gebhart/patrepeval huggingface dataset:
Enteropathogenic and enterohaemorrhagic <i>Escherichia coli</i>: even more subversive elements (2011)

The human pathogens enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC) share a unique mechanism of colonization that results from the concerted action of effector proteins translocated into the host cell by a type III secretion system (T3SS). EPEC and EHEC not only induce characteristic attaching and effacing (A/E) lesions, but also subvert multiple host cell signalling pathways during infection. Our understanding of the mechanisms by which A/E pathogens hijack host cell signalling has advanced dramatically in recent months with the identification of novel activities for many effectors. In addition to further characterization of established effectors (Tir, EspH and Map), new effectors have emerged as important mediators of virulence through activities such as mimicry of Rho guanine nucleotide exchange factors (Map and EspM), inhibition of apoptosis (NleH and NleD), interference with inflammatory signalling pathways (NleB, NleC, NleE and NleH) and phagocytosis (EspF, EspH and EspJ). The findings have highlighted the multifunctional nature of the effectors and their ability to participate in redundant, synergistic or antagonistic relationships, acting in a co-ordinated spatial and temporal manner on different host organelles and cellular pathways during infection.
Selective A<sub>2A</sub>adenosine receptor activation reduces skin pressure ulcer formation and inflammation (2001)

Activation of A(2A) adenosine receptors (A(2A)-AR) by ATL-146e (formerly DWH-146e) prevents inflammatory cell activation and adhesion. Recurrent ischemia-reperfusion (I/R) of the skin results in pressure ulcer formation, a major clinical problem. ATL-146e was evaluated in a novel reproducible rat model of pressure ulcer. A 9-cm(2) region of dorsal rat skin was cyclically compressed at 50 mmHg using a surgically implanted metal plate and an overlying magnet to generate reproducible tissue necrosis. Osmotic minipumps were implanted into 24 rats divided into four equal groups to infuse vehicle (control), ATL-146e (0.004 microg x kg(-1) x min(-1)), ATL-146e plus an equimolar concentration of A(2A) antagonist, ZM-241385, or ZM-241385 alone. Each group received 10 I/R cycles. In non-I/R-treated skin, ATL-146e has no effect on blood flow. I/R-treated skin of the ATL-146e group compared with the vehicle group had 65% less necrotic area, 31% less inhibition of average skin blood flow, and fewer extravasated leukocytes (23 +/- 3 vs. 49 +/- 6 per 500 microm(2)). These data suggest that ATL-146e, acting via an A(2A)-AR, reduces leukocyte infiltration and is a potent prophylactic for I/R injury in skin.
Codebook (2010)

Large-scale software engineering requires communication and collaboration to successfully build and ship products. We conducted a survey with Microsoft engineers on inter-team coordination and found that the most impactful problems concerned finding and keeping track of other engineers. Since engineers are connected by their shared work, a tool that discovers connections in their work-related repositories can help.
A local view of radiation effects in fiber optics (1988)

The reasons for the difficulties that can arise in assessing the potential behaviour of fiber optics in real radiation environments in devising realistic test procedures are considered. Present knowledge of the radiation effects is reviewed by relating the author's own measurements to those of other workers. Some common features of behavior across fiber types are pointed out, and a possible empirical model for the response of undoped core fibers is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
On the Mechanism of Cell Membrane Damage by Complement: Evidence on Insertion of Polypeptide Chains from C8 and C9 into the Lipid Bilayer of Erythrocytes (1977)

The preceding paper (Hammer, C.H., A. Nicholson, and M. M. Mayer, 1975, Proc. Natl. Acad. Sci., 72:5076) presented evidence on insertion of polypeptide chains from the C5b and C7 subunits of C5b, 6, 7 complex into the phospholipid bilayer of erythrocyte membranes. In the present study, EAC1-8 and EAC1-9 (sheep erythrocytes carrying rabbit antibody and complement proteins C1 through C8 or C9, respectively), prepared with either 125I-C8 or 125I-C9, were incubated with trypsin or chymotrypsin and the release of 125I was measured. Only 9 to 19% of the specifically bound radioactivity was released. In addition, elution experiments were performed with 0.02 M EDTA-1.0 M NaCl. This solution did not elute C9 from EAC1-9. By contrast cellbound C9 was recovered from erythrocyte membranes with sodium dodecyl sulfate (SDS). Thus, enzymatic stripping and elution experiments indicate that cellbound C9 behaves like an integral membrane protein, presumably due to insertion into the lipid bilayer. EAC1-9 membranes that had been subjected to extended digestion with trypsin or chymotrypsin were extracted with SDS to recover the enzyme-resistant part of the C9 molecule from the membrane. Even though this domain of C9 carried 90% of the radioiodine associated with native C9, its m.w. was found to be only 18,000 daltons by analysis on SDS-PAGE. This represents one-quarter of the native C9 molecule.
Saturation of the nonlinear refractive index in atomic gases (2013)

Motivated by the ongoing controversy over the origin of the nonlinear index saturation and subsequent intensity clamping in femtosecond filaments, we study the atomic nonlinear polarization induced by high-intensity ultrashort laser pulses in hydrogen by numerically solving the time-dependent Schr\"odinger equation. Special emphasis is given to the efficient modeling of the nonlinear polarization at a central laser frequency corresponding to a wavelength of 800 nm. Here, the recently proposed model of the higher-order Kerr effect (HOKE) and two versions of the standard model for femtosecond filamentation, including either a multiphoton or tunnel ionization rate, are compared. We find that around the clamping intensity the instantaneous HOKE model does not reproduce the temporal structure of the nonlinear response obtained from the quantum-mechanical results. In contrast, the noninstantaneous charge contributions included in the standard models ensure a reasonable quantitative agreement. Therefore, the physical origin for the observed saturation of the overall electron response is confirmed to mainly result from contributions of free or nearly-free electrons.
Interactions between animal cells and gas bubbles: The influence of serum and pluronic F68 on the physical properties of the bubble surface (1994)

We describe a method by which the degree of bubble saturation can be determined by measuring the velocity of single bubbles at different heights from the bubble source in pure water containing increasing concentrations of surfactants. The highest rising velocities were measured in pure water. Addition of surfactants caused a concentration-dependent and height-dependent decrease in bubble velocity; thus, bubbles are covered with surfactants as they rise, and the distance traveled until saturation is reached decreases with increased concentration of surfactant. Pluronic F68 is a potent effector of bubble saturation, 500 times more active than serum. At Pluronic F68 concentrations of 0.1% (w/v), bubbles are saturated essentially at their source. The effect of bubble saturation on the interactions between animal cells and gas bubbles was investigated by using light microscopy and a micromanipulator. In the absence of surfactants, bubbles had a killing effect on cells; hybridoma cells and Chinese hamster ovary (CHO) cells were ruptured when coming into contact with a bubble. Bubbles only partially covered by surfactants adsorbed the cells. The adsorbed cells were not damaged and they also could survive subsequent detachment. Saturated bubbles, on the other hand, did not show any interactions with cells. It is concluded that the protective effect of serum and Pluronic F68 in sparged cultivation systems is based on covering the medium-bubble interface with surfaceactive components and that cell death occurs either after contact of cells with an uncovered bubble or by adsorption of cells through partially saturated bubbles and subsequent transport of cells into the foam region. (c) 1994 John Wiley & Sons, Inc.
Horner-Wittig Reaction of Dimethyl 2,3-<i>O</i>-Isopropylidene-<scp>d</scp>-glyceroylmethylphosphonate and Its Application to the Formal Synthesis of <scp>d</scp>-<i>erythro</i>-C18-Sphingosine (1989)

Abstract Dimethyl 1,2-O-isopropylidene-d-glyceroylmethylphosphonate was found to react with aldehyde in the presence of cesium carbonate in isopropyl alcohol. Using this reaction the formal synthesis of d-erythro-C18-sphingosine was achieved.
The Structural and Thermodynamic Basis for the Formation of Self‐Assembled Peptide Nanotubes (1995)

Nanostructures through self-assembly: Suitably designed planar cyclic peptides like 1 form cylindrical dimers in nonpolar organic solvents. These ensembles are good models for the fundamental description of parallel and antiparallel β-sheet structures as well as for the design of novel peptide nanostructures. The analysis of the structural and thermodynamic aspects of the dimerization process showed that the hydrogen bonds between the peptide backbones are crucial factors for the stability of the ensembles and selective formation of β-sheet arrangements. Furthermore 1 crystallizes to form a novel, porous, solid-state object with an amphiphilic tubular superlattice, which may have potential utility in the molecular inclusion of hydrophilic and hydrophobic substrates.
Tracetree: A Scalable Mechanism to Discover Multicast Tree Topologies in the Internet (2004)

The successful deployment of multicast in the Internet requires the availability of good network management solutions. Discovering multicast tree topologies is an important component of this task. Network managers can use topology information to monitor and debug potential multicast forwarding problems. In addition, the collected topology has several other uses, for example, in reliable multicast transport protocols, in multicast congestion control protocols, and in discovering network characteristics. We present a mechanism for discovering multicast tree topologies using the forwarding state in the network. We call our approach tracetree. First, we present the basic operation of tracetree. Then, we explore various issues related to its functionality (e.g., scalability, security, etc.). Next, we provide a detailed evaluation by comparing it to the currently available alternatives. Finally, we discuss a number of deployment issues. We believe that tracetree provides an efficient and scalable mechanism for discovering multicast tree topologies and therefore fills an important void in the area of multicast network management.
AC van der Pauw Measurements of the Electical Conductivity of Iron-doped Calcium Titanate (1993)

The electrical conductivity of CaFexTi1−xO3−δ (0.10 ≤ × ≤ 0.40) was measured by an AC van der Pauw technique versus oxygen partial pressure (10−20-l atm) and temperature (650–1100 °C). For substitution up to x=0.20 the conductivity was nearly independent of PO2, while at higher degrees of substitution, a ±1/6 dependence was observed over the entire range, with a minimum at intermediate PO2. The results are accounted for by a theory which includes equilibrium between tri- and tetra-valent iron.
A systolic array for approximate string matching (2002)

The edit distance between two strings is defined as the minimum cost of a sequence of editing operations (insertions, deletions and substitutions) that convert one string into the other. This paper presents a linear systolic array for computing the edit distance between two strings over a given alphabet. An encoding scheme is proposed which reduces the number of bits required to represent a state in the computation. The architecture is a parallel realization of the standard dynamic programming algorithm proposed by Wagner and Fischer (1974), and can perform approximate string matching for variable edit costs. More importantly, the architecture does not place any constraint on the lengths of the strings that can be compared. It makes use of simple basic cells and requires regular nearest-neighbor communication, which makes it suitable for VLSI implementation. A prototype of this array is currently being built.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<title>Polymer guided-wave integrated optics: an enabling technology for micro-opto-electro-mechanical systems</title> (1997)

Efficient merging of optical, microelectromechanical (MEM) and microelectronic systems offers significant potential for achieving the microoptoelectromechanical (MOEM) system functionality necessary to meet the performance needs of a number of emerging display, sensing, communications, and control applications. Central to realization of this potential will be the development of a set o microoptical components and processes suitable for co-integration with MEMS devices and support microelectronics. The resulting MEMS 'optical toolbox' will provide the generic building blocks with which photonic functions can be achieved within MOEM systems. An extensive set of bulk and surface micromachined microoptical components supporting free-space optical beam manipulation for optical display, scan, and sense functions is currently under investigation by a number of research groups. Integrated waveguide components have ben less developed within the surface micromachined MEMS environment yet offer substantial opportunities for extending MOEM integrated system capability. This paper explores issues confronting the integration of waveguide technologies within the surface micromachined MEMS environment. Specific focus is placed on initial efforts developing processes for guided wave polymer optics cointegration with the multi-user MEMS process service surface micromachining process. Efforts studying the cointegration of polyimide waveguides with MEMS for integrated optical metrology and state feedback applications will be highlighted.
Near-space flight of a correlated photon system (2014)

We report the successful test flight of a device for generating and monitoring correlated photon pairs under near-space conditions up to 35.5 km altitude. Data from ground based qualification tests and the high altitude experiment demonstrate that the device continues to operate even under harsh environmental conditions. The design of the rugged, compact and power-efficient photon pair system is presented. This design enables autonomous photon pair systems to be deployed on low-resource platforms such as nanosatellites hosting remote nodes of a quantum key distribution network. These results pave the way for tests of entangled photon technology in low earth orbit.
Three-dimensional crystalline SiC nanowire flowers (2004)

Several techniques have already been developed for synthesizing silicon carbide (SiC) material in the form of nanospheres and nanowires/rods. Here, we report the synthesis of a distinctly different kind of SiC nanostructure in the form of three-dimensional crystalline nanowire-based flower-like structures. Interest in such structures centres around the combination of a simple growth process based on SiC nanowire formation, with a resultant structure having potentially complex mechanical and optical properties, the latter a consequence of the wide band gap of bulk SiC. The synthesis of these SiC nanowire flowers is via a vapour–liquid–solid (VLS) process, on which a detailed study of both the chemical and structural composition has been carried out.
Calibration of Wrist-Mounted Robotic Sensors by Solving Homogeneous Transform Equations of the Form AX=XB (1987)

In order to use a wrist-mounted sensor (such as a camera) for a robot task, the position, and orientation of the sensor with respect to the robot wrist frame must be known. We can find the sensor mounting position by moving the robot and observing the resulting motion of the sensor. This yields a homogeneous transform equation of the form AX=XB, where A is the change in the robot wrist position, B is the resulting sensor displacement, and X is the sensor position relative to the robot wrist. The solution to an equation of this form has one degree of rotational freedom and one degree of translational freedom if the angle of rotation of A is neither 0 nor tt radians. To solve for X uniquely, it is necessary to make two arm movements and form a system of two equations of the form: A1X=XB1 and A2X=XB2. A closed-form solution to this system of equations is developed and the necessary conditions for uniqueness is stated.
A peptidomimetic inhibitor of matrix metalloproteinases containing a tetherable linker group (2011)

Successful wound repair and normal turnover of the extracellular matrix relies on a balance between matrix metalloproteinases (MMPs) and their natural inhibitors (the TIMPs). When over-expression of MMPs and abnormally high levels of activation or low expression of TIMPs are encountered, excessive degradation of connective tissue and the formation of chronic ulcers can occur. One strategy to rebalance MMPs and TIMPs is to use inhibitors. We have designed a synthetic pseudopeptide inhibitor with an amine linker group based on a known high-affinity peptidomimetic MMP inhibitor have demonstrated inhibition of MMP-1, -2, -3 and -9 activity in standard solutions. The inhibitor was also tethered to a polyethylene glycol hydrogel using a facile reaction between the linker unit on the inhibitor and the hydrogel precursors. After tethering, we observed inhibition of the MMPs although there was an increase in the IC50s which was attributed to poor diffusion of the MMPs into the hydrogels, reduced activity of the tethered inhibitor or incomplete incorporation of the inhibitor into the hydrogels. When the tethered inhibitors were tested against chronic wound fluid we observed significant inhibition in proteolytic activity suggesting our approach may prove useful in rebalancing MMPs within chronic wounds.
SOS induction in <i>Escherichia coli</i> and Salmonella mutagenicity: a comparison using 330 compounds (1994)

To examine the concordance of two microbial genotoxicity short-term assays, 330 experimental results for the SOS chromotest using tester strain Escherichia coli PQ37 were compared with the results of the Salmonella/mammalian microsome mutagenicity assay with Salmonella typhimurium TA97, TA98, TA100, TA102, TA104, TA1535, TA1537 and/or TA1538. With respect to qualitative features, the concordance between SOS chromotest and Salmonella mutagenicity test results was 86.4% (sensitivity, 78.6%; specificity, 100%; chi 2 = 188.6). None of the non-mutagens (N = 120) were able to induce the SOS system. Additionally, 45 of the 210 S.typhimurium mutagens (21.5%) did not induce the SOS repair system. On closer examination, the majority of these 45 compounds (84%) were mutagens with activities between 0.001 and 10 rev/nmol. Even though the experimental protocols of both systems were not standardized, the correlation coefficient for the experimental results of the two test systems was 0.7 for the 330 chemicals. Except for aliphatic epoxides (r = 0.47), the mutagenicity/SOS induction correlations for congeneric data sets (polycyclic aromatic hydrocarbons, nitroarenes, nitroarenofurans, mycotins) were even better (r = 0.72-0.95). Additionally, computer automated structure evaluation (CASE) analyses of the nature of the structural determinants associated with each endpoint indicate extensive homologies. The data can be taken to indicate that the two phenomena reflect common mechanisms of action.
Performance of asymmetric digital subscriber lines in an impulse noise environment (2003)

The paper presents a numerical study of the impact of impulse noise on asymmetric digital subscriber lines (ADSL). Methods for simulating the effect of impulse disturbances on a discrete multitone system are first presented, and actual measured noise bursts are then used for the simulations as if they were deterministic signals, in order to characterize their effects on ADSL systems. It is shown that, while a combination of coding, interleaving, and 6-dB margin is adequate in protecting ADSL systems from isolated impulses, an impulse train with long duration can cause a significant number of error bits in the system. In this case, a tradeoff among the number of error seconds, the maximum reach, and the coding delay must be made.
Development of an Integrated Mobile Robot System at Carnegie Mellon University: June 1988 (1989)

Abstract : This program focused on the NAVLAB computer-controlled van. During this report period, we addressed major issues in both hardware and software for integrated autonomous mobile robots: 1) We built the NAVLAB mobile robot vehicle by outfitting a commercial truck chassis with computer-controlled drive and steering controls and a set of on-board computer workstations. The NAVLAB serves as a mobile navigation laboratory that allows researchers to interact intensively with the system during testing and execution. This year has seen a continued evolution and improvement of the NAVLAB mechanism, sensors, controller, and Virtual Vehicle interface to higher-level planning and perception software. 2) Previously we designed and implemented the CODGER blackboard system for robot perception and reasoning on a distributed collection of processors. This year we have upgraded it to deal with geometric models and uncertainty in perception and map data. 3) To control the NAVLAB and Terregator mobile robot vehicles, we developed the Driving Pipeline architecture last year for coordinating road following, obstacle avoidance, and vehicle motion control. In our ongoing research, we performed numerous experiments with this system that demonstrate its value. This hardware and software is the basis for the New Generation System (NGS) for robot vision and navigation, which integrates many independent technologies. (edc)
Hernia of Morgagni (1973)

<b>París, F., Tarazona, V., Casillas, M., Blasco, E., Cantó, A., Pastor, J., and Acosta, A. (1973).</b><i>Thorax</i>, <b>28</b>, 631-636. <b>Hernia of Morgagni.</b> Nine patients with Margagni9s hernia of the diaphragm are reported, seven of whom have been operated on. Four patients had gastrointestinal symptoms, two respiratory symptoms, and one retrosternal pain; the other two were asymptomatic. In the first case the diagnosis was made at the time of thoracotomy, in the other eight it was suggested by radiological studies. The standard midline epigastric incision was used for repair in four cases and thoracotomy in two; the last patient was operated on through a preperitoneal subxiphoid route. This route has the advantage of not requiring a wide incision of peritoneum.