gebhart/patrepeval huggingface dataset:
Crystal structure of a recombinant form of the maltodextrin-binding protein carrying an inserted sequence of a B-cell epitope from the preS2 region of hepatitis B virus (1997)

We report the crystal structure of MalE-B133, a recombinant form of the maltodextrin-binding protein (MBP) of Escherichia coli carrying an inserted amino-acid sequence of a B-cell epitope from the preS2 region of the hepatitis B virus (HBV). The structure was determined by molecular replacement methods and refined to 2.7 A resolution. MalE-B133 is an insertion/deletion mutant of MBP in which residues from positions 134 to 142, an external alpha helix in the wild-type structure, are replaced by a foreign peptide segment of 19 amino acids. The inserted residues correspond to the preS2 sequence from positions 132 to 145 and five flanking residues that arise from the creation of restriction sites. The conformation of the recombinant protein, excluding the inserted segment, closely resembles that of wild-type MBP in the closed maltose-bound form. MalE-B133 was shown by previous studies to display certain immunogenic and antigenic properties of the hepatitis B surface antigen (HBsAg), which contains the preS2 region. The crystal structure reveals the conformation of the first nine epitope residues (preS2 positions 132 to 140) exposed on the surface of the molecule. The remaining five epitope residues (preS2 positions 141 to 145) are not visible in electron density maps. The path of the polypeptide chain in the visible portion of the insert differs from that of the deleted segment in the structure of wild-type MBP, displaying a helical conformation at positions 134 to 140 (preS2 sequence numbering). A tripeptide (Asp-Pro-Arg) at the N terminus of the helix forms a stable structural motif that may be implicated in the cross-reactivity of anti-HBsAg antibodies with the hybrid protein.
Evaluation of protease‐activated receptor 2 in murine models of arthritis (2006)

PAR-2 deficiency was found to modulate articular inflammation in murine models of arthritis that require prior immunization and was associated with reduced levels of anti-mBSA IgG and lymph node cell proliferation in AIA. Expression of PAR-2 in RA synovium was significantly higher than that in OA synovium, and this suggests that PAR-2 is implicated in the pathogenesis of immune-mediated forms of arthritis.
Effects of Serotonergic Activation by 5-Hydroxytryptophan on Sleep and Body Temperature of C57BL/6J and Interleukin-6-Deficient Mice are Dose and Time Related (2008)

5-HTP alters sleep-wake behavior and body temperature of mice in a manner similar to that of rats. Increases in NREM sleep after 5-HTP are apparent only during the dark period, which may represent a fundamental property of the serotonergic system. These results suggest that 5-HT should not be considered either wake promoting or NREM sleep promoting. Rather, the role of 5-HT in the regulation of sleep-wake behavior must be considered within the context of the degree to which the system is activated and the time at which the activation occurs.
Novel Conformational States of Peptide Deformylase from Pathogenic Bacterium Leptospira interrogans (2005)

Peptide deformylase is an attractive target for developing novel antibiotics. Previous studies at pH 3.0 showed peptide deformylase from Leptospira interrogans (LiPDF) exists as a dimer in which one monomer is in a closed form and the other is in an open form, with different conformations of the CD-loop controlling the entrance to the active pocket. Here we present structures of LiPDF at its active pH range. LiPDF forms a similar dimer at pH values 6.5-8.0 as it does at pH 3.0. Interestingly, both of the monomers are almost in the same closed form as that observed at pH 3.0. However, when the enzyme is complexed with the natural inhibitor actinotin, the conformation of the CD-loop is half-open. Two pairs of Arg109-mediated cation-pi interactions, as well as hydrogen bonds, have been identified to stabilize the different CD-loop conformations. These results indicate that LiPDF may be found in different structural states, a feature that has never before been observed in the peptide deformylase family. Based on our results, a novel substrate binding model, featured by an equilibrium between the closed and the open forms, is proposed. Our results present crystallographic evidence supporting population shift theory, which is distinguished from the conventional lock-and-key or induced-fit models. These results not only facilitate the development of peptide deformylase-targeted drugs but also provide structural insights into the mechanism of an unusual type of protein binding event.
Video-on-Demand with Multiple Readouts. (1994)

Digital video-on-demand is becoming important, in conjunction with the digitazation of communications and advances in video compression techniques. This paper proposes three new techniques to improve the function and performance of digital video-on-demand systems : multiple readouts of video programs within a few seconds from a disk drive, variable-bit-rate video storage for consistent video quality and efficient multiple readouts, and audio-and-video synchronization that is compatible with a variety of communication networks and video decoding speeds. A new system architecture is also proposed to employ these techniques and video packet transmission. The feasibility of these techniques is experimentally verified. A response time of under one second is achieved from a program request to program initiation on a terminal. In addition, simultaneous access to a video storage server is possible from four terminals if the maximum video bit rate is 2.8 Mbps.
Building external anatomical structures from images using a single off-the-shelf camera (2007)

Three-dimensional (3D) geometric reconstruction and characterization of the human body from bidimensional (2D) images has been a major research topic in Computer Vision. However, it is still a complex problem to solve, when automation, speed and precision are required. Volumetric based methods are a recent and successful solution for 3D structures reconstruction from images. In this work, using an uncalibrated turntable image sequence, acquired with a single off-the-shelf CCD camera, a 3D geometric model of the structure in cause is built. Our main goal is the reconstruction of 3D shapes of external anatomical structures from images, with good precision and photorealistic appearance.
Neutrophil Activation by Bacterial Lipoprotein Versus Lipopolysaccharide: Differential Requirements for Serum and CD14 (2000)

Neutrophil activation plays an important role in the inflammatory response to Gram-negative bacterial infections. LPS has been shown to be a major mediator of neutrophil activation which is accompanied by an early down-regulation of L-selectin and up-regulation of CD1lb/CD18. In this study, we investigated whether lipoprotein (LP), the most abundant protein in the outer membrane of bacteria from the family Enterobacteriaceae, can activate neutrophils and whether this activation is mediated by mechanisms that differ from those used by LPS or Escherichia coli diphosphoryl lipid A (EcDPLA). Neutrophil activation was assessed by measuring down-regulation of L-selectin and up-regulation of CD11b/CD18. When comparing molar concentrations of LP vs EcDPLA, LP was more potent (four times) at activating neutrophils. In contrast to LPS/EcDPLA, LP activation of neutrophils was serum independent. However, LP activation of neutrophils was enhanced by the addition of soluble CD14 and/or LPS-binding protein. In the presence of serum, LP activation of neutrophils was inhibited by different mAbs to CD14. This inhibition was significantly reduced or absent when performed in the absence of serum. Diphosphoryl lipid A from Rhodobacter spheroides (RaDPLA) completely inhibited LPS/EcDPLA activation of neutrophils but only slightly inhibited LP activation of neutrophils. These results suggest that LP activation of human neutrophils can be mediated by a mechanism that is different from LPS activation and that LP is a potentially important component in the development of diseases caused by Gram-negative bacteria of the family Enterobacteriaceae.
Hair fibre production by human hair follicles in whole-organ culture (1994)

We have used both pulse-chase radiolabelling and morphometric techniques to investigate the ability of whole-organ cultures of human hair follicles to synthesize hair fibre. Anagen hair follicles were obtained from human facial skin by microdissection. Follicles were pulse-labelled with 3H-leucine, and radioactivity in alkali-soluble protein (ASP) and alkali-insoluble hair fibre protein (HFP) fractions was determined by differential extraction. There was a slow decline in ASP radioactivity over 7 days of culture, with a half-life of 4 days. In contrast, leucine incorporation into HFP increased linearly from day 1 to day 5, following an initial delay of 17 h. Morphometric analysis revealed that hair follicles and hair fibres grew at the same rate (0.25 mm/day) for 4 days in culture, after which the rate of hair follicle growth declined progressively, whereas fibre growth continued at the initial rate for a further 3 days. Concurrent with the onset of the decline in follicle growth, the base of the hair fibre began to descend towards the follicle base, until hair fibre occupied almost the full length of the hair follicle at day 15. The decline in follicle growth was preceded by a decline in the rate of follicular 3H-thymidine incorporation, with a delay of approximately 1 day. Overall, these data demonstrate that human hair follicles in whole-organ culture are capable of the production of hair fibre, and suggest that cessation of hair growth in vitro results from depletion of the pool of differentiated follicular keratinocytes, secondary to a loss of matrix cell proliferative activity.
Aryltrifluoromethylsulfoxides: Sulfinylation or Aromatics by Triflinate Salts in Acid Medium (2001)

Direct sulfinylation reaction of simple aromatic compounds by triflinate salts in triflic acid led to aryltrifluoromethyl sulfoxides. The para isomer was the major one. The regioselectivity of the reaction was very high when the substituent on the aromatic ring was a halogen atom, a trifluoromethoxy group or an acetanilide function.
Social Preferences and Transport Policy: The case of US speed limits (2009)

This article, in reviewing the long- running US debate on speed limits, illustrates how a different valuation of the trade-off between private mobility needs and safety concerns can shape transport policies. It is argued that the regulatory decentralization debate, together with the speed limit in force in each state, obey the social preferences and valuation given to this trade- off. Such a view is consistent with evidence that higher speed limits are to be found in states with greater private mobility needs, even though their fatality rates might be among the highest in the country. By contrast, lower speed limits and supporters of a low national speed limit are to be found in states that show a greater concern for safety outcomes and which are less dependent on private mobility. By reviewing these events and examining the role played by the main actors and analyzing their motivations, the article identifies important lessons for similar future discussions on transport policy.
O-Allylic Substitution of Hydroxylamine Derivatives Having an N-Electron-Withdrawing Substituent (2003)

The O-allylic substitution of hydroxylamines having an N-electron-withdrawing substituent proceeded smoothly to afford O-allylated products by using [IrCl(cod)]2 or Pd(PPh3)4.
BIFEST (1999)

This paper presents BIFEST, an ATPG system that employs the built-in intermediate voltage test technique in an efficient ATPG process to deal with CMOS bridging faults. Fast and accurate calculations of the intermediate bridging voltages and the variant threshold tolerance margins on a resistive bridging fault model are presented. A PODEM-like, PPSFP-based ATPG process is developed to generate test patterns for faults that are conventionally logic-testable. The remaining faults are then dealt with by special circuits, called built-in intermediate voltage sensors (BIVSs). By this methodology, almost the same fault coverage as that employing I DDQ testing can be achieved with only logic monitoring required.
A reactive molecular dynamics simulation of the silica-water interface (2010)

We report our study of a silica-water interface using reactive molecular dynamics. This first-of-its-kind simulation achieves length and time scales required to investigate the detailed chemistry of the system. Our molecular dynamics approach is based on the ReaxFF force field of van Duin et al. [J. Phys. Chem. A 107, 3803 (2003)]. The specific ReaxFF implementation (SERIALREAX) and force fields are first validated on structural properties of pure silica and water systems. Chemical reactions between reactive water and dangling bonds on a freshly cut silica surface are analyzed by studying changing chemical composition at the interface. In our simulations, reactions involving silanol groups reach chemical equilibrium in approximately 250 ps. It is observed that water molecules penetrate a silica film through a proton-transfer process we call "hydrogen hopping," which is similar to the Grotthuss mechanism. In this process, hydrogen atoms pass through the film by associating and dissociating with oxygen atoms within bulk silica, as opposed to diffusion of intact water molecules. The effective diffusion constant for this process, taken to be that of hydrogen atoms within silica, is calculated to be 1.68 x 10(-6) cm(2)/s. Polarization of water molecules in proximity of the silica surface is also observed. The subsequent alignment of dipoles leads to an electric potential difference of approximately 10.5 V between the silica slab and water.
Fluorescent polycyclic aromatic hydrocarbons as probes for studying the impact of colloids on pollutant transport in groundwater (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFluorescent polycyclic aromatic hydrocarbons as probes for studying the impact of colloids on pollutant transport in groundwaterDebera A. Backhus and Philip M. GschwendCite this: Environ. Sci. Technol. 1990, 24, 8, 1214–1223Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://pubs.acs.org/doi/10.1021/es00078a009https://doi.org/10.1021/es00078a009research-articleACS PublicationsRequest reuse permissionsArticle Views649Altmetric-Citations132LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Existence and consequences of G-quadruplex structures in DNA (2014)

While the discovery of B-form DNA 60 years ago has defined our molecular view of the genetic code, other postulated DNA secondary structures, such as A-DNA, Z-DNA, H-DNA, cruciform and slipped structures have provoked consideration of DNA as a more dynamic structure. Four-stranded G-quadruplex DNA does not use Watson-Crick base pairing and has been subject of considerable speculation and investigation during the past decade, particularly with regard to its potential relevance to genome integrity and gene expression. Here, we discuss recent data that collectively support the formation of G-quadruplexes in genomic DNA and the consequences of formation of this structural motif in biological processes.
Linear programming based techniques for synthesis of network-on-chip architectures (2004)

Network-on-chip (NoC) has been proposed as a solution for the communication challenges of system-on-chip (SoC) design in the nanoscale regime. SoC design offers the opportunity for incorporating custom NoC architectures that are more suitable for a particular application, and do not necessarily conform to regular topologies. This paper presents novel linear programming based techniques for synthesis of custom NoC architectures. In the nanoscale regime, low power consumption would continue to be an important design goal. We first discuss an optimal mixed integer linear programming (MILP) formulation that synthesizes a low power NoC architecture subject to the performance constraints. The MILP formulation is limited by large run times. We next present heuristic techniques that exploit clustering, and 0-1 constraint relaxation to reduce the run times of the formulation. The techniques minimize power as the primary goal, and minimize the number of routers (area) as a secondary goal. We present an analysis of the quality of the results and the solution times of the proposed techniques by extensive experimentation with the realistic benchmarks. The clustering based heuristic generates results whose power consumption is within 11% of the MILP solutions and its average run time is 171.1 seconds. The average run time of the relaxation and rounding based techniques is less than 2 seconds, and the power consumption of their solutions is within 58% of the MILP result.
Mirrorless Lasing in Conducting Polymer poly(2,5-dioctyloxy-p-phenylenevinylene) Films (1996)

We report mirrorless lasing in thin films of poly(2,5-dioctyloxy- p -phenylenevinylene) (DOO-PPV), that we identify as superradiance. We have measured the characteristic properties associated with this phenomenon including spectral narrowing, polarization memory, thickness and intensity dependencies. From the measurements of picosecond transient gain and loss in DOO-PPV we conclude that DOO-PPV films are excellent candidates for solid state lasers.
Expression of mutant p53 in melanoma. (1991)

Mutant p53 has been noted in a variety of human malignancies including carcinomas of lung, breast, and colon, which have also been reported to have frequent karyotype anomalies involving the locus of the p53 gene (17p13). Whereas chromosomal abnormalities of chromosomes 1, 6, and 7 have been noted previously in melanoma, frequent aberrations in chromosome 17 have not been reported previously. Due to the common mutation of this locus in so many types of neoplasms, a range of melanomas from different stages of tumor progression were examined immunohistochemically for expression of mutant p53, in order to assess its prevalence and consider the role of this oncogene in the biological progression of melanoma. Forty-five of 53 (85%) specimens from a range of primary and metastatic melanomas were found to have detectable evidence of p53 gene mutation, by virtue of the immunohistochemical detection of mutant p53 protein. Significantly increased prevalence of mutant p53 was found in metastatic melanoma, compared with primary tumors (P less than 0.05). These findings represent one of the highest incidences of this oncogenic mutation yet recorded in a human malignancy and support the concept that p53 may have a functional role in development of the metastatic tumor phenotype.
The Enzymatic Nature of Human C1r: A Subcomponent of the First Component of Complement (1979)

Abstract The esterase activity of the Clr̄ subcomponent of the first component of complement has been investigated. Clr̄ was found to hydrolyze two amino acid methyl esters; N-acetyl-L-arginine methyl ester and N-acetyl-glycyl-L-lysine methyl ester, and two amino acid p-nitro-phenyl esters, N-carbobenzyloxy-L-tyrosine-p-nitro-phenyl ester and Nα-carbobenzyloxy-L-lysine-p-nitrophenyl ester. A detailed kinetic analysis of the hydrolysis of N-Z-L-Tyr-ONp by Clr̄ revealed that the enzymatic activity per microgram of protein decreased as the Clr̄ concentration was increased. the loss of activity suggested that above 0.5 µM Clr̄ was undergoing aggregation with a loss of active sites. Similarly, when Clr̄ was titrated with the active site titrant p-nitrophenyl-p-guanidinobenzoate the number of titratable sites per milligram of protein decreased with increasing protein concentration. The hydrolysis of N-Z-L-Tyr-ONp by Clr̄ was inhibited by several synthetic inhibitors including phenylmethanesulfonylfluoride, p-amidinophenylmeth-anesulfonylfluoride, diisopropylfluorophosphate, and p-tosyl-L-lysine-chloromethyl ketone. However, the peptide esterase inhibitors Trasylol, hirudin, leupeptin, and Cl̄ esterase inhibitor had no effect on the esterase activity of Clr̄.
A New Sodium Channel α-Subunit Gene (Scn9a) from Schwann Cells Maps to theScn1a, Scn2a, Scn3aCluster of Mouse Chromosome 2 (1996)

We have used a total of 27 AXB/BXA recombinant inbred mouse strains to determine the chromosomal location of a newly identified gene encoding an alpha-subunit isoform of the sodium channel from Schwann cells, Scn9a. Linkage analysis established that Scn9a mapped to the proximal segment of mouse chromosome 2. The segregation of restriction fragment length polymorphisms in 145 progeny from a Mus spretus x C57BL/6J backcross indicates that Scn9a is very tightly linked to Scn1a (gene encoding the type I sodium channel alpha-subunit of the brain) and forms part of a cluster of four Scna genes located on mouse chromosome 2.
Theory and Application of Point-Diffraction Interferometers (1975)

The point-diffraction interferometer is an interferometer for measuring phase variations in which the reference wave is produced by a point discontinuity in the path of the beam. Its simplicity makes it very suitable for testing instruments in situ, and some such tests are described. The general theory shows that other diffracting apertures can be used and relates the technique to phase-contrast microscopy and to scatter-plate interferometry.
Highly reliable high-voltage transistors by use of the SIPOS process (1975)

The npn and pnp high-voltage transistors showing high reliabilities have been developed by using semi-insulating polycrystalline-silicon (SIPOS) films for the surface passivation. SIPOS films are chemically vapor-deposited polycrystalline-silicon doped with oxygen or nitrogen atoms. SIPOS films employed for the surface passivation of high-voltage transistors are composed of triple layers, which are oxygen-doped films of 0.5 µm thickness to stabilize the silicon interface, nitrogen-doped films of 0.15 µm thickness to prevent water or sodium ions from reaching the silicon surface and silicon dioxide films to prevent dielectric breakdown. The npn and pnp SIPOS transistors rated at 800 V and 2500 V have been produced in planar-like structures with field-limiting rings. Furthermore, 10 kV SIPOS transistors with multiple rings have been fabricated and found that operation is stable.