gebhart/patrepeval huggingface dataset:
Singly resonant continuous-wave optical parametric oscillator pumped by a diode laser (1999)

We report on what is believed to be the first singly resonant cw optical parametric oscillator (SRO) that is directly pumped by a diode laser. The SRO consists of a 38-mm-long periodically poled LiNbO(3) crystal in a four-mirror signal-resonant ring cavity. Pumped by 2.5 W of 925-nm diode-laser radiation, the SRO generates 480 mW of single-frequency idler radiation at 2.1mum . The wavelengths of the signal and the idler output are tuned in the ranges of 1.55 to 1.70mum and 2.03 to 2.29mum, respectively, by tuning the wavelength of the diode laser from 924.0 to 925.4 nm.
An Open Label, Phase 2 Study of MABp1 Monotherapy for the Treatment of Acne Vulgaris and Psychiatric Comorbidity. (2015)

Patients had rapid improvement of skin lesions, as well as psychosocial functioning and anxiety. MABp1 may provide a safe and effective means for treating inflammatory acne lesions and. Further studies using this antibody are warranted in this patient population.
CORONAVIRUS: ORGANIZATION, REPLICATION AND EXPRESSION OF GENOME (1990)

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Mechanism and regulation of the nonsense-mediated decay pathway (2016)

The Nonsense-mediated mRNA decay (NMD) pathway selectively degrades mRNAs harboring premature termination codons (PTCs) but also regulates the abundance of a large number of cellular RNAs. The central role of NMD in the control of gene expression requires the existence of buffering mechanisms that tightly regulate the magnitude of this pathway. Here, we will focus on the mechanism of NMD with an emphasis on the role of RNA helicases in the transition from NMD complexes that recognize a PTC to those that promote mRNA decay. We will also review recent strategies aimed at uncovering novel trans-acting factors and their functional role in the NMD pathway. Finally, we will describe recent progress in the study of the physiological role of the NMD response.
Concerted Action of Multiple cis -Acting Sequences Is Required for Rev Dependence of Late Human Immunodeficiency Virus Type 1 Gene Expression (2000)

Based on the human immunodeficiency virus type 1 (HIV-1) gag gene, subgenomic reporter constructs have been established allowing the contributions of different cis-acting elements to the Rev dependency of late HIV-1 gene products to be determined. Modification of intragenic regulatory elements achieved by adapting the codon usage of the complete gene to highly expressed mammalian genes resulted in constitutive nuclear export allowing high levels of Gag expression independent from the Rev/Rev-responsive element system and irrespective of the absence or presence of the isolated major splice donor. Leptomycin B inhibitor studies revealed that the RNAs derived from the codon-optimized gag gene lacking AU-rich inhibitory elements are directed to a distinct, CRM1-independent, nuclear export pathway.
The Impact of Molecular Weight and PEG Chain Length on the Systemic Pharmacokinetics of PEGylated Poly l-Lysine Dendrimers (2008)

The impact of PEGylation on the pharmacokinetics and biodistribution of (3)H-labeled poly l-lysine dendrimers has been investigated after intravenous administration to rats. The volumes of distribution, clearance and consequently the plasma half-lives of the PEGylated dendrimers were markedly dependent on the total molecular weight of the PEGylated dendrimer, but were not specifically affected by the PEG chain length alone. In general, the larger dendrimer constructs (i.e. >30 kDa) had reduced volumes of distribution, were poorly renally cleared and exhibited extended elimination half-lives ( t 1/2 1-3 days) when compared to the smaller dendrimers (i.e. <20 kDa) which were rapidly cleared from the plasma principally into the urine ( t 1/2 1-10 h). At later time points the larger dendrimers concentrated in the organs of the reticuloendothelial system (liver and spleen); however, the absolute extent of accumulation was low. Size exclusion chromatography of plasma and urine samples revealed that the PEGylated dendrimers were considerably more resistant to biodegradation in vivo than the underivatized poly l-lysine dendrimer cores. The results suggest that the size of PEGylated poly l-lysine dendrimer complexes can be manipulated to optimally dictate their pharmacokinetics, biodegradation and bioresorption behavior.
Integrated Asset Modeling, a Quick Solution for Identifying an Infill Well Opportunity (2004)

Abstract This paper describes an integrated asset modeling program designed to determine reserves that can be drained by an infill prospect within a mature asset. This model has proven its ability to reduce risks and improve reservoir decline management. It is able to quickly identify potential benefits of drilling without spending significant time building complex reservoir simulation models. The West Java fields, operated by BP Indonesia, are located in the northwestern part of the Java Island. Production commenced in 1971 on these mature offshore assets with interdependent oil and gas systems. Over 50 separate reservoirs have been identified in these highly stratified structures and many wells produce hydrocarbon from multiple horizons (commingled production). The surface facility network is very complex integrating many producers, various production/compression systems and long pipeline sections. As the fields become mature then there is an increasing need to drill more and more wells to recover untapped reserves and reduce production decline. Quick screenings are required to identify the possibility of drilling an infill well surrounding the existing producers or to access untapped hydrocarbon reserves. An integrated model connecting reservoir tanks, wells, pipeline networks and surface facilities was build support the infill decision. The model can handle naturally flowing, gas lifted and ESPed producing wells. There is no limit on number of wells and/or platforms that can be analyzed. Constraints can be considered at all levels, from well, joint, separator and the overall system. Moreover, production forecasting from the model can also accommodate constraints at the reservoir level.
Two TTX-resistant Na+ currents in mouse colonic dorsal root ganglia neurons and their role in colitis-induced hyperexcitability (2004)

The composition of Na+ currents in dorsal root ganglia (DRG) neurons depends on their neuronal phenotype and innervation target. Two TTX-resistant (TTX-R) Na+ currents [voltage-gated Na channels (Nav)] have been described in small DRG neurons; one with slow inactivation kinetics (Nav1.8) and the other with persistent kinetics (Nav1.9), and their modulation has been implicated in inflammatory pain. This has not been studied in neurons projecting to the colon. This study examined the relative importance of these currents in inflammation-induced changes in a mouse model of inflammatory bowel disease. Colonic sensory neurons were retrogradely labeled, and colitis was induced by instillation of trinitrobenzenesulfonic acid (TNBS) into the lumen of the distal colon. Seven to ten days later, immunohistochemical properties were characterized in controls, and whole cell recordings were obtained from small (<40 pF) labeled DRG neurons from control and TNBS animals. Most neurons exhibited both fast TTX-sensitive (TTX-S)- and slow TTX-R-inactivating Na+ currents, but persistent TTX-R currents were uncommon (<15%). Most labeled neurons were CGRP (79%), tyrosine kinase A (trkA) (84%) immunoreactive, but only a small minority bind IB4 (14%). TNBS-colitis caused ulceration, thickening of the colon and significantly increased neuronal excitability. The slow TTX-R-inactivating Na current density (Nav1.8) was significantly increased, but other Na currents were unaffected. Most small mouse colonic sensory neurons are CGRP, trkA immunoreactive, but not isolectin B4 reactive and exhibit fast TTX-S, slow TTX-R, but not persistent TTX-R Na+ currents. Colitis-induced hyperexcitability is associated with increased slow TTX-R (Nav1.8) Na+ current. Together, these findings suggest that colitis alters trkA-positive neurons to preferentially increase slow TTX-R Na+ (Nav1.8) currents.
Activation of pp60c-src transforming potential by mutations altering the structure of an amino terminal domain containing residues 90-95. (1988)

The overexpression of the c-src gene product, pp60c-src, in avian and rodent embryo cells is not sufficient to induce cellular transformation. In this study we report that structural alterations within an amino terminal domain of pp60c-src, the exon 3 domain (residues 84-115) activate the oncogenic potential of the c-src gene product. Site-directed mutagenesis of the c-src gene was used to generate c-src variants encoding pp60c-src proteins with the following amino acid alterations: tyr 90 to phe (pm90F); tyr 92 to phe (pm92F); arg 95 to either trp, lys, glu or gln (pm95W, 95K, 95E and 95Q, respectively), and deletion of residues 92-95 (dl92). C-src variants encoding proteins with the alteration of arg 95 to trp, glu, or lys, or containing the deletion of residues 92-95, induced alterations in cell morphology and promoted growth in soft agar as well as changes in glucose transport and in vivo tyrosine phosphorylation of cellular proteins (including calpactin I heavy chain, p36). Analysis of in vivo phosphorylation of the transforming variant src proteins revealed little detectable alteration in the phosphorylation of tyr 527, a putative site of tyrosine kinase regulation. Our results suggest that structural alterations within a domain distal to the catalytic (kinase) domain activate pp60c-src kinase activity and, concomitantly, oncogenic potential. Furthermore, we suggest that the exon 3 domain of pp60c-src may contribute to the regulation and/or substrate specificity of the c-src protein.
The identification of three biologically relevant globotriaosyl ceramide receptor binding sites on the Verotoxin 1 B subunit (1999)

The Verotoxin 1 (VT1) B subunit binds to the glycosphingolipid receptor globotriaosylceramide (Gb3). Receptor-binding specificity is associated with the terminally linked Galalpha(1-4) Galbeta disaccharide sequence of the receptor. Recently, three globotriose (Galalpha[1-4] Galbeta [1-4] Glcbeta) binding sites per B-subunit monomer were identified by crystallography. Two of these sites (sites I and II) are located adjacent to phenylalanine-30. Site I was originally predicted as a potential Gb3 binding site on the basis of sequence conservation, and site II was additionally predicted based on computer modelling and receptor docking. The third (site III) was also identified by crystallography and is located at the N-terminal end of the alpha-helix. To determine the biological significance of sites II and III, and to support our previous findings of the significance of site I, we examined the binding properties and cytotoxicity of VT1 mutants designed to block Gb3 binding at each site selectively. The Scatchard analysis of saturation-binding data for each mutant revealed that only the amino acid substitutions predicted to affect site I (D-17E) or site II (G-62T) caused reductions in the binding affinity and capacity of VT1 for Gb3. Similarly, those mutations at sites I and II also caused significant reductions in both Vero and MRC-5 cell cytotoxicity (by seven and five logs, respectively, for G-62T and by four and two logs, respectively, for D-17E). In contrast, the substitution of alanine for W-34 at site III did not reduce the high-affinity binding of the B subunit, despite causing a fourfold reduction in the receptor-binding capacity. The corresponding mutant W-34A holotoxin had a two-log reduction in cytotoxicity on Vero cells and no statistically significant reduction on MRC-5 cells. We conclude that the high-affinity receptor binding most relevant for cell cytotoxicity occurs at sites I and II. In contrast, site III appears to mediate the recognition of additional Gb3 receptor epitopes but with lower affinity. Our results support the significance of the indole ring of W-34 for binding at this site.
Physical Stability of Insulin Formulations (1983)

Insulin aggregation remains a fundamental obstacle to the long-term application of many insulin infusion systems. We here report the effects of physiologic and nonphysiologic compounds on the aggregation behavior of crystalline zinc insulin (CZI) solutions. Under conditions chosen to simulate the most severe that would be encountered in delivery systems (presence of air, continuous motion, and elevated temperature), both highly purified and regular CZI at 5 U/ml formed turbid gels in 5 days. At concentrations of 100 and 500 U/ml stability was increased with turbid gels forming at 12 and 15 days, respectively. Under identical conditions, 5 U/ml CZI formulations containing the physiologic surfactant lysophosphatidylcholine (0.02%) or the synthetic surfactants SDS (1%), Brij 35 (0.1%), Tween (0.01%), or Triton X (0.01%) retained a transmittance at 540 nm of greater than 96% for 67-150 days. These nonionic and ionic surfactants containing the hydrophobic group, CH3(CH2)N, with N = 7-16, remarkably stabilized CZI formulations while those lacking such groups demonstrated little or no effect. The alcohols glycerol (30-50%) and isopropanol (10-50%) were moderately effective stabilizers. Silicone rubber drastically accelerated aggregation in all but one formulation (1% SDS). Emphasis in this study was placed on the properties of 5-U/ml formulations. Controls run at higher concentrations indicated a positive correlation between concentration and stability. It was concluded that the aggregation of insulin into high-molecular-weight polymers may be inhibited by reducing the effective polarity of the solvent. In this regard, anionic and nonionic surfactants containing appropriately long hydrophobic groups demonstrated the greatest degree of stabilization. Finally, of all the medical grade materials likely to be used in pumps, silicone rubber is the most active in promoting insulin aggregation.
Membrane receptor trafficking: Evidence of proximal and distal zones conferred by two independent endoplasmic reticulum localization signals (2003)

The generic membrane trafficking signals of internal RXR and carboxyl-terminal KKXX motifs direct intracellular endoplasmic reticulum (ER) localization of the signal-bearing proteins. These signaling motifs play a critical role in partitioning proteins into designated subcellular compartments by functioning as an intracellular "zip code." In the process of determining the potential distinctions between these two otherwise functionally identical motifs, two functional zones of these signals were revealed. The KKXX signal was effective only when it was positioned closer to the membrane surface. In contrast, under identical conditions, the internal RXR signal was functional when it was positioned distally from the membrane. Different from the C-terminal KKXX signal, the internal RXR motif may be present in multiple copies. The receptor with multivalent RXR motifs displayed similar trafficking behavior to that of the same receptor with one copy of the RXR motif. The distinctive operating ranges from their anchored membrane surface provide experimental evidence for the notion that there are functional zoning layers within which membrane protein signal motifs are active.
High-Density Detection of Restriction-Site-Associated DNA Markers for Rapid Mapping of Mutated Loci in Neurospora (2007)

The wealth of sequence information available for Neurospora crassa and other fungi has greatly facilitated evolutionary and molecular analyses of this group. Although "reverse" genetics, in which genes are first identified by their sequence rather than by their mutant phenotypes, serves as a valuable new approach for elucidating biological processes, classical "forward" genetic analysis is still extremely useful. Unfortunately, mapping mutations and identifying the corresponding genes has typically been slow and laborious. To facilitate forward genetics in Neurospora, we have adapted microarray-based restriction-site-associated DNA (RAD) mapping for use with N. crassa oligonucleotide microarrays. This technique was used to simultaneously detect an unprecedented number of genomewide restriction site polymorphisms from two N. crassa strains: Mauriceville and Oak Ridge. Furthermore, RAD mapping was used to quickly map a previously unknown gene, defective in methylation-7 (dim-7).
Evaluating Spatial Congruency of 3D Audio and Video Objects (2012)

In this paper we demonstrate the evaluation of spatial congruency of object based audio and 3D video reproduction. With current developments in 3D video representation we are able to introduce a depth dimension. Furthermore, audio reproduction systems like Wave Field Synthesis are able to reproduce the sound field of virtual sound sources at various positions in the room, also in front or behind a video screen. When combining these technologies audio objects can be placed at the positions of 3D video objects. Subjective evaluations are needed to investigate the quality of such combinations. In our experiment we displaced the audio and video objects with respect to certain angles and evaluated the noticeable horizontal displacement angle. Displacements of more than 5° are noticeable and become annoying above 10°.
Utilization of Methionine-containing Peptides and Their Derivatives by a Methionine-requiring Auxotroph of Saccharomyces cerevisiae (1974)

A number of peptides containing methionine and glycine, such as Met-Met-Gly, Met-Met-Gly-Met, and Met-Met-Gly-Gly, were synthesized by conventional techniques. The growth response of Saccharomyces cerevisiae G1333, a methionine-requiring auxotroph, toward various di-, tri-, and tetrapeptides containing methionine was measured. The yeast mutant utilized and contained peptidase activity toward most of the peptides investigated. Growth curves varied with the amino acid sequence and composition of the peptide substrate. Only three free peptides, Gly-Met-Gly, Met-Met-Gly-Gly, and Met-Met-Met-Gly failed to satisfy the nutritional requirement of strain G1333. A cell-free extract derived from the auxotroph contained peptidases which liberated methionine from these three peptides. Peptides containing COOH-terminal methionine residues were observed to be better growth substrates than those peptides having different amino acid residues at this position. The yeast auxotroph grew on pentamethionine as well as on methyl ester derivatives of (Met)3, (Met)4, and (Met)5. A number of N-acetylated and t-butyloxycarbonyl di- and tri-peptides containing methionine, such as Ac-Met-Met, Ac-Met-Met-Met, Ac-Met-Gly-Met, Boc-Met-Met-Met, and Boc-Gly-Met-Met served as growth substrates. Several peptide derivatives, all containing a COOH-terminal glycine residue, Ac-Met-Gly, Ac-Met-Gly-Gly, Ac-Gly-Met-Gly, and Boc-Met-Met-Gly, failed to support growth of strain G1333. Comparison of the results obtained for the yeast auxotroph with corresponding data for methionine-requiring auxotrophs of E. coli suggests that the ability of both organisms to utilize similar peptide substrates is different.
Bootstrap Methods: Another Look at the Jackknife (1979)

We discuss the following problem: given a random sample $\mathbf{X} = (X_1, X_2, \cdots, X_n)$ from an unknown probability distribution $F$, estimate the sampling distribution of some prespecified random variable $R(\mathbf{X}, F)$, on the basis of the observed data $\mathbf{x}$. (Standard jackknife theory gives an approximate mean and variance in the case $R(\mathbf{X}, F) = \theta(\hat{F}) - \theta(F), \theta$ some parameter of interest.) A general method, called the "bootstrap," is introduced, and shown to work satisfactorily on a variety of estimation problems. The jackknife is shown to be a linear approximation method for the bootstrap. The exposition proceeds by a series of examples: variance of the sample median, error rates in a linear discriminant analysis, ratio estimation, estimating regression parameters, etc.
Multiple protein-binding sites in the 5'-flanking region regulate c-fos expression. (1986)

We tested sequences flanking the mouse c-fos gene for the ability to form specific DNA-protein complexes with factors present in crude nuclear extracts prepared from mammalian cells. Three such complexes were detected. One complex formed in a region necessary for the induction of c-fos expression by serum growth factors. Two additional complexes formed at sequences that contribute to basal c-fos promoter activity in vivo. These complexes represent three novel sequence-specific DNA-binding activities which appear to participate in the regulation of c-fos transcription.
Candidate AIDS Vaccines (1995)

There is an urgent need to control the global epidemic of human immunodeficiency virus type 1 (HIV-1) infection. Although educational approaches to modify risk-taking behavior are a critical component of prevention, we focus this discussion on the status of vaccine development. The success of active immunization against other infectious diseases makes immunization an attractive approach to preventing HIV-1 infection. The eradication of smallpox1 and progress in the elimination of poliomyelitis, targeted to occur by the year 2000,2 are notable examples of the impact of vaccination.Given the complexity of HIV-1 pathogenesis, however, empirical approaches successful in the development of previous . . .
Effects of a Combined Process of High‐Pressure Carbon Dioxide and High Hydrostatic Pressure on the Quality of Carrot Juice (2002)

ABSTRACT: A combined treatment of high‐pressure carbon dioxide (HPCD) and high hydrostatic pressure (HHP) was investigated as a non‐thermal processing technique to enhance the safety and shelf life of carrot juice. Aerobes were completely inactivated by a combined treatment of 4.90 MPa‐HPCD and 300 MPa‐HHP. A combined treatment of 4.90 MPa‐HPCD and 600 MPa‐HHP effectively inactivated enzymes. The residual activities of polyphenoloxidase, lipoxygenase, and pectinmethylesterase were less than 11.3%, 8.8%, and 35.1%, respectively. Cloud and color were considerably affected by HPCD, but not by HHP. Enzyme activities and the total color difference showed a strong correlation with pH, which was dependent on the pressure of carbon dioxide.