gebhart/patrepeval huggingface dataset:
N‐ and C‐terminal peptide sequences are essential for enzyme assembly, allosteric, and/or catalytic properties of ADP‐glucose pyrophosphorylase (1998)

ADP-glucose pyrophosphorylase is a key regulatory enzyme in starch synthesis in most plant tissues. Unlike the allosteric regulatory dependent properties of the leaf enzyme, the enzymes from non-photosynthetic tissues exhibit varying levels of sensitivity to allosteric regulation, a behavior which may be an inherent property of the enzyme or a product of post-translational modification. As partial proteolysis of the holoenzyme may account for the wide variation of allosteric regulatory behavior exhibited by enzymes from non-photosynthetic tissues, small N- and C-terminal peptide deletions were made on either the potato large and small subunit and co-expressed with the counterpart wild-type subunit in Escherichia coli. Removal of the putative carboxy-terminal allosteric binding region from either subunit type results in an abolishment of enzyme formation indicating that the carboxy terminus of each subunit type is essential for proper subunit folding and/or enzyme assembly as well as its suggested role in allosteric regulation. Removal of a small 10 amino acid peptide from the N-terminus of the small subunit increased its resistance to the allosteric inhibitor Pi as well as its sensitivity to heat treatment. Likewise, removal of the corresponding peptide (17 residues) at the N-terminus of the large subunit also increased its resistance towards Pi inhibition but, in addition, increased its sensitivity to 3-PGA activation. Deletion of an additional 11 residues reversed these changes in allosteric properties but at the expense of a reduced catalytic turnover rate. Combined, these results indicate that the N- and C-terminal regions are essential for the proper catalytic and allosteric regulatory properties of the potato ADP-glucose pyrophosphorylase. The possible significance of these results on the observed insensitivity to effector molecules by ADP-glucose pyrophosphorylases from other non-photosynthetic tissues is discussed.
Enabling high-performance mixed-signal system-on-a-chip (SoC) in high performance logic CMOS technology (2003)

Presents a technique to enable the integration of sensitive analog circuits with a Pentium class microprocessor, on a lossy substrate that sees 190 mVrms of equivalent noise at the center of the die. Measurement results of substrate noise on a Pentium 4/spl reg/ 1 GHz processor show that we can exploit the spectral content of this noise, and use appropriately tuned analog amplification to limit the isolation requirements to 70 dB. By using a combination of measurement and field solver results, we show that a minimal process enhancement (i.e. a deep nwell) will yield 50 dB of isolation. We use measured mismatch data and analysis to conclude that the remaining 20 dB can be achieved by symmetric matched layouts and fully differential circuit topologies. We describe two deep nwell biasing techniques (substrate noise trapping and floating deep nwell) to realize the 50 dB on-die isolation. Finally, we use measurements to show that the deep nwell does not adversely impact the high frequency performance of 140 nm logic CMOS devices.
Extracting Source Code from E-Mails (2010)

E-mails, used by developers and system users to communicate over a broad range of topics, offer a valuable source of information. If archived, e-mails can be mined to support program comprehension activities and to provide views of a software system that are alternative and complementary to those offered by the source code. However, e-mails are written in natural language, and therefore contain noise that makes it difficult to retrieve the important data. Thus, before conducting an effective system analysis and extracting data for program comprehension, it is necessary to select the relevant messages, and to expose only the meaningful information. In this work we focus both on classifying e-mails that hold fragments of the source code of a system, and on extracting the source code pieces inside the e-mail. We devised and analyzed a number of lightweight techniques to accomplish these tasks. To assess the validity of our techniques, we manually inspected and annotated a statistically significant number of e-mails from five unrelated open source software systems written in Java. With such a benchmark in place, we measured the effectiveness of each technique in terms of precision and recall.
Regulation of Folate-mediated One-carbon Metabolism by 10-Formyltetrahydrofolate Dehydrogenase (2006)

10-Formyltetrahydrofolate dehydrogenase (FDH) catalyzes the NADP(+)-dependent conversion of 10-formyltetrahydrofolate to CO(2) and tetrahydrofolate (THF) and is an abundant high affinity folate-binding protein. Although several activities have been ascribed to FDH, its metabolic role in folate-mediated one-carbon metabolism is not well understood. FDH has been proposed to: 1) inhibit purine biosynthesis by depleting 10-formyl-THF pools, 2) maintain cellular folate concentrations by sequestering THF, 3) deplete the supply of folate-activated one-carbon units, and 4) stimulate the generation of THF-activated one-carbon unit synthesis by channeling folate cofactors to other folate-dependent enzymes. The metabolic functions of FDH were investigated in neuroblastoma, which do not contain detectable levels of FDH. Both low and high FDH expression reduced total cellular folate concentrations by 60%, elevated rates of folate catabolism, and depleted cellular 5-methyl-THF and S-adenosylmethionine levels. Low FDH expression increased the formyl-THF/THF ratio nearly 10-fold, whereas THF accounted for nearly 50% of total folate in neuroblastoma with high FDH expression. FDH expression did not affect the enrichment of exogenous formate into methionine, serine, or purines and did not suppress de novo purine nucleotide biosynthesis. We conclude that low FDH expression facilitates the incorporation of one-carbon units into the one-carbon pool, whereas high levels of FDH expression deplete the folate-activated one-carbon pool by catalyzing the conversion of 10-formyl-THF to THF. Furthermore, FDH does not increase cellular folate concentrations by sequestering THF in neuroblastoma nor does it inhibit or regulate de novo purine biosynthesis. FDH expression does deplete cellular 5-methyl-THF and S-adenosylmethionine levels indicating that FDH impairs the folate-dependent homocysteine remethylation cycle.
Lossless compression of medical images by prediction and classification (1994)

A lossless image compression algorithm based on a prediction and classification scheme is presented. The algorithm decomposes an image into four subimages by subsampling pixels at even and odd (both row and column) locations. Because the four subimages have strong correlations to one another, one of them is used as a reference in predicting the other three, and the resulting differences between the predicted subimages and the original subimages are encoded. Even though these differences are decorrelated and tend to be random, there is still a relatively large correlation left between the estimated differences and the subimage used in prediction. For example, the estimated differences tend to be large in a high-detailed region, where pixel values change rapidly, whereas the differences are small in a low-detailed region, where pixel values change smoothly and slowly. This redundancy is exploited by dividing the estimated differences into subsets based on a slope change in the subimage used in prediction. The performance of the proposed algorithm using two different predictors, linear interpolation and third-order polynomial interpolation, is compared with that of the hierarchical interpolation (HINT) scheme and Fourier transform interpolation by measuring the first-order entropies of the estimated differences. With a third-order polynomial interpolation and division into two subsets, an average entropy of 3.1 bits/pixel is achieved for the three predicted difference subimages of the 12 bits/pixel x-ray computed tomography images. It is about 0.86 bits/pixel lower in the first-order entropy than the HINT for the three subimages.
Microporous Metal−Organic Frameworks Formed in a Stepwise Manner from Luminescent Building Blocks (2006)

A series of trivalent lanthanides (Sm, Eu, Gd, Tb, Dy) have been complexed to the dianionic ligand, 4,4'-disulfo-2,2'-bipyridine-N,N'-dioxide, L, in a 3:1 ratio to form trianionic complex building blocks. These units were then cross-linked into a network solid by addition of BaCl2 to form mixed-metal networks of formula {Ba2(H2O)4[LnL3(H2O)2](H2O)nCl}infinity, Ln = Sm3+ (1), Eu3+ (2), Gd3+ (3), Tb3+ (4), Dy3+ (5). The networks were isostructural and contained open channels which readily absorbed and desorbed water accompanied by a spongelike shrinkage and expansion of the host. CO2 sorption measurements confirmed microporosity giving a DR surface area of 718 m2/gm and an average pore size of 6.4 A. Ligand L sensitized all the lanthanide ions with the exception of Gd3+. Studying the series of Ln complexes allowed the determination of the triplet state energy of L which is itself a new ligand for sensitization purposes. The luminescent properties of the lanthanide building blocks were retained in the porous network solid. From the luminescence data, it was possible to attribute the spongelike properties of the network to the Ba2+ coordination sphere rather than the Ln3+ center. Networks were characterized by X-ray crystallography, PXRD, DSC/TGA, water vapor and gas sorption, and luminescence spectroscopy.
A<scp>n</scp> A<scp>merican</scp> T<scp>ext</scp> (1950)

Book reviewed in this article: A TEXTBOOK OF GEOMORPHOLOGY. By Philip G. Worcester
Scattering from surface step edges in strong topological insulators (2011)

We study the characteristics of scattering processes at step edges on the surfaces of strong topological insulators (STIs), arising from restrictions imposed on the $S$ matrix solely by time-reversal symmetry and translational invariance along the step edge. We show that the ``perfectly reflecting'' step edge that may be defined with these restrictions allow modulations in the local density of states (LDOS) near the step edge to decay no slower than $1/x$, where $x$ is the distance from the step edge. This is faster than in two-dimensional electron gases (2DEG)---where the LDOS decays as $1/\sqrt{x}$---and shares the same cause as the suppression of backscattering in STI surface states. We also calculate the scattering at a delta function scattering potential and argue that generic step edges will produce a ${x}^{\ensuremath{-}3/2}$ decay of LDOS oscillations. Experimental implications are also discussed.
First partial three-dimensional model of human monoamine oxidase A (1998)

A survey of the major known structural aspects of monoamine oxidase (MAO) is given and a first partial model of human MAO A is presented. This 3D model has been established using secondary structure predictions and fold recognition methods. It shows two alpha/beta domains (the FAD-binding N-terminal and central domains) and an alpha+beta domain. The C-terminal region is predicted to be responsible for anchoring the protein into the mitochondrial membrane and was not modeled. The covalent binding of the flavin cofactor to a cysteine residue is well predicted. The model is validated with experimental data from the literature and should be useful in designing new experimental studies (site-directed mutagenesis, chemical modification, specific antibodies). This first step towards the 3D structure of monoamine oxidase should contribute to a better understanding of the mechanisms of action and inhibition of this drug target in the treatment of clinical depression.
The state-of-the-art in short term prediction of wind power from a danish perspective (2003)

International audience
CYCLOSPORINE PHARMACOKINETICS AND VARIABILITY FROM A MICROEMULSION FORMULATION—A MULTICENTER INVESTIGATION IN KIDNEY TRANSPLANT PATIENTS (1994)

The steady-state pharmacokinetics and tolerability of a microemulsion formulation of cyclosporine (Sandimmune Neoral) were compared with the commercial formulation (Sandimmune) in 55 clinically stable renal allograft recipients. In study period I (2 weeks' duration), patients entered the study on a stable, individualized twice-daily dosage regimen of the commercial formulation. In period II (2 weeks), they were changed over to the microemulsion formulation at the same dose as at study entry. In period III (2 weeks), dose titration was subsequently allowed if necessary to provide comparable steady-state trough concentrations as at study entry. The commercial formulation was reinstituted during period IV (2 weeks). Safety and tolerability were assessed at weekly clinic visits, and the steady-state pharmacokinetics of cyclosporine in whole blood were characterized at the end of each study period. A milligram-to-milligram dose conversion was adequate when making the initial change between formulations in order to maintain steady-state trough concentrations in the target therapeutic range. Concomitant with this conversion, the steady-state peak concentration and area under the curve increased on average by 59% and 30%, respectively, due to absorption-related differences between the formulations. These increases were not associated with an increase in adverse experiences or changes in blood pressure or clinical laboratory parameters over the first four weeks after the change-over. Trough concentrations were more stable and were more strongly correlated with systemic exposure (area under the curve) during treatment with the microemulsion formulation. Intraindividual coefficients of variation in steady-state peak concentration, time to attain the peak, area under the curve, and percent peak-trough fluctuation ranged from 18% to 74% from the commercial formulation. Variability from the microemulsion formulation was significantly less, ranging from 10% to 22%.
The Analysis of Residuals in Cross-Classified Tables (1973)

In regression analysis and analysis of variance, examination of residuals forms an important part of good statistical practice (see Draper and Smith [1966]). More general uses of residuals have also been explored by Cox and Snell [1968]. In this paper, methods of residual analysis developed for loglinear models for cross-classified tables by Haberman [1972b] are used to examine models for quantal response and for complete and incomplete r X c contingency tables. Section 2 contains a brief summary of results of Haberman [1972b] which are used in this paper. A more complete summary is provided in the appendix. In section 3, residual analysis is used in the hypothesis of row and column independence in a complete r X c table. In section 4, methods are developed appropriate for analysis of quasi-independence models in incomplete r X c tables, and in section 5, methods for use in logit analysis are considered.
Carbonylation of Alcohols, Olefins, and Saturated Hydrocarbons by CO in the Ag(I)–H2SO4 System (1974)

Abstract In the presence of an Ag carbonyl-ion catalyst, prepared in situ from the Ag compound and carbon monoxide in H2SO4, olefins or alcohols reacted with carbon monoxide at room temperature and atmospheric pressure to produce exclusively tertiary carboxylic acids in high yields. The amount of Ag compound sufficient for carrying out the reaction is ca. 0.2 mol/l. The optimum reaction temperature is 0–40°C. The reaction proceeds practically at above a 90% H2SO4 concentration. Saturated hydrocarbons, containing a tertiary hydrogen, also reacted with carbon monoxide in the presence of alcohols or olefins as carbonium ion precursors, thus producing tertiary carboxylic acids.
Gold- and Silver-Mediated Cycloisomerizations of <i>N</i>-Propargylamides (2008)

Substituted N-propargylamides have proven to be valuable substrates for alkyne-activated cycloisomerization reactions. N-Tosyl- N'-propargylurea underwent reaction with AuCl 3 to give the corresponding dihydroimidazolone, while N-propargyl-3-oxobutanamides and esters were used to construct furanyl fused pyrrolidinones and dihydrofuranones via Ag(I)-mediated alkyne activation.
A modular approach to the hardware implementation of digital filters (1976)

Recent advances in the technology of medium and large scale integrated circuits (m.s.i. and l.s.i.) have made possible economical hardware implementations for real-time digital filtering. A flexible design approach for such implementations is presented. The processing mode can be varied to give any hybrid structure between the purely serial and parallel realizations. This leads to a design approach which can be adjusted to suit hardware availability. The resulting structures are modular and are in line with current trends in m.s.i. and l.s.i. technology in that they lend themselves readily to implementations using semiconductor read-only or random access memories.
Modeling of radial uniformity at a wafer interface in a 2f-CCP for SiO2 etching (2005)

Two-frequency capacitively coupled plasmas (2f-CCP) are commonly used as a powerful tool for etching of metallic and dielectric materials. Functional separation between two sources, by which independent control of high-density plasma production and high-energy ion injection onto a wafer surface can be realized, will be strongly required for a precise control of the plasma etcher. When increasing the size of the wafer and aiming at high productivity, radial uniformity in the characteristics of SiO2 etching will become a more essential issue to be addressed. The predicted radial uniformity at the wafer interface and the functional separation have been examined numerically by using VicAddress [in Advances in Low Temperature RF plasmas, edited by T. Makabe (Elsevier, Amsterdam, 2002)] in a 2f-CCP etcher in CF4(5%)∕Ar at 50 mTorr. This etcher was driven at very high frequency (100 MHz) for the production of high-density plasma and at low frequency (1 MHz) for the bias source. The plasma structure and ion velocity distribution at a wafer interface, which have a direct influence on the property of etching, are mainly discussed. Close to the wafer edge, the distortion of the potential intrinsic to the etcher has a greater effect on the ion angular distribution rather than on the ion energy distribution, resulting in a reduction of the radial uniformity of etching.
Beam hardening artefacts in computed tomography with photon counting, charge integrating and energy weighting detectors: a simulation study (2005)

Photon counting x-ray imaging provides efficient rejection of the electronics noise, no pulse height (Swank) noise, less noise due to optimal photon energy weighting and the possibility of energy resolved image acquisition. These advantages apply also to CT when projection data are acquired using a photon counting detector. However, photon counting detectors assign a weighting factor of 1 to all detected photons whereas the weighting factor of a charge integrating detector is proportional to the energy of the detected photon. Therefore, data collected by photon counting and charge integrating detectors represent the 'hardening' of the photon beam passed through the object differently. This affects the beam hardening artefacts in the reconstructed CT images. This work represents the first comparative evaluation of the effect of photon counting, charge integrating and energy weighting photon detectors on beam hardening artefacts in CT. Beam hardening artefacts in CT images were evaluated for 20 cm and 14 cm diameter water cylinders with bone and low contrast inserts, at 120 kVp and 90 kVp x-ray tube voltages, respectively. It was shown that charge integrating results in 1.8% less beam hardening artefacts from bone inserts (i.e., CT numbers in the 'shadow' of the bone are less by 1.8% as compared to CT numbers over the periphery of the image), as compared to photon counting. However, optimal photon energy weighting, which provides highest SNR, results in 7.7% higher beam hardening artefacts from bone inserts as compared to photon counting. The magnitude of the 'cupping' artefacts was lower by 1% for charge integrating and higher by 6.1% for energy weighting acquisitions as compared to photon counting. Only the photon counting systems provide an accurate representation of the beam hardening effect due to its flat energy weighting. Because of their energy dependent weighting factors, the charge integrating and energy weighting systems do not provide accurate representation of the beam hardening effect.
Intravascular photoacoustic imaging to detect and differentiate atherosclerotic plaques (2006)

Atherosclerosis is a systemic disease characterized by the development of a plaque leading to several acute coronary syndromes. Imaging of plaque structure and composition is important in diagnosing the disease and further guiding coronary interventions. Currently, there is no clinical imaging technique capable of providing comprehensive morphological and functional information of the plaques. Several emerging techniques including palpography and thermography are under investigation for intravascular imaging of atherosclerosis. In this paper we present photoacoustic imaging as a means to assess the composition of plaques based on the optical properties of tissue. Specifically, we investigate the feasibility of obtaining intravascular photoacoustic (IVPA) images using a high frequency intravascular ultrasound (IVUS) imaging catheter. Indeed, the combination of intravascular photoacoustic (IVPA) imaging with clinically available intravascular ultrasound (IVUS) is desired for simultaneous functional and morphological imaging of the plaque. The imaging studies were performed using a tissue- mimicking phantom to model the arterial vessel with atherosclerotic plaque. The results of our study suggest that combined IVUS and IVPA imaging has the potential to detect and differentiate atherosclerosis based on both structure and composition of the plaque.
Expression of <i>Rhizobium</i> Chitin Oligosaccharide Fucosyltransferase in Zebrafish Embryos Disrupts Normal Development<sup>a,</sup> (1998)

In this report we present data about the effect of the Rhizobium NodZ enzyme on zebrafish development. We injected zebrafish embryos with a plasmid expressing NodZ protein, and we confirmed that the enzyme is active and has chitin oligosaccharide fucosyltransferase (NodZ) activity in vitro. In addition, the embryos injected with the NodZ-expressing plasmid, but not with a control plasmid, showed malformations or bends in the tail, and in some cases shunted tail structures and fused somites. These results clearly indicate that the likely substrates for this enzyme, chitin oligosaccharides and free N-glycans, have essential functions during early vertebrate embryogenesis.
Traffic density estimation with the cell transmission model (2004)

A macroscopic traffic flow model, called the switching-mode model (SMM), has been derived from the cell transmission model (CTM) and then applied to the estimation of traffic densities at unmonitored locations along a highway. The SMM is a hybrid system that switches among different sets if linear difference equations, or modes, depending on the mainline boundary data and the congestion status of the cells in a highway section. Using standard linear systems techniques, the observability and controllability properties of the SMM modes have been determined. Both the SMM and a density-based version of the CTM have been simulated over a section of I-210 West in Southern California, using several days of loop detector data collected during the morning rush-hour period. The simulation results show that the SMM and CTM produce density estimates that are both similar to one another and in good agreement with measured densities on I-210. The mean percentage error averaged over all the test days was approximately 13% for both models.