gebhart/patrepeval huggingface dataset:
Pulse compression by nonlinear pulse evolution with reduced optical wave breaking in erbium-doped fiber amplifiers (1996)

Nonlinear pulse evolution is studied for a fiber with normal dispersion (ND) and gain. Numerical simulations show that under certain conditions the pulse evolves into a parabolic shape, which has been shown to reduce optical wave breaking. Much as with the square pulse that forms in passive fibers with ND, the interplay of ND and self-phase modulation creates a highly linear chirp, which can be efficiently compressed. Application to an amplifying fiber/grating (prism) pair pulse compressor is considered, with an experimental demonstration of compression from 350 to 77 fs at a gain of 18 dB in an erbium-doped fiber amplifier.
Data-driven RASTA filters in reverberation (2002)

In this work we test the performance of RASTA-style modulation filters derived under reverberant conditions. The modulation filters are constructed through linear discriminant analysis of log critical band energies in a manner described by van Vuuren and Hermansky (1997). In previous work we had observed the properties of the resultant filters under a number of acoustic conditions that were artificially applied to the training speech. Here, we present automatic speech recognition results that compare the performance of these filters under some training and testing reverberant conditions. We also test the effectiveness and robustness of a multi-stream combination using probability streams trained under different reverberant environments. The experiments reveal some performance improvement in severe reverberation.
Phase I Study of SS1P, a Recombinant Anti-Mesothelin Immunotoxin Given as a Bolus I.V. Infusion to Patients with Mesothelin-Expressing Mesothelioma, Ovarian, and Pancreatic Cancers (2007)

SS1P is well tolerated with pleuritis as the DLT at the highest dose level. Evidence of clinical activity was noted in a group of heavily pretreated patients. Phase II clinical trials of SS1P are being planned for malignant mesothelioma and other mesothelin-expressing malignancies.
ANTIBODY RESPONSES AND PROTECTION FROM PYELONEPHRITIS FOLLOWING VACCINATION WITH PURIFIED ESCHERICHIA COLI PAPDG PROTEIN (2004)

Purified PapDG is a tractable vaccine candidate that in our small study demonstrated the ability to elicit adequate serum antibody levels to prevent E. coli mediated pyelonephritis.
CLINICAL STUDY: Endogenous morphine signaling via nitric oxide regulates the expression of CYP2D6 and COMT: autocrine/paracrine feedback inhibition (2007)

We determined changes in mRNA expression in specific enzymes involved in the biosynthesis of morphine in human white blood cells via microarray. Leukocyte exposure to morphine down-regulated catechol-O-methyl transferase (COMT) and CYP2D6 by approximately 50% compared with control values. The treatment did not alter DOPA decarboxylase and dopamine beta-hydroxylase expression, demonstrating the specificity of morphine actions. The verification of the microarray data was accomplished via real-time Taqman reverse transcriptase polymerase chain reaction (RT-PCR) focused on CYP2D6 and COMT expression in different blood samples treated with morphine. The analysis showed similar changes in the expression of CYP2D6 and COMT mRNA. The expression was reduced by 47 +/- 7% for CYP2D6, substantiating the microarray finding of a 54% reduction. Furthermore, exposure of white blood cells to 10(-6) M S-nitroso-N-acetyl-DL-penicillamine (SNAP), a nitric oxide (NO) donor, reduced the expression of CYP2D6 and COMT. Prior naloxone (10(-6) M) or N-nitro-L-arginine methyl ester (L-NAME) (10(-4) M) addition abrogated morphine's down-regulating activity, demonstrating morphine was initiating its actions via stimulating constitutive NO synthase derived NO release via the mu3 opiate receptor splice variant. In the past we demonstrated that UDP-glucurosyltransferase is involved in metabolizing morphine to morphine 6-glucuronide in adrenal chromaffin cells. In the present study its expression was not found in controls and morphine-treated cells, suggesting that morphine 6-glucuronide may not be synthesized in white blood cells. Taken together, it appears that morphine has the ability to modulate its own synthesis via autocrine and paracrine signaling.
Detection of EGFR mutations with mutation-specific antibodies in stage IV non-small-cell lung cancer (2010)

IHC with mutation-specific mAbs against EGFR is a promising method for detecting EGFR mutations in NSCLC patients. However these mAbs should be validated with additional studies to clarify their possible role in routine clinical practice for screening EGFR mutations in NSCLC patients.
Poly(neopentylene carbonate) Hyperstars (2004)

Abstract Summary: Branched aliphatic polycarbonates were synthesized by ring opening polymerization of 5,5‐dimethyl‐1,3‐dioxane‐2‐one (NPC) initiated from polyfunctional alcohols and a commercial hyperbranched polyester (BOLTORN®). Polymerizations in the presence of fumaric acid under bulk conditions allowed high conversion (80%) without gelation. The synthesis of polymers with long chain branches was confirmed by size exclusion chromatography and universal calibration. The Mark–Houwink exponent decreased, indicating an increased density, while increasing the number of arms. The star polymers with up to four arms showed thermal properties T g (20–30 °C) and T m (100–110 °C) similar to linear PNPC. Boltorn™ hyperbranched polymer with radial polycarbonate grafts. magnified image Boltorn™ hyperbranched polymer with radial polycarbonate grafts.
Correlation of picosecond laser-induced latchup and energetic particle-induced latchup in CMOS test structures (1995)

We show that the thresholds for picosecond (psec) laser pulse-induced latchup and energetic particle-induced latchup are well correlated over a range of bulk CMOS test structures designed to be susceptible to latchup. The spatial length of the latchup-sensitive node of the test structures covers a range of values that commonly occur in bulk CMOS devices. The accuracy of this correlation implies that laser-induced latchup can be used for hardness assurance and, under the proper conditions, can be an accurate predictor of latchup threshold linear energy transfer (LET) for most bulk CMOS devices.
Diversity of endotoxin and its impact on pathogenesis (2006)

Lipopolysaccharide or LPS is localized to the outer leaflet of the outer membrane and serves as the major surface component of the bacterial cell envelope. This remarkable glycolipid is essential for virtually all Gram-negative organisms and represents one of the conserved microbial structures responsible for activation of the innate immune system. For these reasons, the structure, function, and biosynthesis of LPS has been an area of intense research. The LPS of a number of bacteria is composed of three distinct regions--lipid A, a short core oligosaccharide, and the O-antigen polysaccharide. The lipid A domain, also known as endotoxin, anchors the molecule in the outer membrane and is the bioactive component recognized by TLR4 during human infection. Overall, the biochemical synthesis of lipid A is a highly conserved process; however, investigation of the lipid A structures of various organisms shows an impressive amount of diversity. These differences can be attributed to the action of latent enzymes that modify the canonical lipid A molecule. Variation of the lipid A domain of LPS serves as one strategy utilized by Gram-negative bacteria to promote survival by providing resistance to components of the innate immune system and helping to evade recognition by TLR4. This review summarizes the biochemical machinery required for the production of diverse lipid A structures of human pathogens and how structural modification of endotoxin impacts pathogenesis.
The DNA Sequence of Human Herpesvirus-6: Structure, Coding Content, and Genome Evolution (1995)

The complete DNA sequence was determined for strain U1102 of human herpesvirus-6, a CD4+ T-lymphotropic virus with disease associations in immunodeficient settings and a possible complicating factor in AIDS. The genome is 159,321 bp in size, has a base composition of 43% G + C, and contains 119 open reading frames. The overall structure is 143 kb bounded by 8 kb of direct repeats, DRL (left) and DRR (right), containing 0.35 kb of terminal and junctional arrays of human telomere-like simple repeats. Since eight open reading frames are duplicated in the repeats, six span repetitive elements and three are spliced, the genome is considered to contain 102 separate genes likely to encode protein. The genes are arranged colinearly with those in the genome of the previously sequenced betaherpesvirus, human cytomegalovirus, and has a distinct arrangement of conserved genes relative to the sequenced gammaherpesviruses, herpesvirus saimiri and Epstein-Barr virus, and the alphaherpesviruses, equine herpesvirus-1, varicella-zoster virus, and herpes simplex virus. Comparisons of predicted amino acid sequences allowed the functions of many human herpesvirus-6 encoded proteins to be assigned and showed the closest relationship in overall number and similarity to human cytomegalovirus products, with approximately 67% homologous proteins as compared to the 21% identified in all herpesviruses. The features of the conserved genes and their relative order suggested a general scheme for divergence among these herpesvirus lineages. In addition to the "core" conserved genes, the genome contains four distinct gene families which may be involved in immune evasion and persistence in immune cells: two have similarity to the "chemokine" chemotactic/proinflammatory family of cytokines, one to their peptide G-protein-coupled receptors, and a fourth to the immunoglobulin superfamily.
Modulation of the histaminergic system and behaviour by α‐fluoromethylhistidine in zebrafish (2003)

The functional role of histamine (HA) in zebrafish brains was studied. Zebrafish did not display a clear circadian variation in brain HA levels. Loading of zebrafish with l-histidine increased HA concentration in the brain. A single injection of the histidine decarboxylase (HDC) inhibitor, alpha-fluoromethylhistidine (alpha-FMH), gave rise to a rapid reduction in zebrafish brain HA. Low HDC activity in the brain after injections verified the effect of alpha-FMH. A reduction in the number of histaminergic fibres but not neurones and an increased expression of HDC mRNA was evident after alpha-FMH. Automated behavioural analysis after alpha-FMH injection showed no change in swimming activity, but abnormalities were detected in exploratory behaviour examined in a circular tank. No significant behavioural changes were detected after histidine loading. The time spent for performance in the T-maze was significantly increased in the first trial 4 days after alpha-FMH injections, suggesting that lack of HA may impair long-term memory. The rostrodorsal telencephalon, considered to correspond to the mammalian amygdala and hippocampus in zebrafish, is densely innervated by histaminergic fibres. These results suggest that low HA decreases anxiety and/or affects learning and memory in zebrafish, possibly through mechanisms that involve the dorsal forebrain.
Molecular phylogeny and species delimitation in the section Longibrachiatum of Trichoderma (2012)

The phylogenetically most derived group of the genus Trichoderma - section Longibrachiatum, includes some of the most intensively studied species, such as the industrial cellulase producer T. reesei (teleomorph Hypocrea jecorina), or the facultative opportunistic human pathogens T. longibrachiatum and H. orientalis. At the same time, the phylogeny of this clade is only poorly understood. Here we used a collection of 112 strains representing all currently recognized species and isolates that were tentatively identified as members of the group, to analyze species diversity and molecular evolution. Bayesian phylogenetic analyses based on several unlinked loci in individual and concatenated datasets confirmed 13 previously described species and 3 previously recognized phylogenetic species all of which were not yet described formally. When the genealogical concordance criterion, the K/θ method and comparison of frequencies of pairwise nucleotide differences were applied to the data sample, 10 additional new phylogenetic species were recognized, seven of which consisted only of a single lineage. Our analysis thus identifies 26 putative species in section Longibrachiatum, what doubles the currently estimated taxonomic diversity of the group, and illustrates the power of combining genealogical concordance and population genetic analysis for dissecting species in a recently diverged group of fungal species.
Asymmetric Y junctions in silicon waveguides for on-chip mode-division multiplexing (2013)

Silicon waveguide asymmetric Y junction mode multiplexers and demultiplexers are demonstrated for applications in on-chip mode-division multiplexing (MDM). We measure demultiplexed crosstalk as low as -30 dB, <-9 dB over the C band, and insertion loss <1.5 dB for multimode links up to 1.2 mm in length. The frequency response of these devices is shown to depend upon Y junction angle and multimode interconnect length. Interference effects are shown to be advantageous for low-crosstalk MDM, even while using compact Y junctions designed to be outside the mode-sorting regime.
17beta-hydroxysteroid dehydrogenase (HSD)/17-ketosteroid reductase (KSR) family; nomenclature and main characteristics of the 17HSD/KSR enzymes (1999)

A number of enzymes possessing 17beta-hydroxysteroid dehydrogenase/17-ketosteroid reductase (17HSD/KSR) activities have been described and cloned, but their nomenclature needs specification. To clarify the present situation, descriptions of the eight cloned 17HSD/KSRs are given and guidelines for the classification of novel 17HSD/KSR enzymes are presented.
Rwc Music Database: Popular, Classical And Jazz Music Databases. (2002)

[TODO] Add abstract here.
Steaming ahead with change (1993)

Discusses briefly the introduction of the British Rail Passenger′s Charter, and explains how the charter has been received and how effective it has been. Describes advantages and disadvantages of the charter. Highlights the achievements of British Rail′s InterCity services.
Increasing the efficiency of SAGE adaptor ligation bydirected ligation chemistry (2004)

The ability of Serial Analysis of Gene Expression (SAGE) to provide a quantitative picture of global gene expression relies not only on the depth and accuracy of sequencing into the SAGE library, but also on the efficiency of each step required to generate the SAGE library from the starting mRNA material. The first critical step is the ligation of adaptors containing a Type IIS recognition sequence to the anchored 3' end cDNA population that permits the release of short sequence tags (SSTs) from defined sites within the 3' end of each transcript. Using an in vitro transcript as a template, we observed that only a small fraction of anchored 3' end cDNA are successfully ligated with added SAGE adaptors under typical reaction conditions currently used in the SAGE protocol. Although the introduction of approximately 500-fold molar excess of adaptor or the inclusion of 15% (w/v) PEG-8000 increased the yield of the adaptor-modified product, complete conversion to the desired adaptor:cDNA hetero-ligation product is not achieved. An alternative method of ligation, termed as directed ligation, is described which exploits a favourable mass-action condition created by the presence of NlaIII during ligation in combination with a novel SAGE adaptor containing a methylated base within the ligation site. Using this strategy, we were able to achieve near complete conversion of the anchored 3' end cDNA into the desired adaptor-modified product. This new protocol therefore greatly increases the probability that a SST will be generated from every transcript, greatly enhancing the fidelity of SAGE. Directed ligation also provides a powerful means to achieve near-complete ligation of any appropriately designed adaptor to its respective target.
Characterization of the cold stress-induced cyanobacterial DEAD-box protein CrhC as an RNA helicase (2000)

We have shown previously that CrhC is a unique member of the DEAD-box family of RNA helicases whose expression occurs specifically under conditions of cold stress. Here we show that recombinant His-tagged CrhC, purified from Escherichia coli, is an ATP-independent RNA binding protein possessing RNA-dependent ATPase activity which is stimulated most efficiently by rRNA and polysome preparations. RNA strand displacement assays indicate that CrhC possesses RNA unwinding activity that is adenosine nucleotide specific. Unwinding of partially duplexed RNA proceeds in the 5'-->3' but not the 3'-->5' direction using standard assay conditions. Immunoprecipitation and far-western analysis indicate that CrhC is a component of a multisubunit complex, interacting specifically with a 37 kDa polypeptide. We propose that CrhC unwinds cold-stabilized secondary structure in the 5'-UTR of RNA during cold stress.
Detection and identification of single dye labeled mononucleotide molecules released from an optical fiber in a microcapillary: First steps towards a new single molecule DNA sequencing technique (1999)

We present efficient detection of single dye labeled mononucleotide molecules released from an optical fiber in a cone shaped microcapillary with an inner diameter of 0.5µm at the small end. A 3µm diameter streptavidin coated optical fiber was doped with dye labeled mononucleotide molecules and positioned about 400µm in front of the detection area. The flow of the negatively charged analyte molecules towards the detection area was established by electrokinetic forces. Adsorption of the dye labeled mononucleotide molecules on the capillary walls as well as the electroosmotic (EOF) flow could be drastically reduced using a 3% polyvinylpyrrolidone (PVP) matrix. We studied bursts of fluorescence photons from single fluorescently labeled mononucleotide molecules Cy5-dCTP and MR121-dUTP. The conjugates were excited by a short-pulse diode laser emitting at a wavelength of 638 nm with a repetition rate of 57 MHz. The setup consists essentially of a confocal microscope for time-correlated single-photon counting (TCSPC). Detection was performed by a single-photon avalanche-photodiode in combination with a PC plug-in card for TCSPC. The time-resolved fluorescence signals of individual molecules were analyzed and identified by a maximum likelihood estimator (MLE). We obtain an overall classification probability of about 96% for the time-resolved identification of Cy5-dCTP and MR121-dUTP via their characteristic fluorescence decay times of 1.42±0.21 ns (Cy5-dCTP) and 2.41±0.32 ns (MR121-dUTP). In addition we report on detection and identification of single Cy5-dCMP and MR121-dUMP molecules degraded enzymatically with the 3′→5′ proofreading activity of T4-DNA-polymerase from statistically labeled DNA strands bound to the optical fiber. The technique presented permits counting and identification of fluorescently labeled mononucleotide molecules cleaved from DNA strands with counting rates>200 nucleotides s-1 and represents a suitable alternative for single molecule sequencing.
How to simultaneously exchange a secret bit by flipping a symmetrically-biased coin (1983)

We present a cryptographic protocol allowing two mutually distrusting parties, A and B, each having a secret bit, to "simultaneously" exchange the values of those bits. It is assumed that initially each party presents a correct encryption of his secret bit to the other party. We develop a new tool to implement our protocol: a slightly biased symmetric coin. The key property of this coin is that from each flip A receives a piece of probabilistic information about B's secret bit which is symmetric to the piece of information B receives about A's secret bit.
A system for assessing motion artifacts in the signal of a micro-optic in-ear vital signs sensor (2008)

Cardiovascular diseases are among the most common causes of death in developed industrial nations. It is of great interest of both physician and patient to determine the cardiovascular risk factors early in order to take preventive measures. To assist these investigations we develop a wearable in-ear measuring system (IN-MONIT) for 24/7 monitoring of heart rate and oxygen saturation (SpO2). The central component is a micro-optic remission/reflection sensor (MORES) located inside the auditory canal. From the measured photoplethysmographic curves the aforementioned vital signs can be derived. In the following we present a recording system for assessing motion artifact influence in the in-ear sensor data. Two accelerometer sensors record posture and motion while at the same time SpO2, heart rate and PPG are measured using both a commercial sensor and the in-ear sensor. The data is transmitted wirelessly to a control PC for storage and further investigation. Using this system we assessed the influence of motion artifacts produced by daily life activities on infrared and red in-ear PPG data and on readings of the reference sensor.
DNA Cloning with Plasmid Vectors (2000)

Adiponectin (Adipo), a multimeric adipocyte-secreted protein abundant in the circulation, is implicated in cardiovascular protective functions. Recent work documented that Adipo locally associates with responsive tissues through interactions with T-cadherin (Tcad), an atypical, glycosylphosphatidylinositol (GPI)-anchored cadherin cell surface glycoprotein. Mice deficient for Tcad lack tissue-associated Adipo, accumulate Adipo in the circulation, and mimic the Adipo knockout (KO) cardiovascular phenotype. In reverse, Tcad protein is visibly reduced from cardiac tissue in Adipo-KO mice, suggesting interdependent regulation of the 2 proteins. Here, we evaluate the effect of Adipo on Tcad protein expression. Adipo and Tcad proteins were colocalized in aorta, heart, and skeletal muscle. Adipo positively regulated levels of Tcad protein in vivo and in endothelial cell (EC) cultures. In Tcad-KO mice, binding of endogenous and exogenously administered Adipo to cardiovascular tissues was dramatically reduced. Consistently, knockdown of Tcad in cultured murine vascular ECs significantly diminished Adipo binding. In search for a possible mechanism, we found that enzymatic cleavage of Tcad with phosphatidylinositol-specific phospholipase C increases plasma Adipo while decreasing tissue-bound levels. Similarly, pretreatment of cultured ECs with serum containing Adipo attenuated phosphatidylinositol-specific phospholipase C-mediated Tcad cleavage. In vivo administration of adenovirus producing Adipo suppressed plasma levels of GPI phospholipase D, the endogenous cleavage enzyme for GPI-anchored proteins. In conclusion, our data show that both circulating and tissue-bound Adipo levels are dependent on Tcad and, in reverse, regulate tissue Tcad levels through a positive feedback loop that operates by suppressing phospholipase-mediated Tcad release from the cell surface.