations between 5 and 20 microM.
Determination of the acoustic nonlinearity parameter in liquid water up to 250&#x00B0;C and 14 MPa (2012)

This work reports, for the first time, the direct measurement of sound speed in liquid water at temperatures up to 250°C and pressures up to 14 MPa. These measurements enabled the determination of the acoustic nonlinearity parameter, B/A, an important property of liquids. From an applications perspective, B/A determines the efficiency of devices that are based on acoustic nonlinear mixing. The objective of the present work was to use a specialized measurement cell for sound speed measurements and the determination of B/A in liquid water as a function of temperature and pressure. Sound speed was measured using Swept Frequency Acoustic Interferometry, while B/A was determined from the derivatives of the sound speed with respect to pressure and temperature. B/A at ambient pressure and temperature was determined to be 4.8, in good agreement with literature values. At 250°C and 14 MPa, B/A was found to be roughly twice its ambient temperature value.
A framework for proactive assistance: Summary (2014)

Advanced Driving Assistance Systems usually provide assistance to drivers only once a high risk situation has been detected. Indeed, it is difficult for an embedded system to understand driving situations, and to predict early enough that it is to become uncomfortable or dangerous. Most of ADAS work assume that interactions between road entities do not exist (or are limited), and that all drivers react in the same manner in similar conditions. We propose a framework that enables to fill these gaps. On one hand, an ontology which is a conceptual description of entities present in driving spaces is used to understand how all the perceived entities interact together with the subject vehicle, and govern its behavior. On the other hand, a dynamic Bayesian Network enables to estimate the driver situation awareness with regard to the perceived objects, based on the ontology inferences, map information, driver actuation and driving style.
<i>Fasciola hepatica</i> Fatty Acid Binding Protein Inhibits TLR4 Activation and Suppresses the Inflammatory Cytokines Induced by Lipopolysaccharide In Vitro and In Vivo (2015)

TLR4, the innate immunity receptor for bacterial endotoxins, plays a pivotal role in the induction of inflammatory responses. There is a need to develop molecules that block either activation through TLR4 or the downstream signaling pathways to inhibit the storm of inflammation typically elicited by bacterial LPS, which is a major cause of the high mortality associated with bacterial sepsis. We report in this article that a single i.p. injection of 15 μg fatty acid binding protein from Fasciola hepatica (Fh12) 1 h before exposure to LPS suppressed significantly the expression of serum inflammatory cytokines in a model of septic shock using C57BL/6 mice. Because macrophages are a good source of IL-12p70 and TNF-α, and are critical in driving adaptive immunity, we investigated the effect of Fh12 on the function of mouse bone marrow-derived macrophages (bmMΦs). Although Fh12 alone did not induce cytokine expression, it significantly suppressed the expression of IL-12, TNF-α, IL-6, and IL-1β cytokines, as well as inducible NO synthase-2 in bmMΦs, and also impaired the phagocytic capacity of bmMΦs. Fh12 had a limited effect on the expression of inflammatory cytokines induced in response to other TLR ligands. One mechanism used by Fh12 to exert its anti-inflammatory effect is binding to the CD14 coreceptor. Moreover, it suppresses phosphorylation of ERK, p38, and JNK. The potent anti-inflammatory properties of Fh12 demonstrated in this study open doors to further studies directed at exploring the potential of this molecule as a new class of drug against septic shock or other inflammatory diseases.
Interference suppression based on soft blanking and iterative likelihood test for LTE uplink (2013)

Interference cancellation is expected to have significant importance for next-generation wireless communication systems due to various co-channel deployment scenarios and dense frequency reuse. In this study, an interference cancellation receiver that exploits the unique characteristics of single-carrier frequency-division multiple access based systems is proposed. The proposed receiver suppresses the co-channel dominant interference by employing a soft window to the frequency-domain samples where the desired and interfering signals overlap. In order to improve the performance, demodulation and regeneration stages are repeated multiple times by initially accommodating a group of reliable symbols before the iterations. The simulation results indicate that proposed methods work particularly well for low overlap ratios compared to interference coordination and no cancellation methods.
[Paradigm shift in clinical trials for neurodegenerative diseases]. (2007)

Neurodegenerative diseases have been construed as incurable disorders. However, therapeutic development for these diseases is now facing a turning point: analyses of cellular and animal models have provided insights into pathogenesis of neurodegenerative diseases, and have indicated rational therapeutic approaches to them. Therefore, how to design clinical trials for neurodegenerative diseases is becoming one of the most challenging issues in the clinical neurology. Given a small number of patients and a slow progression of symptoms, it is important to carry out effective trials using surrogate endpoints or historical control data, if necessary. In particular, pathogenesis-based disease-modifying therapy should be carefully evaluated in clinical trials, because its effect is likely to be suppression of neurodegenerative processes, but not symptom relief. The development of androgen deprivation therapy for spinal and bulbar muscular atrophy (SBMA) is a representative study in this field. SBMA is a hereditary neurodegenerative disease caused by expansion of a trinucleotide CAG repeat, which encodes the polyglutamine tract, in the first exon of the androgen receptor (AR) gene. Animal models carrying human mutant AR gene recapitulate polyglutamine-mediated motor neuron degeneration, providing insights into the pathogenesis of SBMA. There is increasing evidence that testosterone, the ligand of AR, plays a pivotal role in the neurodegeneration in SBMA. The striking success of androgen deprivation therapy in SBMA mouse models has been translated into phase 2, and then phase 3, clinical trials.
Identification of a Bacterium That Specifically Catalyzes the Reductive Dechlorination of Polychlorinated Biphenyls with Doubly Flanked Chlorines (2002)

A microorganism whose growth is linked to the dechlorination of polychlorinated biphenyls (PCBs) with doubly flanked chlorines was identified. Identification was made by reductive analysis of community 16S ribosomal DNA (rDNA) sequences from a culture enriched in the presence of 2,3,4,5-tetrachlorobiphenyl (2,3,4,5-CB), which was dechlorinated at the para position. Denaturing gradient gel electrophoresis (DGGE) analysis of total 16S rDNA extracted from the culture led to identification of three operational taxonomic units (OTUs 1, 2, and 3). OTU 1 was always detected when 2,3,4,5-CB or other congeners with doubly flanked chlorines were present and dechlorinated. Only OTUs 2 and 3 were detected in the absence of PCBs and when other PCBs (i.e., PCBs lacking doubly flanked chlorines) were not dechlorinated. Partial sequences of OTUs 2 and 3 exhibited 98.2% similarity to the sequence of "Desulfovibrio caledoniensis" (accession no. DCU53465). A sulfate-reducing vibrio isolated from the culture generated OTUs 2 and 3. This organism could not dechlorinate 2,3,4,5-CB. From these results we concluded that OTU 1 represents the dechlorinating bacterium growing in a coculture with a Desulfovibrio sp. The 16S rDNA sequence of OTU 1 is most similar to the 16S rDNA sequence of bacterium o-17 (89% similarity), an ortho-PCB-dechlorinating bacterium. The PCB dechlorinator, designated bacterium DF-1, reductively dechlorinates congeners with doubly flanked chlorines when it is supplied with formate or H(2)-CO(2) (80:20).
Iterative context bounding for systematic testing of multithreaded programs (2007)

Multithreaded programs are difficult to get right because of unexpected interaction between concurrently executing threads. Traditional testing methods are inadequate for catching subtle concurrency errors which manifest themselves late in the development cycle and post-deployment. Model checking or systematic exploration of program behavior is a promising alternative to traditional testing methods. However, it is difficult to perform systematic search on large programs as the number of possible program behaviors grows exponentially with the program size. Confronted with this state-explosion problem, traditional model checkers perform iterative depth-bounded search. Although effective for message-passing software, iterative depth-bounding is inadequate for multithreaded software.