gebhart/patrepeval huggingface dataset:
Kirchhoff PreSDM interactive dip‐gather stacking and dip illumination panel generation (2005)

Kirchhoff Pre‐Stack Depth Migration (PreSDM) is used to output image gathers in structure dip angle instead of the traditional offset attributes gathers in sub‐salt areas that are hard to image. These new image gathers can help processors and/or interpreters to better define geological structures through interactively stacking the image gathers in dip within various dip angle ranges based on different interpretations. Illumination panels can also be obtained for structures with different dips. They can be used to determine if observed amplitude anomalies are caused by geology or seismic acquisition and imaging processes. We demonstrate using the Sigsbee 2A synthetic dataset that partial dip‐angle gather stacking and illumination compensation can be used to effectively suppress sub‐salt migration artifacts.
Haemoglobin oxygen saturation as a biomarker: the problem and a solution (2011)

Near-infrared spectroscopy measures of haemoglobin oxygen saturation are often used as an indicator of sufficient oxygen delivery to assess injury susceptibility and tissue damage. They have also often been used as a surrogate measure of oxygen metabolism. Unfortunately, these measures have generally failed to provide robust indicators of injury and metabolism. In this paper, we first review when haemoglobin oxygen saturation does work as a robust indicator, and then detail when and why it fails for assessing brain injury and breast cancer. Finally, we discuss the solution to obtain more robust measures of tissue injury and cancer by combining oxygen saturation measurements with measures of blood flow and volume to more accurately estimate oxygen metabolism.
Comparison of Enzyme-Linked Immunosorbent Assay, Western Blotting, Microagglutination, Indirect Immunofluorescence Assay, and Flow Cytometry for Serological Diagnosis of Tularemia (2004)

The serodiagnostic efficiencies of five different approaches to detecting antibodies (immunoglobulins G, A, and M) developed in clinically proven infections with Francisella tularensis have been assessed. Fifty serum samples from patients suffering from tularemia during an outbreak in Sweden were compared with samples from 50 healthy blood donors (controls) by using an enzyme-linked immunosorbent assay (ELISA), microagglutination (MA), Western blotting (WB), an indirect immunofluorescence assay (IIFA), and flow cytometry (FC). ELISA, WB, and FC were based on the use of preparations of lipopolysaccharides (LPS) of the live vaccine strain of Francisella tularensis subsp. holarctica (ATCC 29684) as a capture antigen. Whole methanol-fixed bacteria were used for IIFA and MA. Optimized protocols yielded a diagnostic sensitivity and specificity of 100% for WB, MA, and FC, 98% for ELISA, and 93% for IIFA. A total of 6,632 serum samples from individuals between the ages of 18 and 79 years, representatively recruited from all regions of Germany, were screened to estimate and confirm the positive predictive value (PVpos) of the ELISA. Serum samples from 15 (0.226%) individuals tested positive for F. tularensis-specific antibodies by ELISA and confirmatory WB. The resulting prevalence-dependent PVpos of 10.2% and specificity of 98.1% were consistent with our findings for tularemia patients and controls. We conclude that the combined usage of a screening ELISA and a confirmatory WB based on LPS as a common antigen, as well as the MA, is a suitable serodiagnostic tool, while the quality of the IIFA is hampered by subjective variations of the results. FC is a promising new approach that might be improved further in terms of multiplex analyses or high-throughput applications.
Massive increase in the stiffness of the human lens nucleus with age: the basis for presbyopia? (2004)

There is a marked increase in the stiffness of the human lens with age. This is most pronounced in the nucleus. Since in vivo data indicate that the nucleus must change shape significantly during accommodation, it is highly likely that these measured changes in physical properties will markedly diminish the ability of the lens to accommodate, and thus may be a major contributing factor to presbyopia. Since there was no measurable difference in the water contents of the nuclear regions of the lenses, this marked increase in stiffness is not due to compaction of the lens nucleus.
Close physical linkage of the FLT1 and FLT3 genes on chromosome 13 in man and chromosome 5 in mouse. (1993)

Receptor-type tyrosine kinases (RTK) with five or seven immunoglobulin-like domains in their extracellular region are encoded by genes grouped in clusters. In human, two such clusters have been individualized, in chromosomal regions 4q11-q12 and 5q33-qter respectively. We define here a third cluster located on chromosome 13q and containing two contiguous RTK genes, FLT1 and FLT3. The former has recently been shown to encode a RTK of a new class while the latter codes for a hematopoietic receptor closely related to the products of the FMS and KIT genes. The physical linkage is also evidenced in mouse, where the two genes appear to lie within a 350 kb Mlu I fragment, on mouse chromosome 5.
Cloning and characterization of a novel human pH‐dependent organic cation transporter, OCTN1 (1997)

cDNA for a novel proton/organic cation transporter, OCTN1, was cloned from human fetal liver and its transport activity was investigated. OCTN1 encodes a 551-amino acid protein with 11 transmembrane domains and one nucleotide binding site motif. It is strongly expressed in kidney, trachea, bone marrow and fetal liver and in several human cancer cell lines, but not in adult liver. When expressed in HEK293 cells, OCTN1 exhibited saturable and pH-dependent [3H]tetraethyl ammonium uptake with higher activity at neutral and alkaline pH than at acidic pH. Furthermore, treatment with metabolic inhibitors reduced the uptake, which is consistent with the presence of the nucleotide binding site sequence motif. Although its subcellular localization and detailed functional characteristics are not clear at present, OCTN1 appears to be a novel proton antiporter that functions for active secretion of cationic compounds across the renal epithelial brush-border membrane. It may play a role in the renal excretion of xenobiotics and their metabolites.
Cloning, Characterization, and Copy Number of the Murine Survival Motor Neuron Gene: Homolog of the Spinal Muscular Atrophy-Determining Gene (1997)

Because of a 500-kb inverted duplication, there are two copies of the survival motor neuron (SMN) gene in humans, cenSMN and telSMN. Both genes produce identical ubiquitously expressed transcripts; however, only mutations in telSMN are responsible for spinal muscular atrophy (SMA), the second most common autosomal recessive childhood disease. We have cloned the murine homolog Smn and mapped the gene to Chromosome 13 within the conserved syntenic region of human chromosome 5q13. We show that the Smn transcript (1.4 kb) is expressed as early as embryonic day 7. In contrast to humans, we found no evidence of alternative splicing. The predicted amino acid sequence between mouse and human SMN is 82% identical, and a putative nuclear localization signal is conserved. FISH data indicate that the duplication of the SMA region observed in humans is not present in the mouse. We also found no evidence of multiple Smn genes using Southern blot hybridization and single-strand conformation analysis. Using these methods, we detected at least four copies of Naip exon 5 clustering distal to Smn. Finally, three biallelic markers were identified within the Smn coding region; two are silent polymorphisms, whereas the third changes a cysteine residue to a tyrosine residue in exon 7. Overall, our results indicate that Smn is single copy within the mouse genome, which should facilitate gene disruption experiments to create an animal model of SMA.
Short-radius drilling expands horizontal well applications (1995)

With the development of advanced tools and technologies, short-radius drilling is poised to redefine the nature of horizontal wells. This paper describes the design and equipment used for drilling short-radius wells and provide several case studies showing the cost advantage of drilling short-radius versus medium- and long-radius wells. One of the inherent advantages of drilling a short-radius well bore are the reduced footage drilled in the curved section and the corresponding additional horizontal section drilled in the pay zone for a given displacement. The paper describes the techniques of well completion and the tools and techniques for setting casings and special tools required for drilling and steering.
Cerebrosides A and C, Sphingolipid Elicitors of Hypersensitive Cell Death and Phytoalexin Accumulation in Rice Plants (1998)

When plants interact with certain pathogens, they protect themselves by generating various chemical and physical barriers called the hypersensitive response. These barriers are induced by molecules called elicitors that are produced by pathogens. In the present study, the most active elicitors of the hypersensitive response in rice were isolated from the rice pathogenic fungus Magnaporthe grisea, and their structures were identified as cerebrosides A and C, sphingolipids that were previously isolated as inducers of cell differentiation in the fungus Schizophyllum commune. Treatment of rice leaves with cerebroside A induced the accumulation of antimicrobial compounds (phytoalexins), cell death, and increased resistance to subsequent infection by compatible pathogens. The degradation products of cerebroside A (fatty acid methyl ester, sphingoid base, and glucosyl sphingoid base) showed no elicitor activity. Hydrogenation of the 8E-double bond in the sphingoid base moiety or the 3E-double bond in the fatty acid moiety of cerebroside A did not alter the elicitor activity, whereas hydrogenation of the 4E-double bond in the sphingoid base moiety led to a 12-fold decrease in elicitor activity. Furthermore, glucocerebrosides from Gaucher's spleen consisting of (E)-4-sphingenine and cerebrosides from rice bran mainly consisting of (4E,8E)-4,8-sphingadienine and (4E,8Z)-4,8-sphingadienine showed no elicitor activity. These results indicate that the methyl group at C-9 and the 4E-double bond in the sphingoid base moiety of cerebrosides A and C are the key elements determining the elicitor activity of these compounds. This study is the first to show that sphingolipids have elicitor activity in plants.
GLYCOSYLATION ENGINEERING (2006)

RETURN TO ISSUEPREVNewsNEXTGLYCOSYLATION ENGINEERINGControlling personalities tame wild sugars on proteins and natural productsSTU BORMANView Author Information C&EN WASHINGTONCite this: Chem. Eng. News 2006, 84, 36, 13–22Publication Date (Print):September 4, 2006Publication History Published online14 November 2010Published inissue 4 September 2006https://pubs.acs.org/doi/10.1021/cen-v084n036.p013https://doi.org/10.1021/cen-v084n036.p013newsACS PublicationsCopyright © 2006 AMERICAN CHEMICAL SOCIETYArticle Views12Altmetric-Citations5LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options SUBJECTS:Pharmaceuticals,Post-translational modification Get e-Alerts
Protein Kinase C β2-Dependent Phosphorylation of Core 2 GlcNAc-T Promotes Leukocyte-Endothelial Cell Adhesion (2003)

Increased leukocyte-endothelial cell adhesion is a key early event in the development of retinopathy and atherogenesis in diabetic patients. We recently reported that raised activity of glycosylating enzyme [beta]1,6 acetylglucosaminyltransferase (core 2 GlcNAc-T) is responsible for increased leukocyte-endothelial cell adhesion and capillary occlusion in retinopathy. Here, we demonstrate that elevated glucose increases the activity of core 2 GlcNAc-T and adhesion of human leukocytes to retinal capillary endothelial cells, in a dose-dependent manner, through diabetes-activated serine/threonine protein kinase C beta2 (PKCbeta2)-dependent phosphorylation. This regulatory mechanism, involving phosphorylation of core 2 GlcNAc-T, is also present in polymorphonuclear leukocytes isolated from type 1 and type 2 diabetic patients. Inhibition of PKCbeta2 activation with the specific inhibitor, LY379196, attenuated serine phosphorylation of core 2 GlcNAc-T and prevented increased leukocyte-endothelial cell adhesion. Raised activity of core 2 GlcNAc-T was associated with a threefold increase in O-linked glycosylation of P-selectin glycoprotein ligand-1 on the surface of leukocytes of diabetic patients compared with age-matched control subjects. PKCbeta2-dependent phosphorylation of core 2 GlcNAc-T may thus represent a novel regulatory mechanism for activation of this key enzyme in mediating increased leukocyte-endothelial cell adhesion and capillary occlusion in diabetic retinopathy.
Separation of a mixture of independent signals using time delayed correlations (1994)

The problem of separating n linearly superimposed uncorrelated signals and determining their mixing coefficients is reduced to an eigenvalue problem which involves the simultaneous diagonalization of two symmetric matrices whose elements are measureable time delayed correlation functions. The diagonalization matrix can be determined from a cost function whose number of minima is equal to the number of degenerate solutions. Our approach offers the possibility to separate also nonlinear mixtures of signals.
A triple polysilicon stacked flash memory cell with wordline self-boosting programming (2002)

A novel triple polysilicon stacked flash cell by the wordline boosting is proposed as a solution for a low voltage operation. The third gate named as booster gate is simply stacked and self-aligned on the conventional control gate. The successively coupled booster gate bias in addition to the precharged control gate voltage is a key to increase the floating gate potential. A new NAND flash cell array with 0.51 /spl mu//sup 2/ cell size is fabricated using the 0.32 /spl mu/m process technology. A triple stacked polysilicon structure is patterned with a single self-alignment etching technology. With the booster gate bias, significantly enhanced coupling to the floating gate is obtained through the self-boosted control gate voltage. Thus, for the first time, a 11 V programming voltage is achieved at 300 /spl mu/s programming time in the multi-bit NAND flash cell.
Synthesis of Poly(propylene glycol)‐block‐Polyethylenimine Triblock Copolymers for the Delivery of Nucleic Acids (2011)

LPEIs, which are efficient DNA transfection agents, were found to be far less effective for the delivery of siRNAs. Here, two amphiphilic triblock copolymers LPEI(50) -b-PPG(36) -b-LPEI(50) (2) and LPEI(14) -b-PPG(68) -b-LPEI(14) (4) have been synthesized. The transfection assays showed that compound 2 was efficient for DNA transfection whilst it was almost inactive for siRNA delivery. In contrast, polymer 4 was inefficient for DNA transfection while it showed capabilities for siRNA delivery. Taken together, our results indicate that the properties required for DNA and siRNA delivery are different. Moreover, we show that introduction of a hydrophobic segment that allows self-assembly confers siRNA delivery capacities.
A genomic perspective on human proteases (2001)

Over 400 human proteases documented in secondary databases can already be delineated in genomic sequence. A Genome Ontology annotation of 30585 sequences in the provisional human proteome set recognises 498 proteases, i.e. 1.6%. Homology searches against finished sequence and comparisons between mouse and zebrafish are likely to increase this total. However, the data already indicate that the mechanistic class, sequence family and domain distribution of the genomic complement of proteases is unlikely to shift significantly from that already observed in the transcript data. Genomically derived novel sequences will require bioinformatic analysis and biochemical verification. The increasing availability of annotated genomic data will enable studies of splice variants, transcriptional control, polymorphisms, pseudogenes, inactive homologues and evolution. Comparative work on complete human protease families should produce a more integrated picture of their biochemistry and physiology. Genomic data will also lead to the identification of new protease involvement in disease processes and their evaluation as drug targets.
Amino acid sequence of the UP1 calf thymus helix-destabilizing protein and its homology to an analogous protein from mouse myeloma. (1985)

A complete amino acid sequence has been determined for the UP1 single-stranded DNA binding protein from calf thymus that was first described by G. Herrick and B. M. Alberts [(1976) J. Biol. Chem. 251, 2124-2132]. Peptides required to establish the UP1 sequence were isolated by reversed-phase HPLC of digests produced by endoproteinase Lys-C, trypsin, chymotrypsin, Staphylococcus aureus V8 protease, and cyanogen bromide cleavage of UP1. The purified peptides were coupled to aminopolystyrene prior to solid-phase sequencing. UP1 contains 195 amino acids and has a molecular weight of 22,162. UP1 has a blocked NH2 terminus and contains a single NG,NG-dimethylarginine residue near its COOH terminus. Gas-phase sequencing of tryptic peptides derived from an analogous protein from mouse myeloma cells [Planck, S. R. & Wilson, S. H. (1980) J. Biol. Chem. 255, 11547-11556] revealed that this mouse helix-destabilizing protein shares a high degree of sequence homology with UP1. Of the 59 amino acids in the mouse protein that have so far been found to be homologous with UP1, 48 correspond exactly to sequences found in UP1. Most of the 11 differences that have been found between the sequences of these two proteins are conservative in nature, involving primarily the interchange of chemically similar amino acids. One 9-residue mouse sequence that is not obviously homologous to UP1 may be a result of the larger size of the mouse myeloma protein as compared to UP1. Since none of the UP1 or mouse myeloma helix-destabilizing protein sequence appears to be homologous to that of any previously sequenced protein, we presume that these two proteins represent a distinct class of single-stranded nucleic acid binding proteins that probably play a role in metabolism of single-stranded RNA or DNA in vivo.
A Microhomology-Mediated Break-Induced Replication Model for the Origin of Human Copy Number Variation (2009)

Chromosome structural changes with nonrecurrent endpoints associated with genomic disorders offer windows into the mechanism of origin of copy number variation (CNV). A recent report of nonrecurrent duplications associated with Pelizaeus-Merzbacher disease identified three distinctive characteristics. First, the majority of events can be seen to be complex, showing discontinuous duplications mixed with deletions, inverted duplications, and triplications. Second, junctions at endpoints show microhomology of 2-5 base pairs (bp). Third, endpoints occur near pre-existing low copy repeats (LCRs). Using these observations and evidence from DNA repair in other organisms, we derive a model of microhomology-mediated break-induced replication (MMBIR) for the origin of CNV and, ultimately, of LCRs. We propose that breakage of replication forks in stressed cells that are deficient in homologous recombination induces an aberrant repair process with features of break-induced replication (BIR). Under these circumstances, single-strand 3' tails from broken replication forks will anneal with microhomology on any single-stranded DNA nearby, priming low-processivity polymerization with multiple template switches generating complex rearrangements, and eventual re-establishment of processive replication.
Synthesis of a Well-Defined Glycopolymer by Nitroxide-Controlled Free Radical Polymerization (1998)

This is the first report of the synthesis of a well-defined glycopolymer by free radical polymerization. N-(p-vinylbenzyl)-[O-β-d-galactopyranosyl-(1→4)]-d-gluconamide (VLA), a styrene derivative with an oligosaccharide moiety, was polymerized in N,N-dimethylformamide solution at 90 °C by the nitroxide-mediated free radical polymerization technique. Acetylated VLA gave polymers with a molecular weight from about 2000 to 40 000, an Mw/Mn ratio of about 1.1 in all cases, and a conversion of up to about 90%, where Mw and Mn are the weight- and number-average molecular weights. Indispensable for this success were (1) the use of di-tert-butyl nitroxide (DBN) rather than other nitroxides such as TEMPO, (2) the acetylation of VLA, and (3) the use of a radical initiator DCP (dicumyl peroxide) as an accelerator. DBN provided a well-controlled polymerization of VLA at 90 °C (VLA becomes unstable at higher temperatures, e.g., >120 °C). The acetylation effectively prevented the chain transfer that leads to dead polymers and broad polydispersities. DCP remarkably accelerated the rate of polymerization (the rate of chain extension), which otherwise was impractically slow, without causing any appreciable broadening of polydispersity.
Virus-Receptor Interaction in an Adenovirus System (1968)

HeLa or KB cells each contain around 10(4) receptor sites for adenovirus type 2. These are inactivated by treatment of live cells with subtilisin. The receptor activity of the enzyme-treated cells is regained after 4 to 8 hr of incubation in complete medium. A technique that utilizes the difference in buoyant density between free virus and virus-receptor complex was developed to demonstrate receptor activity. Cellular fractionation revealed that receptors were confined mainly to the plasma membrane fraction and that negligible receptor activity could be demonstrated in enzyme-treated cells. Subtilisin probably did not penetrate the cell membrane; thus, the receptors are limited to the cell surface. Purified fiber of the virion completely prevents attachment of adenovirus types 2 and 5 to receptor sites at a ratio of 10(5) protein molecules per cell. Adsorption studies indicate that 10(5) to 10(6) receptor sites are available for the structural protein. The fiber does not affect attachment of poliovirus type 1.