gebhart/patrepeval huggingface dataset:
Seismic waveform inversion in the frequency domain; Part 1, Theory and verification in a physical scale model (1999)

Abstract Seismic waveforms contain much information that is ignored under standard processing schemes; seismic waveform inversion seeks to use the full information content of the recorded wavefield. In this paper I present, apply, and evaluate a frequency-space domain approach to waveform inversion. The method is a local descent algorithm that proceeds from a starting model to refine the model in order to reduce the waveform misfit between observed and model data. The model data are computed using a full-wave equation, viscoacoustic, frequency-domain, finite-difference method. Ray asymptotics are avoided, and higher-order effects such as diffractions and multiple scattering are accounted for automatically. The theory of frequency-domain waveform/wavefield inversion can be expressed compactly using a matrix formalism that uses finite-difference/finite-element frequency-domain modeling equations. Expressions for fast, local descent inversion using back-propagation techniques then follow naturally. Implementation of these methods depends on efficient frequency-domain forward-modeling solutions; these are provided by recent developments in numerical forward modeling. The inversion approach resembles prestack, reverse-time migration but differs in that the problem is formulated in terms of velocity (not reflectivity), and the method is fully iterative. I illustrate the practical application of the frequency-domain waveform inversion approach using tomographic seismic data from a physical scale model. This allows a full evaluation and verification of the method; results with field data are presented in an accompanying paper. Several critical processes contribute to the success of the method: the estimation of a source signature, the matching of amplitudes between real and synthetic data, the selection of a time window, and the selection of suitable sequence of frequencies in the inversion. An initial model for the inversion of the scale model data is provided using standard traveltime tomographic methods, which provide a robust but low-resolution image. Twenty-five iterations of wavefield inversion are applied, using five discrete frequencies at each iteration, moving from low to high frequencies. The final results exhibit the features of the true model at subwavelength scale and account for many of the details of the observed arrivals in the data.
Computational design of Candida boidinii xylose reductase for altered cofactor specificity (2009)

In this study we introduce a computationally-driven enzyme redesign workflow for altering cofactor specificity from NADPH to NADH. By compiling and comparing data from previous studies involving cofactor switching mutations, we show that their effect cannot be explained as straightforward changes in volume, hydrophobicity, charge, or BLOSUM62 scores of the residues populating the cofactor binding site. Instead, we find that the use of a detailed cofactor binding energy approximation is needed to adequately capture the relative affinity towards different cofactors. The implicit solvation models Generalized Born with molecular volume integration and Generalized Born with simple switching were integrated in the iterative protein redesign and optimization (IPRO) framework to drive the redesign of Candida boidinii xylose reductase (CbXR) to function using the non-native cofactor NADH. We identified 10 variants, out of the 8,000 possible combinations of mutations, that improve the computationally assessed binding affinity for NADH by introducing mutations in the CbXR binding pocket. Experimental testing revealed that seven out of ten possessed significant xylose reductase activity utilizing NADH, with the best experimental design (CbXR-GGD) being 27-fold more active on NADH. The NADPH-dependent activity for eight out of ten predicted designs was either completely abolished or significantly diminished by at least 90%, yielding a greater than 10(4)-fold change in specificity to NADH (CbXR-REG). The remaining two variants (CbXR-RTT and CBXR-EQR) had dual cofactor specificity for both nicotinamide cofactors.
Exploring Shape Variations by 3D‐Model Decomposition and Part‐based Recombination (2012)

Abstract We present a system that allows new shapes to be created by blending between shapes taken from a database. We treat the shape as a composition of parts; blending is performed by recombining parts from different shapes according to constraints deduced by shape analysis. The analysis involves shape segmentation, contact analysis, and symmetry detection. The system can be used to rapidly instantiate new models that have similar symmetry and adjacency structure to the database shapes, yet vary in appearance.
Structure of the chromosomal gene for murine interleukin 3. (1985)

We have isolated the mouse interleukin 3 (IL-3) gene from a mouse sperm DNA library based on homology with the mouse mast-cell growth-factor (MCGF) cDNA sequence. The nucleotide sequence determined for the gene and its flanking regions reveals that the IL-3 gene is composed of four introns and five exons. The nucleotide sequence of the exons agrees with that determined for the MCGF cDNA. A "TATA"-like sequence preceded by a G + C-rich region is found in the 5' flanking region. At the 3' region of the second intron are nine repeats of a closely related 14-base-pair (bp) sequence. These repeated sequences share extensive homology with a 20-bp repeated sequence found in the human genome, which was shown to have enhancer activity. Eight out of nine repeats form a 73-bp duplicated sequence and each 73-bp repeat contains sequences homologous to the core sequence suggested for enhancer elements. These sequences may play a role in the expression of the IL-3 gene in concanavalin A- or antigen-stimulated T lymphocytes. Stable transformants of L cells generated by co-transformation of the IL-3 gene with pSV2neo constitutively express MCGF activity indicating that the isolated gene is functional in vivo.
Spatial resolution of fodrin proteolysis in postischemic brain. (1993)

One of the major obstacles in investigating in vivo proteolytic phenomena has been the inaccessibility to spatial information as to where in the tissue the reaction proceeds because the orthodox method employing electrophoretic analysis requires homogenization of samples and thus results in loss of such spatial information. To overcome this technical drawback, we have developed methodology to produce antibodies that specifically distinguish a proteolyzed form of a given protein from its intact form. Here we describe our immunohistochemical observation of calpain-catalyzed fodrin proteolysis in postischemic gerbil hippocampus, using an antibody exclusively specific to the proteolyzed 150-kDa form of fodrin alpha subunit. Our data establish a novel discovery that transient (10 min) global forebrain ischemia followed by reperfusion induces at least two distinct phases of fodrin proteolysis in hippocampus: an early phase in molecular layer and in stratum oriens of CA3 and CA1 sectors within 15 min and a late drastic and persistent phase in the entire CA1 after 4-24 h. The former may be one of the early events initiating the complex cascade leading to the delayed neuronal death, while the latter should be considered as a more direct cause for the actual degeneration in CA1.
The Story of PLP (1983)

The development of information systems during the 1970's was primarily directed to the needs of commercial businesses and manufacturers. Now, with the advances in communications technology and the significant increase in microprocessor capabilities, the informational needs of the entire consumer market can be satisfied. However, to minimize the variables in developing products for the mass market that includes businesses as well as residences, the systerns that are required to provide the informational vehicle must reach a high level of standardization. Since 1978, the international arena has attempted to standardize the character sets and coding of a class of information systems referred to as Videotex. The first agreement reached was in November 1980 by the International Telegraph and Telephone Consultative Committee (CCITT), in Geneva. This CCITT recommendation was referred to as "International Information Exchange for Interactive Videotex, Recommendation S.100," and included three incompatible coding schemes. In May 1981, a Presentation Level Protocol (PLP) was announced by AT&T which combined all of the functions of the three incompatible coding schemes of S.100, with more complete graphical and color capabilities, into a unified coding syntax. This article covers the rationale for PLP prior to May 1981 and recent progress toward a North American standard for videotex.
Applying a neural network to recover missed RFID readings (2010)

Since the emergence of Radio Frequency Identification technology (RFID), the community has been promised a cost effective and efficient means of identifying and tracking large sums of items with relative ease. Unfortunately, due to the unreliable nature of the passive architecture, the RFID revolution has been reduced to a fraction of its intended audience due to anomalies such as missed readings. Previous work within this field of study have focused on restoring the data at the recording phase which we believe does not allow enough evidence for consecutive missed readings to be corrected. In this study, we propose a methodology of intelligently imputing missing observations through the use of an /emph{Artificial Neural Network} (ANN) in a static environment. Through experimentation, we discover the most effective algorithm to train the network and establish that the ANN restores a cleaner data set than other intelligent classifier methodologies.
Recent Developments in Carbon Nanotube Membranes for Water Purification and Gas Separation (2010)

Carbon nanotubes (CNTs) are nanoscale cylinders of graphene with exceptional properties such as high mechanical strength, high aspect ratio and large specific surface area. To exploit these properties for membranes, macroscopic structures need to be designed with controlled porosity and pore size. This manuscript reviews recent progress on two such structures: (i) CNT Bucky-papers, a non-woven, paper like structure of randomly entangled CNTs, and (ii) isoporous CNT membranes, where the hollow CNT interior acts as a membrane pore. The construction of these two types of membranes will be discussed, characterization and permeance results compared, and some promising applications presented.
High-Performance Multi-Wafer SiC Epitaxy – First Results of Using a 10x100mm Reactor (2010)

In this paper, we present first results of epitaxial layer deposition using a novel warm-wall CVD multi-wafer system AIX 2800G4 WW from AIXTRON with a capability of processing 10x100mm wafers per run. Intra-wafer and wafer-to-wafer homogeneities of doping and thickness for full-loaded 10x100mm runs will be shown and compared to results of the 6x100mm setup of our hot-wall reactor VP2000HW by AIXTRON used for device production since 2001.
Identification and detection of the periostin gene in cardiac development (2004)

Periostin, a member of the fasciclin gene family, acts as a cell adhesion molecule through binding to cell surface integrins. Periostin expression has previously been shown to increase substantially following transforming growth factor beta (TGF-beta) and bone morphogenetic protein stimulation. As these molecules are indispensable for cardiac development, we sought to clone the chicken ortholog of periostin and evaluate its spatiotemporal expression pattern during heart morphogenesis. We show by Northern analysis, whole mount and section in situ hybridization experiments that periostin is predominantly expressed in the developing endothelium of the ventricular trabeculae as well as in the endothelium and mesenchyme of the outflow tract and atrioventricular endocardial cushions. Cardiac expression continues into fetal development where periostin is seen predominantly in the valve leaflets and supporting chordae tendinae.
Fatty Acid Oxidation in the Heart (1996)

Summary The heart is known for its ability to produce energy from fatty acids (FA) because of its important β-oxidation equipment, but it can also derive energy from several other substrates including glucose, pyruvate, and lactate. The cardiac ATP store is limited and can assure only a few seconds of beating. For this reason the cardiac muscle can adapt quickly to the energy demand and may shift from a 100% FA-derived energy production (after a lipid-rich food intake) or any balanced situation (e.g., diabetes, fasting, exercise). These situations are not similar for the heart in terms of oxygen requirement because ATP production from glucose is less oxygen-consuming than from FA. The regulation pathways for these shifts, which occur in physiologic as well as pathologic conditions (ischemia-reperfusion), are not yet known, although both insulin and pyruvate dehydrogenase activation are clearly involved. It becomes of strategic importance to clarify the pathways that control these shifts to influence the oxygen requirement of the heart. Excess FA oxidation is closely related to myocardial contraction disorders characterized by increased oxygen consumption for cardiac work. Such an increased oxygen cost of cardiac contraction was observed in stunned myocardium when the contribution of FA oxidation to oxygen consumption was increased. In rats, an increase in n-3 polyunsaturated FA in heart phospholipids achieved by a fish-oil diet improved the recovery of pump activity during postischemic reperfusion. This was associated with a moderation of the ischemia-induced decrease in mitochondrial palmitoylcarnitine oxidation. In isolated mitochondria at calcium concentrations close to that reported in ischemic cardiomyocytes, a futile cycle of oxygen wastage was reported, associated with energy wasting (constant AMP production). This occurs with palmitoylcarnitine as substrate but not with pyruvate or citrate. The energy wasting can be abolished by CoA-SH and other compounds, but not the oxygen wasting. Again, the calcium-induced decrease in mitochondrial ADP/O ratio was reduced by increasing the n-3 polyunsaturated FA in the mitochondrial phospholipids. These data suggest that in addition to the amount of circulating lipids, the quality of FA intake may contribute to heart energy regulation through the phospholipid composition. On the other hand, other intervention strategies can be considered. Several studies have focused on palmitoylcarnitine transferase I to achieve a reduction in β-oxidation. In a different context, trimetazidine was suggested to exert its anti-ischemic effect on the heart by interfering with the metabolic shift, either at the pyruvate dehydrogenase level or by reducing the β-oxidation. Further studies will be required to elucidate the complex system of heart energy regulation and the mechanism of action of potentially efficient molecules.
Gender Preselection in Domestic Animals Using Flow Cytometrically Sorted Sperm1 (1992)

Preselecting the gender of offspring in both humans and animals has been of keen interest since the beginning of recorded history. Numerous attempts have been made to accomplish gender preselection in both humans and animals. However, virtually all attempts have ended in failure, primarily because they lacked a scientific basis upon which to determine a measurable difference. Some methods have been derived from folklore, in which case there was virtually no possibility for success. This paper deals briefly with the numerous “physical separation” methods that have been proposed and(or) used to separate X- and Y-chromosome-bearing sperm, but the main emphasis is given to the technique of flow cytometry for sperm validation and X- and Y-bearing sperm separation. Flow cytometric analysis of sperm DNA is very useful for evaluating the proportions of X- and Y-bearing sperm in a sample of semen. Similarly, flow cytometric sorting of X-and Y-bearing sperm has also proven itself to be the only laboratory method that skews the sex ratio of semen. This flow cytometric sorting method has been used successfully to produce progeny from rabbits and swine surgically inseminated from separate populations of X- and Y-bearing sperm.
ANTAGONISM OF d -CYCLOSERINE INHIBITION OF MYCOBACTERIAL GROWTH BY d -ALANINE (1963)

Zygmunt, Walter A. (Mead Johnson & Co., Evansville, Ind.). Antagonism of d-cycloserine inhibition of mycobacterial growth by d-alanine. J. Bacteriol. 85:1217-1220. 1963.-Reversal of the antimycobacterial activity of d-4-amino-3-isoxazolidinone (d-cycloserine) by alanine in two species of mycobacteria actively growing on chemically defined media was compared. In both instances, d-alanine was the most effective reversal agent. The specificity with which the d isomer reversed the antimycobacterial activity of d-cycloserine was more pronounced than that observed with other species of bacteria. Mycobactin, a growth factor for certain mycobacteria, showed no reversal activity.
Diabetic neuropathy (1989)

Many factors contribute to the nerve damage of diabetes--metabolic (myo-inositol), microvascular, glycosylation and ageing. The variety of clinical syndromes indicates the complexity of the disease. Measurement of peripheral and autonomic nerve function is improving allowing the establishment of prospective natural history and therapeutic studies. There is a need for standardization of clinical definition and staging.
Genetic Variants of HIV-1 in Thailand (1992)

Serosurveys conducted prior to 1988 indicated a very low level of HIV-1 infection in Thailand, even among high-risk groups. The Ministry of Health has reported a dramatic increase in HIV-1 infection during the last three years. The geographic and demographic distribution of the epidemic is broad, involving multiple provinces and risk groups. Foci of higher incidence and prevalence have been noted in the urban center of Bangkok and in the northern provinces of Chiang Mai and Chiang Rai. Here we report the results of genetic characterization of 16 HIV-1 isolates from Thailand using a combination of polymerase chain reaction (PCR) typing and DNA sequencing. The complete sequence of gp160 (env) of five isolates, partial env sequence of six additional isolates, and the gag gene of two isolates were determined. Two highly distinct HIV-1 variants were found. One variant resembled those prevalent in North America and Europe; five of the isolates were of this type. The remaining eleven isolates were very similar to one another and represented a variant unlike any previously described. Phylogenetic tree analysis of complete env and gag genes placed the two variants on widely separated branches. Protein sequence comparisons indicate both general and specific features that distinguish the Northern Thailand variant both from the Bangkok variant and from virtually all previously sequenced HIV-1 isolates. A simple PCR test for distinguishing the two variants has been developed for use in epidemiologic surveys.
Additive insulinotropic effects of exogenous synthetic human gastric inhibitory polypeptide and glucagon-like peptide-1-(7-36) amide infused at near-physiological insulinotropic hormone and glucose concentrations. (1993)

Gastric inhibitory polypeptide (GIP) and glucagon-like peptide-1-(7-36) amide (GLP-1) are glucose-dependent insulinotropic gut hormones that may explain the greater insulin secretory response with oral compared to i.v. glucose (incretin effect). To study their individual and combined contributions, in eight healthy volunteers, on separate occasions, synthetic human GIP (1 pmol/kg.min) and/or GLP-1 (0.3 pmol/kg.min) or placebo were infused i.v. (-30 to 120 min), while at 0 min, a glucose infusion "isoglycemic" to the profile after an oral glucose load of 50 g/400 mL was started. After the administration of 50 g oral glucose, immunoreactive GIP rose several-fold to 337 +/- 43 pmol/L, while there was only a transient (10-30 min) and moderate increment in immunoreactive GLP-1 (from basal, 25-30, to 41 +/- 4 pmol/L). Isoglycemic i.v. glucose infusions led to smaller B-cell responses (estimated incretin effect, 41 +/- 5%). With single infusions of GIP or GLP-1 (circulating concentrations, 464 +/- 73 and 54 +/- 3 pmol/L, respectively), B-cell responses were significantly augmented compared to i.v. glucose alone and were no longer significantly different from those after oral glucose. The combination of GIP and GLP-1 led to B-cell responses that were significantly higher than those with either hormone alone (additive mode of cooperation). Plasma GIP concentrations were similar after endogenous secretion (oral glucose) and i.v. infusion, while exogenously administered GLP-1 led to plasma levels that were maintained at an elevated level for a longer period during exogenous infusion than after stimulation by oral glucose. When, in seven volunteers, a lower dose (0.15 pmol/kg.min) of GLP-1 was infused during isoglycemic glucose infusion experiments only for the duration of elevated plasma levels in the oral glucose challenges (0-30 min), a significant, but transient, increment in insulin and C-peptide concentrations was observed, which was equivalent to 26 +/- 10% of the estimated incretin effect. Therefore, in conclusion, circulating GIP seems to make a major contribution to the incretin effect after oral glucose, and GLP-1 appears to mediate a smaller proportion. GIP and GLP-1 can interact in an additive manner in normal man.
Intragenic regions required for LamB export. (1984)

Escherichia coli strains containing a series of lamB-lacZ fusions have been isolated and characterized. Each of these fusions specifies a hybrid protein with LamB sequences at the NH2 terminus and a large functional COOH-terminal fragment of beta-galactosidase. The amount of LamB present in the various hybrid proteins ranges from as few as 4 amino acids to a complete signal sequence (25 amino acids) plus 49 amino acids of the mature protein. With respect to hybrid protein export these fusions fall into three classes. Hybrid proteins with an incomplete LamB signal sequence or those that have a complete signal sequence plus 27 or fewer amino acids of the mature LamB protein are not exported and remain in the cytoplasm. In contrast, fusion strains attempt to export hybrid proteins that contain a complete signal sequence plus 39 or 43 amino acids of mature LamB. However, these proteins are not localized to the outer membrane. Finally, a hybrid protein that is slightly larger, containing 49 amino acids of mature LamB, is found in the outer membrane in appreciable amounts. These fusions, together with previously described lamB-lacZ fusions, have enabled us to define more precisely the minimal amount of lamB required to initiate the process of protein export. Moreover, they genetically locate a signal that appears to guide LamB to the outer membrane. This signal is within a region of amino acid homology shared by other major outer membrane proteins [ Nikaido , H. &amp; Wu, H. C. P. (1984) Proc. Natl. Acad. Sci. USA 81, 1048-1052].
Handling mobility in a wireless ATM network (2002)

The world of wireless telecommunications is rapidly changing. The capabilities of wireless networks are improving at a steady pace. This paper presents a protocol implementation for providing mobility in an asynchronous transfer mode (ATM) network. The vision of the authors is of one "ATM-based wireless telecommunications network" that is capable of supporting a variety of today's applications with room to grow for advanced applications of the future. The next generation wireless networks are called personal communication services (PCS) networks and will provide for global user mobility, a life-long user identification numbering system and the ability to accommodate varying data rates.