gebhart/patrepeval huggingface dataset:
Conformational Spread: The Propagation of Allosteric States in Large Multiprotein Complexes (2004)

The phenomenon of allostery is conventionally described for small symmetrical oligomeric proteins such as hemoglobin. Here we review experimental evidence from a variety of systems-including bacterial chemotaxis receptors, muscle ryanodine receptors, and actin filaments-showing that conformational changes can also propagate through extended lattices of protein molecules. We explore the statistical mechanics of idealized linear and two-dimensional arrays of allosteric proteins and show that, as in the analogous Ising models, arrays of closely packed units can show large-scale integrated behavior. We also discuss proteins that undergo conformational changes driven by the hydrolysis of ATP and give examples in which these changes propagate through linear chains of molecules. We suggest that conformational spread could provide the basis of a solid-state "circuitry" in a living cell, able to integrate biochemical and biophysical events over hundreds of protein molecules.
The Catalytic Dehydration of 2,3-Butanediol to Butadiene. II. Adsorption Equilibria (1950)

Further understanding of the reaction in which 2,3-butanediol is dehydrated over thorium oxide to methyl vinyl carbinol and butadiene has been gained by measuring the adsorption on thoria of water, methyl ethyl ketone and the above-mentioned diol, carbinol, and diene, at temperatures up to 200 °C. In some instances satisfactory isotherms could not be obtained because sufficient chemisorption occurred, followed by polymerization or dehydration reactions, to reduce seriously the area of thoria surface available for adsorption. There was evidence to suggest that water, alone of the vapours concerned, was taken up in greater amount than could be accounted for by adsorption. The bearing of this on the dehydration and its relation to the structure of the catalyst is briefly discussed. A suggestion in a previous paper(1) that water is the product which retards the catalytic dehydration is confirmed. At temperatures little above 50 °C, methyl vinyl carbinol is dehydrated by thoria to butadiene, while methyl ethyl ketone at room temperature undergoes self-condensation on thoria to yield a methyl heptenone. Also at quite low temperatures dimerization of butadiene brings about appreciable reduction of available surface. Some loss of activity on this account must therefore be expected when thoria is used to dehydrate 2,3-butanediol, even though butadiene is adsorbed only weakly.
Power electronics for the next century-first step (2002)

Preparations for the development of the next century power electronics started almost 3 years ago under the auspices of NASA/JPL's New Millennium Program (NMP). Solicitation of product development ideas from the industry members to miniaturize the power electronics, during initial NMP workshops, resulted in conceiving a product which combined the enabling High Density Interconnect (HDI) and the Application Specific Integrated Circuit (ASIC) technologies to achieve the NMP objectives. An industry team was formed to develop a Power Actuation and Switching Module (PASM) which would quadruple the capability of such a module over the existing hybrid technology and enable the development of many other space power system modules such as the shunt regulator module, battery charger module, dc-dc converter module with the eventual goal of the entire Power conditioning, Management And Distribution (PMAD) system on a single slice. JPL's decision to fly the PASM on Deep Space One (DS-1) as a Category 3 Experiment and quickly validate this technology provided additional impetus to this unique team of the industry and the government to bring this project to a successful end. This paper describes in detail the PASM development program including its electrical and mechanical design, and its integration and ongoing performance on DS-1. A road map for the future HDI based products is also included.
The Fate and Behavior of Mercury in Coal-Fired Power Plants (2002)

For the past 22 years in the Netherlands, the behavior of Hg in coal-fired power plants has been studied extensively. Coal from all over the world is fired in Dutch power stations. First, the Hg concentrations in these coals were measured. Second, the fate of the Hg during combustion was established by performing mass balance studies. On average, 43 +/- 30% of the Hg was present in the flue gases downstream of the electrostatic precipitator (ESP; dust collector). In individual cases, this figure can vary between 1 and 100%. Important parameters are the Cl content of the fuel and the flue gas temperature in the ESP. On average, 54 +/- 24% of the gaseous Hg was removed in the wet flue-gas desulfurization (FGD) systems, which are present at all Dutch coal-power stations. In individual cases, this removal can vary between 8% (outlier) and 72%. On average, the fate of Hg entering the power station in the coal was as follows: <1% in the bottom ash, 49% in the pulverized fuel ash (ash collected in the ESP), 16.6% in the FGD gypsum, 9% in the sludge of the wastewater treatment plant, 0.04% in the effluent of the wastewater treatment plant, 0.07% in fly dust (leaving the stack), and 25% as gaseous Hg in the flue gases and emitted into the air. The distribution of Hg over the streams leaving the FGD depends strongly on the installation. On average, 75% of the Hg was removed, and the final concentration of Hg in the emitted flue gases of the Dutch power stations was only -3 microg/m3(STP) at 6% O2. During co-combustion with biomass, the removal of Hg was similar to that during 100% coal firing. Speciation of Hg is a very important factor. An oxidized form (HgCl2) favors a high degree of removal. The conversion from Hg0 to HgCl2 is positively correlated with the Cl content of the fuel. A catalytic DENOX (SCR) favors the formation of oxidized Hg, and, in combination with a wet FGD, the total removal can be as high as 90%.
Complex cepstrum-based decomposition of speech for glottal source estimation (2009)

Homomorphic analysis is a well-known method for the separation of non-linearly combined signals. More particularly, the use of complex cepstrum for source-tract deconvolution has been discussed in various articles. However there exists no study which proposes a glottal flow estimation methodology based on cepstrum and reports effective results. In this paper, we show that complex cepstrum can be effectively used for glottal flow estimation by separating the causal and anticausal components of a windowed speech signal as done by the Zeros of the Z-Transform (ZZT) decomposition. Based on exactly the same principles presented for ZZT decomposition, windowing should be applied such that the windowed speech signals exhibit mixed-phase characteristics which conform the speech production model that the anticausal component is mainly due to the glottal flow open phase. The advantage of the complex cepstrum-based approach compared to the ZZT decomposition is its much higher speed. Index Terms: Speech Analysis, Homomorphic Processing, Glottal Source Estimation
Force and Flow Transition in Plowed Granular Media (2010)

We use plate drag to study the response of granular media to localized forcing as a function of volume fraction ϕ. A bifurcation in the force and flow occurs at the onset of dilatancy ϕc. Below ϕc rapid fluctuations in the drag force F(D) are observed. Above ϕc fluctuations in F(D) are periodic and increase in magnitude with ϕ. Velocity field measurements indicate that the bifurcation in F(D) results from the formation of stable shear bands above ϕc which are created and destroyed periodically during drag. A friction-based wedge flow model captures the dynamics for ϕ>ϕc.
Wafer-level defect-based testing using enhanced voltage stress and statistical test data evaluation (2003)

In this paper, we illustrate the effectiveness of wafer-level enhanced voltage stress (EVS) along with low voltage sweep (LVS), I/sub DDQ/ and other parametric tests to screen early life failure defects. Our experiment shows temporary undetected defects after repeated exposure to certain applied voltages. We demonstrate a statistical methodology to screen die with suspected early life failure defects.
Covalent modification of porous implants using extracellular matrix proteins to accelerate neovascularization (2006)

Healing associated with many polymeric biomedical implants commonly involves the formation of an avascular fibrous capsule. The lack of either formation or persistence of blood vessels in formed fibrous capsules, as well as a lack of new blood vessels within porous polymeric implants, often results in poor performance of the implant. The current study evaluated the use of extracellular matrix protein modification of a commonly used biomedical implant material, expanded polytetrafluoroethylene (ePTFE), as a mechanism to increase the neovascularization both within these porous implants and in tissue that forms in the peri-implant area. Discs of ePTFE were covalently modified with different extracellular matrix proteins including collagen type IV, fibronectin, and laminin type I. Discs were implanted into the adipose tissue of adult rats, and following a 5-week implant phase, histologic analysis of peri-implant tissue angiogenesis and implant neovascularization was performed. Striking differences were observed in angiogenic and neovascularization responses to matrix-modified ePTFE when compared with control, untreated ePTFE. Fibronectin treatment resulted in an extensive inflammatory response but, relative to the degree of inflammation, limited evidence of tissue angiogenesis or polymer neovascularization. Collagen type IV treatment groups exhibited a significant increase in angiogenesis in the peri-implant tissue with minimal evidence of implant neovascularization. In contrast to all other implant modifications, laminin type 1-treated ePTFE samples stimulated an extensive peri-implant tissue angiogenic response and a coordinate neovascularization of the porous interstices of the biomaterial.
Atmospheric Monitoring with LIDAR method for TA Experiment (2005)

M. Chikawa, T. Benno, N. Hayashida, S. Udo, M Teshima and Telescope Array Experiment collaborations b (a) Department of Physics, Kinki University, Osaka 577-8502 Japan (b) Institute for Cosmic Ray Research, University of Tokyo, Chiba 272-8582 Japan (c)Max-Planck-Institute for Physics, Foehringer Ring 6, 80805 Munchen, Germany Presenter: M.Chikawa (mchikawa@phys.kindai.ac.jp), jap-chikawa-M-abs1-he15-poster
Copper transport from ceruloplasmin: characterization of the cellular uptake mechanism (1990)

Copper uptake from 67Cu-labeled ceruloplasmin (67CuCp) was studied in K-562 cells, a human erythroleukemic cell line. 67CuCp was prepared by an ascorbate-catalyzed exchange of recrystallized ceruloplasmin with 67CuCl2. The labeled protein was treated with Chelex-100 and gel filtration to ensure that 67Cu was tightly bound to the structure. 67CuCp bound specifically to the K-562 cells at 4 degrees C. The binding was linear with protein in the range of 200-800 nM and in the presence of 3% albumin. In this concentration range, 67CuCl2 showed no binding that could be interpreted as specific; 80-90% of the cell-bound 67Cu was removed by washing the cells with acid buffer. When binding was attempted at 37 degrees C, a significant fraction of the 67Cu resisted acid washing and with time accumulated in the cells. Fractionating the cytosolic components on Percoll gradients located the 67Cu in buoyant fractions of densities 1.030-1.05, with a peak at 1.035. Repeating the experiment with 125I-labeled ceruloplasmin failed to localize any 125I label in Percoll fractions; very little 125I was detected in the cytosol. Double-labeled 67Cu-125I-ceruloplasmin confirmed that copper and not the protein moiety of ceruloplasmin was taken up by the cells. The uptake reaction was inhibited by 1 mM bathocuproine sulfonate and by 1 mM sodium iproniazid. Ascorbate (100 microM) strongly stimulated uptake. These studies provide evidence that K-562 cells are able to extract copper atoms from ceruloplasmin and transport the copper to the cytosol.(ABSTRACT TRUNCATED AT 250 WORDS)
Efficient metabolic pathway engineering in transgenic tobacco and tomato plastids with synthetic multigene operons (2013)

The engineering of complex metabolic pathways requires the concerted expression of multiple genes. In plastids (chloroplasts) of plant cells, genes are organized in operons that are coexpressed as polycistronic transcripts and then often are processed further into monocistronic mRNAs. Here we have used the tocochromanol pathway (providing tocopherols and tocotrienols, collectively also referred to as "vitamin E") as an example to establish principles of successful multigene engineering by stable transformation of the chloroplast genome, a technology not afflicted with epigenetic variation and/or instability of transgene expression. Testing a series of single-gene constructs (encoding homogentisate phytyltransferase, tocopherol cyclase, and γ-tocopherol methyltransferase) and rationally designed synthetic operons in tobacco and tomato plants, we (i) confirmed previous results suggesting homogentisate phytyltransferase as the limiting enzymatic step in the pathway, (ii) comparatively characterized the bottlenecks in tocopherol biosynthesis in transplastomic leaves and tomato fruits, and (iii) achieved an up to tenfold increase in total tocochromanol accumulation. In addition, our results uncovered an unexpected light-dependent regulatory link between tocochromanol metabolism and the pathways of photosynthetic pigment biosynthesis. The synthetic operon design developed here will facilitate future synthetic biology applications in plastids, especially the design of artificial operons that introduce novel biochemical pathways into plants.
AS ROCHAS ULTRABÁSICAS DA SERRA DO ESPINHAÇO, MG (1972)

An alpine-type serpentine belt, situated in the transition zone between the mioand eugeosyncline of the Pre-cambrian Minas Series in the State of Minas Gerais, Brazil, shows an extension of at least 300 km. From petrographic evidence, a four step evolution and alteration scheme can be deduced:  1 ) peridotite;  2 ) serpentinization;  3) chloritization and amphibolization;  4) talquification + carbonatization. Some of the ultrabasic bodies show a chromite mineralization with economic possibilities in part. Regional correlations may indicate a major extension of this serpentine belt, specially to the north, accompanying the quartzites of the Minas Series.
Synthesis, HPLC Enantioresolution, and X‐ray Analysis of a New Series of C5‐methyl Pyridazines as <i>N</i>‐Formyl Peptide Receptor (FPR) Agonists (2013)

The synthesis of three racemates and the corresponding non-chiral analogues of a C5-methyl pyridazine series is described here, as well as the isolation of pure enantiomers and their absolute configuration assignment. In order to obtain optically active compounds, direct chromatographic methods of separation by HPLC-UV were investigated using four chiral stationary phases (CSPs: Lux Amylose-2, Lux Cellulose-1, Lux Cellulose-2 and Lux Cellulose-3). The best resolution was achieved using amylose tris(5-chloro-2-methylphenylcarbamate) (Lux Amylose-2), and single enantiomers were isolated on a semipreparative scale with high enantiomeric excess, suitable for biological assays. The absolute configuration of optically active compounds was unequivocally established by X-ray crystallographic analysis and comparative chiral HPLC-UV profile. All compounds of the series were tested for formyl peptide receptor (FPR) agonist activity, and four were found to be active, with EC50 values in the micromolar range.
The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed (2013)

Nucleosome occupancy plays a key role in regulating access to eukaryotic genomes. Although various chromatin regulatory complexes are known to regulate nucleosome occupancy, the role of DNA sequence in this regulation remains unclear, particularly in mammals. To address this problem, we measured nucleosome distribution at high temporal resolution in human cells at hundreds of genes during the reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV). We show that nucleosome redistribution peaks at 24 h post-KSHV reactivation and that the nucleosomal redistributions are widespread and transient. To clarify the role of DNA sequence in these nucleosomal redistributions, we compared the genes with altered nucleosome distribution to a sequence-based computer model and in vitro-assembled nucleosomes. We demonstrate that both the predicted model and the assembled nucleosome distributions are concordant with the majority of nucleosome redistributions at 24 h post-KSHV reactivation. We suggest a model in which loci are held in an unfavorable chromatin architecture and "spring" to a transient intermediate state directed by DNA sequence information. We propose that DNA sequence plays a more considerable role in the regulation of nucleosome positions than was previously appreciated. The surprising findings that nucleosome redistributions are widespread, transient, and DNA-directed shift the current perspective regarding regulation of nucleosome distribution in humans.
Characterization of Complement Factor H Binding to<i>Yersinia enterocolitica</i>Serotype O:3 (2008)

A number of bacteria bind factor H (FH), the negative regulator of the alternative complement pathway, to avoid complement-mediated killing. Here we show that a gram-negative enteric pathogen, Yersinia enterocolitica serotype O:3, uses two virulence-related outer membrane (OM) proteins to bind FH. With Y. enterocolitica O:3 mutant strains displaying different combinations of surface factors relevant to complement resistance, we demonstrated that the major receptor for FH is the OM protein YadA. Another OM protein, Ail, also contributes to FH binding provided that it is not blocked by distal parts of the lipopolysaccharide (i.e., the O antigen and the outer core hexasaccharide). Importantly, we demonstrated that surface-bound FH was functional; both YadA- and Ail-bound FH displayed cofactor activity for factor I-mediated cleavage of C3b. With truncated recombinant FH constructs, we located the binding site of Ail specifically to short consensus repeats 6 and 7 of FH, while YadA showed a novel type of FH-binding pattern and appears to bind FH throughout the entire FH molecule. We thus conclude that Y. enterocolitica, via YadA and Ail, recruits functionally active FH to its surface. FH binding appears to be an important mechanism of the complement resistance of this pathogen.
Application of a Ring Pseudorandom Aperture for Transverse Section Tomography (1977)

Tomographic images of gamma ray sources have been obtained by the use of a one-dimensional pseudorandom aperture and computerized digital reconstruction. The binary code is laid out on the surface of a cylinder. The source to be imaged must be located within the cylinder and detectors are placed outside and facing inward. The length of the code is matched to the cylinder circumference so that its rotation provides a complete pseudorandom time modulation for each source-detector combination. Counts from each detector are separately stored as a function of the rotation phase angle. Subsequent correlation computations give the reconstructed source intensity along any angle within the fan for each detector. Experimentally measured variances confirm the predictions of a theoretical analysis of the statistics of pseudorandom imaging given elsewhere. We have used only three detectors to date, but the scheme will easily accommodate a complete detector ring to maximize the photon counting efficiency and permit a full tomographic reconstruction of the section.
Fluorescence Ureteral Visualization in Human Laparoscopic Colorectal Surgery Using Methylene Blue (2016)

Ureteral fluorescence imaging using MB proved to be safe and feasible. However, the present technique does not provide practical advantage over conventional laparoscopic imaging for identification of the ureter during laparoscopic colorectal surgery. Future research is necessary to explore more extensive dose finding, alternative fluorescent dyes, or improvement of the imaging system to make this application clinically beneficial.
Fourier-Transform-Limited Performance of a Lithographically Scribed Planar Holographic Bragg Reflector (2004)

Planar holographic Bragg reflectors (HBRs) are computer-generated two-dimensional (2-D) slab-waveguide-based refractive-index gratings. HBRs provide the spectral filtering function of fiber Bragg gratings but-enabled by the 2-D slab waveguide geometry-add the capability to spatially route signals. Here, we report on a silica-on-silicon-based focusing HBR providing 17 GHz, essentially Fourier-transform-limited, spectral resolution. This result comprises the first time deep ultraviolet projection lithography is successfully applied to the fabrication of a 2-D Bragg reflector on the centimeter scale. The 2-D Bragg filter occupies a compact 0.3 cm/sup 2/ footprint and provides diffraction-limited spatial input-output beam mapping.
THE ROLE OF AFFERENT LYMPHATICS IN THE REJECTION OF SKIN HOMOGRAFTS (1968)

Experiments have been carried out on guinea pigs of two isogenic strains to elucidate the role of afferent lymphatic vessels in the rejection of orthotopic skin homografts. Graft beds were prepared in partially isolated skin flaps with an intact sustaining vascular "umbilical cord" in which a lymphatic connection with the host could be retained or abolished at will. In the absence of demonstrable lymphatic connections between flap and host, intra-flap homografts long outlived similar grafts transplanted to conventional sites in intact skin and, rather than being specifically rejected, died as a consequence of ischemic necrosis of the flap. When lymphatic drainage was retained, intra-flap homografts were rejected in the usual manner. Hosts of long-term intra-flap homografts did not develop sensitivity, as evidenced by the "first set" type rejection of subsequent test grafts, or by the long-term survival of a second skin graft transplanted to a new flap raised on the opposite side of the host's body. Intra-flap skin homografts were rejected if (a) the hosts had been presensitized, (b) they were grafted concomitantly with a skin homograft placed in a conventional site, or inoculated with a suspension of donor lymphoid cells, or (c) if the lymphatic drainage was restored by reimplantation of the hitherto partially isolated flap to an appropriate vascular bed. These findings and others indicate that an intact lymphatic drainage in its bed is essential for an orthotopic skin homograft to sensitize its host. Various experiments were carried out in which intra-flap homografts were used as "indicators" for the acquisition of specific active or adoptive immunity by their hosts. By transplanting skin homografts to conventional beds concomitantly with intra-flap grafts and then excising the former at various intervals, it has been found that a graft must be in residence for a minimum period of 4 days to evoke the development of a detectable level of sensitivity in the host. Furthermore, by replacing either freshly prepared or long-term skin flaps bearing skin homografts in vascular beds on the trunk and determining the subsequent survival times of the homografts, evidence has been obtained suggesting that reestablishment of a functional lymphatic system in a free skin graft may take as long as 9 days. Using intra-flap homografts as indicators of adoptive immunization of the host, we found that as few as 50 x 10(6) isologous peripheral blood leukocytes from a specifically sensitized animal will transfer an effective level of sensitivity. We also found that hyperimmune serum, in relatively large amount, exerts a weak but definite adverse effect upon either freshly or recently transplanted intra-flap grafts.