gebhart/patrepeval huggingface dataset:
How frequent are correlated changes in families of protein sequences? (1994)

A loss-of-function point mutation in a protein is often rescued by an additional mutation that compensates for the original physical change. According to one hypothesis, such compensation would be most effective in maintaining a structural motif if the two mutated residues were spatial neighbors. If this hypothesis were correct, one would expect that many such compensatory mutations have occurred during evolution and that present-day protein families show some degree of correlation in the occurrence of amino acid residues at positions whose side chains are in contact. Here, a statistical theory is presented which allows evaluation of correlations in a family of aligned protein sequences by assigning a scalar metric (such as charge or side-chain volume) to each type of amino acid and calculating correlation coefficients of these quantities at different positions. For the family of myoglobins it is found that there is a high correlation between fluctuations in neighboring charges. The correlation is close to what would be expected for total conservation of local charge. For the metric side-chain volume, on the other hand, no correlation could be found.
Simultaneous core sample measurements of elastic properties and resistivity at reservoir conditions employing a modified triaxial cell – a feasibility study (2009)

ABSTRACT Adaptations of existing triaxial cells for ultrasonic P‐ and S‐wave measurements are well documented. This paper proposes further modification of such a cell so that also resistivity measurements can be carried out simultaneously at reservoir conditions. By employing the top cap and the pedestal of the cell as electrodes, axial resistivity measurements are now feasible. In order to minimize the polarization effect of this two‐electrode arrangement, careful analyses have been carried out to optimize the choice of electrode coating and measurement frequency band. Radial resistivity measurements are also included in the system by introducing a strap‐electrode system. In a reservoir under production changes in both saturations, temperature (if steam injection) and stresses can take place. Therefore the modified triaxial system should be able to measure the integrated effects on the acoustic parameters and electric responses caused by variations in each of these parameters. The feasibility of the system to obtain such reliable information is demonstrated, employing a small selection of core samples. In the future such combined measurements on reservoir core samples can be used to link both seismic and electromagnetic observations to the actual earth model and constrain both modelling and inversion.
Micromechanical bulk acoustic wave resonator (2003)

We describe the use of bulk acoustic mode in micromechanical silicon resonators operating at radio frequencies. Based on measured data from the fabricated resonator (f/sub r//spl sim/14 MHz, Q>100 000) we analyze the characteristic impedance and signal levels in such microdevices and compare the values with conventional quartz crystals. We find that the high impedance level of microresonators can be met with integration of the readout electronics and that silicon can accommodate significantly larger vibration energy densities than quartz. Based on the results, we anticipate a wide application range for the micromechanical bulk acoustic wave structures in future wireless communication devices and microsensors.
Control of the optical Kerr effect in chirped-pulse-amplification systems using model-based phase shaping (2009)

Using phase shaping, the impact of the Kerr effect in a fiber-based chirped-pulse amplification (CPA) system is experimentally controlled. The technique is based on an analytical model describing the spectral phase owing to self-phase modulation in CPA systems. The method relies neither on complex phase measurements nor on time-consuming optimization routines. Nearly transform-limited pulses with energies as high as 1 mJ are produced, and a B integral being as high as 8 rad is accumulated in the main amplifier. The value of the B integral is determined by the method itself.
A study of binary tree traversal algorithms and a tag-free threaded representation (1986)

Abstract Starting from a stack-based binary tree traversal algorithm for preorder and/or inorder, we derive an algorithm recently discovered by J. M. Morris which requires neither stack nor tag fields. This algorithm may also be derived from the familiar threaded binary tree traversal algorithm. By demonstrating how searching may proceed in parallel with traversal, we show that the algorithm is “almost read-only”. This leads to a new representation for threaded binary trees requiring no tag fields. We show how to perform the usual operations efficiently for this representation, including strictly read-only traversal. In addition, we analyse the performance of variants of the traversal algorithm for binary trees represented with/without threads and with/without tag fields. Keywords: TreesTraversalsNovel Tag-Free Threaded RepresentationC.R. Categories: E.l[Data]Data Structures-treesF.2.2 [Analysis of Algorithms and Problem Complexity]Nonnumerical Algorithms and Problems-traversals
Crystal structure of potassium phyllodiantimonidogallate, KGaSb<sub>2</sub> (1991)

Article Crystal structure of potassium phyllodiantimonidogallate, KGaSb2 was published on December 1, 1991 in the journal Zeitschrift für Kristallographie - Crystalline Materials (volume 197, issue 1-4).
Cell-cell adhesion in plant grafting is facilitated by β-1,4-glucanases (2020)

Plant grafting is conducted for fruit and vegetable propagation, whereby a piece of living tissue is attached to another through cell-cell adhesion. However, graft compatibility limits combinations to closely related species, and the mechanism is poorly understood. We found that <i>Nicotiana</i> is capable of graft adhesion with a diverse range of angiosperms. Comparative transcriptomic analyses on graft combinations indicated that a subclade of β-1,4-glucanases secreted into the extracellular region facilitates cell wall reconstruction near the graft interface. Grafting was promoted by overexpression of the β-1,4-glucanase. Using <i>Nicotiana</i> stem as an interscion, we produced tomato fruits on rootstocks from other plant families. These findings demonstrate that the process of cell-cell adhesion is a potential target to enhance plant grafting techniques.
Concentration and temperature dependence on diffusivities of CO<sub>2</sub> and N<sub>2</sub> for poly(dimethyl, methylphenyl siloxane) (2007)

Abstract Experimental determination of solubility and diffusion coefficients of CO 2 and N 2 in poly(dimethyl, methylphenyl siloxane) (PMPS) for the pressure range 0–150 kPa and the temperature range of −10°C to 45°C is discussed. The absorption isotherms were measured by pressure decay equilibrium. Diffusion coefficients were determined by modeling the transient absorption data by Fickian diffusion. The value of solubility coefficient for CO 2 at 35°C was 1.21 ± 0.02 cm 3 CO 2 (STP)/(cm 3 polymer.atm) and it increased to 2.07 ± 0.01 cm 3 CO 2 (STP)/(cm 3 polymer.atm) at 1°C. The absorption isotherms of CO 2 obtained were linear for the pressure range 0–200 kPa and the enthalpy of sorption value was −10.82 kJ/mole for CO 2 . However, the diffusion coefficients of CO 2 changed with feed pressure. The diffusion coefficient of CO 2 in PMPS at 22°C and 128.6 kPa equilibrium pressure was 7.22 × 10 −6 cm 2 /s and thus the permeability value at these conditions was 1392 Barrers. The diffusion coefficients of CO 2 at 0°C and equilibrium pressures of 125.8 kPa and 10.5 kPa were 5.72 × 10 −6 cm 2 /s and 4.31 × 10 −6 cm 2 /s, respectively. Consequently, the CO 2 permeability in PMPS decreases by about 20% when the pressure is reduced from 125.8 to 10.5 kPa at 0°C. © 2007 American Institute of Chemical Engineers AIChE J, 2008
High data rate pulse regeneration using non-linear transmission line technology (NLTL) (2002)

The application of Non-Linear Transmission Line (NLTL) technology to the restoration of signal integrity in electro-optic back-planes technology is reported. The non-linear transmission line synthesized uses coplanar wave-guide because it has better performance than the micro-strip line.
Active control of the dynamics of a dual-spin spacecraft (1975)

Covers advancements in spacecraft and tactical and strategic missile systems, including subsystem design and application, mission design and analysis, materials and structures, developments in space sciences, space processing and manufacturing, space operations, and applications of space technologies to other fields.
The Production Algorithm of Pseudo-Random Number Generator Based on Compound Non-Linear Chaos System (2006)

Pseudo-random number generator designs based on the traditional characteristic polynomial and the register slow in speed, and short life cycle. This paper a compound chaos system is designed using the nonlinear Logistic mapping system and the partition mapping. A production algorithm of pseudo-random number generator based on the compound non-linear chaos system is introduced. Theoretical and experimental results show that the random sequences produced by this pseudo-random number generator has good cryptology performance, making the design an ideal pseudo-random number generator. A new chaos stream cipher encryption system is designed based on the algorithm. Experimental results show that this stream cipher is desirable in terms of security, costeffectiveness and pseudo-randomness .
High expression of TIAF-1 in chronic kidney and liver allograft rejection and in activated T-helper cells1 (2003)

TIAF-1 mRNA and protein are predominantly up-regulated in kidney and liver allografts with chronic rejection. This does not seem to be related to the cyclosporine A therapy. Expression of TIAF-1 in the lymphocytes during chronic allograft rejection may be related to the predominance of a Th2 response in this condition. The expression in the transplanted tissue may protect these cells from apoptosis.
A 201.4 GOPS 496 mW Real-Time Multi-Object Recognition Processor With Bio-Inspired Neural Perception Engine (2010)

A 201.4 GOPS real-time multi-object recognition processor is presented with a three-stage pipelined architecture. Visual perception based multi-object recognition algorithm is applied to give multiple attentions to multiple objects in the input image. For human-like multi-object perception, a neural perception engine is proposed with biologically inspired neural networks and fuzzy logic circuits. In the proposed hardware architecture, three recognition tasks (visual perception, descriptor generation, and object decision) are directly mapped to the neural perception engine, 16 SIMD processors including 128 processing elements, and decision processor, respectively, and executed in the pipeline to maximize throughput of the object recognition. For efficient task pipelining, proposed task/power manager balances the execution times of the three stages based on intelligent workload estimations. In addition, a 118.4 GB/s multi-casting network-on-chip is proposed for communication architecture with incorporating overall 21 IP blocks. For low-power object recognition, workload-aware dynamic power management is performed in chip-level. The 49 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> chip is fabricated in a 0.13 ¿m 8-metal CMOS process and contains 3.7 M gates and 396 KB on-chip SRAM. It achieves 60 frame/sec multi-object recognition up to 10 different objects for VGA (640 × 480) video input while dissipating 496 mW at 1.2 V. The obtained 8.2 mJ/frame energy efficiency is 3.2 times higher than the state-of-the-art recognition processor.
<p>COVID’s Razor: RAS Imbalance, the Common Denominator Across Disparate, Unexpected Aspects of COVID-19</p> (2020)

A modern iteration of Occam's Razor posits that "the simplest explanation is usually correct." Coronavirus Disease 2019 involves widespread organ damage and uneven mortality demographics, deemed unexpected from what was originally thought to be "a straightforward respiratory virus." The simplest explanation is that both the expected and unexpected aspects of COVID-19 share a common mechanism. Silent hypoxia, atypical acute respiratory distress syndrome (ARDS), stroke, olfactory loss, myocarditis, and increased mortality rates in the elderly, in men, in African-Americans, and in patients with obesity, diabetes, and cancer-all bear the fingerprints of the renin-angiotensin system (RAS) imbalance, suggesting that RAS is the common culprit. This article examines what RAS is and how it works, then from that baseline, the article presents the evidence suggesting RAS involvement in the disparate manifestations of COVID-19. Understanding the deeper workings of RAS helps one make sense of severe COVID-19. In addition, recognizing the role of RAS imbalance suggests potential routes to mitigate COVID-19 severity.
VISCOSITY STUDIES OF SYSTEM CaO‐MgO‐Al <sub>2</sub> O <sub>3</sub> ‐SiO <sub>2:</sub> II, CaO‐Al <sub>2</sub> O <sub>3</sub> ‐SiO <sub>2</sub> * (1948)

A bstract Viscosity data are presented covering those compositions in the CaO‐Al 2 O 3 ‐SiO 2 system which are liquid at 1500°C. The pattern of isokoms on the CaO‐Al 2 O 3 ‐SiO 2 face of the compositional tetrahedron which represents the CaO‐MgO‐Al 2 O 3 ‐SiO 2 system is a system of lines which roughly parallel the lines along which the lime content is constant. There are, however, considerable deviations from this parallelism in regions of very low and very high alumina content.
Bio-Removal Techniques of Nitrogen for Coking Wastewater (2005)

Based on engineering practice of coking wastewater treatment technology,some control methods of activated sludge culture and domestication during the opening adjustment for coking wastewater bio-removal of nitrogen treatment system have been introduced.The factors influencing nitrification and de-nitrification are discussed and experiences about adjustment and operation of coking wastewater is also summed up.
Kinetic Mechanism of Histidine-Tagged Homocitrate Synthase from <i>Saccharomyces cerevisiae</i> (2004)

Kinetic data have been collected suggesting a preferred sequential ordered kinetic mechanism for the histidine-tagged homocitrate synthase (HCS) from Saccharomyces cerevisiae with alpha-ketoglutarate binding before AcCoA and CoA released before homocitrate. Oxaloacetate is also a substrate for HCS, but with lower affinity than alpha-ketoglutarate. In agreement with the ordered kinetic mechanism desulfo-CoA is uncompetitive and citrate is competitive vs alpha-ketoglutarate. Varying AcCoA, citrate is a noncompetitive inhibitor as predicted, but CoA is noncompetitive vs AcCoA suggesting binding of CoA to E:homocitrate and E:alpha-ketoglutarate. The product CoA behaves in a manner identical to the dead-end analogue desulfo-CoA, suggesting an E:alpha-ketoglutarate:CoA dead-end complex. Data further suggest an irreversible reaction overall, in agreement with the downhill nature of the reaction as a result of homocitryl-CoA hydrolysis. Fluorescence titration data generally agree with the steady state data, but show finite binding of CoA and AcCoA to free enzyme, suggesting that the mechanism may be random with a high degree of synergism of binding between the reactants.
Expression in<i>Escherichia</i>of chemically synthesized gene for the human immune Interferon (1983)

A 454 base pair fragment of double stranded DNA consisting of a gene for a human immune interferon (hIFN-gamma), initiation and termination signals plus appropriate restriction endonuclease sites, was totally synthesized. The synthesis involved preparation of 62 oligodeoxyribonucleotides by rapid, solid phase procedures, and enzymatic ligation of the oligonucleotides. This synthetic gene was expressed in E. coli under the control of the lac UV5 promoter. The product has antiviral activity which was acid labile and completely neutralized by antiserum to hIFN-gamma but not by antiserum to hIFN-alpha or hIFN-beta. Molecular weight of hIFN-gamma produced by E. coli was estimated to be about 32,000 and 17,000 by gel filtration and SDS-polyacrylamide gel electrophoresis respectively.
Excitation of sideband emissions by a modulated electron beam during the CHARGE 2B Mission (1994)

Sideband wave emissions are secondary peaks in wave power observed at frequencies above and below the primary peak. Observed sideband amplitudes are usually reduced compared to the primary wave amplitude. During the recent CHARGE 2B ionospheric rocket mission, sideband waves were observed during an electron beam injection experiment. The beam current was modulated causing a peak in wave power at the modulation frequency and at certain times sidebands were observed along with the primary wave emission. A nonlinear coupling mechanism between the primary wave and a lower‐frequency wave is explored here to explain the presence of the sideband emissions. Comparison of the theoretical results with the wave data confirm this mechanism as a viable explanation for the observed sidebands.
Designing an Oral Sex Condom Promotion Program for Female Sex Workers in Singapore (2000)

In 1996, a health promotion program began to increase condom use for oral sex among female brothel-based sex workers in Singapore. It was initiated based upon increasing evidence of HIV transmission through oral sex as well as increased oral sex among these workers and their clients. Condom use for oral sex increased from 42.2 percent in 1996 prior to the program to 91.7 percent in mid-2000, with a corresponding decline in pharyngeal gonorrhea from its peak of 10.7 percent to 3.6 percent (compared to no significant changes in the two-year period before intervention). A significant increase in oral condom use with decreased pharyngeal gonorrhea incidence was observed among sex workers where brothel educational interventions took place compared with matched controls without brothel interventions. This case study describes the application of a health promotion framework to effect behavior change. Major differences in the behavioral risk-education strategies and message contents between this program and our earlier program on condom use for vaginal sex also are highlighted.
Activation of a mitogen‐activated protein kinase pathway in <i>Arabidopsis</i> by chitin (2004)

SUMMARY Chitin, a polysaccharide composed of beta-1-->4-linked N-acetyl-d-glucosamine, has been shown or implicated as a signal in plant defence and development. However, the key components of chitin perception and downstream signalling in non-leguminous plants are largely unknown. In recent years, mitogen-activated protein kinases (MAPKs) and their cascades were shown to transduce various extracellular stimuli into internal cellular responses. To investigate the possible involvement of MAPKs in chitin signalling in plants, the model plant Arabidopsis thaliana was treated with crab-shell chitin and also with the purified chitin oligomers (degree of polymerization, d.p. = 2-8). Both mRNA levels and kinase activity of two MAPK genes, AtMPK6 and AtMPK3, were monitored after treatment. The mRNA of AtMPK3 was strongly up-regulated by both chitin and its larger oligomers (d.p. = 6-8), but the mRNA of AtMPK6 did not appear to be regulated by these treatments. However, the kinase activity of both MAPKs was induced by chitin and the larger oligomers (d.p. = 6-8), with AtMPK6 much more strongly induced. In addition, WRKY22, WRKY29, WRKY33 and WRKY53, which encode four WRKY transcription factors that recognize TTGAC(C/T) W-box elements in promoters of numerous plant defence-related genes, were up-regulated by these treatments. WRKY33 and WRKY53 expression was induced by the transgenic expression of the tobacco MAPKK NtMEK2 active mutant NtMEK2(DD), suggesting a potential role for these WRKY transcription factors in relaying the signal generated from the MAPK cascade to downstream genes. These data suggest that AtMPK6/AtMPK3 and WRKY transcription factors (such as WRKY33 and WRKY53) may be important components of a pathway involved in chitin signalling in Arabidopsis plants.
Block copolymers by radical polymerization 3. Block copolymers of styrene, methyl acrylate, <i>n</i>‐methyl‐<i>n</i>‐vinylacetamide, 1‐vinyl‐2‐pyrrolidone (1982)

Abstract A polyazoinitiator obtained from 2,2′‐azoisobutyronitrile (AIBN) and a diol is used to prepare block copolymers according to the Smets procedure. Partial decomposition of the polyazoinitiator in presence of a monomer results in an azogroup‐containing prepolymer. Block copolymers are obtained decomposing the remaining azo groups in presence of a second monomer. Examples investigated are styrene/methyl acrylate, styrene/ N ‐methyl‐ N ‐vinylacetamide, methyl acrylate/ N ‐methyl‐ N ‐vinylacetamide, 1‐vinyl‐2‐pyrrolidone/acrylonitrile. Homopolymers are produced simultaneously. Up to 70% of block copolymers are formed in these reactions. Block copolymers of styrene/methyl acrylate have hard/soft segmented molecules. It is an elastic material with spherical, cylindrical and lamellar, resp. domain structures, depending on the composition.
Range-Modulated Pencil Beam Algorithm for Proton Dose Calculations (2001)

The range-modulated pencil beam algorithm (RMPBA) has been developed for proton treatment planning on the basis of the pencil beam algorithm (PBA) to reduce the calculation time yet realize sufficient accuracy. It uses the depth-dose distribution of the range-modulated beam as a central-axis term of pencil beams. The spread of the range-modulated pencil beam is derived by assuming that the protons pass through the average thickness of the ridge-filter. The accuracy of dose calculations by the RMPBA is verified by comparison with dose measurements in water performed using a silicon semiconductor detector. The results of the measured dose distributions agree well with those of the calculations using the RMPBA. Furthermore, the calculation time required by the RMPBA is one-sixth of that required by the PBA in the case of the six-step ridge-filter. Therefore, the dose-calculation method by the RMPBA will be useful and applicable to actual treatment planning of proton therapy.
Tumor Necrosis Factor α Stimulates Lipolysis in Adipocytes by Decreasing Gi Protein Concentrations (1999)

Prolonged treatment (12-24 h) of adipocytes with tumor necrosis factor alpha (TNFalpha) stimulates lipolysis. We have investigated the hypothesis that TNFalpha stimulates lipolysis by blocking the action of endogenous adenosine. Adipocytes were incubated for 48 h with TNFalpha, and lipolysis was measured in the absence or presence of adenosine deaminase. Without adenosine deaminase, the rate of glycerol release was 2-3-fold higher in the TNFalpha-treated cells, but with adenosine deaminase lipolysis increased in the controls to approximately that in the TNFalpha-treated cells. This suggests that TNFalpha blocks adenosine release or prevents its antilipolytic effect. Both N6-phenylisopropyl adenosine and nicotinic acid were less potent and efficacious inhibitors of lipolysis in treated cells. A decrease in the concentration of alpha-subunits of all three Gi subtypes was detected by Western blotting without a change in Gs proteins or beta-subunits. Gi2alpha was about 50% of control, whereas Gi1alpha and Gi3alpha were about 20 and 40% of control values, respectively. The time course of Gi down-regulation correlated with the stimulation of lipolysis. Furthermore, down-regulation of Gi by an alternative approach (prolonged incubation with N6-phenylisopropyl adenosine) stimulated lipolysis. These findings indicate that TNFalpha stimulates lipolysis by blunting endogenous inhibition of lipolysis. The mechanism appears to be a Gi protein down-regulation.