gebhart/patrepeval huggingface dataset:
The Devil and Holy Water: Protein and Carbon Nanotube Hybrids (2013)

Integrating carbon nanotubes (CNTs) with biological systems to form hybrid functional assemblies is an innovative research area with great promise for medical, nanotechnology, and materials science applications. The specifics of molecular recognition and catalytic activity of proteins combined with the mechanical and electronic properties of CNTs provides opportunities for physicists, chemists, biologists, and materials scientists to understand and develop new nanomachines, sensors, or any of a number of other molecular assemblies. Researchers know relatively little about the structure, function, and spatial orientation of proteins noncovalently adsorbed on CNTs, yet because the interaction of CNTs with proteins depends strongly on the tridimensional structure of the proteins, many of these questions can be answered in simple terms. In this Account, we describe recent research investigating the properties of CNT/protein hybrids. Proteins act to solvate CNTs and may sort them according to diameter or chirality. In turn, CNTs can support and immobilize enzymes, creating functional materials. Additional applications include proteins that assemble ordered hierarchical objects containing CNTs, and CNTs that act as protein carriers for vaccines, for example. Protein/CNT hybrids can form bioscaffolds and can serve as therapeutic and imaging materials. Proteins can detect CNTs or coat them to make them biocompatible. One of the more challenging applications for protein/CNT hybrids is to make CNT substrates for cell growth and neural interfacing applications. The challenge arises from the structures' interactions with living cells, which poses questions surrounding the (nano)toxicology of CNTs and whether and how CNTs can detect biological processes or sense them as they occur. The surface chemistry of CNTs and proteins, including interactions such as π-π stacking interactions, hydrophobic interactions, surfactant-like interactions, and charge-π interactions, governs the wealth of structures, processes, and functions that appear when such different types of molecules interact. Each residue stars in one of two main roles, and understanding which residues are best suited for which type of interaction can lead to the design of new hybrids. Nonlocally, the peptide or protein primary, secondary, and tertiary structures govern the binding of proteins by CNTs. The conjugation of proteins with CNTs presents some serious difficulties both experimentally and culturally (such as bridging the "jargon barrier" across disciplines). The intersection of these fields lies between communities characterized by distinctly different approaches and methodologies. However, the examples of this Account illustrate that when this barrier is overcome, the exploitation of hybrid CNT-protein systems offers great potential.
On the Utility of Chirp Modulation for Digital Signaling (1973)

The issue of signal selection in binary data transmission is presented. The question of the relative utility of linear frequency sweeping (LFS or chirp), compared to PSK and FSK, in terms of error probability and spectrum usage, is discussed. The transmission media considered are the coherent, partially coherent, Rayleigh, and Rician channel models. Theoretically, LFS has unconditionally superior characteristics in the partially coherent and fading cases, for certain ranges of channel conditions. This is due to the more negative values of cross-coherence parameters possible with the LFS signal set over the FSK signal set. For the fading channel, theoretical supremacy of LFS over FSK depends upon the specular-to-Rayleigh signal power ratio and the adjustability of in-phase cross coherence, with a constraint upon quadrature phase cross coherence. From a practical standpoint, coherent reception of the LFS signal set has severe limitations. These are manifested primarily in two aspects: the need for phase synchronization of a chirp signal set, and the fact that the optimum value of cross coherence is highly sensitive to synchronization channel signal-to-noise ratio (SNR), and/or spectral-to-Rayleigh signal power ratio. The latter would require that modulation characteristics track the channel conditions in order to achieve the supremacy in performance theoretically predicted by optimization of the cross-coherence parameter in LFS.
Intravirion reverse transcripts in the peripheral blood plasma on human immunodeficiency virus type 1-infected individuals (1994)

Variable levels of viral DNA have been demonstrated within human immunodeficiency virus type 1 (HIV-1) virions purified from cell cultures. In the present studies, it is demonstrated that DNase-resistant viral DNA is associated with HIV-1 virions purified from the peripheral blood plasma of both symptomatic and asymptomatic HIV-1-infected individuals. The differences in viral DNA copy numbers, detected by quantitative PCR in various regions of the HIV-1 genome, indicated that the intravirion HIV-1 DNA is frequently, but perhaps not totally, the result of partial reverse transcription. These in vivo data suggest that it may be valuable to further investigate the impact of virion-associated viral DNA upon the efficiency of intra- and interhost HIV-1 transmission modes.
Intestinal Fucose as a Mediator of Host–Microbe Symbiosis (2015)

Fucose is an L-configuration sugar found abundantly in the mammalian gut. It has long been known to be induced there by the presence of bacteria, but only recently have some of the molecular mechanisms behind this process been uncovered. New work suggests that fucose can have a protective role in both gut-centered and systemic infection and inflammation. This review highlights recent studies showing that, in addition to acting as a food source for beneficial gut symbionts, host fucose can suppress the virulence of pathogens and pathobionts. The relevance of gut fucosylation to human diseases also is discussed.
Making Bertha Drive—An Autonomous Journey on a Historic Route (2014)

Abstract-125 years after Bertha Benz completed the first overland journey in automotive history, the Mercedes Benz S-Class S 500 INTELLIGENT DRIVE followed the same route from Mannheim to Pforzheim, Germany, in fully autonomous manner. The autonomous vehicle was equipped with close-to-production sensor hardware and relied solely on vision and radar sensors in combination with accurate digital maps to obtain a comprehensive understanding of complex traffic situations. The historic Bertha Benz Memorial Route is particularly challenging for autonomous driving. The course taken by the autonomous vehicle had a length of 103 km and covered rural roads, 23 small villages and major cities (e.g. downtown Mannheim and Heidelberg). The route posed a large variety of difficult traffic scenarios including intersections with and without traffic lights, roundabouts, and narrow passages with oncoming traffic. This paper gives an overview of the autonomous vehicle and presents details on vision and radar-based perception, digital road maps and video-based self-localization, as well as motion planning in complex urban scenarios.
Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization (1996)

Pseudomonas sp. strain ADP metabolizes atrazine to carbon dioxide and ammonia via the intermediate hydroxyatrazine. The genetic potential to produce hydroxyatrazine was previously attributed to a 1.9-kb AvaI DNA fragment from strain ADP (M. L. de Souza, L. P. Wackett, K. L. Boundy-Mills, R. T. Mandelbaum, and M. J. Sadowsky, Appl. Environ. Microbiol. 61:3373-3378, 1995). In this study, sequence analysis of the 1.9-kb AvaI fragment indicated that a single open reading frame, atzA, encoded an activity transforming atrazine to hydroxyatrazine. The open reading frame for the chlorohydrolase was determined by sequencing to be 1,419 nucleotides and encodes a 473-amino-acid protein with a predicted subunit molecular weight of 52,421. The deduced amino acid sequence matched the first 10 amino acids determined by protein microsequencing. The protein AtzA was purified to homogeneity by ammonium sulfate precipitation and anion-exchange chromatography. The subunit and holoenzyme molecular weights were 60,000 and 245,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration chromatography, respectively. The purified enzyme in H2(18)O yielded [18O]hydroxyatrazine, indicating that AtzA is a chlorohydrolase and not an oxygenase. The most related protein sequence in GenBank was that of TrzA, 41% identity, from Rhodococcus corallinus NRRL B-15444R. TrzA catalyzes the deamination of melamine and the dechlorination of deethylatrazine and desisopropylatrazine but is not active with atrazine. AtzA catalyzes the dechlorination of atrazine, simazine, and desethylatrazine but is not active with melamine, terbutylazine, or desethyldesisopropylatrazine. Our results indicate that AtzA is a novel atrazine-dechlorinating enzyme with fairly restricted substrate specificity and contributes to the microbial hydrolysis of atrazine to hydroxyatrazine in soils and groundwater.
The analysis of the intramacrophagic virulome ofBrucella suisdeciphers the environment encountered by the pathogen inside the macrophage host cell (2002)

The pathogen Brucella suis resides and multiplies within a phagocytic vacuole of its host cell, the macrophage. The resulting complex relationship has been investigated by the analysis of the set of genes required for virulence, which we call intramacrophagic virulome. Ten thousand two hundred and seventy-two miniTn5 mutants of B. suis constitutively expressing gfp were screened by fluorescence microscopy for lack of intracellular multiplication in human macrophages. One hundred thirty-one such mutants affected in 59 different genes could be isolated, and a function was ascribed to 53 of them. We identified genes involved in (i) global adaptation to the intracellular environment, (ii) amino acid, and (iii) nucleotide synthesis, (iv) sugar metabolism, (v) oxidoreduction, (vi) nitrogen metabolism, (vii) regulation, (viii) disulphide bond formation, and (ix) lipopolysaccharide biosynthesis. Results led to the conclusion that the replicative compartment of B. suis is poor in nutrients and characterized by low oxygen tension, and that nitrate may be used for anaerobic respiration. Intramacrophagic virulome analysis hence allowed the description of the nature of the replicative vacuole of the pathogen in the macrophage and extended our understanding of the niche in which B. suis resides. We propose calling this specific compartment "brucellosome."
Macrophage infiltration in acute coronary syndromes. Implications for plaque rupture. (1994)

Macrophage-rich areas are more frequently found in patients with unstable angina and non-Q-wave myocardial infarction. This suggests that macrophages are a marker of unstable atherosclerotic plaques and may play a significant role in the pathophysiology of acute coronary syndromes.
Dial a program—An HF remote selection cable television system (1970)

A new concept in cable television systems is described in which the general form of the network is similar to the local distribution network of a telephone system. Each television set is provided with an individual connection to a program exchange where the subscriber may select, by means of a remotely operated switch, the program of his choice from the unlimited number of programs available at the exchange. The system is based on the technology of HF multipair cable television systems extensively used in Great Britain. The system is flexible in use and the facilities for two-way transmission, subscription TV, audience rating, etc., are explained.
Solution-state structure of a fully alternately 2′-F/2′-OMe modified 42-nt dimeric siRNA construct (2010)

A high-resolution solution structure of a stable 42-nt RNA dimeric construct has been derived based on a high number of NMR observables including nuclear overhauser effects (NOEs), J-coupling constants and residual dipolar couplings (RDCs), which were all obtained with isotopically unlabeled molecules. Two 21-nt siRNA that efficiently hybridize consist of ribose units that were alternately substituted by 2'-fluoro or 2'-methoxy groups. Structure calculations utilized a set of H-F RDC values for all 21 2'-fluoro modified nucleotides under conditions of weak alignment achieved by Pf1 phages. A completely 2'-F/2'-OMe modified dimeric RNA construct adopts an antiparallel double-helical structure consisting of 19 Watson-Crick base pairs with additional 3' UU overhangs and a 5' phosphate group on the antisense strand. NMR data suggest that the stability of individual base pairs is not uniform throughout the construct. While most of the double helical segment exhibits well dispersed imino resonances, the last three base pairs either display uncharacteristic chemical shifts of imino protons or absence of imino resonances even at lower temperatures. Accessibility of imino protons to solvent exchange suggests a difference in stability of duplex ends, which might be of importance for incorporation of the guide siRNA strand into a RISC.
Defective Neuromuscular Synapses in Mice Lacking Amyloid Precursor Protein (APP) and APP-Like Protein 2 (2005)

Biochemical and genetic studies place the amyloid precursor protein (APP) at the center stage of Alzheimer's disease (AD) pathogenesis. Although mutations in the APP gene lead to dominant inheritance of familial AD, the normal function of APP remains elusive. Here, we report that the APP family of proteins plays an essential role in the development of neuromuscular synapses. Mice deficient in APP and its homolog APP-like protein 2 (APLP2) exhibit aberrant apposition of presynaptic marker proteins with postsynaptic acetylcholine receptors and excessive nerve terminal sprouting. The number of synaptic vesicles at presynaptic terminals is dramatically reduced. These structural abnormalities are accompanied by defective neurotransmitter release and a high incidence of synaptic failure. Our results identify APP/APLP2 as key regulators of structure and function of developing neuromuscular synapses.
Speckle phase averaging in high-resolution color holography (1997)

Interest in wavelength multiplexing in holography derives naturally from the need for realistic color rendition as well as from resolution requirements. Imaging in coherent illumination is compromised by speckle. Speckle is prejudicial to quality, sharpness, contrast—in a word, to the fidelity of reproduction or holographic reconstruction. In incoherent light these patterns are canceled by spatial phase averaging. Incoherent light can indeed be regarded as a superposition of a very large number of coherent components whose phase factors are distributed at random. It is demonstrated that the averaging effect, ultimately caused by the law of large numbers, is achieved by the superposition of only three components, thus allowing simultaneously a true color rendition and an improvement in spatial resolution. The spatial statistical behavior of the amplitude of the sum of three intrinsically coherent waves, when they are incoherently superposed in an imaging system, is investigated. A random variable representing the amplitude of this sum is introduced. Then the cumulative probability function and the probability density function of the resulting amplitude are calculated. The white-light (infinite-wave illumination) case and the purely coherent (one-wave) case are analyzed. The results are interpreted with a heuristic vector model.
A Live Attenuated Influenza A(H5N1) Vaccine Induces Long-Term Immunity in the Absence of a Primary Antibody Response (2014)

NCT01109329.
Operating characteristics of single-quantum-well AlGaAs/GaAs high-power lasers (1988)

The operating characteristics of six types of graded-index separate confinement heterostructure single-quantum-well wide-stripe lasers grown by metalorganic chemical vapor deposition are reported. The lasers exhibited intrinsic mode losses as low as 3 cm/sup -1/ and internal quantum efficiencies near unity. Measured differential gain coefficients range from 3.7 to 6.5 cm/A, and extrapolated transparency current densities range from 54 to 145 A/cm/sup 2/. These wide-stripe lasers are typically multilongitudinal mode and exhibit narrowing of the gain envelope and lateral far-field pattern as the cavity length increases. The high value of T/sub 0/(>200 K) at long cavity lengths in conjunction with the low current density permits junction-side-up operation to CW optical powers of 0.5-0.7 W/facet, at which level catastrophic facet damage occurs on the uncoated devices. A maximum power conversion efficiency of 57% was measured on the laser structure exhibiting the lowest threshold current.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
What sets the long-term level of sympathetic nerve activity: is there a role for arterial baroreceptors? (2004)

Much of our knowledge of the influence of the sympathetic nervous system on the control of blood pressure is built on experimental approaches that focus very much on time scales <24 h. Although direct recordings of sympathetic nerve activity (SNA) over short time scales provide important information, it is difficult to place their relevance over the longer term where the development of chronic changes in blood pressure are likely to be a mixture of hormonal, renal, and neural influences. Recently new experimental approaches are now revealing a possible role for arterial baroreceptors in the chronic regulation of SNA. These studies reveal that chronic increases in blood pressure are associated with chronic changes in SNA that may be due to nonresetting of the blood pressure-SNA baroreflex relationship. This review discusses the implications of such information, highlighting new technologies for long-term recording of SNA that appear to hold much promise for revealing the role of SNA to the kidney for the long-term control of blood pressure.
Syntheses and spectral properties of β‐iodoureas and 2‐amino‐4,4‐diphenyl‐2‐oxazolines (1991)

Abstract The syntheses of N ‐( trans ‐2‐iodocyclohexyl)‐ 1–4 , N ‐(2‐iodo‐3,3‐dimethylbutyl) 5 , and N ‐(2‐iodo‐1,1‐diphenylethyl)ureas 6, 7 and the cyclization of 6 and 7 into 2‐amino‐2‐oxazoline derivatives 8, 9 are reported. The structures of prepared compounds are based on analytical and spectroscopic data.
Improved Localization of Cortical Activity By Combining EEG and MEG with MRI Cortical Surface Reconstruction (2002)

We describe a comprehensive linear approach to the problem of imaging brain activity with high temporal as well as spatial resolution based on combining EEG and MEG data with anatomical constraints derived from MRI images. The “inverse problem” of estimating the distribution of dipole strengths over the cortical surface is highly underdetermined, even given closely spaced EEG and MEG recordings. We have obtained much better solutions to this problem by explicitly incorporating both local cortical orientation as well as spatial covariance of sources and sensors into our for-
New protein crosslinking reagents that are cleaved by mild acid (1989)

New homo- and heterobifunctional cross-linking reagents have been synthesized. These reagents are based on ortho ester, acetal, and ketal functionalities that undergo acid-catalyzed dissociation but are base stable. The protein-reactive group in all the homobifunctional reagents is a maleimide group; the heterobifunctional acetal cross-linker has a maleimide group at one end and an N-hydroxysuccinimide ester at the other. These reagents have been used to cross-link diphtheria toxin (DT) to itself to give covalently cross-linked DT dimer or to conjugate DT monomer to the anti-CD5 antibody, T101. The hydrolysis of these cross-linked proteins was studied as a function of pH. Cleavage rates vary from minutes to hours at the pH of acidified cellular vesicles (approximately pH 5.4), ortho esters being the fastest, acetals the slowest, and ketals intermediate, but the cross-linked products are approximately 100 times more stable at the vascular pH of 7.4 and 1000 times more stable at a storage pH of 8.4 in all cases. The utility of these reagents in the reversible blockade of a toxic protein functional domain was demonstrated by using cross-linked DT dimer where the blocking and unblocking of toxin binding sites correlates with cellular toxicity. Of the different cross-linkers described, the acetone ketal, bis(maleimidoethoxy)propane (BMEP), appears to be the most promising in the construction of highly efficacious immunotoxins.
<title>Trends in optical design of projection lenses for UV and EUV lithography</title> (2000)

The continuing trend towards higher integration density of microelectronic circuits requires steadily decreasing feature sizes. The SIA roadmap defines the technologies needed to meet this challenges. One of the fundamental requirements for lithography with a resolution of 100 nm and below is the development of new high-performance optical designs for projection lenses.
Toxicity, Binding, and Permeability Analyses of Four Bacillus thuringiensis Cry1 δ-Endotoxins Using Brush Border Membrane Vesicles of Spodoptera exigua and Spodoptera frugiperda (1999)

The binding and pore formation properties of four Bacillus thuringiensis Cry1 toxins were analyzed by using brush border membrane vesicles from Spodoptera exigua and Spodoptera frugiperda, and the results were compared to the results of toxicity bioassays. Cry1Fa was highly toxic and Cry1Ac was nontoxic to S. exigua and S. frugiperda larvae, while Cry1Ca was highly toxic to S. exigua and weakly toxic to S. frugiperda. In contrast, Cry1Bb was active against S. frugiperda but only marginally active against S. exigua. Bioassays performed with iodinated Cry1Bb, Cry1Fa, and Cry1Ca showed that the effects of iodination on toxin activity were different. The toxicities of I-labeled Cry1Bb and Cry1Fa against Spodoptera species were significantly less than the toxicities of the unlabeled toxins, while Cry1Ca retained its insecticidal activity when it was labeled with 125I. Binding assays showed that iodination prevented Cry1Fa from binding to Spodoptera brush border membrane vesicles. 125I-labeled Cry1Ac, Cry1Bb, and Cry1Ca bound with high-affinities to brush border membrane vesicles from S. exigua and S. frugiperda. Competition binding experiments performed with heterologous toxins revealed two major binding sites. Cry1Ac and Cry1Fa have a common binding site, and Cry1Bb, Cry1C, and Cry1Fa have a second common binding site. No obvious relationship between dissociation of bound toxins from brush border membrane vesicles and toxicity was detected. Cry1 toxins were also tested for the ability to alter the permeability of membrane vesicles, as measured by a light scattering assay. Cry1 proteins toxic to Spodoptera larvae permeabilized brush border membrane vesicles, but the extent of permeabilization did not necessarily correlate with in vivo toxicity.