gebhart/patrepeval huggingface dataset:
Evidence Supporting the Formation of 2,3-Epoxy-3-methylindoline:  A Reactive Intermediate of the Pneumotoxin 3-Methylindole (1998)

The existence of a cytochrome P450-dependent 2,3-epoxide of the potent pneumotoxin 3-methylindole was indirectly confirmed using stable isotope techniques and mass spectrometry. Determination of hydride shift and incorporation of labeled oxygen in 3-methyloxindole and 3-hydroxy-3-methyloxindole, metabolites that may be in part dependent on the presence of the epoxide, were utilized as indicators of the epoxide's existence. One mechanism for the formation of 3-methyloxindole involves cytochrome P450-mediated epoxidation followed by ring opening requiring a hydride shift from C-2 to C-3. Through incubations of goat lung microsomes with [2-2H]-3-methylindole, the retention of 2H in 3-methyloxindole was found to be 81%, indicating a majority of the oxindole was produced by the mechanism described above. 3-Hydroxy-3-methylindolenine is an imine reactive intermediate that could be produced by ring opening of the 2,3-epoxide. The imine may be oxidized to 3-hydroxy-3-methyloxindole by the cytosolic enzyme aldehyde oxidase. Activities of this putative detoxification enzyme were determined in both hepatic and pulmonary tissues from goats, rats, mice, and rabbits, but the activities could not be correlated to the relative susceptibilities of the four species to 3-methylindole toxicity. The 18O incorporation into either 3-methyloxindole or 3-hydroxy-3-methyloxindole from both 18O2 and H218O was determined. The 18O incorporation into 3-methyloxindole from 18O2 was 91%, strongly implicating a mechanism requiring cytochrome P450-mediated oxygenation. Incorporation of 18O into 3-hydroxy-3-methyloxindole indicated that the alcohol oxygen originated from molecular oxygen, also implicating an epoxide precursor. These studies demonstrate the existence of two new reactive intermediates of 3-methylindole and describe the mechanisms of their formation and fate.
Torsional and Lateral Vibrations of Polycrystalline Diamond Compact PDC Bits in Directional Drilling (2016)

Abstract Drillstring vibration has adverse effect on rate of penetration, causes equipment failure and increase in non productive time (NPT). In carrying out this research work on torsional and lateral vibrations of Polycrystalline Diamond Compact (PDC) bits in directional drilling, harmonic and modal finite element analyses were adopted for the obvious advantage that it is able to approximate the real structure with a finite number of degrees of freedom. The effect of weight on bit on rate of penetration, resonance, damping effect of drilling mud and friction between drillstring and the wellbore were analyzed. In the cause of the analysis, different critical load, critical speed for the finite element of the drillstring and the BHA and saturation points were developed for the different components of the drillstring from the Euler model to determine the crippling loads that will cause each component to buckle and propagate lateral and torsional vibration. The effect of angle inclination was also considered in the design of the vibration analysis model for directional wells application. A new concept, managing WOB while drilling was also advanced to avoid reaching the founder's point in real time drilling operation. The deductions and findings resulted in the development of a computer model, vibraCOM which detects, analyses and mitigates torsional and lateral drillstring vibrations realtime for practical applications. The results shows that it is better to drill below the critical speed of the finite elements of the drillstring and BHA to avoid resonance and to ensure the axial forces acting on the BHA is below the critical load.
Recent developments in the analysis of protein complexes<sup>1</sup> (2003)

The goal of this review is to analyse how recent technical developments contributed to the biochemical characterisation of protein complexes. Improvement of tags used for protein purification, including in our own laboratory, and the development of new strategies have allowed the use of generic procedures for the purification of a wide variety of protein complexes. Together with increased mass spectrometry sensitivity and automation, this made high throughput studies of protein complexes possible and allowed proteome-wide analyses of protein complexes. However, knowledge of protein complex composition, even at the cellular level, will not be sufficient to understand their function. We suggest that the next level of analysis in this area will be the definition of internal subunit arrangement in complexes as a first step toward more detailed structural analyses.
Enhanced CD4+ T-Cell Recovery with Earlier HIV-1 Antiretroviral Therapy (2013)

A transient, spontaneous restoration of CD4+ T-cell counts occurs in the 4-month time window after HIV-1 infection. Initiation of ART during this period is associated with an enhanced likelihood of recovery of CD4+ counts. (Funded by the National Institute of Allergy and Infectious Diseases and others.).
Serum Lipids in Infection (1969)

Abstract Striking elevations in concentrations of total serum lipids were observed in patients with infection caused by gram-negative bacilli. The elevated levels of total lipid in these patients were due mainly to marked increases in serum concentrations of triglycerides or free fatty acids or both. In contrast, patients with severe infection caused by gram-positive cocci had normal concentrations of total serum lipids. Those with fever but no infection and those with influenza had normal concentrations of total serum lipids and normal levels of the major lipid classes. Patients with infectious or serum hepatitis demonstrated a moderate hyperlipidemia, which resulted from increased concentrations of serum triglycerides and free cholesterol. Lipoprotein electrophoresis demonstrated that the hyperlipidemia in patients with severe infection caused by gram-negative bacilli was related to increased levels of pre-beta-lipoproteins. In patients with hepatitis there were increased levels of pre-beta-lipoproteins...
Simulation-based hierarchical sizing and biasing of analog firm IPs (2009)

This paper presents a simulation-based hierarchical sizing and biasing tool for analog integrated circuits design. The tool allows the designer to express the sizing procedure in terms of sizing and biasing operators. These operators are technology independent, hence the documented procedure can be easily ran over different technologies. A procedure has been proposed for a single-ended two-stage operational amplifier and evaluated over 130 nm, 65 nm and 45 nm technologies. The results prove the efficiency of the proposed tool.
Nitration and Aromatic Reactivity (1971)

First published in 1971 this volume claims that nitration is important for two reasons. First, because it is the most general process for the preparation of aromatic nitro-compounds, and secondly, on account of the part it has played in the development of theoretical organic chemistry. The special concern of this monograph is with those nitrating systems in which mechanistic studies have established, or made probable, the identity of the agent through which they effect nitration. It presents a summary of the understanding of the nitration process. A discussion of the various types of nitrating systems leads to the conclusion that nitration is generally effected through the nitronium ion. The mechanism of the substitution is examined, and discussed in terms of reactivity for particular groups of aromatic compounds.
Activation of Ca2+ signaling in neutrophils by the mast cell-released immunophilin FKBP12. (1995)

The immunophilins of the FK506-binding protein (FKBP) family are intracellular proteins that bind the immunosuppresants FK506 and rapamycin. In this study we show that HMC-1 mast cells sensitized with IgE release FKBP12 upon stimulation with anti-IgE. The release is rapid and not affected by actinomycin D or cycloheximide, suggesting that it is due to exocytosis from a storage compartment. FKBP12 from HMC-1 mast cells exhibits biological activity. When applied extracellularly to human neutrophils, it induces transient changes in the intracellular Ca2+ concentration ([Ca2+]i) due to Ca2+ release from intracellular stores. Inhibition of [Ca2+]i changes by ruthenium red and ryanodine indicates that ryanodine receptor/Ca2+ release channels are involved in FKBP12-induced Ca2+ signaling. Neutrophil activation by mast cell-derived FKBP12 is prevented by complexing FKBP12 with FK506 or rapamycin. These results demonstrate that extracellular FKBP12 functions as a cytokine in cell-to-cell communication. They further suggest a pathophysiological role for FKBP12 as a mediator in immediate or type I hypersensitivity and may have implications for novel therapeutic strategies in the treatment of allergic disorders with FK506 and rapamycin.
Compressed‐Sensing multispectral imaging of the postoperative spine (2012)

This study shows that the inherently sparse nature of MSI data allows modest undersampling followed by CS reconstruction with no loss of diagnostic quality.
Study of the relationship between shear modification and melt fracture in extrusion of LDPE (1998)

Successive passes through an extruder can modify the melt morphology of low-density polyethylene (LDPE) by applying a shearing process. The major effects of shear modification are to decrease the elastic properties, as evidenced by the decrease in extrudate swell at the exit of a capillary and in melt viscosity at a low-frequency region. The effect of shear modification is also shown by the delay in the onset of melt fracture upon extrusion. The critical shear stress resulted from extrudate appearance, and apparent discontinuity in the flow curve of LDPE shows a similar value with polypropylene rather than those of LLDPE and HDPE. The shearing histories experienced by these materials did not result in any measurable change in molecular weight, so that the chemical modification process such as degradation and crosslinking may be ruled out. These behaviors were also confirmed to the fact that the extrudate swell was fully reversible by annealing in a molten state. The effects of shear modification on rheological properties could be explained by the changes in melt morphology owing to the disentanglement of temporary couplings between long branches. Also, a reduction in melt elasticity by shear modification of LDPE can be used as an effective tool to improve the surface roughness of extrudates in the cable-making process. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 70: 2187–2195, 1998
Temperature sensing in BOTDA system by using artificial neural network (2015)

The use of an artificial neural network (ANN) for extraction of a temperature profile from a local Brillouin gain spectrum in a Brillouin optical time‐domain analysis fibre sensor system is proposed and demonstrated. An ANN is applied to process the Brillouin time‐domain trace in order to extract the temperature information along the fibre after the data acquisition process. The results show that the ANN provides higher accuracy and larger tolerance to measurement error than Lorentzian curve fitting does, especially for a large frequency scanning step. Hence the measurement time can be greatly reduced by adopting a larger frequency scanning step without sacrificing accuracy.
Organization of the human β-1,2-N-acetylglucosaminyltransferase I gene (MGAT1), which controls complex and hybrid N-glycan synthesis (1997)

UDP-GlcNAc: alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I (EC 2.4.1.101; GlcNAc-T I) is a medial-Golgi enzyme which catalyses the first step in the conversion of oligomannose-type to N-acetyl-lactosamine- and hybrid-type N-glycans and is essential for normal embryogenesis in the mouse. Previous work indicated the presence of at least two exons in the human GlcNAc-T I gene MGAT1, exon 2 containing part of the 5' untranslated region and the complete coding and 3' untranslated regions, and exon 1 with the remainder of the 5' untranslated region. We now report the cloning and sequencing of a human genomic DNA fragment containing exon 1, which is between 5.6 and 15 kb upstream of exon 2. Transient transfection, ribonuclease protection and reverse transcriptase-mediated PCR indicated the absence of transcription start sites in intron 1 between exons 1 and 2. Northern analysis, ribonuclease protection, primer extension analysis and rapid amplification of 5'-cDNA ends showed that there are multiple transcription start sites for exon 1 compatible with the expression by several human cell lines and tissues of two transcripts, a broad band ranging in size from 2.7 to 3.0 kb and a sharper band at 3.1 kb. The 5' flanking region of exon 1 has a GC content of 81% and has no canonical TATA or CCAAT boxes but contains potential binding sites for transcription factors Sp1, GC-binding factor and epidermal growth factor receptor-specific transcription factor. Chloramphenicol acetyltransferase (CAT) expression was observed on transient transfection into HeLa cells of a fusion construct containing the gene for CAT and a genomic DNA fragment from the 5' flanking region of exon 1. It is concluded that MGAT1 is a typical housekeeping gene although there is, in addition, tissue-specific expression of the larger 3.1 kb transcript.
PhagePhisher: a pipeline for the discovery of covert viral sequences in complex genomic datasets (2016)

Obtaining meaningful viral information from large sequencing datasets presents unique challenges distinct from prokaryotic and eukaryotic sequencing efforts. The difficulties surrounding this issue can be ascribed in part to the genomic plasticity of viruses themselves as well as the scarcity of existing information in genomic databases. The open-source software PhagePhisher (http://www.putonti-lab.com/phagephisher) has been designed as a simple pipeline to extract relevant information from complex and mixed datasets, and will improve the examination of bacteriophages, viruses, and virally related sequences, in a range of environments. Key aspects of the software include speed and ease of use; PhagePhisher can be used with limited operator knowledge of bioinformatics on a standard workstation. As a proof-of-concept, PhagePhisher was successfully implemented with bacteria-virus mixed samples of varying complexity. Furthermore, viral signals within microbial metagenomic datasets were easily and quickly identified by PhagePhisher, including those from prophages as well as lysogenic phages, an important and often neglected aspect of examining phage populations in the environment. PhagePhisher resolves viral-related sequences which may be obscured by or imbedded in bacterial genomes.
First Step toward Model-Free, Anonymous Object Tracking with Recurrent Neural Networks (2015)

In this paper, we propose and study a novel visual object tracking approach based on convolutional networks and recurrent networks. The proposed approach is distinct from the existing approaches to visual object tracking, such as filtering-based ones and tracking-by-detection ones, in the sense that the tracking system is explicitly trained off-line to track anonymous objects in a noisy environment. The proposed visual tracking model is end-to-end trainable, minimizing any adversarial effect from mismatches in object representation and between the true underlying dynamics and learning dynamics. We empirically show that the proposed tracking approach works well in various scenarios by generating artificial video sequences with varying conditions; the number of objects, amount of noise and the match between the training shapes and test shapes.
Mechanism of anchoring of OmpA protein to the cell wall peptidoglycan of the gram‐negative bacterial outer membrane (2011)

The outer membrane protein A (OmpA) plays important roles in anchoring of the outer membrane to the bacterial cell wall. The C-terminal periplasmic domain of OmpA (OmpA-like domain) associates with the peptidoglycan (PGN) layer noncovalently. However, there is a paucity of information on the structural aspects of the mechanism of PGN recognition by OmpA-like domains. To elucidate this molecular recognition process, we solved the high-resolution crystal structure of an OmpA-like domain from Acinetobacter baumannii bound to diaminopimelate (DAP), a unique bacterial amino acid from the PGN. The structure clearly illustrates that two absolutely conserved Asp271 and Arg286 residues are the key to the binding to DAP of PGN. Identification of DAP as the central anchoring site of PGN to OmpA is further supported by isothermal titration calorimetry and a pulldown assay with PGN. An NMR-based computational model for complexation between the PGN and OmpA emerged, and this model is validated by determining the crystal structure in complex with a synthetic PGN fragment. These structural data provide a detailed glimpse of how the anchoring of OmpA to the cell wall of gram-negative bacteria takes place in a DAP-dependent manner.
FLUVIAL SEDIMENT STORAGE IN WETLANDS<sup>1</sup> (1989)

ABSTRACT: The important ecological and hydrological roles of wetlands are widely recognized, but the geomorphic functions of wetlands are also critical. Wetlands can be defined in geomorphic, as well as in hydrological or biological terms, and a geomorphic definition of wetlands is proposed. An analysis of fluvial sediment budget studies shows that wetlands typically serve as short‐term sediment sinks or longer‐term sediment storage sites. In ten study basins of various sizes, an estimated 14 to 58 percent of the total upland sediment production is stored in alluvial wetland or other aquatic environments. Of the sediment reaching streams, 29 to 93 percent is stored in alluvial wetland or channel environments. For basins of more than 100 km 2 , more than 15 percent of total upland sediment production and more than 50 percent of sediment reaching streams is deposited in wetlands. The data underestimates the magnitude of wetland sediment storage due to the lack of data from large river systems. A theoretical analysis of river channel sediment delivery shows that wetland and aquatic sediment storage is inevitable in fluvial systems and systematically related to basin size. Results suggest that wetlands should be managed in the context of drainage basins, rather than as discrete, independent units.
T cell tolerance to self antigens in New Zealand hybrid mice with lupus-like disease. (1989)

We determined if self-reactive T cells are able to escape thymic tolerance in autoimmune New Zealand mice. T cells utilizing V beta 17a and V beta 11 encoded receptors have been shown to be clonally eliminated in nonautoimmune mice expressing I-E because of their potential self-reactivity. Similarly, V beta 8.1+ and V beta 6+ T cells are tolerized in the thymus of nonautoimmune mice that express Mls-1a. These T cell subsets were quantitated in the lymph nodes and spleens of (NZB x NZW)F1 and (NZB x SWR)F1 mice. In young mice from both autoimmune strains, deletion was similar to that observed in control animals matched for I-Ed and Mls-1a expression. Furthermore, older female autoimmune mice with elevated levels of IgG antinuclear antibodies and severe lupus-like renal disease did not demonstrate evidence of a global tolerance defect. We also found that the levels of residual V beta 17a+ cells in MHC-matched control F1 strains were further reduced by up to 80% in autoimmune (NZB x SWR)F1 mice. The greater in vivo elimination corresponded to an enhanced ability of NZB spleen cells, compared with other H-2d spleen cells, to stimulate V beta 17a+ hybridomas in vitro. The increased stimulation in culture could not be attributed to quantitative differences in I-E Ag expression. The results suggest that autoreactive T cells have been eliminated in these autoimmune mice by normal mechanisms of self-tolerance. Furthermore, the data demonstrate the existence of an NZB minor locus not present in other H-2d strains that influences T cell repertoire and enhances stimulation of T cells potentially reactive to self class II MHC Ag.
Serological detection of Helicobacter pylori antibodies in children and their parents (1994)

The antibody response to Helicobacter pylori was examined in 56 children (ages 5 to 18) to determine whether serological tests can be used for diagnosis. Twenty-four children (43%) were H. pylori positive and 32 children (57%) were H. pylori negative by culture and histological examination of endoscopic biopsy specimens. The immune response was also examined in 39 nonendoscoped parents of the children. H. pylori-specific immunoglobulin G (IgG) and IgA antibodies were detected by the flow microsphere immunofluorescent assay (FMIA). IgG was also detected by using the Pyloristat enzyme-linked immunosorbent assay (ELISA). The sensitivity, specificity, and positive and negative predictive values for the FMIA for IgG were 100, 97, 96, and 100%, respectively. The respective values for the Pyloristat ELISA for IgG were 96, 94, 92, and 97%. The respective values for the FMIA for IgA were 50, 100, 100, and 73%. Both assays identified the same 19 parents as IgG positive, while FMIA identified 17 of the 19 parents as IgA positive.
Expression of mutated Nck SH2/SH3 adaptor respecifies mesodermal cell fate in <i>Xenopus laevis</i>  development (1997)

Nck is a widely expressed SH2/SH3 adaptor protein containing one SH2 and three SH3 domains. Although Nck is assumed to mediate the formation of protein-protein complexes during signaling, little is currently known about its specific function. We have constructed a series of Nck SH3 and SH2 domain mutants, expressed them in Xenopus laevis embryos, and monitored injected embryos for developmental abnormalities. This approach allows correlation of developmental phenotypes with the presence or absence of specific Nck protein-binding domains. We show that microinjection of RNA-encoding Nck with an inactivating mutation in the third SH3 domain (NckK229) into dorsal blastomeres of early embryos caused anterior truncation with high frequency, and membrane localization of both the first and second SH3 domains together was sufficient to induce this anterior-truncation phenotype. Molecular marker analysis of explants revealed that the expression of NckK229 ventralized dorsal mesoderm. Lineage tracing experiments demonstrated that the expression of Nck K229 in dorsal blastomeres affected the migratory properties of mesoderm cells in gastrulation and led to the adoption of a more posterior fate. These data suggest that protein(s) that bind the first and second SH3 domains of Nck can affect the response to signals that establish dorso-ventral patterning, and that protein(s) that bind the third SH3 domain antagonize the ventralizing effect of the first two SH3 domains.
Synthesis of prodigiosene–estrogen conjugates: optimization of protecting group strategies and anticancer properties (2015)

The tripyrrolic prodigiosene skeleton was conjugated to several estrogen ligands. The conjugation was achieved via an ester linker that proved to be unusually sensitive to hydrolysis during synthesis. This work describes the determination of an appropriate protecting group for the hydroxy groups of the estrogen linker. The anticancer properties of the target prodigiosene–estrogen conjugates were evaluated against breast cancer cells and some show selectivity for ER+ breast cancer cell lines.