gebhart/patrepeval huggingface dataset:
Functional properties of the carboxy-terminal host cell-binding domains of the two toxins, TcdA and TcdB, expressed by Clostridium difficile (2008)

The biological and ligand-binding properties of recombinant C-terminal cell-binding domains (CBDs) and subdomains of the two large exotoxins, Toxin A (TcdA) and Toxin B (TcdB) expressed by Clostridium difficile were examined in the hemagglutination and Verocytotoxicity neutralization assays and by qualitative affinity chromatography using Sepharose-linked alpha Gal(1,3)betaGal(1,4)beta Glc as well as the direct electrospray ionization mass spectrometry (ES-MS) assay. These studies revealed that, whereas the full-length TcdA CBD agglutinated rabbit erythrocytes, neutralized TcdA-mediated Vero cell death and bound to alpha Gal(1,3)betaGal(1,4)beta Glc-derivatized Sepharose, the TcdB CBD was inactive in these functional assays. Moreover, retention by alpha Gal(1,3)betaGal(1,4)beta Glc-derivatized Sepharose corresponded to the number of available TcdA subdomain ligand-binding sites. By contrast, the ES-MS assays revealed that both the TcdA and TcdB CBD bind to 8-methoxycarbonyloctyl-alpha Gal(1,3)betaGal(1,4)beta Glc sequences with similar avidities. Additional ES-MS experiments using chemically altered alpha Gal(1,3)betaGal(1,4)beta Glc sequences also revealed that the TcdA and TcdB CBD will tolerate a fair amount of structural variation in their complementary glycan ligands. Although the studies are consistent with the known ligand-binding properties of the TcdA and TcdB holotoxins, they also revealed subtle heretofore unrecognized functional differences in their receptor recognition properties.
Evidence for splicing of avian sarcoma virus 5′-terminal genomic sequences onto viral-specific RNA in infected cells (1978)

The 5'-terminal nucleotide sequences of the avian sarcoma virus (ASV) genome are transcribed by the reverse transcriptase in vitro into a DNA transcript that represents the entire distance ( approximately 100 nucleotides) between the tRNA(Trp) primer molecule and the 5' terminus. We have used these DNA(100) transcripts in hybridization reactions with ASV-specific RNA from infected avian cells and find nucleotide sequences complementary to these transcripts on all of the various size classes of viral mRNA identified. Similar hybridization results were obtained with a specific DNA transcript complementary to viral genomic nucleotide sequences between the tRNA(Trp) primer molecule and up to, but not including, the terminal redundant sequences (DNA(70)), indicating that the observed hybridization of DNA(100) to all size classes of viral RNA in infected cells did not reflect hybridization of DNA(100) to the terminal redundant sequences at the 3' end of the viral genome. Escherichia coli RNase H hydrolysis of RNA.DNA hybrids consisting of genomic 35S RNA obtained from virus and DNA(100) transcripts indicated that viral genomic sequences complementary to these DNA transcripts were not present at sites distal to the ends of the RNA genome and therefore not adjacent to the corresponding gene sequences representing the various species of viral mRNA from infected cells. These studies suggest that the 5'-terminal genomic nucleotide sequences, or a portion thereof, are somehow added or "spliced" onto each ASV-specific mRNA species in infected cells either during or after transcription of proviral DNA for some as yet undetermined purpose.
Electron Microscopy of Unstained, Hydrated Protein Crystal at 4 K (1982)

Electron radiation damage is the most fundamental problem in studying biological specimen at high resolution. Knapek and Dubochet have reported a factor of 30-300 in reducing the damage of small organic crystals at 4 K compared to 300 K. Chiu and co-workers have made a preliminary report that there was a factor of 10 in reducing the damage of structural details between 4 to 6 Å in a hydrated, unstained protein crystal with the Munich superconducting lens microscope. This paper presents our current data on the damage study of glucose embedded crotoxin complex with the Berlin superconducting lens microscope operated at 100 keV and our preliminary result on imaging this protein crystal to 9.5 Å resolution in a medium dose condition.
Hydrodynamics of flow through gels with applications to the eye (1983)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1983.
Specific Lesion Subsets (2003)

One of the early lessons in interventional cardiology was the discovery that certain angiographic features were associated with poor acute outcome, in particular, abrupt or threatened occlusion [1,2]. Because these lesion characteristics accounted for a major portion of the morbidity related to balloon angioplasty, guidelines were developed in an effort to risk-stratify patients based on angiographic criteria and to dissuade intervention in high-risk subgroups [3].
Characterization of DDRI‐18 (3,3′‐(1<i>H</i>,3′<i>H</i>‐5,5′‐bibenzo[<i>d</i>]imidazole‐2,2′‐diyl)dianiline), a novel small molecule inhibitor modulating the DNA damage response (2012)

We identified a chemical compound, DDRI-18, that has chemosensitization activity. Although the target molecule and mechanism of action of DDRI-18 remain unknown, DDRI-18 is an effective chemosensitizing agent and may improve the therapy with classical anticancer drugs.
Some Theoretical Considerations on the Combustion and Disruption of Free Slurry Droplets (1989)

Abstract The combustion and disruption or free slurry droplets are studied theoretically to elucidate a mechanism for the overall disruptive burning process. The disruptive burning process consists of three stages; a d2-law stage, a shell formation stage, and a disruption stage. It is proposed that the agglomeration of particles near the droplet surface due to capillary forces causes the shell formation and that the pyrolysis of additives due to the temperature rise in the outer surface of the shell produces an impermeable shell immediately and eventually disruption activity. A simple mathematical model is formulated to predict the shell formation and disruption time, and the fragmented shell thickness. The model simulation results for the disruptive burning of boron/JP-IO slurry droplets show good agreements with Takahashi er al. (1988a, b)'s experimental results. The disruption time increases with increasing initial slurry droplet diameter or increasing initial boron loading. The thickness of the fragmented shell increases as the initial diameter or the initial boron loading is increased. Finally, results show that the disruption time increases significantly whereas the thickness of the fragmented shell increases slightly as the environmental oxygen concentration is increased.
Carcinogenicity, DNA adduct formation and K-<i>ras</i> activation by 7<i>H</i>-dibenzo[<i>c, g</i>]carbazole in strain A/J mouse lung (1996)

N-Heterocyclic polynuclear aromatic hydrocarbons (NHA) are environmental pollutants formed during the combustion of organic materials. 7-H-Dibenzo[c,g]carbazole (DBC) is a potent carcinogen in lung, liver and skin. We undertook these studies to determine whether tissue specificity for DBC lung carcinogenicity in the strain A/J mouse is mirrored by formation of DBC-DNA adducts in lung tissue and whether these adducts are consistent with mutation patterns in the K-ras gene. Strain A/J mice were given a single i.p. injection of DBC at doses of 0, 5, 10, 20 or 40 mg/kg and levels of DNA adducts in the lung were monitored by 32P-postlabeling on days 1, 3, 5, 7, 14 and 21. The remaining animals were sacrificed 8 months after DBC treatment and lung tumor multiplicity and K-ras mutation patterns in the tumors were determined. The lung tumor response to DBC was dose related, with an average of 4.7 +/- 1.2 tumors/mouse at 5 mg/kg and 48.1 +/- 5.5 tumors/mouse at 40 mg/kg. As many as seven DBC-DNA adducts were observed in the lung. DNA binding levels in the lung were highest at 40 mg/kg, with maximum binding at 5-7 days. At lower dose levels the maximum binding to DNA decreased and shifted to earlier time points. The DBC-DNA adduct in the lung with the highest level of binding at all dose levels was DBC-DNA adduct 3. The majority of DBC-induced mutations in the K-ras gene in the lung were A-->T (80%) transversions in the third base of codon 61, a mutation that has not been previously observed in chemically induced lung tumors in strain A/J mice.
A New Sigmoidal Transformation for Weakly Singular Integrals in the Boundary Element Method (2003)

The power of the sigmoidal transformation in weakly singular integrals has been demonstrated by the recent works [A. Sidi, in Numerical Integration IV, H. Brass and G. Hämmerlin, eds., Birkhäuser--Verlag, Berlin, 1993, pp. 359--373; P. R. Johnston, Internat. J. Numer. Methods Engrg., 45 (1999), pp. 1333--1348; P. R. Johnston, Internat. J. Numer. Methods Engrg., 47 (2000), pp. 1709--1730; D. Elliott, Math. Methods Appl. Sci., 20 (1997), pp. 121--132; D. Elliott, J. Austral. Math. Soc. Ser. B, 40 (1998), pp. E77--E137]. Especially, application of this transformation is useful for efficient numerical evaluation of the singular integrals appearing in the usual boundary element method. In this paper, a new sigmoidal transformation containing a parameter b is presented. It is shown that the present transformation, with the Gauss--Legendre quadrature rule, can improve the asymptotic truncation error of the traditional sigmoidal transformations by controlling the parameter. For some examples, we compare the numerical results of the present method with those of the well-known Sidi- and Elliott-transformations to show the superiority of the former.
Incidental Cardiac and Pericardial Abnormalities on Chest CT (2008)

Recognition and detection of various cardiac and pericardial abnormalities on chest CT as the evaluation of noncardiac disease is important for its early diagnosis and proper management.
Optimizing survey design for diffracted multiple attenuation with 3D SRME (2009)

We describe a methodology that can be used in designing a survey suitable for subsequent application of advanced multiple attenuation methods for the purpose of tackling complex diffracted multiples. The problem of diffracted multiple attenuation is tackled through an application of surface-related multiple elimination in three dimensions (3D SRME). The impact of changes in acquisition geometry is assessed by performing multiple attenuation on synthetic data. We demonstrate that 3D SRME can successfully attenuate surface-related diffracted multiples, provided the necessary full wavefield is either acquired or reconstructed. We focus our study on the impact of acquisition geometry on the quality of multiple suppression and show that acquiring higher-density data can lead to significant improvements in diffracted multiple attenuation. Finally, we demonstrate that 3D SRME was able to achieve a high degree of diffracted multiple attenuation in a field survey acquired with the geometry studied in synthetic data experiments.
Examination of Nylon Spinneret Holes by Scanning Electron Microscopy† (1959)

ABSTRACT A method is described for the examination of small holes which has been applied to the study of a nylon spinneret. A resolution of 1000 AU is demonstrated with the probable prospect of a five-fold improvement.
A 280 <inline-formula> <tex-math notation="LaTeX">$\mu$ </tex-math> </inline-formula>W Dynamic Zoom ADC With 120 dB DR and 118 dB SNDR in 1 kHz BW (2018)

This paper presents a dynamic zoom analog-to-digital converter for use in low-bandwidth (<;1 kHz) instrumentation applications. It employs a high-speed asynchronous successive approximation register (SAR) ADC that dynamically updates the references of a fully differential ΔΣ ADC. Compared to previous zoom ADCs, faster reference updates relax the loop filter requirements, thus allowing the adoption of energy-efficient amplifiers. Fabricated in a 0.16-μm CMOS process, the prototype occupies 0.26 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and achieves 119.1-dB peak signal-to-noise ratio (SNR), 118.1-dB peak signal-to-noise-and-distortion-ratio (SNDR), and 120.3-dB dynamic range (DR) in a 1-kHz bandwidth while consuming 280 μW. This results in a Schreier figure of merit (FoM) of 185.8 dB.
Dynamic Light Scattering from Block Copolymer Melts near the Order−Disorder Transition (1996)

Dynamic light scattering measurements have been performed on four symmetric diblock copolymer melts, as a function of temperature, both above and below the order−disorder transition (ODT). The materials were poly(ethylenepropylene)−poly(ethylethylene) (PEP−PEE) with Mw = 5.0 × 104, poly(vinylcyclohexane) (PVCH)−PEE with Mw = 5.3 × 104, PVCH−polyethylene (PE) with Mw = 1.6 × 104, and PE−PEE with Mw = 2.7 × 104. Up to four relaxation modes were resolved. In all cases, the correlation functions exhibited a very strong, very slow diffusive mode, similar to that previously observed in polymeric and small-molecule glass formers and attributed to long-range density fluctuations. Via the Kawasaki−Stokes−Einstein relation, a correlation length or cluster size, ξ, was associated with this process. Above the ODT, ξ was on the order of 100 nm and independent of temperature. However, below the ODT, ξ apparently increased by at least 2 orders of magnitude for PVCH−PE and PE−PEE, while remaining nearly independent of temperature for the other two copolymers. For PEP−PEE, the angle dependence of the scattered intensity also reflected a correlation length of 100 nm. The cluster mode was subtracted from the correlation functions, and the residual decays were reanalyzed by Laplace inversion. Two other modes, the diffusive heterogeneity mode and the structural internal mode, were then resolved, in accordance with theory. For the PEP−PEE sample, the heterogeneity diffusion coefficient was in quantitative agreement with the self-diffusion coefficient as measured by forced Rayleigh scattering, and at least in the disordered state, the relaxation time of the internal mode was in quantitative agreement with the longest relaxation time determined by rheological measurements. For this sample, a fourth, diffusive mode was also apparent, with a time scale intermediate between the longest relaxation time and the translational diffusion of the chains. The temperature dependence of this mode was weaker than that of the viscosity or the chain diffusion, and its specific origin is unclear; however, it appears to be correlated with the frequency at which time−temperature superposition breaks down in the rheological properties.
Structural Generation of Virtual Prototypes for Smart Sensor Development in SystemC-AMS from Simulink Models (2023)

We present a flow to reuse system-level analog/mixed-signal (AMS) models developed in MATLAB/Simulink for the extension of virtual prototypes in SystemC. To prevent time-consuming co-simulation, our flow translates the Simulink model into an equivalent SystemC-AMS model. Translation is supported either by wrapping code generated by MATLAB's Embedded Coder or by instantiating previously generated models. Thus, a one-to-one mapping of the model's hierarchy is possible which allows deep insights into the architecture and good traceability. The conducted case study on an accelerometer model shows the applicability of our approach. The generated hierarchical model is half as fast as a monolithic version but allows better observability and traceability of the system. It is tens of times faster than simulation in Simulink. The extended virtual prototype aims to support software engineers during development and validation of firmware in smart sensors.
Structure-function studies of the herpes simplex virus type 1 DNA polymerase (1990)

The analysis of the deduced amino acid sequence of the herpes simplex virus type 1 (HSV-1) DNA polymerase reported here suggests that the polymerase structure consists of domains carrying separate biological functions. The HSV-1 enzyme is known to possess 5'-3'-exonuclease (RNase H), 3'-5'-exonuclease, and DNA polymerase catalytic activities. Sequence analysis suggests an arrangement of these activities into distinct domains resembling the organization of Escherichia coli polymerase I. In order to more precisely define the structure and C-terminal limits of a putative catalytic domain responsible for the DNA polymerization activity of the HSV-1 enzyme, we have undertaken in vitro mutagenesis and computer modeling studies of the HSV-1 DNA polymerase gene. Sequence analysis predicts that the major DNA polymerization domain of the HSV-1 enzyme will be contained between residues 690 and 1100, and we present a three-dimensional model of this region, on the basis of the X-ray crystallographic structure of the E. coli polymerase I. Consistent with these structural and modeling studies, deletion analysis by in vitro mutagenesis of the HSV-1 DNA polymerase gene expressed in Saccharomyces cerevisiae has confirmed that certain amino acids from the C terminus (residues 1073 to 1144 and 1177 to 1235) can be deleted without destroying HSV-1 DNA polymerase catalytic activity and that the extreme N-terminal 227 residues are also not required for this activity.
Implementing a distributed combat simulation on the Time Warp operating system (1988)

Utilizing the Time Warp Operating System, the CTLS project at JPL has produced a distributed combat simulation called STB-87 and measured its performance on the JPL Mark III Hypercube. By applying the spiral model of software development, the CTLS project will produce a series of software test beds, to culminate in the completion of a working prototype theater level simulation three to five years hence. STB-87, the first software test bed, is a ground-based combat simulation decomposed into objects which communicate via time-stamped messages. The use of incremental object-based design, coding, and testing has been helpful when developing a parallel simulation. The performance measurements show that, with the appropriate choice of object granularity, STB-87 is able to achieve a speedup factor of 12 running on a 32-node Mark III Hypercube.
Compositional effects on the growth of Mg(M)O films (2010)

The influence of the composition on the crystallographic properties of deposited Mg(M)O (with M=Al, Cr, Ti, Y, and Zr) films is studied. For a flexible control of the composition, dual reactive magnetron sputtering was used as deposition technique. Two different approaches to predict the composition are discussed. The first is an experimental way based on the simple relationship between the deposition rate and the target-substrate distance. The second is a route using a Monte Carlo based particle trajectory code. Both methods require a minimal experimental input and enable the user to quickly predict the composition of complex thin films. Good control and flexibility allow us to study the compositional effects on the growth of Mg(M)O films. Pure MgO thin films were grown with a (111) preferential out-of-plane orientation. When adding M to MgO, two trends were noticed. The first trend is a change in the MgO lattice parameters compared to pure MgO. The second tendency is a decrease in the crystallinity of the MgO phase. The experimentally determined crystallographic properties are shown to be in correspondence with the predicted properties from molecular dynamics simulations.
Sterol Binding by the Tombusviral Replication Proteins Is Essential for Replication in Yeast and Plants (2017)

Membranous structures derived from various organelles are important for replication of plus-stranded RNA viruses. Although the important roles of co-opted host proteins in RNA virus replication have been appreciated for a decade, the equally important functions of cellular lipids in virus replication have been gaining full attention only recently. Previous work with <i>Tomato bushy stunt tombusvirus</i> (TBSV) in model host yeast has revealed essential roles for phosphatidylethanolamine and sterols in viral replication. To further our understanding of the role of sterols in tombusvirus replication, in this work we showed that the TBSV p33 and p92 replication proteins could bind to sterols <i>in vitro</i> The sterol binding by p33 is supported by cholesterol recognition/interaction amino acid consensus (CRAC) and CARC-like sequences within the two transmembrane domains of p33. Mutagenesis of the critical Y amino acids within the CRAC and CARC sequences blocked TBSV replication in yeast and plant cells. We also showed the enrichment of sterols in the detergent-resistant membrane (DRM) fractions obtained from yeast and plant cells replicating TBSV. The DRMs could support viral RNA synthesis on both the endogenous and exogenous templates. A lipidomic approach showed the lack of enhancement of sterol levels in yeast and plant cells replicating TBSV. The data support the notion that the TBSV replication proteins are associated with sterol-rich detergent-resistant membranes in yeast and plant cells. Together, the results obtained in this study and the previously published results support the local enrichment of sterols around the viral replication proteins that is critical for TBSV replication.<b>IMPORTANCE</b> One intriguing aspect of viral infections is their dependence on efficient subcellular assembly platforms serving replication, virion assembly, or virus egress via budding out of infected cells. These assembly platforms might involve sterol-rich membrane microdomains, which are heterogeneous and highly dynamic nanoscale structures usurped by various viruses. Here, we demonstrate that TBSV p33 and p92 replication proteins can bind to sterol <i>in vitro</i> Mutagenesis analysis of p33 within the CRAC and CARC sequences involved in sterol binding shows the important connection between the abilities of p33 to bind to sterol and to support TBSV replication in yeast and plant cells. Together, the results further strengthen the model that cellular sterols are essential as proviral lipids during viral replication.
IMS Multimedia Telephony over Cellular Systems: VoIP Evolution in a Converged Telecommunication World (2007)

IMS Multimedia Telephony service has been standardized in 3GPP as the replacement of the circuit switched telephony service in cellular networks. The multimedia telephony service consists of several service components such as voice, video and text. 'IMS Multimedia Telephony over Cellular Systems' provides a comprehensive overview of the service that will enable enriched telephony for mobile users. Enriched telephony fulfils the user's desire to communicate in new ways, for example by sharing pictures and video clips. In addition to an overview of the Multimedia Telephony service, the book focuses on the modern media processing methods, which allows the quality of the packet switched voice and video telephony not only to match but also possibly exceed the quality of circuit switched telephony. Such key components as adaptive jitter buffering and adaptation of conversational media are explained in detail. Key features: * Detailed description of how Multimedia Telephony sessions are set-up and controlled * Analysis showing the capacity and quality of VoIP and Multimedia Telephony in cellular networks * Coverage of other IMS services such as PoC specified by 3GPP and OMA * Description of suitable QoS and radio bearers for Multimedia Telephony * Explanation of the modern radio interface, especially High Speed Packet Access, which is based on concepts such as link adaptation and fast hybrid ARQ The possibilities for the current and future standards covered in this book make it an indispensable resource for engineers, designers and researchers in VoIP, telecommunication companies and universities teaching and conducting research in telecommunications. It will also be of interest to managers needing an in-depth knowledge of the engineering and key issues of this complex technology, and students aspiring to develop a career in this area.