gebhart/patrepeval huggingface dataset:
A Tale of Tails: Dissecting the Enhancing Effect of Tailed Primers in Real-Time PCR (2016)

Non-specific tail sequences are often added to the 5'-terminus of primers to improve the robustness and overall performance of diagnostic assays. Despite the widespread use of tailed primers, the underlying working mechanism is not well understood. To address this problem, we conducted a detailed in vitro and in silico analysis of the enhancing effect of primer tailing on 2 well-established foot-and-mouth disease virus (FMDV) RT-qPCR assays using an FMDV reference panel. Tailing of the panFMDV-5UTR primers mainly affected the shape of the amplification curves. Modelling of the raw fluorescence data suggested a reduction of the amplification efficiency due to the accumulation of inhibitors. In depth analysis of PCR products indeed revealed the rapid accumulation of forward-primer derived artefacts. More importantly, tailing of the forward primer delayed artefacts formation and concomitantly restored the sigmoidal shape of the amplification curves. Our analysis also showed that primer tailing can alter utilisation patterns of degenerate primers and increase the number of primer variants that are able to participate in the reaction. The impact of tailed primers was less pronounced in the panFMDV-3D assay with only 5 out of 50 isolates showing a clear shift in Cq values. Sequence analysis of the target region of these 5 isolates revealed several mutations in the inter-primer region that extend an existing hairpin structure immediately downstream of the forward primer binding site. Stabilisation of the forward primer with either a tail sequence or cationic spermine units restored the sensitivity of the assay, which suggests that the enhancing effect in the panFMDV-3D assay is due to a more efficient extension of the forward primer. ur results show that primer tailing can alter amplification through various mechanisms that are determined by both the assay and target region. These findings expand our understanding of primer tailing and should enable a more targeted and efficient use of tailed primers.
The Effects of Adipokines on Cartilage and Meniscus Catabolism (2011)

Obesity is one of the primary risk factors for osteoarthritis. Increased adiposity is associated not only with alterations in joint loading, but also with increased systemic and joint concentrations of adipose tissue-derived cytokines, or "adipokines", that promote a state of chronic, low-grade inflammation that may act in concert with other cytokines in the joint to increase joint degeneration. However, the direct effect of adipokines, such as leptin, visfatin, and interleukin-6 (IL-6), on joint tissues, such as articular cartilage and meniscus, are not fully understood. In this study, we examined the hypothesis that these adipokines act synergistically with interleukin-1 (IL-1) to increase catabolism and the production of proinflammatory mediators in cartilage and meniscus. Explants of porcine cartilage and meniscus were treated with physiologically relevant concentrations of leptin, IL-6, or visfatin, alone or in combination with IL-1. Visfatin and IL-1 promoted the catabolic degradation of both cartilage and meniscus, as evidenced by increased metalloproteinase activity, nitric oxide production, and proteoglycan release. However, leptin or IL-6 at physiologic concentrations had no effect on the breakdown of these tissues. These findings suggest that the effects of obesity-induced osteoarthritis may not be through a direct effect of leptin or IL-6 on cartilaginous tissues, but support a potential role for increased visfatin levels in this regard. These data provide an important first step in understanding the role of adipokines in regulating cartilage and meniscus metabolism; however, these adipokines may have different effects in the context of the whole joint and must be evaluated further.
Viable ultramicrocells in drinking water (2008)

Chlorinated tap water filtrate (0.2 and 0.1 microm) still harbours opportunistic micro-organisms that can pose some health threat.
Independent anatomical and functional measures of the V1/V2 boundary in human visual cortex (2005)

The cerebral cortex has both anatomical and functional specialization, but the level of correspondence between the two in the human brain has remained largely elusive. Recent successes in high-resolution magnetic resonance imaging of myeloarchitecture patterns in the cortex suggest that it may now be possible to compare directly human anatomy and function in vivo. We independently investigated the anatomical and functional borders between primary and secondary human visual areas (V1 and V2) in vivo. Functional borders were mapped with functional magnetic resonance imaging (fMRI) using a narrow, vertical black and white contrast-reversing wedge. In three separate scanning sessions, anatomical images were collected at three different slice orientations (300 microm x 300 microm, slice thickness, 1.5 mm). The anatomical signature of V1 was determined by the presence of a hypointense band in the middle of the cortical gray matter. The band was identified in between 81% and 33% (mean 57%) of V1 defined using fMRI, and less than 5% of the identified band was in cortex outside V1. Intensity profiles taken through the gray matter on the V1 and V2 sides of the functional border indicate a measurable difference in the size of the hypointense band for all subjects. This is the first demonstration that the definition of V1 by fMRI closely matches the anatomically defined striate cortex in the human brain. The development of very high-resolution structural MRI may permit the definition of cortical areas based on myeloarchitecture when functional definition is not possible.
Mixed infection of <i>Porphyromonas gingivalis</i> and <i>Bacteroides forsythus</i> in a murine abscess model: involvement of gingipains in a synergistic effect (2001)

Several microorganisms including Porphyromonas gingivalis and Bacteroides forsythus have been implicated to be etiologically important agents of periodontal disease. In this study, we determined the ability of combinations of periodontopathogenic microorganisms to cause tissue destruction in a murine abscess model. Although all bacterial combinations used in this study produced larger abscesses than did monoinfection of each bacterium, the combination of P. gingivalis and B.forsythus showed a synergistic effect on abscess formation. Since these two bacteria have been frequently found together in lesions of periodontitis, these results suggest the significance of their co-infection in the progression of periodontitis. P. gingivalis produces extracellular and cell-associated cysteine proteinases (gingipains) which appear to be involved in its virulence. The rgpA rgpB double and kgp mutants induced significantly smaller abscesses than the wild type. Moreover, the rgpA rgpB kgp triple (gingipain-null) mutant hardly showed lesion formation at all with the experimental conditions used in this study, indicating that these genes encoding gingipains are important for virulence of P. gingivalis. Mixed infection of these P. gingivalis mutants with B. forsythus showed an additive effect on abscess formation, indicating that the gingipains of P. gingivalis may play an important role in the pathological synergism between P. gingivalis and B. forsythus.
현대도예의 움직임에 관한 현상학적 접근 (2011)

장르의 해체 및 표현매체의 다양성과 더불어 현대도예는 점차 다원화되는 양상을 보이며, 작품 읽기에 있어 전통적인 틀을 벗어난 새로운 접근방식이 필요하게 되었다.
 최근 인간 중심의 ‘몸(body)’을 통한 현상학적 공간 개념은 새로운 시대, 공간을 해석하기 위한 적합한 수단으로 다루어지고 있다.
 ‘현상학(phenomenology)’의 대표적인...
Strength and Performance Enhancement of Bonded Joints by Spatial Tailoring of Adhesive Compliance via 3D Printing (2016)

Adhesive bonding continues to emerge as a preferred route for joining materials with broad applications including advanced structures, microelectronics, biomedical systems, and consumer goods. Here, we study the mechanics of deformation and failure of tensile-loaded single-lap joints with a compliance-tailored adhesive. Tailoring of the adhesive compliance redistributes stresses and strains to reduce both shear and peel concentrations at the ends of the adhesive that determine failure of the joint. Utilizing 3D printing, the modulus of the adhesive is spatially varied along the bondlength. Experimental strength testing, including optical strain mapping, reveals that the strain redistribution results in a greater than 100% increase in strength and toughness concomitant with a 50% increase in strain-to-break while maintaining joint stiffness. The tailoring demonstrated here is immediately realizable in a broad array of 3D printing applications, and the level of performance enhancement suggests that compliance tailoring of the adhesive is a generalizable route for achieving superior performance of joints in other applications, such as advanced structural composites.
The pyroelectric energy harvesting capabilities of PMN–PT near the morphotropic phase boundary (2011)

This paper reports on direct thermal to electrical energy conversion by performing the Olsen cycle on pyroelectric materials. The energy harvesting capability of commercially available [001] oriented 68PbMg1/3Nb2/3O3?32PbTiO3 (PMN?32PT) single crystal capacitors was measured experimentally. An energy density of 100? mJ?cm?3/cycle, corresponding to 4.92?mW?cm?3, was obtained by successively dipping the material in oil baths at temperatures 80 and 170??C and cycling the electric field between 2 and 9? kV?cm?1. Similarly, an energy density of 55?mJ?cm?3/cycle was obtained between 80 and 140??C. An estimated 40% of this energy resulted from the strain polarization due to the rhombohedral to tetragonal phase transition. The strain from this transition disappeared when the maximum operating temperature exceeded the Curie temperature of about 150??C. The optimal low electric field used in the Olsen cycle maximizing the energy harvested was found to be around 2?kV?cm?1. In addition, the material suffered from (i)?dielectric breakdown for electric fields larger than 9? kV?cm?1 and (ii)?cracking from thermal stress for operating temperature differences in excess of 90??C. A physical model predicting the total amount of energy harvested was also derived, accounting for thermal expansion as well as temperature dependent dielectric constant and spontaneous polarization. The model predictions fell within 20% of the experimental results in the temperature range between 80 and 170??C and electric fields ranging from 2 to 9?kV?cm?1.
Generation of Ketenes from Acid Chlorides Using NaH/Crown Ether Shuttle-Deprotonation for Use in Asymmetric Catalysis (2002)

[reaction: see text] We describe methodology for the in situ generation of reactive monosubstituted ketenes from acid chlorides through a shuttle deprotonation process using NaH as an inexpensive stoichiometric base and a crown ether cocatalyst. We have successfully applied this new procedure to the catalytic, asymmetric synthesis of beta-lactams and alpha-haloesters.
A Soft Computing Model for Predicting Yarn Tenacity (2007)

A soft computing model for predicting yarn tenacity from fiber properties and yarn parameters is developed. Because the number of samples is limited, the artificial neural network to be established must be a small-scale one. This soft computing model includes two stages. Firstly, the fiber properties and yarn parameters were selected by utilizing a ranking method for identifying the most relevant fiber properties and yarn parameters as the input variables to fit the small-scale artificial neural network model. The first part of this method takes human knowledge of yarn tenacity into account. The second part utilizes a data sensitivity criterion based on a distance method. Secondly, the artificial neural network model of the relationship between fiber properties, yarn parameters and yarn tenacity is established. The results show that the artificial neural network model yields an accurate prediction, and a reasonably effective artificial neural network model can be achieved with relatively few data points integrated with the input variable selecting method developed in this research. The results also show that there is great potential for this research in the field of computer-assisted design in spinning technology.
Impact of Dielectric Constant on Embedded Antenna Efficiency (2014)

The impact of dielectric constant on radiation efficiency of embedded antenna located inside human body or another liquid environment is investigated both analytically and numerically. Our research is analysed and simulated at 403 MHz in the MedRadio band (401–406 MHz) and within a block of 2/3 human muscle phantom. Good agreement is achieved between analysis and simulation results. This work provides a guidance in selecting insulator for embedded antennas.
Circular High-Impedance Surfaces Characterization (2012)

In this letter, characterization of circular high-impedance surfaces (HISs) is investigated. The reflection phase characterization used for rectangular HISs is here extended to circular lattices. Circular HISs discussed in this letter present a 2-D periodicity, and consequently the phase diagram is determined for concentric and radial polarizations. The effect of mapping a rectangular HIS into a circular one is investigated in order to give some insights regarding the design of such metasurface. The presented characterization constitutes a useful tool for the design of low-profile antennas using HIS as reflector.
A Direct Methanol Fuel Cell Based on a Novel Low-Cost Nanoporous Proton-Conducting Membrane (1999)

We report here a low‐cost and improved direct methanol fuel cell (DMFC), based on a novel nanoporous proton‐conducting membrane (NP-PCM). The use of the NP-PCM in DMFC offers several advantages over the Nafion‐based DMFC; lower membrane cost (by more than two orders of magnitude), smaller pores (by a factor of two), and lower methanol crossover (by up to an order of magnitude), which lead to much higher fuel utilization. The NP‐PCM also has higher conductivity (by up to four times). In addition, the ionic conductivity of the NP‐PCM, unlike Nafion, is not affected by heavy metal impurities, thus it may permit the use of cheaper catalysts and hardware materials. The maximum power density achieved so far, at and at ambient oxygen pressure, is . ©2000 The Electrochemical Society
Structural Determinants of the Capacity of Heparin to Inhibit the Formation of the Human Amplification C3 Convertase (1981)

The ability of heparin glycosaminoglycan to prevent formation of the properdin-stabilized amplification C3 convertase is independent of antithrombin binding activity and requires substitution of the amino sugar and a degree of oxygen (O)-sulfation which could be on the uronic acid or the amino sugar. Preparations of heparin glycosaminoglycan isolated by different techniques from different species (rat, human, and porcine) exhibited an equivalent capacity to inhibit generation of the amplification C3 convertase. Hyaluronic acid, which is devoid of O-sulfation, had no inhibitory activity; chondroitin 4-sulfate of rat and whale origins, chondroitin 6-sulfate of rat and shark origins, and dermatan sulfate from porcine skin are O-sulfated on the galactosamine and had minimal activity. Porcine heparin glycosaminoglycan, isolated on the basis of affinity for antithrombin III, had no greater anticomplementary activity than porcine glycosaminoglycan, which failed to bind antithrombin III and had essentially no anticoagulant activity. Nitrogen (N)-desulfation of porcine heparin reduced anticomplementary activity to the level of the other sulfated mucopolysaccharides, and both N-resulfation and N-acetylation restored the original activities, thereby indicating a requirement for N-substitution, but not N-sulfation. N-resulfation of N-desulfated and O-desulfated heparin did not restore any activity, thus indicating that O-sulfation and N-substitution represent independent, critical structural requirements for the anticomplementary activity of heparin glycosaminoglycan. Inasmuch as N-desulfated-N-acetylated heparin had no anticoagulant activity, the nature of the N-substitution completely distinguishes the plasma-protein effector pathway that is inhibited.
A two-level heuristic for machine loading and assembly routing in a flexible assembly system (2002)

The paper presents integer programming formulations and an approximative lexicographic approach for a bicriterion loading and routing problem in a flexible assembly system. The problem objective is to determine an assignment of tasks to assembly stations for a set of products so as to balance station workloads and minimize total interstation transfer time. In the approach proposed, first the station workloads are balanced using a linear relaxation-based heuristic and then assembly routes are selected based on a network flow model. An illustrative example is provided and some results of computational experiments are reported.
A profile of impaired insulin degradation in relation to late‐life cognitive decline: A preliminary investigation (2008)

These preliminary analyses of a possible phenotype of impaired insulin degradation provide supportive evidence that deficits in insulin degradation may be related to late-life verbal memory decline.
<i>Fasciola hepatica</i>: a technique for the study of gut penetration by juvenile flukes (1981)

A method using light and electron microscopes is described which is suitable for the examination of gut penetration by juvenile Fasciola hepatica. It involved the ligation of small sections of the small intestine of rats and the introduction of artificially excysted flukes into these gut loops. By restricting the area of infection in this way it was possible to either recover flukes from the gut lumen or to prepare ultrathin sections for electron microscopy of flukes penetrating the gut wall. In addition, flukes were recovered from the body cavity at various times after preparation of loops in resistant and naive rats. It was found that more flukes reached the body cavity in naive rats than in resistant rats, demonstrating a resistance to infection in the gut loops of sensitized rats.
Simultaneous detection of the C282Y, H63D and S65C mutations in the hemochromatosis gene using quenched-FRET real-time PCR (2008)

Hereditary hemochromatosis (HH) is a common autosomal disorder of iron metabolism mainly affecting Caucasian populations. Three recurrent disease-associated mutations have been detected in the hemochromatosis gene (HFE): C282Y, H63D, and S65C. Although HH phenotype has been associated with all three mutations, C282Y is considered the most relevant mutation responsible for hemochromatosis. Clinical complications of HH include cirrhosis of the liver, congestive cardiac failure and cardiac arrhythmias, endocrine pancreatic disease, which can be prevented by early diagnosis and treatment. Therefore, a reliable genotyping method is required for presymptomatic diagnosis. We describe the simultaneous detection of the C282Y, H63D and S65C mutations in the hemochromatosis gene by real-time PCR followed by melting curve analysis using fluorescence resonance energy transfer (FRET) probes. The acceptor fluorophore may be replaced by a quencher, increasing multiplex possibilities. Real-time PCR results were compared to the results of sequencing and conventional PCR followed by restriction digestion and detection by agarose gel electrophoresis (PCR-RFLP). Genotypes from 80 individuals obtained both by the conventional PCR-RFLP method and quenched-FRET real-time PCR were in full agreement. Sequencing also confirmed the results obtained by the new method, which proved to be an accurate, rapid and cost-effective diagnostic assay. Our findings demonstrate the usefulness of real-time PCR for the simultaneous detection of mutations in the HFE gene, which allows a reduction of a significant amount of time in sample processing compared to the PCR-RFLP method, eliminates the use of toxic reagents, reduces the risk of contamination in the laboratory, and enables full process automation.
[Studies on the dynamics of biological characteristics of CD133+ cells from human umbilical cord blood during short-term culture]. (2003)

This study was to investigate dynamics of biological properties of CD133(+) cells from human umbilical cord blood (UCB) during short-term culture containing the combination of hematopoietic growth factors and the feasibility of in vitro expansion of CD133(+) cells. The biology activities including analysis of cell cycle, immunophenotype, telomerase activity, expression of adhesion molecules and expansion potential of CD133(+) cells were monitored during ex-vivo expansion, and compared with those of CD34(+) cells. The results showed that the contents of CD133(+) and CD34(+) cells in fresh UCB were (1.05 +/- 0.73)% and (1.40 +/- 0.56)% respectively. About 79.62% of CD34(+) cells expressed CD133, and more than 97% of CD133(+) cells were CD133(+)CD34(+), markedly higher than that in CD34(+) fraction (P < 0.01). No significant differences were observed in content of cells expressing CD38, CD13, CD14, CD61 and glycophorin-A between the two fractions. Expansion of CD133(+), CD133(+)CD34(+) and CD34(+)CD38(-) cells at 10 days and those of CFU-mix, HPP-CFC and CD34(+)CD38(-) cells at 6 days from CD133(+) cells group were significantly higher than those from the CD34(+) cell group (P < 0.05). Analysis of immunophenotype showed that CD133(+)CD34(+) cells declined gradually while CD133(-)CD34(+) and CD133(-)CD34(-) cells increased during ex-vivo expansion; basal telomerase activities of fresh UCB CD133(+) and CD34(+) cells were low but significantly exceeded that of CD34(-) fraction (P < 0.05). At first week of expansion, telomerase activity was significantly upregulated, after two weeks, telomerase activity remarkably declined, and decreased to baseline or below the limits of detection in day 20. More than 90% of CD133(+) cells expressed CD49d and CD11a, and, more than 85% of the cells expressed CD54, about 50% of cells expressed CD62L. At the early stage of expansion, expression of CD49d was upregulated, expression of CD11a remaining no change, while as expression of CD54 and CD62L was downregulated. Expression of all adhesion molecules was decreased gradually with extend of culture. But expression of these adhesion molecules on CD34(+) subsets were not affected significantly during expansion. It is concluded that CD133(+) population may be a more primitive hematopoietic stem/progenitor cells (HSPC) than CD34(+) cells, CD133(+) cells have great expansion potential for ex-vivo expansion and is a suitable target cell for ex-vivo expansion of HSPC. Downregulation of adhesion molecules and telomerase activity may be one of the reasons for delayed engraftment of expanded products.
A principle of organization which facilitates broad Lamarckian-like adaptations by improvisation (2015)

The hypothesis raises a critical, but thus far overlooked adaptation problem and explains how random variation can self-organize to confer a wide range of individual-specific adaptations beyond the existing outcomes of natural selection. It portrays gene regulation as an inseparable synergy between natural selection and adaptation by improvisation. The latter provides a basis for Lamarckian adaptation that is not limited to a specific mechanism and readily accounts for the remarkable resistance of tumors to treatment.