gebhart/patrepeval huggingface dataset:
Binding of the Bi (III) Complex of Naringin with<b><i>β</i></b>-Cyclodextrin/Calf Thymus DNA: Absorption and Fluorescence Characteristics (2014)

Naringin-Bi (III) complex (Narb) was prepared and analysed by UV-Visible absorption and fluorescence measurements. The inclusion complex of Narb with β -Cyclodextrin ( β -CD) was characterized by the UV-Visible absorption, Infrared, scanning dlectron microscopic, and X-ray diffractometric techniques. The stoichiometry of the inclusion complex of Narb with β -CD was 1 : 1 with a binding constant of 5.18 × 10 2 mol −1 dm 3 . The interaction of Narb with Calf Thymus DNA (ctDNA) was investigated in the presence and the absence of β -CD. The binding constants for the interaction of Narb with ctDNA in the absence and the presence of β -CD were 1.29 × 10 5 mol −1 dm 3 and 6.89 × 10 4 mol −1 dm 3 , respectively. The Stern-Volmer constants for the interaction of Narb with ctDNA in the absence and the presence of β -CD were 1.25 × 10 4 mol −1 dm 3 and 5.10 × 10 3 mol −1 dm 3 , respectively. The lowering of the binding affinity and the<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:msub><mml:mrow><mml:mi>K</mml:mi></mml:mrow><mml:mrow><mml:mtext>sv</mml:mtext></mml:mrow></mml:msub></mml:mrow></mml:math>were observed for the interaction of Narb with ctDNA in the presence of β -CD.
O-Antigen Delays Lipopolysaccharide Recognition and Impairs Antibacterial Host Defense in Murine Intestinal Epithelial Cells (2009)

Although Toll-like receptor (TLR) 4 signals from the cell surface of myeloid cells, it is restricted to an intracellular compartment and requires ligand internalization in intestinal epithelial cells (IECs). Yet, the functional consequence of cell-type specific receptor localization and uptake-dependent lipopolysaccharide (LPS) recognition is unknown. Here, we demonstrate a strikingly delayed activation of IECs but not macrophages by wildtype Salmonella enterica subsp. enterica sv. (S.) Typhimurium as compared to isogenic O-antigen deficient mutants. Delayed epithelial activation is associated with impaired LPS internalization and retarded TLR4-mediated immune recognition. The O-antigen-mediated evasion from early epithelial innate immune activation significantly enhances intraepithelial bacterial survival in vitro and in vivo following oral challenge. These data identify O-antigen expression as an innate immune evasion mechanism during apical intestinal epithelial invasion and illustrate the importance of early innate immune recognition for efficient host defense against invading Salmonella.
In vitro activation of heat shock transcription factor DNA-binding by calcium and biochemical conditions that affect protein conformation. (1990)

The transcription of heat shock genes in response to physiological stress requires activation of heat shock transcription factor (HSF). Although the transcriptional response is most commonly induced by temperature elevation, the biochemical events involved in HSF activation in vivo can also be triggered at normal physiological temperatures by chemicals that inhibit metabolic processes. We have used a HeLa cell-free system in which HSF DNA-binding is activated by conditions that affect protein conformation, including increasing concentrations of hydrogen ions, urea, or nonionic detergents. Treatment with calcium ions also results in a concentration- and time-dependent activation of HSF in vitro. Pretreatment with each of these biochemical conditions reduces the temperature dependence for HSF activation in vitro. These results suggest that HSF is activated either directly by undergoing a conformational change or indirectly through interactions with unfolded proteins.
NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site (2011)

The Neurospora VS ribozyme is a small nucleolytic ribozyme with unique primary, secondary and global tertiary structures, which displays mechanistic similarities to the hairpin ribozyme. Here, we determined the high-resolution NMR structure of a stem-loop VI fragment containing the A730 internal loop, which forms part of the active site. In the presence of magnesium ions, the A730 loop adopts a structure that is consistent with existing biochemical data and most likely reflects its conformation in the VS ribozyme prior to docking with the cleavage site internal loop. Interestingly, the A730 loop adopts an S-turn motif that is also present in loop B within the hairpin ribozyme active site. The S-turn appears necessary to expose the Watson-Crick edge of a catalytically important residue (A756) so that it can fulfill its role in catalysis. The A730 loop and the cleavage site loop of the VS ribozyme display structural similarities to internal loops found in the active site of the hairpin ribozyme. These similarities provided a rationale to build a model of the VS ribozyme active site based on the crystal structure of the hairpin ribozyme.
Semantic query optimization in recursive databases (2003)

Semantic query optimization is the process of using semantic knowledge expressed in the form of integrity constraints to transform a query into a semantically equivalent one; one that is thought to be less expensive to process. The authors analyze the possibilities of semantic optimization in a deductive database that includes recursive relations and, consequently, integrity constraints that include recursive literals. They propose a compiled approach to utilizing semantic knowledge in recursive query processing, assuming recursive queries are processed using compiled iterative methods. Also, a method of residue propagation for obtaining implied constraints that are often useful in optimization is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template (2011)

Natural and synthetic biological networks must function reliably in the face of fluctuating stoichiometry of their molecular components. These fluctuations are caused in part by changes in relative expression efficiency and the DNA template amount of the network-coding genes. Gene product levels could potentially be decoupled from these changes via built-in adaptation mechanisms, thereby boosting network reliability. Here, we show that a mechanism based on an incoherent feedforward motif enables adaptive gene expression in mammalian cells. We modeled, synthesized, and tested transcriptional and post-transcriptional incoherent loops and found that in all cases the gene product adapts to changes in DNA template abundance. We also observed that the post-transcriptional form results in superior adaptation behavior, higher absolute expression levels, and lower intrinsic fluctuations. Our results support a previously hypothesized endogenous role in gene dosage compensation for such motifs and suggest that their incorporation in synthetic networks will improve their robustness and reliability.
Stimulation of IL-2 production in murine lymphocytes by substance P and related tachykinins. (1993)

Substance P (SP), a tachykinin neuropeptide, has been previously reported to stimulate IL-2 production in murine T cell lines activated with phorbol esters. Here we extend these observations by establishing the stimulatory effect of SP and related tachykinins on IL-2 production by normal murine lymphocytes and on purified CD4+ T cells. SP proved to be the most efficient IL-2 inducer, exerting its maximal effect at concentrations that were 4 to 5 orders of magnitude lower than the optimal stimulatory concentrations of physalaemin, NKA, or NKB. SP stimulated IL-2 production in a dose-dependent manner, with an optimal concentration range of 10(-10) to 10(-14) M, comparable with physiologic concentrations of SP found in blood and other organs. The effect of SP was carried by the carboxyl-terminal part of the molecule (SP4-11). The specificity of SP activity was confirmed by the inhibitory effect of spantide, a tachykinin antagonist, and of CP-96,345, a nonpeptide antagonist specific for NK-1-type receptors. In unfractionated spleen cell cultures SP induced de novo IL-2 protein synthesis. SP could induce IL-2 production either directly, or in combination with Con A or anti-CD3 antibody treatments. The effect of SP in conjunction with Con A was synergistic, whereas the effect in conjunction with anti-CD3 antibodies was additive, suggesting different molecular mechanisms for these stimulatory factors. In the absence of additional costimuli the effect of SP in unfractionated spleen cell cultures was partially mediated through the induction of IL-1, and both SP and IL-1 were required for IL-2 induction in purified CD4+ T cells. In contrast to its stimulatory effect on the generation of IL-2, SP did not induce IFN-gamma production in murine spleen cells. The stimulatory effect of SP on IL-2 production suggests that some of the already described immunostimulatory activities of SP could be mediated through the up-regulation of IL-2 production in normal lymphocytes.
On the semantics of temporal specifications of component-behavior for dynamic architectures (2017)

In component-based design, temporal logic is a means to specify the temporal behavior of components. If these components are deployed to a dynamic architecture, they can be activated and deactivated over time. Thus, the traditional semantics of temporal specifications of component-behavior does no longer reflect the actual behavior of the components within such dynamic architectures. To address this problem, we provide an alternative semantics of temporal specifications of component-behavior for dynamic architectures, taking into account component activation and deactivation. We show soundness and relative completeness of our semantics w.r.t. the traditional one. The new semantics can then be used to support in the formal specification of dynamic architectures by separating the specification of component-behavior from other aspects such as component activation and architecture reconfiguration.
An elastin gene mutation producing abnormal tropoelastin and abnormal elastic fibres in a patient with autosomal dominant cutis laxa (1998)

Elastin is the protein responsible for the characteristic elastic properties of many tissues including the skin, lungs and large blood vessels. Loss-of-function mutations in the elastin gene are known to cause the heart defect supravalvular aortic stenosis (SVAS). We and others have identified deletions, nonsense mutations and splice site mutations in SVAS patients that abolish the function of one elastin gene. We have now identified an elastin mutation in a patient with a completely different phenotype, the rare autosomal dominant condition cutis laxa. A frameshift mutation in exon 32 of the elastin gene is predicted to replace 37 amino acids at the C-terminus of elastin by a novel sequence of 62 amino acids. mRNA and immunoprecipitation studies show that the mutant allele is expressed. Electron microscopy of skin sections shows abnormal branching and fragmentation in the amorphous elastin component, and immunocytochemistry shows reduced elastin deposition in the elastic fibres and fewer microfibrils in the dermis. These findings suggest that the mutant tropoelastin protein is synthesized, secreted and incorporated into the elastic matrix, where it alters the architecture of elastic fibres. Interference with cross-linking would reduce elastic recoil in affected tissues and explain the cutis laxa phenotype.
QuickSilver: A Flexible, Extensible, and High-Speed Architecture for Multi-Modality Imaging (2006)

A flexible, extensible, high-speed architecture, called Quicksilvertrade and specifically geared to the requirements of small animal imaging, has been developed. The architecture is composed of ring-based event processing modules (EPMs) with nearest neighbor, high-speed digital communication transmitting event packets via a "store and forward" concept. Each EPM is capable of transmitting up to 15.6M events/sec to other EPMs. Coincidence determination is performed at the EPM level around the "ring". This distributes the load and eliminates the need for a separate coincidence processor. Each EPM is capable of transmitting up to 1.9M coincidence events/sec to an event routing subsystem (ERS) for acquisition and processing. The ERS has 2 transport interfaces for acquiring events: an IEEE 1394A interface and a PCI interface. The IEEE 1394A interface can support up to 5.3M events/sec and the PCI interface can support up to 16.7M events/sec. Thus this architecture provides a new level of capability for small animal PET imaging, but is also extremely well suited for PET research, single photon emission computed tomography (SPECT) imaging, and use with X-ray CT and magnetic resonance imaging (MRI).
Design and operational characteristics of a high-speed (millisecond) system for the measurement of thermophysical properties at high temperatures (1971)

Design and constructional details of a high-speed system for the measurement of selected thermophysical properties of electri cal conductors at te~pe.ratures aoove 2000 K in e~p erime nt~ of subsecond duration are described. Operation al characten stlcs of such a system are given. VarIous phenomena that affect the design and successful operation of the system are discussed and, .whenever possible, quantitative results are given. Certain experimental ch ecks to assess the operation of th e system are also described.
A Model for Secondary Monitor Unit Calculations of PBS Proton Therapy Treatment Plans (2019)

This work demonstrates the potential for reasonably accurate secondary verification of MUs in pencil beam scanning proton therapy for SFUD treatment plans with the proposed method. Required inputs are few, and are readily accessible, facilitating automation and clinical application. Further investigation will expand the current model to accommodate a broader range of potential optimization problems, and intensity-modulated proton therapy treatment plans.
Chemical-Free Recovery of Elemental Selenium from Selenate-Contaminated Water by a System Combining a Biological Reactor, a Bacterium–Nanoparticle Separator, and a Tangential Flow Filter (2018)

Biological selenate (SeO<sub>4</sub><sup>2-</sup>) reduction to elemental selenium nanoparticles (SeNPs) has been intensively studied but little practiced because of the additional cost associated with separation of SeNPs from water. Recovery of the SeNPs as a valuable resource has been researched to make the approach more competitive. Separation of the intracellular SeNPs from the biomass usually requires the addition of chemicals. In this research, a novel approach that combined a biological reactor, a bacterium-SeNP separator, and a tangential flow ultrafiltration module (TFU) was investigated to biologically reduce selenate and separate the SeNPs, biomass, and water from each other. This approach efficiently removed and recovered selenium while eliminating the use of chemicals for separation. The three units in the approach worked in synergism to achieve the separation and recovery. The TFU module retained the biomass in the system, which increased the biomass retention time and allowed for more biomass decay through which intracellular SeNPs could be released and recovered. SeNP aggregates were separated from bacterial aggregates due to their different interactions with a tilted polyethylene sheet in the bacterium-SeNP separator. SeNP aggregates stayed on the polyethylene sheet while bacterial aggregates settled down to the bottom of the separator.
Factors influencing the uptake of cholesterol by isolated brush border membranes from rabbit small intestine. (1986)

The uptake of [3H] cholesterol by isolated brush border membranes from rabbit small intestine was studied under different conditions. In initial experiments the uptake from taurocholate-micellized suspensions was found to be greatly enhanced by Ca2+. Maximum stimulation was obtained with 10 mM Ca2+ and this condition was adopted for some of the subsequent experiments. In the presence of this cation, the uptake was too rapid to allow kinetic studies and only equilibrium values could be measured. Addition of lecithins to the micelles had an inhibitory effect on the equilibrium uptake in the presence of Ca2+ and on the rate of uptake in the absence of this cation which increased with acyl chain length. Admixture of the sterol with dipalmitoylphosphatidylethanolamine stimulated the uptake whereas admixture with dipalmitoylphosphatidylglycerol as well as with 1-monoolein alone or together with oleic acid had little or no effect on uptake in the presence of Ca2+. Again with this cation present, preincubation of membranes with the dipalmitoyl analogue of lecithin increased the equilibrium uptake of the sterol and abolished the inhibitory effect of the choline lipid. This inhibitory effect could be seen only with untreated membranes when lecithin and cholesterol were micellized together. In the absence of Ca2+, preincubation with dipalmitoylphosphatidylcholine had no marked effect on the rate of cholesterol uptake and the suppressive effect of lecithin on this rate could be seen even with lipid-treated membranes provided the lecithin and sterol were micellized together.(ABSTRACT TRUNCATED AT 250 WORDS)
All Disordered Regions of Native Cellulose Show Common Low-Frequency Dynamics (2000)

We present inelastic neutron scattering (INS) experiments on various types of cellulose revealing the universal nature of the disordered regions from the point of view of low-energy dynamics. Using INS in combination with the deuteration of polar groups technique, we have studied the dynamic response of hydroxyl groups, χ‘ ‘ within cellulose: from regions accessible to water was found to be distinctly different from obtained from the inaccessible crystal cores. The shape of does not depend on the sample origin and, therefore, is independent of its crystallinity. Our study includes the comparison of different native cellulose specimens with (i) a completely disordered reference sample and (ii) a sample where the intracrystalline hydroxyl groups have been deuterated. Thus, we can state that the accessible regions are identical to disordered regions. These regions, which include the crystal surfaces, possess a common dynamic signature.
Bit-Shift Model Taking Account of the Effect of Written Bits. (2000)

The estimation of error rates is becoming increasingly important with the continued growth in the density of magnetic recording. It is known that the error rate is strongly affected by the overwrite performance, while it strictly depends on the bit shift caused by hard-transition shift (HTS) or non-linear transition shift (NLTS). We designed a bit-shift model based on the mechanism of bit-shift occurrence. Our model confirms that the overwrite depends on the overwritten transition density and can be characterized by HTS and NLTS. This paper discusses simulations of the dependencies of the write gap length, the write field, and the spacing on overwrite.
Maxillary unilateral molar distalization with sliding mechanics: a preliminary investigation (2001)

Fifteen patients, eight males and seven females with a mean age of 13.32 years, were selected for unilateral molar distalization. Dentally, all presented with a unilateral Class II molar relationship. The subjects were all in the permanent dentition with second molars erupted and with a well aligned lower dental arch. For maxillary molar distalization a new intra-oral appliance was developed, the Keles Slider, which comprised two premolar and two molar bands. The anchorage unit was a Nance button with an anterior bite plane. From the palatal side, the point of distal force application was carried towards the level of centre of resistance of the maxillary first molar. A Ni-Ti coil spring was used and 200 g distal force was applied to the Class II first molar. Lateral cephalograms were taken and analysed before and 2 months after molar distalization. The Class II molars were distalized bodily, on average, 4.9 mm (P < 0.001). Mesial migration of the Class II first premolars was 1.3 mm (P < 0.05), incisor protrusion was 1.8 mm (P < 0.05) and incisor proclination 3.2 degrees (P < 0.05). The overbite was reduced by 3.1 mm (P < 0.001) and the overjet increased 2.1 mm (P < 0.01). For stabilization, the corrected Class II unilateral molar relationship was maintained with a Nance button for 2 months. The results show that this newly developed device achieved bodily distal molar movement with minimum anchorage loss.
Spectroscopic and Electrochemical Properties of a Series of Mixed-Metal d<sup>6</sup>,d<sup>8</sup>Bimetallic Complexes of the Form [(bpy)<sub>2</sub>M(BL)PtCl<sub>2</sub>]<sup>2+</sup>(bpy = 2,2‘-Bipyridine; BL = dpq (2,3-Bis(2- pyridyl)quinoxaline) or dpb (2,3-Bis(2-pyridyl)- benzoquinoxaline); M = Os<sup>II</sup>or Ru<sup>II</sup>) (1996)

A series of new polymetallic complexes have been prepared which couple d6 pseudooctahedral lightabsorbing centers to a d8 square planar platinum site. These systems have lowest lying excited states that are M → BL charge transfer in nature. Hence, optical excitation directs charge flow toward the coupled platinum site. Synthetic variation of the lightabsorbing metal and the bridging ligand has been quite useful in the interpretation of the spectroscopic and electrochemical properties of these systems.
New technology of runway friction coefficient measurement and its towed implementation (2016)

The paper deals with the conceptual model of a towed measuring complex implementing a new runway friction coefficient measurement technology. The technology is based on the principle of controlled deceleration of the measuring wheel to simulate them in the process of measuring in anti-lock braking modes. Simulated modes are close to a real mode of braking aircraft wheels during landing formed by aviation automation systems. To improve accuracy of reproduction of electromechanical braking device characteristics, an automatic adaptive braking control system is offered. Based on the Burkhard model and additive random noise, a complex of mathematical models of distribution of friction coefficient values along the runway has been developed. A complex of mathematical models includes a variety of descriptive characteristics (snow, wet asphalt with snow, very wet asphalt and wet asphalt). Computer models of friction coefficient measurement processes have been obtained. Series of experiments depending the results of friction coefficient measurements with simulated anti-lock braking mode on variations of their shape, intensity and frequency of braking and the average values of the slip anti-lock braking mode cycles have been carried out. It is shown that at any statistically representative interval of the runway (200 m), the average value of measured friction coefficient varies depending on the change of form the anti-lock braking cycles. Design documentation has been developed; experimental model of a new towing measurement system has been designed and has passed debugging tests. Its semi-natural tests based at the test bench with a controlled drum simulator of “treadmill” and airfield tests are also planned.
Analysis, Specification and Generation of Mobile Computer Data Synchronisation (2005)

In current technologies, mobile computer data synchronisation protocols are typically programmed at a low-level. The disadvantages of this are that they are error-prone and time consuming. This paper analyses current Palm OS data synchronisation problems and applies embedded domain-specific language (EDSL) techniques in the problem domain to improve the current situation. The key advantage is that domain developers can describe problems using their natural terms and concepts at high conceptual level. Our approach allows equivalent code to be generated automatically from higher-level specifications, enabling domain developers to express their ideas quickly and concisely, to work more productively and to avoid certain kinds of coding error.