gebhart/patrepeval huggingface dataset:
Synthesis of oligoribonucleotides via the phosphite-triester approach on a polymer support. (1986)

Four ribonucleoside phosphoramidites bearing 5'-O-dimethoxytrityl and 2'-O-tetrahydrofuranyl groups were synthesized with the use of bis(diisopropylamino)-methoxyphosphine in yields of 68-92%. By the same procedure, the phosphoramidite derivatives of dimers were also prepared for block condensation.We measured the time course of the condensation reaction of ribonucleoside phosphoramidite and nucleoside linked to long-chain alkylamine-controlled pore glass (LCA-CPG) resin. It took 30 min for complete coupling if the nucleoside phosphoramidite was activated with 1-H-tetrazole. However, when 5-p-nitrophenyltetrazole was used for the activation, the condensation reaction was complete within 5 min. The behavior of the block condensation reaction using dimers was similar to that of monomers in the case of 5-p-nitrophenyltetrazole activation.We synthasized oligoribonucleotides UUUU, CUCUCUU and GGCGCGCC in yields of 51, 33 and 3%, respectively, by the phosphite-triester approach by means of either stepwise or block condensation on the LCA-CPG resin.
Neutralizing Human Anti Crotoxin scFv Isolated from a Nonimmunized Phage Library (2000)

Combinatorial phage display technology offers a new possibility for making human antibodies which could be used in immune therapy. We explored the use of this technology to make human scFvs specific for crotoxin, the main toxic component of the venom of the South-American rattlesnake Crotalus durissus terrificus. Crotoxin, a phospholipase A2 neurotoxin constituted by the association of two subunits, exerts its lethal action by blocking neuromuscular transmission. This is the first report of human anticrotoxin scFvs (scFv 1, scFv 6 and scFv 8) isolated from a naive library of more than 1010 scFv clones with in vivo neutralizing activity. Nevertheless, differences are observed at the level of biological and immunological effects. Only scFv 8 is able to reduce the myotoxicity induced by crotoxin and scFv 1 is capable of altering the in vitro enzymatic activity of this toxin. All three scFvs recognize a region of one subunit located at the junction with the other one. Moreover these scFvs share strong amino acid homologies at the level of either the heavy or the light chain. Taken together, our results suggest that the use of human anticrotoxin scFvs may lead to a new and less aggressive passive immune therapy against poisoning by the venom of Crotalus durissus terrificus.
Gas Chromatographic Simulated Distillation-Mass Spectrometry for the Determination of the Boiling Point Distributions of Crude Oils (2000)

The coupling of gas chromatographic simulated distillation with mass spectrometry for the determination of the distillation profiles of crude oils is reported. The method provides the boiling point distributions of both weight and volume percent amounts. The weight percent distribution is obtained from the measured total ion current signal. The total ion current signal is converted to weight percent amount by calibration with a reference crude oil of a known distillation profile. Knowledge of the chemical composition of the crude oil across the boiling range permits the determination of the volume percent distribution. The long-term repeatability is equivalent to or better than the short-term repeatability of the currently available American Society for Testing and Materials (ASTM) gas chromatographic method for simulated distillation. Results obtained by the mass spectrometric method are in very good agreement with results obtained by conventional methods of physical distillation. The compositional information supplied by the method can be used to extensively characterize crude oils.
The polymerase subunit of DNA polymerase III of Escherichia coli. I. Amplification of the dnaE gene product and polymerase activity of the alpha subunit. (1985)

The Escherichia coli dnaE gene, which encodes the alpha subunit of DNA polymerase III (pol III) holoenzyme, has been cloned in a plasmid containing the PL promoter of phage lambda and thermally induced to overproduce the alpha subunit. In cells carrying this plasmid (pKH167), the alpha subunit was amplified, after heat induction, to a level of about 0.2% of the total cellular protein. Polymerase activity was assayed in three ways: (i) gap-filling by pol III holoenzyme and subassemblies of it, (ii) the extensive replication of a primed, single-stranded DNA circle only by pol III holoenzyme, and (iii) complementation of a crude, inactive pol III holoenzyme (temperature-sensitive dnaE mutant fraction) in replication of a primed, single-stranded DNA circle. Amplification of the alpha subunit raised the polymerase level 10-fold in assay (i), indicative of the dependence of pol III gap-filling activity on this polypeptide; pol III holoenzyme activity remained unaffected (assay (ii)), but the complementation activity was raised 5-fold (assay (iii)). Thus, the elevated alpha subunit (free or in a subassembly form) can substitute in vitro for a defective alpha subunit in pol III holoenzyme, but cannot increase the in vivo level of about eight pol III holoenzyme molecules per cell. This low level of pol III holoenzyme is fixed in wild type cells (bearing no plasmid) despite the presence of a 5-fold excess of the alpha subunit, as inferred from the various assays. These results suggest that the low level of pol III holoenzyme is determined by a factor or factors other than the level of the alpha subunit.
Cutting Edge: Different Toll-Like Receptor Agonists Instruct Dendritic Cells to Induce Distinct Th Responses via Differential Modulation of Extracellular Signal-Regulated Kinase-Mitogen-Activated Protein Kinase and c-Fos (2003)

Dendritic cells (DCs) are pivotal in determining the class of an adaptive immune response. However, the molecular mechanisms within DCs that determine this decision-making process are unknown. Here, we demonstrate that distinct Toll-like receptor (TLR) ligands instruct human DCs to induce distinct Th cell responses by differentially modulating mitogen-activated protein kinase signaling. Thus, Escherichia coli LPS and flagellin, which trigger TLR4 and TLR5, respectively, instruct DCs to stimulate Th1 responses via IL-12p70 production, which depends on the phosphorylation of p38 and c-Jun N-terminal kinase 1/2. In contrast, the TLR2 agonist, Pam3cys, and the Th2 stimulus, schistosome egg Ags: 1) barely induce IL-12p70; 2) stimulate sustained duration and magnitude of extracellular signal-regulated kinase 1/2 phosphorylation, which results in stabilization of the transcription factor c-Fos, a suppressor of IL-12; and 3) yield a Th2 bias. Thus, distinct TLR agonists differentially modulate extracellular signal-regulated kinase signaling, c-Fos activity, and cytokine responses in DCs to stimulate different Th responses.
A role for intracellular calcium in tight junction reassembly after ATP depletion-repletion (1999)

The integrity of the tight junction (TJ), which is responsible for the permeability barrier of the polarized epithelium, is disrupted during ischemic injury and must be reestablished for recovery. Recently, with the use of an ATP depletion-repletion model for ischemia and reperfusion injury in Madin-Darby canine kidney cells, TJ proteins such as zonula occludens-1 (ZO-1) were shown to reversibly form large complexes and associate with cytoskeletal proteins (T. Tsukamoto and S. K. Nigam, J. Biol. Chem. 272: 16133-16139, 1997). In this study, we examined the role of intracellular calcium in TJ reassembly after ATP depletion-repletion by employing the cell-permeant calcium chelator 1, 2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid-AM (BAPTA-AM). Lowering intracellular calcium during ATP depletion is associated with significant inhibition of the reestablishment of the permeability barrier following ATP repletion as measured by transepithelial electrical resistance and mannitol flux, marked alterations in the subcellular localization of occludin by immunofluorescent analysis, and decreased solubility of ZO-1 and other TJ proteins by Triton X-100 extraction assay, suggesting that lowering intracellular calcium potentiates the interaction of TJ proteins with the cytoskeleton. Coimmunoprecipitation studies indicated that decreased solubility may partly result from the stabilization of large TJ protein-containing complexes with fodrin. Although ionic detergents (SDS and deoxycholate) appeared to cause a dissociation of ZO-1-containing complexes from the cytoskeleton, sucrose gradient analyses of the solubilized proteins suggested that calcium chelation leads to self-association of these complexes. Together, these results raise the possibility that intracellular calcium plays an important facilitatory role in the reassembly of the TJ damaged by ischemic insults. Calcium appears to be necessary for the dissociation of TJ-cytoskeletal complexes, thus permitting functional TJ reassembly and paracellular permeability barrier recovery.
Mitochondrial-type iron–sulfur cluster biosynthesis genes (IscS and IscU) in the apicomplexan Cryptosporidium parvum (2003)

Several reports have indicated that the iron-sulfur cluster [Fe-S] assembly machinery in most eukaryotes is confined to the mitochondria and chloroplasts. The best-characterized and most highly conserved [Fe-S] assembly proteins are a pyridoxal-5'-phosphate-dependent cysteine desulfurase (IscS), and IscU, a protein functioning as a scaffold for the assembly of [Fe-S] prior to their incorporation into apoproteins. In this work, genes encoding IscS and IscU homologues have been isolated and characterized from the apicomplexan parasite Cryptosporidium parvum, an opportunistic pathogen in AIDS patients, for which no effective treatment is available. Primary sequence analysis (CpIscS and CpIscU) and phylogenetic studies (CpIscS) indicate that both genes are most closely related to mitochondrial homologues from other organisms. Moreover, the N-terminal signal sequences of CpIscS and CpIscU predicted in silico specifically target green fluorescent protein to the mitochondrial network of the yeast Saccharomyces cerevisiae. Overall, these findings suggest that the previously identified mitochondrial relict of C. parvum may have been retained by the parasite as an intracellular site for [Fe-S] assembly.
A modern view of phenylalanine ammonia lyase (2007)

Phenylalanine ammonia lyase (PAL; E.C.4.3.1.5), which catalyses the biotransformation of L-phenylalanine to trans-cinnamic acid and ammonia, was first described in 1961 by Koukol and Conn. Since its discovery, much knowledge has been gathered with reference to the enzyme's catabolic role in microorganisms and its importance in the phenyl propanoid pathway of plants. The 3-dimensional structure of the enzyme has been characterized using X-ray crystallography. This has led to a greater understanding of the mechanism of PAL-catalyzed reactions, including the discovery of a recently described cofactor, 3,5-dihydro-5-methyldiene-4H-imidazol-4-one. In the past 3 decades, PAL has gained considerable significance in several clinical, industrial, and biotechnological applications. The reversal of the normal physiological reaction can be effectively employed in the production of optically pure L-phenylalanine, which is a precursor of the noncalorific sweetener aspartame (L-phenylalanyl-L-aspartyl methyl ester). The enzyme's natural ability to break down L-phenylalanine makes PAL a reliable treatment for the genetic condition phenylketonuria. In this mini-review, we discuss prominent details relating to the physiological role of PAL, the mechanism of catalysis, methods of determination and purification, enzyme kinetics, and enzyme activity in nonaqueous media. Two topics of current study on PAL, molecular biology and crystal structure, are also discussed.
Phage randomization in a charybdotoxin scaffold leads to CD4‐mimetic recognition motifs that bind HIV‐1 envelope through non‐aromatic sequences (2001)

Binding of HIV-1 gp120 to T-cell receptor CD4 initiates conformational changes in the viral envelope that trigger viral entry into host cells. Phage epitope randomization of a beta-turn loop of a charybdotoxin-based miniprotein scaffold was used to identify peptides that can bind gp120 and block the gp120-CD4 interaction. We describe here the display of the charybdotoxin scaffold on the filamentous phage fUSE5, its use to construct a beta-turn library, and miniprotein sequences identified through library panning with immobilized Env gp120. Competition enzyme-linked immunosorbent assay (ELISA) identified high-frequency phage selectants for which specific gp120 binding was competed by sCD4. Several of these selectants contain hydrophobic residues in place of the Phe that occurs in the gp120-binding beta-turns of both CD4 and previously identified scorpion toxin CD4 mimetics. One of these selectants, denoted TXM[24GQTL27], contains GQTL in place of the CD4 beta-turn sequence 40QGSF43. TXM[24GQTL27] peptide was prepared using solid-phase chemical synthesis, its binding to gp120 demonstrated by optical biosensor kinetics analysis and its affinity for the CD4 binding site of gp120 confirmed by competition ELISA. The results demonstrate that aromatic-less loop-containing CD4 recognition mimetics can be formed with detectable envelope protein binding within a beta-turn of the charybdotoxin miniprotein scaffold. The results of this work establish a methodology for phage display of a charybdotoxin miniprotein scaffold and point to the potential value of phage-based epitope randomization of this miniprotein for identifying novel CD4 mimetics. The latter are potentially useful in deconvoluting structural determinants of CD4-HIV envelope recognition and possibly in designing antagonists of viral entry.
Quantitative and Statistical Performance Evaluation of Arbiter Physical Unclonable Functions on FPGAs (2010)

The quantitative performance indicators of Physical Unclonable Functions (PUFs)-Randomness, Steadiness, Correctness, Diffuseness and Uniqueness-are strictly defined and applied to the evaluation of 45 arbiter PUFs on Virtex-5 FPGAs. The indicators effectively reflect the characteristics of PUFs ranging from 0 to 1 with 1 being the highest performance. The indicators enable the easy measurement and intuitive understanding of PUF performances. The experimental results shows that the arbiter PUFs have excellent overall intra-device performances though a slight bit bias is indicated. The inter-device performance is moderate and will suffice for the practical use of PUFs for device authentication and so on. Additionally, the reliability of the obtained PUF performances is statistically discussed in terms of the Confidence Interval and the number of devices. This paper presents in detail the definitions of the performance indicators and the quantitative and statistical evaluation results of the arbiter PUFs.
Postural orientation and equilibrium: what do we need to know about neural control of balance to prevent falls? (2006)

Postural control is no longer considered simply a summation of static reflexes but, rather, a complex skill based on the interaction of dynamic sensorimotor processes. The two main functional goals of postural behaviour are postural orientation and postural equilibrium. Postural orientation involves the active alignment of the trunk and head with respect to gravity, support surfaces, the visual surround and internal references. Sensory information from somatosensory, vestibular and visual systems is integrated, and the relative weights placed on each of these inputs are dependent on the goals of the movement task and the environmental context. Postural equilibrium involves the coordination of movement strategies to stabilise the centre of body mass during both self-initiated and externally triggered disturbances of stability. The specific response strategy selected depends not only on the characteristics of the external postural displacement but also on the individual's expectations, goals and prior experience. Anticipatory postural adjustments, prior to voluntary limb movement, serve to maintain postural stability by compensating for destabilising forces associated with moving a limb. The amount of cognitive processing required for postural control depends both on the complexity of the postural task and on the capability of the subject's postural control system. The control of posture involves many different underlying physiological systems that can be affected by pathology or sub-clinical constraints. Damage to any of the underlying systems will result in different, context-specific instabilities. The effective rehabilitation of balance to improve mobility and to prevent falls requires a better understanding of the multiple mechanisms underlying postural control.
Harnessing Type I and Type III CRISPR-Cas systems for genome editing (2015)

CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are widespread in archaea and bacteria, and research on their molecular mechanisms has led to the development of genome-editing techniques based on a few Type II systems. However, there has not been any report on harnessing a Type I or Type III system for genome editing. Here, a method was developed to repurpose both CRISPR-Cas systems for genetic manipulation in Sulfolobus islandicus, a thermophilic archaeon. A novel type of genome-editing plasmid (pGE) was constructed, carrying an artificial mini-CRISPR array and a donor DNA containing a non-target sequence. Transformation of a pGE plasmid would yield two alternative fates to transformed cells: wild-type cells are to be targeted for chromosomal DNA degradation, leading to cell death, whereas those carrying the mutant gene would survive the cell killing and selectively retained as transformants. Using this strategy, different types of mutation were generated, including deletion, insertion and point mutations. We envision this method is readily applicable to different bacteria and archaea that carry an active CRISPR-Cas system of DNA interference provided the protospacer adjacent motif (PAM) of an uncharacterized PAM-dependent CRISPR-Cas system can be predicted by bioinformatic analysis.
Evaluating Empirical Models for the Detection of High-Risk Components: Some Lessons Learned (1995)

Introduction Software complexity metrics are often used as indirect metrics of reliability since they can be obtained relatively early in the software development life cycle. Using complexity metrics to identify high-risk components, i.e. components which likely contain faults, allows software engineers to focus the verification effort on them, thus achieving a reliable product at a lower cost. Since in this study the direct metric of reliability is the class to which the software component belongs (high-risk or low-risk), the prediction problem is reduced to a classification model. Classification problems have traditionally been solved by various methods, which originate from different problem-solving paradigms such as statistical analysis, machine learning, and neural networks. This study compares different modeling techniques which cover all the three classification paradigms: principal component analysis, discriminant analysis, logistic regression, logical classification m
Catalytic and Electrocatalytic Methane Oxidation with Solid Gxide Membranes (1991)

Abstract Natural gas is an inexpensive, abundant natural resource of which about 90% is methane [1]. Methane is a raw material of great synthetic importance. Nevertheless, methane is primarily used only as fuel from which CO2 and H2O are the combustion products. Total proven natural gas reserves and resources are over 1,500 trillion cubic feet, enough to last 75 years at the present rate of consumption (21. Recently, there has been a glut in natural gas, to which the response has been to conserve gas by capping wells. Furthermore, there is enough geopressured gas in the southern United States to possibly last a thousand years [2].
Browsing in hypertext: a cognitive study (1992)

Several dimensions of browsing are examined to find out: what browsing is and what cognitive processes are associated with it; whether there is a browsing strategy and, if so, whether there are any differences between how subject-area experts and novices browse; and how this knowledge can be applied to improve the design of hypertext systems. Two groups of students, subject-area experts and novices, were studied while browsing a Macintosh HyperCard application. Three browsing strategies were identified: (1) search-oriented browse: scanning and reviewing information relevant to a fixed task; (2) review-browse: scanning and reviewing interesting information in the presence of transient browse goals that represent changing tasks; and (3) scan-browse: scanning for interesting information without review. Most subjects used review-browse interspersed with search-oriented browse. Within this strategy, comparisons showed that experts browsed in more depth, and viewed information differently than did novices. Based on these findings, suggestions are made to hypertext developers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Increased CD8+ central memory T cells in patients with multiple sclerosis (2007)

A T-cell-mediated autoimmune process against central nervous system myelin is believed to underlie the pathogenesis of multiple sclerosis (MS). Formation of immunological memory is based on the differentiation of naïve T cells to memory T cells after exposure to antigens and specific cytokines. The aim of this study was to analyse peripheral blood mononuclear cells in patients with MS for different T-cell subsets including naïve and memory T cells. Flow cytometry and enzyme-linked immunosorbent assay were used to analyse memory T-cell subsets and plasma concentration of interleukin-15 (IL-15) in peripheral blood of MS patients, patients with other neurological disorders and healthy controls. MS patients had a skewed distribution of T cells with an increased level of CD8+/CCR7+/CD45RA - central memory T cells (TCM) compared to healthy controls. In addition, MS patients showed significantly higher levels of plasma IL-15 than healthy controls did. Upregulated CD8+ TCM in MS patients may reflect a persistent chronic inflammatory response that may have been induced during early stages of the disease. This derangement may be important for maintaining chronic inflammation in MS.