gebhart/patrepeval huggingface dataset:
Fast neutron - gamma pulse shape discrimination of liquid scintillation signals for time correlated measurements (2003)

We describe a neutron/gamma pulse shape discrimination (PSD) system that overcomes count rate limitations of previous methods for distinguishing neutrons from gammas in liquid scintillation detectors. Previous methods of PSD usually involve pulse shaping time constants that allow throughput of tens of thousands counts per second. Time correlated measurements require many millions of counts per second to accurately characterize nuclear material samples. To rapidly inspect many test articles, a high-throughput system is desired. To add neutron - gamma distinction to the analysis provides a much desired enhancement to the characterizations. However, if the PSD addition significantly slows down the inspection throughput, this PSD feature defeats any analysis advantage. Our goal for the fast PSD system is to provide sorted timing pulses to a fast, multi-channel, time-correlation processor at rates approaching several million counts per second enabling high throughput, enhanced inspection of nuclear materials.
The E8 Lattice and Error Correction in Multi-Level Flash Memory (2011)

A construction using the E8 lattice and Reed-Solomon codes for error-correction in flash memory is given. Since E8 lattice decoding errors are bursty, a Reed-Solomon code over GF($2^8$) is well suited. This is a type of trellis-coded modulation, where the Euclidean distance of the lattice (which is an eight-dimensional constellation) is combined with the Hamming distance of the code. This system is compared with the conventional technique for flash memories, BCH codes using Gray-coded PAM. This construction has a performance advantage of 1.7 to 2.0 dB for an uncoded data density of 3 bits/cell.
Array-Based Vapor Sensing Using Chemically Sensitive, Carbon Black−Polymer Resistors (1996)

We describe herein the construction of a simple, low-power, broadly responsive vapor sensor. Carbon black−organic polymer composites have been shown to swell reversibly upon exposure to vapors. Thin films of carbon black−organic polymer composites were deposited across two metallic leads, and swelling-induced resistance changes of the films signaled the presence of vapors. To identify and classify vapors, arrays of such vapor-sensing elements were constructed, with each element containing the same carbon black conducting phase but a different organic polymer as the insulating phase. The differing gas−solid partition coefficients for the various polymers of the sensor array produced a pattern of resistance changes that can be used to classify vapors and vapor mixtures. This type of sensor array resolved common organic solvents, including molecules of different classes (such as aromatics from alcohols) as well as those within a particular class (such as benzene from toluene and methanol from ethanol). The response of an individual composite to varying concentrations of solvent was consistent with the predictions of percolation theory. Accordingly, significant increases in the signals from array elements were observed for carbon black−polymer composites that were operated near their percolation thresholds.
Functional Domains of a Geminivirus Replication Protein (1997)

Tomato golden mosaic virus, a member of the geminivirus family, has a single-stranded DNA genome that is replicated and transcribed in infected plant cells through the concerted action of viral and host factors. One viral protein, AL1, contributes to both processes by binding to a directly repeated, double-stranded DNA sequence located in the overlapping (+) strand origin of replication and AL1 promoter. The AL1 protein, which occurs as a multimeric complex in solution, also catalyzes DNA cleavage during initiation of rolling circle replication. To identify the tomato golden mosaic virus AL1 domains that mediate protein oligomerization, DNA binding, and DNA cleavage, a series of truncated AL1 proteins were produced in a baculovirus expression system and assayed for each activity. These experiments localized the AL1 oligomerization domain between amino acids 121 and 181, the DNA binding domain between amino acids 1 and 181, and the DNA cleavage domain between amino acids 1 and 120. Deletion of the first 29 amino acids of AL1 abolished DNA binding and DNA cleavage, demonstrating that an intact N terminus is required for both activities. The observation that the DNA binding domain includes the oligomerization domain suggested that AL1-AL1 protein interaction may be a prerequisite for DNA binding but not for DNA cleavage. The significance of these results for AL1 function during geminivirus replication and transcription is discussed.
3D QSAR Analyses of Novel Tyrosine Kinase Inhibitors Based on Pharmacophore Alignment (2001)

In an effort to develop a quantitative ligand-binding model for the receptor tyrosine kinases, a pharmacophore search was first used to identify structural features that are common in two novel sets of 12 molecules of the 3-substituted indolin-2-ones and 19 compounds of the benzylidene malononitriles with low-to-high affinity for HER2, a kind of receptor tyrosine kinase. The common pharmacophore model based on these 31 compounds was used as a template to obtain the aligned molecular aggregate, which provided a good starting point for 3D-QSAR analysis of only the 19 benzylidene malononitriles. Two molecular field analysis (MFA) techniques, including CoMFA and CoMSIA, were used to derive the quantitative structure-activity relationships of the studied molecules. From the studied results, it was obvious that the 3D-QSAR models based on the pharmacophore alignment were superior to those based on the simple atom-by-atom fits. Considering the flexibility of the studied molecules and the difference between the active conformers and the energy-lowest conformers, the pharmacophore model can usually provide the common features for the flexible regions. Moreover, the best CoMSIA model based on the pharmacophore hypothesis gave good statistical measure from partial least-squares analysis (PLS) (q(2) = 0.71), which was slightly better than the CoMFA one. Our study demonstrated that pharmacophore modeling and CoMSIA research could be effectively combined. Results obtained from both methods helped with understanding the specific activity of some compounds and designing new specific HER2 inhibitors.
Change Impact Analysis Based on a Taxonomy of Change Types (2010)

Software change impact analysis (CIA) is a key technique for identifying unpredicted and potential effects caused by changes made to software. Different change types often have different impact mechanisms, even some changes do not impact other entities in programs in spite of some dependences existed between these entities and the modified entity. In this paper, we propose a static CIA technique, which considers different impact mechanisms and rules of different change types, to calculate the impact sets. Precision improvement of the impact sets relies on 3 aspects: change types of a modified entity, dependences between the modified entity and other entities, and the intuition that to win at the start -- if the initial impact set is estimated more accurately, then the final impact set depending on this initial impact set will be more precise. Experimental case study demonstrates the effectiveness of our technique, and its potential applications in software maintenance.
Cellulose crystallinity – a key predictor of the enzymatic hydrolysis rate (2010)

The enzymatic hydrolysis of cellulose encounters various limitations that are both substrate- and enzyme-related. Although the crystallinity of pure cellulosic Avicel plays a major role in determining the rate of hydrolysis by cellulases from Trichoderma reesei, we show that it stays constant during enzymatic conversion. The mode of action of cellulases was investigated by studying their kinetics on cellulose samples. A convenient method for reaching intermediate degrees of crystallinity with Avicel was therefore developed and the initial rate of the cellulase-catalyzed hydrolysis of cellulose was demonstrated to be linearly proportional to the crystallinity index of Avicel. Despite correlation with the adsorption capacity of cellulases onto cellulose, at a given enzyme loading, the initial enzymatic rate continued to increase with a decreasing crystallinity index, even though the bound enzyme concentration stayed constant. This finding supports the determinant role of crystallinity rather than adsorption on the enzymatic rate. Thus, the cellulase activity and initial rate data obtained from various samples may provide valuable information about the details of the mechanistic action of cellulase and the hydrolysable/reactive fractions of cellulose chains. X-ray diffraction provides insight into the mode of action of Cel7A from T. reesei. In the conversion of cellulose, the (021) face of the cellulose crystal was shown to be preferentially attacked by Cel7A from T. reesei.
Helicobacter pylori (1997)

Helicobacter pylori is a gram-negative bacterium which causes chronic gastritis and plays important roles in peptic ulcer disease, gastric carcinoma, and gastric lymphoma. H. pylori has been found in the stomachs of humans in all parts of the world. In developing countries, 70 to 90% of the population carries H. pylori. In developed countries, the prevalence of infection is lower. There appears to be no substantial reservoir of H. pylori aside from the human stomach. Transmission can occur by iatrogenic, fecal-oral, and oral-oral routes. H. pylori is able to colonize and persist in a unique biological niche within the gastric lumen. All fresh isolates of H. pylori express significant urease activity, which appears essential to the survival and pathogenesis of the bacterium. A variety of tests to diagnose H. pylori infection are now available. Histological examination of gastric tissue, culture, rapid urease testing, DNA probes, and PCR analysis, when used to test gastric tissue, all require endoscopy. In contrast, breath tests, serology, gastric juice PCR, and urinary excretion of [15N]ammonia are noninvasive tests that do not require endoscopy. In this review, we highlight advances in the detection of the presence of the organism and methods of differentiating among types of H. pylori, and we provide a background for appropriate chemotherapy of the infection.
Increased virulence of Neisseria meningitidis after in vitro iron-limited growth at low pH (1981)

At low pH (6.6) and under conditions of iron limitation, Neisseria meningitidis group B (strain SD1C) exhibited an atypical outer membrane protein profile and an increased relative virulence for the mouse. Cells grown in a buffered medium were effectively deprived of iron by the addition of ethylenediamine-diorthohydroxyphenylacetate. The pH of the medium selected for characteristic colonial morphologies: type M3 predominated at pH 6.6, and type M5 predominated at pH 7.7. A mixed population of M1, M3, and M5 colonies was observed at pH 7.2. Isolated outer membrane proteins were analyzed by sodium dodecyl 99 99 sulfate-polyacrylamide gel electrophoresis, and surface exposed proteins were labeled by the [125I]lactoperoxidase method and subsequently identified by autoradiography. Cells grown at pH 6.6 elaborated a major outer membrane protein (protein III; molecular weight, 69,000), which was also present in the outer membrane of iron-limited cells grown at pH 7.2. At pH 7.2 in an iron-sufficient medium, protein III was present only in small quantities in sodium dodecyl sulfate-polyacrylamide gel was present only in small quantities in sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels. A study of the relative virulence (50% lethal dose) of the meningococcus for C57/BL mice revealed that iron-limited cells grown at low pH had an increased relative virulence 1,200-fold (50% lethal dose, 4.0 CFU) greater than that of cells grown in the same medium but at pH 7.2 and with sufficient iron. These studies indicate that pH and iron can be important factors in the determination of meningococcal virulence.
Low Pin-count Debug Interfaces for Multi-device Systems (2009)

Boundary-Scan Architecture (JTAG) is widely used as a debug interface, providing a path for a debugger to access debug com-ponents in complex systems-on-chip (SoCs). By its very nature JTAG accommodates systems containing multiple devices. How-ever, JTAG was primarily intended as a component and board test interface, and is not ideally suited as a debug interface. Its shortcomings have led the industry to search for an alternative. As a result, JTAG interfaces have started to be displaced by dedicated debug interfaces. This paper examines some of these alternatives, and concludes that a dedicated serial wire debug interface can be delivered with lower pin-count and higher per-formance, whilst maintaining support for multi-device systems and interoperability with test. I.
Exceptionally High Acetylene Uptake in a Microporous Metal−Organic Framework with Open Metal Sites (2009)

Six prototype microporous metal-organic frameworks (MOFs) HKUST-1, MOF-505, MOF-508, MIL-53, MOF-5, and ZIF-8 with variable structures and porosities were examined for their acetylene storage, highlighting HKUST-1 as the highest acetylene storage material ever reported with an uptake of 201 cm(3)/g at 295 K and 1 atm. To locate the acetylene binding sites within HKUST-1, neutron powder diffraction studies on acetylene loaded HKUST-1 were carried out and have conclusively established the significant contribution of open Cu(2+) sites for acetylene storage by their strong preferred interactions with acetylene molecules. The binding properties of acetylene gas at different sites were further investigated by first-principles calculations.
Analysis of Glycosphingolipids by Fluorophore-Assisted Carbohydrate Electrophoresis Using Ceramide Glycanase from Mercenaria mercenaria (1994)

Polyacrylamide gel electrophoresis of fluorophore-labeled saccharides is a simple and sensitive separation method for glycan analysis. This method requires an aldehydic reducing carbon on the saccharide in order to react with the amine group of the fluorophore (8-aminonaphthalene-1,3,6-trisulfonic acid or 2-aminoacridone). We have used exoglycosidase-free ceramide glycanase from hard-shelled clam to expose the reducing terminal of the glycan in glycosphingolipid by cleaving the linkage between the glycan and the ceramide. The released glycan was used for fluorophore-assisted carbohydrate electrophoresis, in order to qualitatively determine its monosaccharide composition, chain length, and glycosidic linkages using linkage-specific glycosidases, including a beta 1-3,4 galactosidase from clam.
Comparative analyses of the two proliferating cell nuclear antigens from the hyperthermophilic archaeon, <i>Thermococcus kodakarensis</i> (2012)

The DNA sliding clamp is a multifunctional protein involved in cellular DNA transactions. In Archaea and Eukaryota, proliferating cell nuclear antigen (PCNA) is the sliding clamp. The ring-shaped PCNA encircles double-stranded DNA within its central hole and tethers other proteins on DNA. The majority of Crenarchaeota, a subdomain of Archaea, have multiple PCNA homologues, and they are capable of forming heterotrimeric rings for their functions. In contrast, most organisms in Euryarchaeota, the other major subdomain, have a single PCNA forming a homotrimeric ring structure. Among the Euryarchaeota whose genome is sequenced, Thermococcus kodakarensis is the only species with two genes encoding PCNA homologues on its genome. We cloned the two genes from the T. kodakarensis genome, and the gene products, PCNA1 and PCNA2, were characterized. PCNA1 stimulated the DNA synthesis reactions of the two DNA polymerases, PolB and PolD, from T. kodakarensis in vitro. PCNA2, however, only had an effect on PolB. We were able to disrupt the gene for PCNA2, whereas gene disruption for PCNA1 was not possible, suggesting that PCNA1 is essential for DNA replication. The sensitivities of the Δpcna2 mutant strain to ultraviolet irradiation (UV), methyl methanesulfonate (MMS) and mitomycin C (MMC) were indistinguishable from those of the wild-type strain.
Derivatization Followed by Reductive Cleavage (DFRC Method), a New Method for Lignin Analysis:  Protocol for Analysis of DFRC Monomers (1997)

A new method for selective and efficient cleavage of arylglycerol−β-aryl (β-O-4) ether linkages in lignins is introduced. The acronym “DFRC” relates to the reactions involved, derivatization followed by reductive cleavage. Derivatization, accompanied by cell wall solubilization, is accomplished with acetyl bromide in acetic acid; reductive cleavage of resulting β-bromo ethers utilizes zinc in an acidic medium. Following acetylation, degradation monomers (4-acetoxycinnamyl acetates) are quantified by GC, providing data analogous to those from analytical thioacidolysis. Keywords: Acetyl bromide; lignin; β-aryl ether; thioacidolysis; reductive elimination
Chemical Modifications Designed to Improve Peptide Stability: Incorporation of Non-Natural Amino Acids, Pseudo-Peptide Bonds, and Cyclization (2010)

Functions and properties of native peptides vary from highly specific antibiotics or cytotoxic antitumor drugs, to hormones, neurotransmitters, immunomodulators, etc. Despite their potential utility as therapeutic agents, there are problems connected with the use of natural peptides, due to the low stability against proteolysis, resulting in a short duration of in vivo activity, and in a low bioavailability. One way to overcome these disadvantages is the use of modified peptides, the so called peptidomimetics. Overall, the less peptide character in a drug candidate, the more stable it is towards protease cleavage. A huge number of non-peptidic scaffolds have been reported in the literature; nevertheless, several cases have failed to reproduce the activity of the precursor peptide when the scaffold itself contains relevant pharmacophore elements. Therefore, quasi-peptides still maintain their appeal for applications in medicinal chemistry. For the large number of different unnatural amino acids and peptidomimetics, the overview cannot be all-inclusive. This review focuses on modified peptides in which the peptide character is still preponderant, with particular emphasis on the chemical methodologies utilized to introduce the modifications.
Intravenous immunoglobulin in neurological disease: a specialist review. (2002)

Treatment of neurological disorders with intravenous immunoglobulin (IVIg) is an increasing feature of our practice for an expanding range of indications. For some there is evidence of benefit from randomised controlled trials, whereas for others evidence is anecdotal. The relative rarity of some of the disorders means that good randomised control trials will be difficult to deliver. Meanwhile, the treatment is costly and pressure to "do something" in often distressing disorders considerable. This review follows a 1 day meeting of the authors in November 2000 and examines current evidence for the use of IVIg in neurological conditions and comments on mechanisms of action, delivery, safety and tolerability, and health economic issues. Evidence of efficacy has been classified into levels for healthcare interventions (tables 1 and 2).
Immunohistochemical localization of N-acetylaspartate in rat brain (1991)

N-acetylaspartate (NAA) is one of the most prevalent compounds in the mammalian nervous system. As such, NAA largely contributes to the major peak on water-suppressed proton magnetic resonance spectra. Highly specific antibodies to NAA demonstrate that this compound is discretely localized in a substantial number of neurons throughout the extent of the rat CNS. N-acetylaspartylglutamate (NAAG) is a structurally related neuronal dipeptide which is less widely distributed than NAA. NAAG and NAA immunoreactivities were extensively colocalized in many brainstem areas, where NAAG containing neurons were more numerous than in forebrain structures.
Arg-X-Lys/Arg-Arg motif as a signal for precursor cleavage catalyzed by furin within the constitutive secretory pathway (1991)

Many peptide hormones are produced from larger precursors by endoproteolysis at pairs of basic amino acids (e.g. Lys-Arg and Arg-Arg) within the regulated secretory pathway in endocrine cells. However, many other secretory and membrane proteins appear to be produced from precursors through cleavage at multiple, rather than paired, basic residues within the constitutive secretory pathway in non-endocrine cells. By surveying various precursors processed constitutively, we noticed that most of them have the consensus sequence, Arg-X-Lys/Arg-Arg (RXK/RR), at the cleavage site. When expressed in endocrine and non-endocrine cells, a precursor with the RXKR sequence was cleaved in both types of cells, whereas that with the Lys-Arg pair was cleaved only in the endocrine cells. When the RXKR precursor was coexpressed with furin and PC3, both of which are mammalian homologues of the yeast precursor-processing endoprotease Kex2, in non-endocrine cells, enhancement of the precursor cleavage by furin but not by PC3 was observed. By contrast, when the Lys-Arg precursor was coexpressed with the two mammalian proteases in endocrine cells with no endogenous processing activity at dibasic sites, it was cleaved only by PC3. These results indicate that the basic pair and the RXK/RR sequence are the signals for precursor cleavages catalyzed by PC3 within the regulated secretory pathway and by furin within the constitutive pathway, respectively.
Alkoxyalkyl Esters of Cidofovir and Cyclic Cidofovir Exhibit Multiple-Log Enhancement of Antiviral Activity against Cytomegalovirus and Herpesvirus Replication In Vitro (2002)

The incidence of cytomegalovirus (CMV) retinitis is declining in AIDS patients but remains a significant clinical problem in patients with organ transplants and bone marrow transplants. Prophylaxis with ganciclovir (GCV) or valganciclovir reduces the incidence of CMV disease but may lead to the emergence of drug-resistant virus with mutations in the UL97 or UL54 gene. It would be useful to have other types of oral therapy for CMV disease. We synthesized hexadecyloxypropyl and octadecyloxyethyl derivatives of cyclic cidofovir (cCDV) and cidofovir (CDV) and found that these novel analogs had 2.5- to 4-log increases in antiviral activity against CMV compared to the activities of unmodified CDV and cCDV. Multiple-log increases in activity were noted against laboratory CMV strains and various CMV clinical isolates including GCV-resistant strains with mutations in the UL97 and UL54 genes. Preliminary cell studies suggest that the increase in antiviral activity may be partially explained by a much greater cell penetration of the novel analogs. 1-O-Hexadecyloxypropyl-CDV, 1-O-octadecyloxyethyl-CDV, and their corresponding cCDV analogs are worthy of further preclinical evaluation for treatment and prevention of CMV and herpes simplex virus infections in humans.