gebhart/patrepeval huggingface dataset:
Effects of second-generation platinum analogs on isolated PM-2 DNA and their cytotoxicity in vitro and in vivo. (1980)

Using PM-2 DNA and cytotoxicity assay systems, we have studied several second-generation platinum analogs and compared these to the parent compound cis-diamminedichloroplatinum(II). These results indicate that all planar platinum(II) congeners induced similar effects upon interaction with PM-2 DNA, i.e., alteration of the tertiary DNA conformations. The reactivity of the analogs with DNA depended on the activity of the leaving groups. Octahedral platinum(IV) compounds, however, induced breakage of covalently closed circular PM-2 DNA, and the effects were not inhibited by either chloride or ethylenediaminetetraacetate. This suggests that breakage of isolated PM-2 DNA may be related to the axial trans bonds rather than the equatorial cis bonds of the solvated platinum(IV) compounds, since the activity of the dichloroplatinum(II) compounds has been shown to be inhibited by chloride ions. Studies on the in vitro and in vivo cytotoxicity of the platinum analogs demonstrated that the reactivity of analogs against PM-2 DNA correlated with in vitro and in vivo potencies. The reactivity with PM-2 DNA appeared to depend on the characteristics of the leaving group.
Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel (1997)

Newly described phylogenetic lineages within the domain Archaea have recently been found to be significant components of marine picoplankton assemblages. To better understand the ecology of these microorganisms, we investigated the relative abundance, distribution, and phylogenetic composition of Archaea in the Santa Barbara Channel. Significant amounts of archaeal rRNA and rDNA (genes coding for rRNA) were detected in all samples analyzed. The relative abundance of archaeal rRNA as measured by quantitative oligonucleotide hybridization experiments was low in surface waters but reached higher values (20 to 30% of prokaryotic rRNA) at depths below 100 m. Probes were developed for the two major groups of marine Archaea detected. rRNA originating from the euryarchaeal group (group II) was most abundant in surface waters, whereas rRNA from the crenarchaeal group (group I) dominated at depth. Clone libraries of PCR-amplified archaeal rRNA genes were constructed with samples from 0 and 200 m deep. Screening of libraries by hybridization with specific oligonucleotide probes, as well as subsequent sequencing of the cloned genes, indicated that virtually all archaeal rDNA clones recovered belonged to one of the two groups. The recovery of cloned rDNA sequence types in depth profiles exhibited the same trends as were observed in quantitative rRNA hybridization experiments. One representative of each of 18 distinct restriction fragment length polymorphism types was partially sequenced. Recovered sequences spanned most of the previously reported phylogenetic diversity detected in planktonic crenarchaeal and euryarchaeal groups. Several rDNA sequences appeared to be harbored in archaeal types which are widely distributed in marine coastal waters. In total, data suggest that marine planktonic crenarchaea and euryarchaea of temperate coastal habitats thrive in different zones of the water column. The relative rRNA abundance of the crenarchaeal group suggests that its members constitute a significant fraction of the prokaryotic biomass in subsurface coastal waters.
Twin-disc tests of iron oxides in dry and wet wheel−rail contacts (2015)

The wheel−rail contact system is open to the environment; as a result there are various kinds of contaminants present between railway wheels and rails. In addition to water, oil and sand, which are applied intentionally or unintentionally, iron oxides are constantly present on surfaces. A twin-disc rolling-sliding tribometer has been used to study the influence of iron oxides on the adhesion coefficient and wear rates of wheel and rail materials. Iron oxides were created in a climate chamber and tests were performed under both dry and wet conditions. The adhesion coefficient, wear rates and surface roughness were investigated. Results indicate that an increase in slip ratio increases the adhesion coefficient, and the wear rate also increases in the dry condition. In wet conditions, the effect of iron oxides lasts for a long time and greatly influences adhesion and wear. The adhesion curve peaks at a much larger creep with the presence of thin oxides than for thick oxides.
Laser catheter ablation of simulated ventricular tachycardia (1987)

Catheter-directed laser injury of the left ventricular endocardium for ablation of ventricular tachycardia was studied in a canine model of simulated ventricular tachycardia. Bipolar plunge electrodes were placed at thoracotomy into the left ventricular endocardium in nine anesthetized dogs. Ventricular tachycardia was simulated by pacing at 200 beats per minute. After four days of recovery, catheter-directed neodymium:yttrium-aluminum-garnet laser injury was produced at the site of earliest recorded electrical activation during pacing tachycardia as detected by endocardial catheter mapping. Immediately after laser injury and again five days after injury, pacing tachycardia was attempted. Failure to pace after laser injury was defined as successful arrhythmia ablation. In 3/9 (33%) experiments, the laser-injured tissue surrounded the tachycardia source (pacing wires), and pacing-simulated ventricular tachycardia was prevented. When the laser injury did not involve the tachycardia source, 6/9 animals, due to limitations of the mapping system, pacing was not prevented. One animal developed sustained ventricular tachycardia during laser injury, with conversion to sinus rhythm by lidocaine. One animal, without recognized ventricular arrhythmia, died five days after laser injury. No unusual findings were noted at autopsy. These preliminary data suggest that catheter-directed laser-induced injury can ablate arrhythmia sources. Further studies are indicated in a more physiologic model, and the safety and risks of the procedure need further evaluation.
Strict detailed balance is unnecessary in Monte Carlo simulation (1999)

Detailed balance is an overly strict condition to ensure a valid Monte Carlo simulation. We show that, under fairly general assumptions, a Monte Carlo simulation need satisfy only the weaker balance condition. Not only does our proof show that sequential updating schemes are correct, but also it establishes the correctness of a whole class of new methods that simply leave the Boltzmann distribution invariant.
An Effective Algorithm for Automatic Detection and Exact Demarcation of Breath Sounds in Speech and Song Signals (2007)

Automatic detection of predefined events in speech and audio signals is a challenging and promising subject in signal processing. One important application of such detection is removal or suppression of unwanted sounds in audio recordings, for instance in the professional music industry, where the demand for quality is very high. Breath sounds, which are present in most song recordings and often degrade the aesthetic quality of the voice, are an example of such unwanted sounds. Another example is bad pronunciation of certain phonemes. In this paper, we present an automatic algorithm for accurate detection of breaths in speech or song signals. The algorithm is based on a template matching approach, and consists of three phases. In the first phase, a template is constructed from mel frequency cepstral coefficients (MFCCs) matrices of several breath examples and their singular value decompositions, to capture the characteristics of a typical breath event. Next, in the initial processing phase, each short-time frame is compared to the breath template, and marked as breathy or nonbreathy according to predefined thresholds. Finally, an edge detection algorithm, based on various time-domain and frequency-domain parameters, is applied to demarcate the exact boundaries of each breath event and to eliminate possible false detections. Evaluation of the algorithm on a database of speech and songs containing several hundred breath sounds yielded a correct identification rate of 98% with a specificity of 96%
High-resolution tool for measuring photomask flatness (2003)

As lithography wavelengths reduce, the depth of focus decreases rapidly as well, resulting in the need for flatter photomasks with specifications under 0.25 microns. With the introduction of EUV mask technology, the overlay error budget drives the flatness requirements considerably lower to just 50 nanometers or so. This paper describes a new tool that utilizes near normal incidence interferometry to perform flatness measurements on polished 6025 photomasks that are coated or uncoated. Achieving a low measurement uncertainty required a robust optical and mechanical design. Even nanometer level measurement errors due to gravity sag have to be considered. Supporting the substrate during measurement creates deformations due to gravity that must be dealt with for an accurate evaluation of the flatness. Two improvements to the recently introduced Corning Tropel UltraFlat Mask System that first minimize and then remove the remaining gravity sag errors in photomask flatness measurements will also be discussed.
ADAM9 Expression Is Associate with Glioma Tumor Grade and Histological Type, and Acts as a Prognostic Factor in Lower-Grade Gliomas (2016)

The A disintegrin and metalloproteinase 9 (ADAM9) protein has been suggested to promote carcinoma invasion and appears to be overexpressed in various human cancers. However, its role has rarely been investigated in gliomas and, thus, in the current study we have evaluated ADAM9 expression in gliomas and examined the relevance of its expression in the prognosis of glioma patients. Clinical characteristics, RNA sequence data, and the case follow-ups were reviewed for 303 patients who had histological, confirmed gliomas. The ADAM9 expression between lower-grade glioma (LGG) and glioblastoma (GBM) patients was compared and its association with progression-free survival (PFS) and overall survival (OS) was assessed to evaluate its prognostic value. Our data suggested that GBM patients had significantly higher expression of ADAM9 in comparison to LGG patients (p < 0.001, t-test). In addition, among the LGG patients, aggressive astrocytic tumors displayed significantly higher ADAM9 expression than oligodendroglial tumors (p < 0.001, t-test). Moreover, high ADAM9 expression also correlated with poor clinical outcome (p < 0.001 and p < 0.001, log-rank test, for PFS and OS, respectively) in LGG patients. Further, multivariate analysis suggested ADAM9 expression to be an independent marker of poor survival (p = 0.002 and p = 0.003, for PFS and OS, respectively). These results suggest that ADAM9 mRNA expression is associated with tumor grade and histological type in gliomas and can serve as an independent prognostic factor, specifically in LGG patients.
Advanced materials for use in soft self-healing devices (2017)

Devices integrated with self-healing ability can benefit from long-term use as well as enhanced reliability, maintenance and durability. This progress report reviews the developments in the field of self-healing polymers/composites and wearable devices thereof. One part of the progress report presents and discusses several aspects of the self-healing materials chemistry (from non- covalent to reversible covalent-based mechanisms), as well as the required main approaches used for functionalizing the composites to enhance their electrical conductivity, magnetic, dielectric, electroactive and/or photoactive properties. The second and complementary part of the progress report links the self-healing materials with partially or fully self-healing device technologies, including wearable sensors, supercapacitors, solar cells and fabrics. Some of the strong and weak points in the development of each self-healing device are clearly highlighted and criticized, respectively. Several ideas regarding further improvement of soft self-healing devices are proposed.
Socioeconomic and traditional importance of date palm. (2012)

The date palm fruit is a drupe exhibiting a high diversity in texture, shape, color and chemical composition depending on the genotype, environment, season and cultural practices. The fruit typically characterize the variety. The socio-economic value of dates is particularly known from oases, where date palms grow and fruits were historically the medium of exchange between populations. The geographical distribution of date palm cultivars is not yet well studied and the international demand on some of them will have disastrous impacts on the sustainability of this crop in the long term. This impoverishes germplasm and narrows the diversity grown among oases. In addition, despite the presence of several reports on the chemical composition and the nutritional value of dates, many other potentialities of the fruits remain to be explored. Many claims report on the antibacterial, antifungal, antitumor, antiulcer and immuno-modulatory properties of dates. Recently, the antioxidant activity of some cultivars was investigated and attributed to phenolic compounds. Dates are very rich in phenolics, in quality and quantity, which opens many fields of investigation in terms of new potential uses. This study summarizes the recent progress in date research, providing an up-to-date overview of the worldwide production/commercialization and the traditional and medicinal uses. Other current and future applications of dates also are highlighted.
COP-15 in Copenhagen: How the Merging of Movements Left Civil Society Out in the Cold (2010)

What happened to non-governmental organizations' participation at the COP-15 round of climate negotiations in Copenhagen? Although the climate regime has been seen as relatively open to civil society, everything changed in Copenhagen and civil society became increasingly disenfranchised. This article discusses the three main forces that led to civil society's disenfranchisement at this round of the climate negotiations: increased registration, poor planning by the Danish organizers and the United Nations Framework Convention on Climate Change Secretariat, and the merging of movements. I conclude by discussing implications of the increase in civil society disenfranchisement to the climate regime and to the study of global environmental politics more broadly.
1.5μm band travelling-wave semiconductor optical amplifiers with window facet structure (1989)

1.5μ band travelling-wave semiconductor optical amplifiers (TWAs), characterised by their window facet structure and symmetrised active waveguide, have been developed. 1.5 dB spectral gain ripple and 1.3 dB TE-TM mode gain difference at 22 dB signal gain were achieved simultaneously. An average facet reflectivity as low as 0.06% was estimated.
Identification of the namH Gene, Encoding the Hydroxylase Responsible for the N-Glycolylation of the Mycobacterial Peptidoglycan (2004)

The peptidoglycan of most bacteria consists of a repeating disaccharide unit of beta-1,4-linked N-acetylmuramic acid and N-acetylglucosamine. However, the muramic acid moieties of the mycobacterial peptidoglycan are N-glycolylated, not N-acetylated. This is a rare modification seen only in the peptidoglycan of mycobacteria and five other closely related genera of bacteria. The N-glycolylation of sialic acids is a unique carbohydrate modification that has been studied extensively in eukaryotes. However, the significance of the N-glycolylation of bacterial peptidoglycan is unknown. The goal of this project was to identify the gene encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. We developed a novel assay for the mycobacterial UDP-N-acetylmuramic acid hydroxylation reaction and demonstrated that Mycobacterium smegmatis has an enzyme activity that can convert UDP-N-acetylmuramic acid to UDP-N-glycolylmuramic acid. We identified the gene namH encoding the mycobacterial UDP-N-acetylmuramic acid hydroxylase by computer data base searching and motif comparisons with the eukaryotic enzymes responsible for the N-glycolyation of sialic acids. The namH gene is not essential for in vitro growth as we were successful in deleting the gene in M. smegmatis. The M. smegmatis mutant is devoid of UDP-N-acetylmuramic acid hydroxylase activity and synthesizes only N-acetylated muropeptide precursors. Furthermore, the mutant exhibits increased susceptibility to beta-lactam antibiotics and lysozyme. Our studies suggest that the N-glycolylation of mycobacterial peptidoglycan may play a role in lysozyme resistance or may contribute to the structural stability of the cell wall architecture.
The Synthesis of Biologically Active Peptides and Proteins (1969)

The proteins are key components of all living organisms, and their fundamental role in biology cannot be overestimated. These very large and extremely complex substances are major constituents of blood, muscle, skin, bone, nerve, and, in fact, of every tissue and organ of the body. All of the enzymes that catalyze biochemical reactions and many of the hormones that regulate them are proteins. If we are to understand, and eventually control, the events that occur in the body, we must first understand the composition, structure, and function of the individual proteins. One way is to study proteins isolated from natural sources. Another way is to make the proteins in the laboratory and to study the synthetic material. Although the total chemical synthesis of a protein was out of the question a decade ago, it was not unreasonable to begin thinking of the day when a synthesis might be achieved and
Fixed Switching Frequency Digital Sliding-Mode Control of DC-DC Power Supplies Loaded by Constant Power Loads with Inrush Current Limitation Capability (2019)

This paper proposes a digital sliding-mode controller for a DC-DC boost converter under constant power-loading conditions. The controller has been designed in two steps: the first step is to reach the sliding-mode regime while ensuring inrush current limiting; and the second one is to move the system to the desired operating point. By imposing sliding-mode regime, the equivalent control and the discrete-time large-signal dynamic model of this system are derived. The analysis shows that unlike with a resistive load, the boost converter under a fixed-frequency digital sliding-mode current control with external voltage loop open and loaded by a constant power load, is unstable. Furthermore, as with a resistive load, the system presents a right-half plane zero in the control-to-output transfer function. After that, an outer controller is designed in the z-domain for system stabilization and output voltage regulation. The results show that the system exhibits good performance in startup in terms of inrush current limiting and in transient response due to load and input voltage disturbances. Numerical simulations from a detailed switched model are in good agreement with the theoretical predictions. An experimental prototype is implemented to verify the mathematical analysis and the numerical simulation, which results in a perfect agreement in small-signal and steady-state behavior but also in a small discrepancy in the current limitation due a small propagation delay. Some efficient solutions have been proposed to mitigate the inrush current in the experimental results.
Measurement of the ratio of primary to total bile acids in serum by enzymatic fluorometric microassay and its clinical significance in patients with liver disease. (1985)

An enzymatic fluorometric microassay using 3 alpha- or 7 alpha-hydroxysteroid dehydrogenase was devised to determine serum total or primary bile acids. The present microassay using 50 microliter of a serum sample was run as a two-step method; the first step is the reaction of substrates with NAD+ and the hydroxysteroid dehydrogenase to produce as much NADH as possible in the incubation system and the second step is that of NADH with resazurin coupled with 1-methoxy phenazinemethosulfate to produce fluorescent resorfin. The assay is specific for 3 alpha- or 7 alpha-hydroxy bile acids, sensitive (a detection limit of 1.5 microM with a linear range of 1.5-80 microM), reproducible (CV = less than 5%) and inexpensive. As measured by this microassay, the ratio of serum primary to total bile acids (P/T ratio) in 10 normal subjects was 62.1 +/- 0.7% and was significantly elevated in the early phase of acute hepatitis (p less than 0.01), followed by return to the normal level after 4 weeks.
Endocytic and exocytic pathways of the neuronal secretory process and trans synaptic transfer of wheat germ agglutinin‐horseradish peroxidase <i>in vivo</i> (1985)

The lectin wheat germ agglutinin (WGA) conjugated to horseradish peroxidase (HRP) was employed to study the endocytic and exocytic pathways of the secretory process in neurons and the potential for trans-synaptic transfer of molecules within the CNS. WGA-HRP binds to surface membrane oligosaccharides and enters cells by adsorptive endocytosis. The lectin conjugate was administered intranasally or into the cerebral ventricles of mice; postinjection survival times ranged from 5 minutes to 6 days. Due to binding of the lectin to ependymal cells subsequent to an intraventricular injection, only select populations of neurons (i.e., hippocampal formation; paraventricular nuclei; midbrain raphe; VI, X, XII motor nuclei; among others) were exposed extracellularly to WGA-HRP and became labeled by retrograde axoplasmic transport from axon terminals or by direct cell body/dendritic uptake. WGA-HRP delivered intranasally was endocytosed by first-order olfactory neurons and transported by anterograde axoplasmic flow to the terminal field within the glomerular layer of the main olfactory bulb; eventually perikarya of the mitral cell layer were labeled, presumably by anterograde trans-synaptic transfer of the lectin conjugate. In the variety of neurons analyzed ultrastructurally following exposure to WGA-HRP, the proposed sequence of intracellular pathways through which peroxidase reaction product was traced over time was: cell surface membrane----endocytic structures----endosomes (presecondary lysosomes)----transfer vesicles----transmost Golgi saccule----vesicles, vacuoles, and/or dense core granules. WGA-HRP also labeled vesicles and tubules that were channeled to and/or derived from spherical endosomes, dense bodies, and multivesicular bodies. The peroxidase-positive, membrane-delimited products of the trans Golgi saccule contributed to anterograde axonal transport vectors and accumulated within axon terminals. A second contribution to these vectors was provided by peroxidase-labeled tubules and dense bodies believed to represent components of the lysosomal compartment. Profiles of the axonal reticulum comparable to those that stained cytochemically for glucose-6-phosphatase activity, a marker for the endoplasmic reticulum, were not associated with the transport of WGA-HRP. Trans-synaptic transfer of WGA-HRP from primary olfactory neurons to postsynaptic cells in the olfactory bulb was reflected in peroxidase-positive endocytic vesicles, endosomes, dense bodies, and the trans Golgi saccule.(ABSTRACT TRUNCATED AT 400 WORDS)
Studies towards the Synthesis of Aculeatin C (2007)

Efficient activation/deprotection reactions of functional groups by PIFA reagent allowed for the construction of the polyspirocyclic core of aculeatin C according to a new polyspiro annulation approach. Addition of TFA increased the yield and the selectivity to the benefit of the desired conformer.