gebhart/patrepeval huggingface dataset:
Improved performance interferometer designs for optical coherence tomography (2003)

In this paper we show that by using alternative optical components in fibre optic OCT, power conserving interferometers can be constructed that have such properties that a Fizeau interferometer configuration can achieve a higher SNR than that of a conventional Michelson arrangement and a comparable SNR to a Michelson optimised for power conservation.
A Competitive Mechanism for Staphylococcal Toxin SSL7 Inhibiting the Leukocyte IgA Receptor, FcαRI, Is Revealed by SSL7 Binding at the Cα2/Cα3 Interface of IgA (2005)

Leukocyte recruitment and effector functions like phagocytosis and respiratory burst are key elements of immunity to infection. Pathogen survival is dependent upon the ability to overwhelm, evade or inhibit the immune system. Pathogenic group A and group B streptococci are well known to produce virulence factors that block the binding of IgA to the leukocyte IgA receptor, Fc alphaRI, thereby inhibiting IgA-mediated immunity. Recently we found Staphylococcus aureus also interferes with IgA-mediated effector functions as the putative virulence factor SSL7 also binds IgA and blocks binding to Fc alphaRI. Herein we report that SSL7 and Fc alphaRI bind many of the same key residues in the Fc region of human IgA. Residues Leu-257 and Leu-258 in domain C alpha2 and residues 440-443 PLAF in C alpha3 of IgA lie at the C alpha2/C alpha3 interface and make major contributions to the binding of both the leukocyte receptor Fc alphaRI and SSL7. It is remarkable this S. aureus IgA binding factor and unrelated factors from streptococci are functionally convergent, all targeting a number of the same residues in the IgA Fc, which comprise the binding site for the leukocyte IgA receptor, Fc alphaRI.
Relation of C-Reactive Protein and Coronary Heart Disease in the MRFIT Nested Case-Control Study (1996)

The authors measured the relation between C-reactive protein, alpha 1 acid glycoprotein and albumin, an acute phase protein, and subsequent risk of myocardial infarction and coronary heart disease death in a nested case-control study among the Multiple Risk Factor Intervention Trial (MRFIT) participants. There were 98 myocardial infarction cases, 148 coronary heart disease deaths, and 491 controls. The cases and controls were followed for up to 17 years for deaths and 6-7 years for myocardial infarction cases and controls. There was a significant association between available distribution of C-reactive protein and subsequent coronary heart disease mortality. For smokers at baseline, the risk of coronary heart disease deaths in quartile 4 of C-reactive protein as compared with quartile 1 was 4.3 (95% confidence interval 1.74-10.8). The association persisted when adjusted for characteristics related to smoking and smoking cessation during the trial and to pulmonary function. There was no relation between alpha 1 acid glycoprotein and either myocardial infarction or coronary heart disease death. Albumin was inversely related to coronary heart disease death only for deaths that occurred between 7 and 13 years after baseline, consistent with previous MRFIT analyses. This is the first prospective study in "healthy but high risk individuals" to document the relation between C-reactive protein and coronary heart disease mortality.
A photometric approach to digitizing cultural artifacts (2001)

In this paper we present a photometry-based approach to the digital documentation of cultural artifacts. Rather than representing an artifact as a geometric model with spatially varying reflectance properties, we instead propose directly representing the artifact in terms of its reflectance field --- the manner in which it transforms light into images. The principal device employed in our technique is a computer-controlled lighting apparatus which quickly illuminates an artifact from an exhaustive set of incident illumination directions and a set of digital video cameras which record the artifact's appearance under these forms of illumination. From this database of recorded images, we compute linear combinations of the captured images to synthetically illuminate the object under arbitrary forms of complex incident illumination, correctly capturing the effects of specular reflection, subsurface scattering, self-shadowing, mutual illumination, and complex BRDF's often present in cultural artifacts. We also describe a computer application that allows users to realistically and interactively relight digitized artifacts.
Protein‐Based Nanomedicine Platforms for Drug Delivery (2009)

Protein-based nanomedicine platforms for drug delivery comprise naturally self-assembled protein subunits of the same protein or a combination of proteins making up a complete system. They are ideal for drug-delivery platforms due to their biocompatibility and biodegradability coupled with low toxicity. A variety of proteins have been used and characterized for drug-delivery systems, including the ferritin/apoferritin protein cage, plant-derived viral capsids, the small Heat shock protein (sHsp) cage, albumin, soy and whey protein, collagen, and gelatin. There are many different types and shapes that have been prepared to deliver drug molecules using protein-based platforms, including various protein cages, microspheres, nanoparticles, hydrogels, films, minirods, and minipellets. The protein cage is the most newly developed biomaterial for drug delivery and therapeutic applications. The uniform size, multifunctionality, and biodegradability push it to the frontier of drug delivery. In this Review, the recent strategic development of drug delivery is discussed with emphasis on polymer-based, especially protein-based, nanomedicine platforms for drug delivery. The advantages and disadvantages are also discussed for each type of protein-based drug-delivery system.
A major estrogen-regulated protein secreted from the liver of Xenopus laevis is a member of the serpin superfamily. Nucleotide sequence of cDNA and hormonal induction of mRNA. (1992)

Estrogen treatment of Xenopus frogs causes four mRNAs to become highly abundant in the liver. Three of these mRNAs have been previously identified as coding for vitellogenin, ferritin, and serum retinol binding protein. We show here that the fourth abundant liver messenger RNA comprises about 1500 nucleotides and codes for a 45-kDa secreted protein, designated Ep45. A clone complementary to Ep45 mRNA was isolated, and its identity was confirmed by hybridization selection of mRNA that translated in vitro into the Ep45 precursor. Nucleotide sequence analysis of the nearly full length cDNA revealed a total length of 1454 base pairs consisting of: 36 nucleotides of the 5' noncoding region, 1308 base pairs encoding an open reading frame of 436 amino acids, and 110 nucleotides of the 3' untranslated region. Ep45 mRNA may originate from as many as four closely spaced transcription start sites, which are 15 to 21 bases upstream of the first nucleotide of the cDNA clone. The Xenopus laevis genome appears to contain a single Ep45 gene. The deduced amino acid sequence indicates that Ep45 has features typical of a secreted protein, including a signal peptide of 16 amino acids and three potential sites for N-linked glycosylation, and is related to the serine protease inhibitors, a large family of proteins with very diverse physiological functions. Ep45 mRNA was absent in the liver of normal male frogs and increased at least 100-fold in response to estradiol-17 beta. Thus, both Ep45 and vitellogenin mRNAs are switched from undetectable to very high levels, a pattern of expression not found for any other mRNAs in Xenopus liver.
Self-Assembly and Bonding of Alkanephosphonic Acids on the Native Oxide Surface of Titanium (2001)

Alkanephosphonic acids assemble from solution on the native oxide surface of titanium to form alkane chain ordered films which, however, are easily removed by solvent rinse. In contrast, assembling the alkanephosphonic acid from solution on the native oxide surface of titanium followed by gentle heating gives an alkane chain ordered film of the acid which is strongly surface-bound; this film resists removal by solvent washing or simple mechanical peel testing. Surface imaging by atomic force microscopy shows comprehensive surface coverage by aggregated islands, with elevations of each consistent with monolayer formation. ω-Carboxyalkanephosphonic acids are also easily bound to the native oxide surface of Ti through self-assembly/heating. Infrared analysis is consistent with surface attachment through the phosphonate headgroup.
Integration of amorphous and polycrystalline silicon thin-film transistors through selective crystallization of amorphous silicon (1999)

Selective exposure of a hydrogenated amorphous silicon (a-Si:H) film to a room-temperature hydrogen plasma using a patterned masking layer and a subsequent anneal at 600 °C, results in patterned polycrystalline and amorphous silicon regions. However, most of the hydrogen in the amorphous silicon is lost, leading to severe degradation in its properties. In this letter, we report the rehydrogenation of amorphous silicon films following this anneal to give a-Si:H thin-film transistors with a mobility as high as 1.2 cm2/V s and ON/OFF current ratios of ∼106. This process was used to integrate amorphous and polycrystalline silicon transistors on a single substrate with only one more lithography and processing step than that required for a single type of transistor.
Organotrifluoroborates: Protected Boronic Acids that Expand the Versatility of the Suzuki Coupling Reaction (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Plasma-Assisted Deposition at Atmospheric Pressure (1995)

In plasma-assisted deposition methods the activation energy necessary for the initiation of chemical reactions is transferred via charged particles. Due to this fact in many cases the process temperature can be kept small, if gas discharges at pressures below 1 hPa are used. On the other hand low pressure requires a great deal of vacuum equipment. Processes at atmospheric pressure are more favourable, if similar results compared to existing methods can be achieved. Basis for a new plasma-assisted deposition method at atmospheric pressure are barrier discharges. Those discharges consist of a large number of transient microdischarges in parallel which are distributed statistically on the surface to be coated. Starting with some basic considerations on the repetitive generation of microdischarges, the deposition of thin polymeric films on glass surfaces is described, using barrier discharges at atmospheric pressure and acetylene. Uniform polymeric films up to 1 µm are obtained, if trains of voltage pulses are used. Parameters influencing the deposition rate and the film quality are discussed. In addition, it is estimated whether further improvements of the deposition process are possible.
Redefining the relevance of established cancer cell lines to the study of mechanisms of clinical anti-cancer drug resistance (2011)

Although in vitro models have been a cornerstone of anti-cancer drug development, their direct applicability to clinical cancer research has been uncertain. Using a state-of-the-art Taqman-based quantitative RT-PCR assay, we investigated the multidrug resistance (MDR) transcriptome of six cancer types, in established cancer cell lines (grown in monolayer, 3D scaffold, or in xenograft) and clinical samples, either containing >75% tumor cells or microdissected. The MDR transcriptome was determined a priori based on an extensive curation of the literature published during the last three decades, which led to the enumeration of 380 genes. No correlation was found between clinical samples and established cancer cell lines. As expected, we found up-regulation of genes that would facilitate survival across all cultured cancer cell lines evaluated. More troubling, however, were data showing that all of the cell lines, grown either in vitro or in vivo, bear more resemblance to each other, regardless of the tissue of origin, than to the clinical samples they are supposed to model. Although cultured cells can be used to study many aspects of cancer biology and response of cells to drugs, this study emphasizes the necessity for new in vitro cancer models and the use of primary tumor models in which gene expression can be manipulated and small molecules tested in a setting that more closely mimics the in vivo cancer microenvironment so as to avoid radical changes in gene expression profiles brought on by extended periods of cell culture.
Diketo acid inhibitor mechanism and HIV-1 integrase: Implications for metal binding in the active site of phosphotransferase enzymes (2002)

The process of integrating the reverse-transcribed HIV-1 DNA into the host chromosomal DNA is catalyzed by the virally encoded enzyme integrase (IN). Integration requires two metal-dependent reactions, 3' end processing and strand transfer. Compounds that contain a diketo acid moiety have been shown to selectively inhibit the strand transfer reaction of IN in vitro and in infected cells and are effective as inhibitors of HIV-1 replication. To characterize the molecular basis of inhibition, we used functional assays and binding assays to evaluate a series of structurally related analogs. These studies focused on investigating the role of the conserved carboxylate and metal binding. We demonstrate that an acidic moiety such as a carboxylate or isosteric heterocycle is not required for binding to the enzyme complex but is essential for inhibition and confers distinct metal-dependent properties on the inhibitor. Binding requires divalent metal and resistance is metal dependent with active site mutants displaying resistance only when the enzymes are evaluated in the context of Mg(2+). The mechanism of action of these inhibitors is therefore likely a consequence of the interaction between the acid moiety and metal ion(s) in the IN active site, resulting in a functional sequestration of the critical metal cofactor(s). These studies thus have implications for modeling active site inhibitors of IN, designing and evaluating analogs with improved efficacy, and identifying inhibitors of other metal-dependent phosphotransferases.
A Generalization of the Gamma Distribution (1962)

This paper concerns a generalization of the gamma distribution, the specific form being suggested by Liouville's extension to Dirichlet's integral formula [3]. In this form it also may be regarded as a special case of a function introduced by L. Amoroso [1] and R. d'Addario [2] in analyzing the distribution of economic income. (Also listed in [4] and [5].) In essence, the generalization (1) herein is accomplished by supplying a positive parameter, $p$, as an exponent in the exponential factor of the gamma distribution. The moment generating function is shown, and cumulative probabilities are related directly to the incomplete gamma function (tabulated in [6]). Distributions are given for various functions of independent "generalized gamma variates" thus defined, special attention being given to the sum of such variates. Convolution results occur in alternating series form, with coefficients whose evaluation may be tedious and lengthy. An upper bound is provided for the modulus of each term, and simplified computation methods are developed for some special cases. A corollary is derived showing that the researches of Robbins in [7] apply to a larger class of problems than was treated in [7]. Extensions of his methods lead to iterative formulae for the coefficients in series obtained for an even larger class of problems.
Selection of the Constitutive Mutant of Bacillus firmus var. alkalophilus and its Characteristics of Cydodextrin Glucanotransferase Production (1995)

To investigate the role of induction on CGTase production for alkalophilic Bacillus firm us var. alkalophilus H609, the constitutive mutants that form a halo around its colonies at non-inducible AG agar media containing amylose and glucose were selected. The selected constitutive mutants could produce CGTase in the range of 18.9 to 28.8 units/ml in the alkaline basal medium, and finally a constitutive mutant Bacillus firmus var. alkalophilus CM46 was selected. The constitutive nature of CM46 was also confirmed in protein level using SDS-PAGE. The effects of induction and catabolite repression for both parent strain Bacillus firmus var. alkalophilus H609 and constitutive mutant CM46 were also compared by adding soluble starch and glucose during cultivation. The selected mutant CM46 was a non-inducible but a catabolite regulated type mutant. Even though inductive regulation was released, the specific CGTase activity defined as CGTase activity per cell concentration was not increased compared with that of parent strain. The cell growth and CGTase production patterns of constitutive mutant Bacillus firmus var. alkalophilus CM46 were compared with the parent strain to identify CGTase production characteristics.
Hypoxia-inducible Expression of a Natural cis-Antisense Transcript Inhibits Endothelial Nitric-oxide Synthase (2007)

The destabilization of endothelial nitric-oxide synthase (eNOS) mRNA in hypoxic endothelial cells may be important in the etiology of vascular diseases, such as pulmonary hypertension. Recently, an overlapping antisense transcript to eNOS/NOS3 was implicated in the post-transcriptional regulation of eNOS. We demonstrate here that expression of sONE, also known as eNOS antisense (NOS3AS) or autophagy 9-like 2 (APG9L2), is robustly induced by hypoxia or functional deficiency of von Hippel-Lindau protein. sONE is also up-regulated in the aortas of hypoxic rats. In hypoxic endothelial cells, sONE expression negatively correlates with eNOS expression. Blocking the hypoxic induction of sONE by RNA interference attenuates the fall in both eNOS RNA and protein. We provide evidence that the induction of sONE primarily involves transcript stabilization rather than increased transcriptional activity and is von Hippel-Lindaubut not hypoxia-inducible factor 2alpha-dependent. We also demonstrate that sONE transcripts are enriched in the nucleus of normoxic cells and that hypoxia promotes an increase in the level of cytoplasmic and polyribosome-associated, sONE mRNA. The finding that eNOS expression can be regulated by an overlapping cis-antisense transcript in a stimulus-dependent fashion provides evidence that sense/antisense interactions may play a previously unappreciated role in vascular disease pathogenesis.
Measurement Of Multiphase Flow Water Fraction And Water-cut (2007)

This paper describes a microwave transmission multiphase flow water‐cut meter that measures the amplitude attenuation and phase shift across a pipe diameter at multiple frequencies using cavity‐backed antennas. The multiphase flow mixture permittivity and conductivity are derived from a unified microwave transmission model for both water‐ and oil‐continuous flows over a wide water‐conductivity range; this is far beyond the capability of microwave‐resonance‐based sensors currently on the market. The water fraction and water cut are derived from a three‐component gas‐oil‐water mixing model using the mixture permittivity or the mixture conductivity and an independently measured mixture density. Water salinity variations caused, for example, by changing formation water or formation/injection water breakthrough can be detected and corrected using an online water‐conductivity tracking technique based on the interpretation of the mixture permittivity and conductivity, simultaneously measured by a single‐modality microwave sensor.
Intrusion detection: a bioinformatics approach (2004)

We address the problem of detecting masquerading, a security attack in which an intruder assumes the identity of a legitimate user. Many approaches based on hidden Markov models and various forms of finite state automata have been proposed to solve this problem. The novelty of our approach results from the application of techniques used in bioinformatics for a pair-wise sequence alignment to compare the monitored session with past user behavior. Our algorithm uses a semiglobal alignment and a unique scoring system to measure similarity between a sequence of commands produced by a potential intruder and the user signature, which is a sequence of commands collected from a legitimate user. We tested this algorithm on the standard intrusion data collection set. As discussed, the results of the test showed that the described algorithm yields a promising combination of intrusion detection rate and false positive rate, when compared to published intrusion detection algorithms.
The myotonic dystrophies: diagnosis and management (2010)

There are currently two clinically and molecularly defined forms of myotonic dystrophy: (1) myotonic dystrophy type 1 (DM1), also known as 'Steinert's disease'; and (2) myotonic dystrophy type 2 (DM2), also known as proximal myotonic myopathy. DM1 and DM2 are progressive multisystem genetic disorders with several clinical and genetic features in common. DM1 is the most common form of adult onset muscular dystrophy whereas DM2 tends to have a milder phenotype with later onset of symptoms and is rarer than DM1. This review will focus on the clinical features, diagnosis and management of DM1 and DM2 and will briefly discuss the recent advances in the understanding of the molecular pathogenesis of these diseases with particular reference to new treatments using gene therapy.
Report: AT&T's Pay-Per-View Television Trial (1987)

Pay-per-view service is a television entertainment service wherein consumers can watch a scheduled movie or live event on their home television sets and be charged specifically for the viewing. It is a usage-sensitive pricing system for television entertainment similar to the movie services found in some hotels in which viewers pay only for those programs they watch. The prospect of multimillion-dollar revenues from the sale of first-run movies, live sporting events, and other premium television entertainment on a pay-per-view basis has continued to entice movie studios, event producers, cable and network television operators, and other purveyors of home video entertainment. For pay-per-view to be a viable business, an efficient system for ordering, distributing, and billing of the pay-per-view programs is necessary.
mus308 mutants of Drosophila exhibit hypersensitivity to DNA cross-linking agents and are defective in a deoxyribonuclease. (1990)

Mutagen-sensitive strains that identify 16 different Drosophila genes have been screened for alterations in DNA metabolic enzymes. A characteristic defect in an acid-active deoxyribonuclease was observed in strains carrying the six available mutant alleles of the mus308 gene. Since that enzyme is detected at normal levels in a mutant strain that is deficient in the previously identified enzymes DNase 1 and DNase 2, it represents a new Drosophila nuclease that is designated Nuclease 3. The mus308 mutants were originally distinguished from all other mutagen-sensitive mutants of Drosophila because they exhibit hypersensitivity to the DNA cross-linking agent nitrogen mustard without expressing a concurrent sensitivity to the monofunctional agent methyl methanesulfonate. Further observations of hypersensitivity to the mutagens trimethylpsoralen, diepoxybutane and cis-platinum now establish a more general sensitivity of these mutants to agents capable of generating DNA cross-links. In spite of the hypersensitivity of the mus308 mutants to DNA cross-linking agents, the initial incision step of DNA cross-link repair is normal in mus308 cells as assayed by the alkaline elution procedure. The Drosophila mus308 mutants show promise of providing a useful model for analogous defects in other organisms including man.