gebhart/patrepeval huggingface dataset:
Susceptibility of lipopolysaccharide-defective mutants of Pseudomonas aeruginosa strain PAO to dyes, detergents, and antibiotics (1978)

Lipopolysaccharide-defective mutants of Pseudomonas aeruginosa strain PAO have been isolated on the basis of their resistance to lipopolysaccharide-specific bacteriophages. These mutants have been differentiated by their agglutination in NaCl and acriflavine, phage sensitivity, and chemical analysis of the lipopolysaccharides. The susceptibility of the wild-type strain and four mutants to a series of twenty-six agents, including dyes, detergents, antibiotics, and lysozyme, was examined. The roughest mutant (AK-43) exhibited increased susceptibility to sodium deoxycholate, hexadecylpyridinium chloride, benzalkonium chloride, ampicillin, penicillin G, erythromycin, colymycin, and polymyxin B. The role of cell envelope fractions in antibiotic resistance in P. aeruginosa is discussed.
Adipokines and cardiovascular risk factors in patients with autoimmune thyroiditis and subclinical hypothyroidism (2014)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Efficient, visible organic light-emitting diodes utilizing a single polymer layer doped with quantum dots (2008)

We demonstrate organic light-emitting diodes (OLEDs) using a single active layer consisting of CdSe∕ZnS quantum dots (QDs) dispersed in poly (9,9-dioctylfluorene) (PFO). The diodes have an external quantum efficiency of ∼0.5% and reach 0.1A∕cm2 at 6.5V. These results are comparable to complex, multilayer QD OLEDs. Built-in potential measurements show that the QD valence levels are shifted to lower binding energy when compared to quantum confinement based estimates, and are close to PFO valence levels. Devices using red and green QDs emit predominantly from the QDs but the spectrum of blue QDs is perturbed by interactions with PFO.
Creation of High-Refractive-Index Amorphous Titanium Oxide Thin Films from Low-Fractal-Dimension Polymeric Precursors Synthesized by a Sol–Gel Technique with a Hydrazine Monohydrochloride Catalyst (2012)

Amorphous titanium dioxide (TiO(2)) thin films exhibiting high refractive indices (n ≈ 2.1) and high transparency were fabricated by spin-coating titanium oxide liquid precursors having a weakly branched polymeric structure. The precursor solution was prepared from titanium tetra-n-butoxide (TTBO) via the catalytic sol-gel process with hydrazine monohydrochloride used as a salt catalyst, which serves as a conjugate acid-base pair catalyst. Our unique catalytic sol-gel technique accelerated the overall polycondensation reaction of partially hydrolyzed alkoxides, which facilitated the formation of liner polymer-like titanium oxide aggregates having a low fractal dimension of ca. (5)/(3), known as a characteristic of the so-called "expanded polymer chain". Such linear polymeric features are essential to the production of highly dense amorphous TiO(2) thin films; mutual interpenetration of the linear polymeric aggregates avoided the creation of void space that is often generated by the densification of high-fractal-dimension (particle-like) aggregates produced in a conventional sol-gel process. The mesh size of the titanium oxide polymers can be tuned either by water concentration or the reaction time, and the smaller mesh size in the liquid precursor led to a higher n value of the solid thin film, thanks to its higher local electron density. The reaction that required no addition of organic ligand to stabilize titanium alkoxides was advantageous to overcoming issues from organic residues such as coloration. The dense amorphous film structure suppressed light scattering loss owing to its extremely smooth surface and the absence of inhomogeneous grains or particles. Furthermore, the fabrication can be accomplished at a low heating temperature of <80 °C. Indeed, we successfully obtained a transparent film with a high refractive index of n = 2.064 (at λ = 633 nm) on a low-heat-resistance plastic, poly(methyl methacrylate), at 60 °C. The result offers an efficient route to high-refractive-index amorphous TiO(2) films as well as base materials for a wider range of applications.
<title>Gas-cooled probe protectors</title> (1999)

The design and testing of a gas cooled probe protector shell is described. Standard optical probes are limited to relatively low temperature and mild environmental conditions. By enclosing such probes in concentric air- cooled stainless steel tubes with a brazed sapphire window at the end, their operating limits can be greatly extended. Gas cooling eliminates the facility requirements and leak hazards of water-cooled probes. Low gas flow rates have been demonstrated to maintain a probe at less than 100 degree(s)C in a 600 degree(s)C quiescent environment.
Structural and functional characterization of a cell surface binding protein of vaccinia virus. (1990)

The nature of the interaction between the enveloped DNA-containing poxviruses and the surfaces of host cells as a first step in virus infection is not known. In this investigation we have identified and defined structural and functional properties of a 32-kDa protein of vaccinia virus. This protein is part of the virus envelope and binds to the cell surface of various cultured cells. The gene encoding the 32-kDa viral protein was mapped and sequenced. It was found to code a 35,426-Da protein with a large N-terminal domain with sequence homology to carbonic anhydrases and a C-terminal domain with sequences similar to those of the attachment glycoprotein VP7 of rotavirus and to transmembrane proteins. A potential cell surface binding domain was within the last 50 amino acid residues of the C terminus. The 32-kDa protein is basic, predicted pI 8.67, is synthesized at late times post-infection, may form dimers held by disulfide bonds at the single cysteine 262, and is apparently non-glycosylated. The 32-kDa protein is a vaccinia virus antigen, with predicted antigenic sites located near amino acids 108-110 (carbonic anhydrase domain) and 298-299 (transmembrane domain). Several lines of evidence suggest that the 32-kDa protein is needed for efficient virus replication in cultured cells but that in addition to this protein other viral proteins are involved in the process of virus entry into cells.
Endotoxin downregulates rat hepatic ntcp gene expression via decreased activity of critical transcription factors. (1998)

Sodium-dependent uptake of bile acids across the hepatic basolateral membrane is rapidly and profoundly diminished during sepsis, thus contributing to the pathogenesis of sepsis-associated cholestasis. This effect is mediated by endotoxin or effector cytokines, which reduce expression of several hepatobiliary transporters, including the sodium-dependent bile acid transporter gene, ntcp. We test here the hypothesis that endotoxin treatment leads to impaired binding activity of ntcp promoter trans-acting factors, resulting in reduction of ntcp mRNA expression. After endotoxin administration, ntcp mRNA levels reached their nadir by 16 h, and nuclear run-on assays demonstrated a marked reduction in ntcp gene transcription. At 16 h after treatment, nuclear binding activities of two key factors that transactivate the ntcp promoter, hepatocyte nuclear factor (HNF) 1 and Footprint B binding protein (FpB BP), decreased to 44 and 47% of pretreatment levels, respectively, while levels of the other known ntcp promoter transactivator, signal transducer and activator of transcription 5, were unaffected. In contrast, the universal inflammatory response factors nuclear factor kappaB and activating protein 1 were both upregulated significantly. Examination of nuclear extracts obtained at sequential time points revealed that the maximal decrease in nuclear activities of both HNF1 and FpB BP preceded the nadir of ntcp mRNA expression by 6-10 h. Furthermore, these two nuclear factors returned towards normal levels before the recovery of ntcp mRNA levels observed by 48 h. Since HNF1alpha mRNA levels were unchanged at all time points, HNF1 is likely to be regulated posttranscriptionally by endotoxin. We conclude that the downregulation of ntcp gene expression by endotoxin is mediated at the level of transcription through tandem reductions in the nuclear binding activity of two critical transcription factors. These findings provide new insight into the coordinated downregulation of hepatobiliary transporters during sepsis.
Source Code Plagiarism Detection using Multi Layered Approach for C Language Programs (2014)

Source code plagiarism is a growing concern in academia. Programming assignments are used to evaluate students in programming courses. Therefore, checking programming assignments for plagiarism is essential. If a course consists of a large number of students, it is impractical for a human inspector to check each assignment, and while automated tools are available, none is accurate, robust and fast enough to detect plagiarism in the programming assignments. Thus, there is a prominent need for automated and accurate plagiarism detection tool.
Estimation of voice source and vocal tract characteristics based on multi-frame analysis (2003)

This paper presents a new approach for estimating voice source and vocal tract filter characteristics of voiced speech. When it is required to know the transfer function of a system in signal processing, the input and output of the system are experimentally observed and used to calculate the function. However, in the case of source-filter separation we deal with in this paper, only the output (speech) is observed and the characteristics of the system (vocal tract) and the input (voice source) must simultaneously be estimated. Hence the estimate becomes extremely difficult, and it is usually solved approximately using oversimplified models. We demonstrate that these characteristics are separable under the assumption that they are independently controlled by different factors. The separation is realised using an iterative approximation along with the Multi-frame Analysis method, which we have proposed to find spectral envelopes of voiced speech with minimum interference of the harmonic structure.
Effects of Dietary Fiber and Its Components on Metabolic Health (2010)

Dietary fiber and whole grains contain a unique blend of bioactive components including resistant starches, vitamins, minerals, phytochemicals and antioxidants. As a result, research regarding their potential health benefits has received considerable attention in the last several decades. Epidemiological and clinical studies demonstrate that intake of dietary fiber and whole grain is inversely related to obesity, type two diabetes, cancer and cardiovascular disease (CVD). Defining dietary fiber is a divergent process and is dependent on both nutrition and analytical concepts. The most common and accepted definition is based on nutritional physiology. Generally speaking, dietary fiber is the edible parts of plants, or similar carbohydrates, that are resistant to digestion and absorption in the small intestine. Dietary fiber can be separated into many different fractions. Recent research has begun to isolate these components and determine if increasing their levels in a diet is beneficial to human health. These fractions include arabinoxylan, inulin, pectin, bran, cellulose, β-glucan and resistant starch. The study of these components may give us a better understanding of how and why dietary fiber may decrease the risk for certain diseases. The mechanisms behind the reported effects of dietary fiber on metabolic health are not well established. It is speculated to be a result of changes in intestinal viscosity, nutrient absorption, rate of passage, production of short chain fatty acids and production of gut hormones. Given the inconsistencies reported between studies this review will examine the most up to date data concerning dietary fiber and its effects on metabolic health.
Automatic analogue network synthesis using genetic algorithms (1995)

Genetic algorithms provide a basis for automatic synthesis of analogue electronic networks. Passive linear networks have been generated to meet both frequency-domain and time-domain specifications. The networks generated are both novel and effective. It should be possible to extend the technique to deal with active networks.
Effects of Soil Fumigation with Methyl Bromide and Chloropicrin on Root Health and Yield of Strawberry (1991)

Soil fumigation with methyl bromide and chloropicrin (MBC) reduced the severity of black root rot of strawberry in experiments at four locations in California. At three of these sites, fumigation increased root density by 19-61% over the untreated controls. Improvement of root health by fumigation was correlated with increased yields of berries at all four locations. Accumulative harvests from fumigated plots were 24-29% greater than the untreated controls. At a fifth location, fumigation with MBC had no significant effect on root growth, root rot severity, or yields, and this may have been partly attributable to low disease levels. In comparison to MBC, preplant soil applications of metham-sodium and metalaxyl had no effect on root disease levels, root development, or yield (.)
Mitochondrial content is central to nuclear gene expression: Profound implications for human health (2016)

We review a recent paper in Genome Research by Guantes et al. showing that nuclear gene expression is influenced by the bioenergetic status of the mitochondria. The amount of energy that mitochondria make available for gene expression varies considerably. It depends on: the energetic demands of the tissue; the mitochondrial DNA (mtDNA) mutant load; the number of mitochondria; stressors present in the cell. Hence, when failing mitochondria place the cell in energy crisis there are major effects on gene expression affecting the risk of degenerative diseases, cancer and ageing. In 2015 the UK parliament approved a change in the regulation of IVF techniques, allowing "Mitochondrial replacement therapy" to become a reproductive choice for women at risk of transmitting mitochondrial disease to their children. This is the first time that this technique will be available. Therefore understanding the interaction between mitochondria and the nucleus has never been more important.
Non-Hydroxamate Histone Deacetylase Inhibitors (2010)

A number of histone deacetylase (HDAC) inhibitors have been developed as anticancer agents and most of them are hydroxamic acid derivatives, typified by suberoylanilide hydroxamic acid (SAHA), Trichostatin A (TSA) and NVPLAQ824. However, hydroxamic acids have been associated with poor pharmacokinetics and severe toxicity. In addition, although isozyme-selective HDAC inhibitors are considered useful not only as tools for probing the biology of an enzyme but as drugs with low toxicity, many of the hydroxamate HDAC inhibitors do not distinguish well among the HDAC isozymes. Thus, there has been considerable interest in developing non-hydroxamate HDAC inhibitors. To date, small fatty acids, o-aminoanilides, electrophilic ketones, N-formyl hydroxylamines, thiols and mercaptoamides have been reported as non-hydroxamate HDAC inhibitors, and some of them show antiproliferative activity comparable to hydroxamates. Interestingly, hydroxamate HDAC inhibitors such as SAHA and TSA do not discriminate well among the HDAC isozymes whereas many non-hydroxamate HDAC inhibitors have shown selectivity. These non-hydroxamate HDAC inhibitors should pave the way for the development of tools for biological research and new medicines with few side effects. In this review, we introduce nonhydroxamate HDAC inhibitors describing their design, enzyme inhibition, cancer cell growth inhibition and isozyme selectivity.
Mapping in Vivo Chromatin Interactions in Yeast Suggests an Extended Chromatin Fiber with Regional Variation in Compaction (2008)

The higher order arrangement of nucleosomes and the level of compaction of the chromatin fiber play important roles in the control of gene expression and other genomic activities. Analysis of chromatin in vitro has suggested that under near physiological conditions chromatin fibers can become highly compact and that the level of compaction can be modulated by histone modifications. However, less is known about the organization of chromatin fibers in living cells. Here, we combine chromosome conformation capture (3C) data with distance measurements and polymer modeling to determine the in vivo mass density of a transcriptionally active 95-kb GC-rich domain on chromosome III of the yeast Saccharomyces cerevisiae. In contrast to previous reports, we find that yeast does not form a compact fiber but that chromatin is extended with a mass per unit length that is consistent with a rather loose arrangement of nucleosomes. Analysis of 3C data from a neighboring AT-rich chromosomal domain indicates that chromatin in this domain is more compact, but that mass density is still well below that of a canonical 30 nm fiber. Our approach should be widely applicable to scale 3C data to real spatial dimensions, which will facilitate the quantification of the effects of chromatin modifications and transcription on chromatin fiber organization.
Chemical reversal of the RNA gain of function in myotonic dystrophy (2009)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
High-temperature molten salt thermal energy storage systems (1980)

The results of comparative screening studies of candidate molten carbonate salts as phase change materials (PCM) for advanced solar thermal energy storage applications at 540 to 870 C (1004 to 1600 F) and steam Rankine electric generation at 400 to 540 C (752 to 1004 F) are presented. Alkali carbonates are attractive as latent heat storage materials because of their relatively high storage capacity and thermal conductivity, low corrosivity, moderate cost, and safe and simple handling requirements. Salts were tested in 0.1 kWhr lab scale modules and evaluated on the basis of discharge heat flux, solidification temperature range, thermal cycling stability, and compatibility with containment materials. The feasibility of using a distributed network of high conductivity material to increase the heat flux through the layer of solidified salt was evaluated. The thermal performance of an 8 kWhr thermal energy storage (TES) module containing LiKCO3 remained very stable throughout 5650 hours and 130 charge/discharge cycles at 480 to 535 C (896 to 995 F). A TES utilization concept of an electrical generation peaking subsystem composed of a multistage condensing steam turbine and a TES subsystem with a separate power conversion loop was defined. Conceptual designs for a 100 MW sub e TES peaking system providing steam at 316 C, 427 C, and 454 C (600 F, 800 F, and 850 F) at 3.79 million Pa (550 psia) were developed and evaluated. Areas requiring further investigation have also been identified.
Membrane oxygenators: current developments in design and application (1988)

Cardiopulmonary bypass (CPB) procedures require a blood-gas exchanger (oxygenator) to temporarily replace the respiratory function of the lungs. In the past the majority of CPB procedures have been carried out with bubble oxygenators which effect gas exchange by dispersion of bubbles into the blood. Membrane oxygenators, on the other hand, utilize a hydrophobic gas permeable membrane between the blood and gas phases. Bubble oxygenators are being superseded by membrane types for CPB due to improvements in membrane technology and mass transfer efficiency. These advances are reviewed in this paper and are illustrated by reference to the gas exchange and operating characteristics of a number of clinical oxygenators designed for adult CPB. Membrane oxygenators are also being used for long-term support in the treatment of acute respiratory failure. Operated in a partial bypass circuit, the oxygenator may have to function for several days or weeks. In one particular treatment method, the rate of spontaneous breathing is controlled by the partial or total removal of the metabolic CO2 production by the membrane oxygenator. For this method, known as extracorporeal CO2 removal (ECCO2R), the oxygenator must be optimized for CO2 transfer at low blood flow rates. The suitability of clinical oxygenators for ECCO2R is discussed in terms of gas exchange and functionality over a prolonged operation.
Comparison of the Fouling Release Properties of Hydrophobic Fluorinated and Hydrophilic PEGylated Block Copolymer Surfaces:  Attachment Strength of the Diatom <i>Navicula</i> and the Green Alga <i>Ulva</i> (2006)

To understand the role of surface wettability in adhesion of cells, the attachment of two different marine algae was studied on hydrophobic and hydrophilic polymer surfaces. Adhesion of cells of the diatom Navicula and sporelings (young plants) of the green macroalga Ulva to an underwater surface is mainly by interactions between the surface and the adhesive exopolymers, which the cells secrete upon settlement and during subsequent colonization and growth. Two types of block copolymers, one with poly(ethylene glycol) side-chains and the other with liquid crystalline, fluorinated side-chains, were used to prepare the hydrophilic and hydrophobic surfaces, respectively. The formation of a liquid crystalline smectic phase in the latter inhibited molecular reorganization at the surface, which is generally an issue when a highly hydrophobic surface is in contact with water. The adhesion strength was assessed by the fraction of settled cells (Navicula) or biomass (Ulva) that detached from the surface in a water flow channel with a wall shear stress of 53 Pa. The two species exhibited opposite adhesion behavior on the same sets of surfaces. While Navicula cells released more easily from hydrophilic surfaces, Ulva sporelings showed higher removal from hydrophobic surfaces. This highlights the importance of differences in cell-surface interactions in determining the strength of adhesion of cells to substrates.
Solenoid surface coils in magnetic resonance imaging (1986)

A nonplanar solenoidal surface radiofrequency coil is used as a receiver with a conventional transmitter coil in a magnetic resonance imaging system. The improved signal-to-noise ratio, compared with that of conventional fixed saddle or solenoid receiver coils, permits higher resolution imaging and thinner image sections. In addition, the problem of signal dropoff that occurs in deep structures with planar and other noncircumferential surface coils is eliminated. Solenoid surface coils are particularly useful in imaging deep structures in anatomic regions that do not fit standard head and body coils, such as the neck, knees, and other smaller body parts.
Mayer Bond Order as a Metric of Complexation Effectiveness in Lead Halide Perovskite Solutions (2016)

One of the most appealing features of solar cells made from hybrid organic–inorganic perovskites is that they can be processed directly from solution, leading to low cost, energy-efficient processing. Numerous studies have shown that the composition of these solutions and the choice of solvent (or solvent blend) affects the efficiency of the resulting solar cell. Despite the importance of this correlation for performance, the choice of solvent(s) used to deposit the perovskite precursors has been largely a matter of experimental trial-and-error. In this work, we present a coherent theory explaining the molecular origin of the efficacy of solvent choice, which lends itself to the creation of a fast quantum mechanical-based screening process that facilitates the design of effective new solvents. We also provide the first theoretical confirmation of complexation of HOIP precursors in solution, including their structure and relative stability. We show that the Mayer bond order of a solvent’s polar atoms predicts the solubility of the perovskite lead halide precursors in the solvent much more reliably than the relative polarity and Hansen polar solubility parameter suggested in the literature as being figures of merit.