gebhart/patrepeval huggingface dataset:
Characterization of Immuno-stimulating Polysaccharides Isolated from Korean Persimmon Vinegar (2008)

In this study, polysaccharides were isolated from Korean persimmon vinegar to characterize the polysaccharides existing as soluble forms within traditional Korean fermented beverages, and their immuno-stimulating activities were examined. Three successive chromatographies were used to purify the main polysaccharide in the persimmon vinegar, PV-1b-I, to homogeneity from the crude polysaccharide (PV-0). The molecular mass of PV-1b-I was estimated as 110 kDa and it contained significant proportions of mannose (46.8%), galactose (28.5%) and arabinose (19.1%). PV-1b-I strongly reacted with β-glucosyl Yariv reagent, suggesting the presence of an arabino-3,6-galactan moiety. PV-1b-I also induced high levels of macrophage activation and mitogenicity on murine splenocytes in vitro. The intravenous administration of PV-1b-I significantly augmented NK cytotoxicity against YAC-1 tumor cells. PV-1b-I also showed potent anticomplementary activity in a dose-dependent manner. Finally, C3 activation products were identified by crossed immunoelectrophoresis using anti-human C3 and the anti-complementary activity of PV-1b-I under Ca²+-free conditions, suggesting that this PV-1b-I causes complementary activations via both alternative and classical pathways. From these results, one can conclude that Korean persimmon vinegar contains select polysaccharides in addition to healthy components, and these polysaccharides appear to provide immuno-stimulating activities beneficial to human health.
Matrix formalism for calculation of electric field intensity of light in stratified multilayered films (1990)

A new algorithm has been proposed for the calculation of the electric field intensity in stratified multilayered films when light is incident on the system. The algorithm utilizes matrix formulas based on Abeles's formulas for the calculation of reflectance and transmittance. Equations for calculating patial absorptance due to a certain depth in the films are also derived. Some examples of the application of the electric field description are given for the analysis of three kinds of reflection spectroscopic methods which use metal surfaces: reflection-absorption, surface electromagnetic wave, and metal overlayer ATR methods. The algorithm given here offers a useful tool in understanding the mechanism of light absorption in various spectroscopic methods, and is convenient to use where intensity of the IR spectrum is of interest.
The Use of Melting Curves as a Novel Approach for Validation of Real-time PCR Instruments (2011)

Validation of PCR thermal cycler performance is crucial in order to obtain reliable results. In this study, high resolution melting curve (HRM) analysis is presented as a novel validation method for real-time PCR instruments. By applying HRM analysis using a defined PCR amplicon and EvaGreen dye, information about the temperature accuracy and thermal homogeneity of the heating block was obtained. This pilot study shows the potential of our technique for temperature validation of real-time quantitative PCR thermal cyclers. Our data correlated well with the temperature accuracy data obtained from the Mobile Temperature Acquisition System (MTAS; r2 = 0.93), which conforms to the National Institute of Standards and Technology criteria, and our method was reproducible in independent runs (r2 = 0.95). The advantages of this HRM-based method include: (i) temperature measurement under real world conditions in the reaction liquid in closed reaction tubes; (ii) temperature measurement of all wells; and (iii) applicability to all real-time PCR instruments capable of HRM analysis.
Skin graft rejection by beta 2-microglobulin-deficient mice. (1992)

Mice homozygous for a beta 2-microglobulin (beta 2-m) gene disruption lack beta 2-m protein and are deficient for functional major histocompatibility complex class I (MHC-I) molecules. The mutant mice have normal numbers of CD4+8- T helper cells, but lack MHC-I-directed CD4-8+ cytotoxic T lymphocytes (CTLs). In this study we used the beta 2-m mutant mice to study the importance of MHC-I-directed immunity in skin graft rejection. Our results indicate that MHC-I-directed CD8+ CTLs are not essential in the rejection of allografts with whole MHC or multiple minor H differences. However, the absence of MHC-I-guided immunity profoundly reduces the ability of mutant mice to reject H-Y disparate grafts. In addition, we show that natural killer cells which vigorously reject MHC-I-deficient bone marrow grafts, are not effective in the destruction of MHC-I-deficient skin grafts.
Construction of the gyrB Database for the Identification and Classification of Bacteria. (1998)

Nucleotide sequences of small-subunit rRNA (16S rRNA) are most commonly used for the identification and characterization of bacteria and their complex communities. However, 16S rRNA evolves slowly and is often not very convenient to resolve bacterial strains at the species level. We have therefore attempted to develop a rapid and more convenient system for bacterial identification using the gyrB gene sequences. We chose the gyrB gene, because (i) it is rarely transmitted horizontally, (ii) its molecular evolution rate is higher than that of 16S rRNA, and (iii) the gene is distributed ubiquitously among bacterial species. We PCR-amplified the 1.2 kb-long gyrB segments from about 1,000 bacterial species by using degenerate primers and determined their nucleotide sequences. The resultant data have been assembled into the gyrB database accessible via WWW.
The Formation and the Plane Indices of Etched Facets of Wet Etching Patterned Sapphire Substrate (2012)

A two-step chemical wet etching processes were used to investigated the formation and the plane indexes of exposed etched facets of wet etching patterned sapphire substrate (PSS). It was found when SiO2 mask still remained on the top c-plane, the structure of PSS comprised of a hexagonal pyramid covered with six facets with a flat top c-plane. When SiO2 mask were etched away, beside six facets on the bottom, there were 3 extra facets exposed on the top.
Narrowband fiber grating filters (1990)

Two techniques for the fabrication of fiber gratings with a narrowband filter response are reported. In the first technique, the reflection bandwidth is reduced by increasing the grating length. Fiber gratings 10 mm long have been made with a bandwidth of approximately 0.3 nm. In the second technique, a phase shift is incorporated into the grating to form a resonant structure. Fiber resonators with resonant dips in reflection and peaks in transmission having full-width half-maximum (FWHM) bandwidths of approximately 0.08 nm have been fabricated. A corresponding narrowband transmission peak was also measured.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Der Experimentator: Molekularbiologie/ Genomics (2009)

Lieber EXPERIMENTATOR, wir präsentieren Ihnen hier das Grundlagenwissen sowie Tipps und Tricks für den Umgang mit Nucleinsäuren. Sie werden sofort merken, dass der Autor Lust und Frust der täglichen L
Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau (2020)

Little is known about life in the boron-rich hot springs of Trans-Himalayas. Here, we explore the geomicrobiology of a 4438-m-high spring which emanates ~70 °C-water from a boratic microbialite called Shivlinga. Due to low atmospheric pressure, the vent-water is close to boiling point so can entropically destabilize biomacromolecular systems. Starting from the vent, Shivlinga's geomicrobiology was revealed along the thermal gradients of an outflow-channel and a progressively-drying mineral matrix that has no running water; ecosystem constraints were then considered in relation to those of entropically comparable environments. The spring-water chemistry and sinter mineralogy were dominated by borates, sodium, thiosulfate, sulfate, sulfite, sulfide, bicarbonate, and other macromolecule-stabilizing (kosmotropic) substances. Microbial diversity was high along both of the hydrothermal gradients. Bacteria, Eukarya and Archaea constituted >98%, ~1% and <1% of Shivlinga's microbiome, respectively. Temperature constrained the biodiversity at ~50 °C and ~60 °C, but not below 46 °C. Along each thermal gradient, in the vent-to-apron trajectory, communities were dominated by Aquificae/Deinococcus-Thermus, then Chlorobi/Chloroflexi/Cyanobacteria, and finally Bacteroidetes/Proteobacteria/Firmicutes. Interestingly, sites of >45 °C were inhabited by phylogenetic relatives of taxa for which laboratory growth is not known at >45 °C. Shivlinga's geomicrobiology highlights the possibility that the system's kosmotrope-dominated chemistry mitigates against the biomacromolecule-disordering effects of its thermal water.
Surfactant Compositions with High Sweepout Effect for Increasing Well Injectivity and Improved Oil Recovery (2003)

A004 SURFACTANT COMPOSITIONS WITH HIGH SWEEPOUT EFFECT FOR INCREASING WELL INJECTIVITY AND ENHANCED OIL RECOVERY 1 G.B.FRIDMAN 1 O.B.SOBANOVA 1 I.L. FYODOROVA 1 A.SH. SHAKIROV 2 1 JSC NIIneftepromchim 420045 Russia Kazan N.Yershov st. 29 e-mail: neftpx@mi.ru 2 JSC “Tatnefteotdacha” One of the important trends in oil field exploitation is operation with the injection well stock involving well completion for injection and maintaining the required injectivity in them. Last years the problem of enhanced oil recovery is particularly urgent along with the challenges of improved oil recovery. The scientists of JSC NIIneftepromchim have been developing the new methods based on
A class of optimal fixed-byte error protection codes for computer systems (2002)

Error control codes are now being successfully applied to computer systems, especially to memory systems. This paper proposes a new class of error control codes to protect the fixed-byte in computer words from errors. The fixed-byte stores valuable and important information such as control and address information in communication messages or pointer information in database words. 'Fixed-byte' means the clustered information digits in the word whose position is determined in advance. As a simple class of these unequal error protection codes, this paper proposes two types of optimal fixed-byte error protection codes: single-bit error correction and fixed b-bit byte error correction (SEC-FbEC) codes and single-bit error correction, double-bit error detection, and fixed b-bit byte error detection (SEC-DED-FbED) codes. The obtained optimal SEC-FbEC codes where byte length b=7 bits and information length k=64 bits, for example, require a check-bit length of only 8 bits, which is the same as that of the conventional SEC-DED codes with k=64 bits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<i>In Vitro</i> and <i>In Vivo</i> Evaluation of Novel Glibenclamide Derivatives as Imaging Agents for the Non-Invasive Assessment of the Pancreatic Islet Cell Mass in Animals and Humans (2005)

Pancreatic islet cell mass (PICM) is a major determinant of the insulin secretory capacity in humans. Currently, the only method for accurate assessment of the PICM is an autopsy study. Thus, development of a technique allowing the non-invasive quantification of PICM is of great interest. The aim of this study was to develop such a non-invasive technique featuring novel fluorine- and (99m)Tc-labelled glibenclamide derivatives. Despite the structural modifications necessary to introduce fluorine into the glibenclamide molecule, all derivatives retained insulin stimulating capacity as well as high affinity binding to human SUR1 when compared to the original glibenclamide. Contrastingly, the lipophilicity of the fluorine-labelled derivatives was altered depending on the particular modification. In the human PET-study a constant but weak radioactive signal could be detected in the pancreas using a fluorine-labelled glibenclamide derivative. However, a reliable assessment and visualisation of the PICM could not be obtained. It can be assumed that the high uptake of the fluorine-labelled tracer e.g. into the the liver and the high plasma protein binding leads to a relatively low signal-to-noise ratio. In case of the presented fluorine-labelled glibenclamide based compounds this could be the result of their invariably high lipophilicity. The development of a (99 m)Tc-labelled glibenclamide derivative with a lower lipophilicity and differing in vivo behaviour, glibenclamide based compounds for non-invasive imaging of the pancreatic islet cell mass may be possible.
Flipping Biological Switches: Solving for Optimal Control: A Dissertation (2015)

Switches play an important regulatory role at all levels of biology, from molecular switches triggering signaling cascades to cellular switches regulating cell maturation and apoptosis. Medical therapies are often designed to toggle a system from one state to another, achieving a specified health outcome. For instance, small doses of subpathologic viruses activate the immune system’s production of antibodies. Electrical stimulation revert cardiac arrhythmias back to normal sinus rhythm. In all of these examples, a major challenge is finding the optimal stimulus waveform necessary to cause the switch to flip. This thesis develops, validates, and applies a novel model-independent stochastic algorithm, the Extrema Distortion Algorithm (EDA), towards finding the optimal stimulus. We validate the EDA’s performance for the Hodgkin-Huxley model (an empirically validated ionic model of neuronal excitability), the FitzHugh-Nagumo model (an abstract model applied to a wide range of biological systems that that exhibit an oscillatory state and a quiescent state), and the genetic toggle switch (a model of bistable gene expression). We show that the EDA is able to not only find the optimal solution, but also in some cases excel beyond the traditional analytic approaches. Finally, we have computed novel optimal stimulus waveforms for aborting epileptic seizures using the EDA in cellular and network models of epilepsy. This work represents a first step in developing a new class of adaptive algorithms and devices that flip biological switches, revealing basic mechanistic insights and therapeutic applications for a broad range of disorders.
Blue Pr^3+-doped ZBLAN fiber upconversion laser (1996)

We demonstrate blue laser emission from a direct semiconductor laser-diode-pumped Pr(3+)-doped upconversion fiber laser. This laser produced more than 1 mW of power at a wavelength of 492 nm from pump lasers operating at 830 and 1020 nm.
Computational challenges of sequence classification in microbiomic data (2011)

Next-generation sequencing technologies have opened up an unprecedented opportunity for microbiology by enabling the culture-independent genetic study of complex microbial communities, which were so far largely unknown. The analysis of metagenomic data is challenging: potentially, one is faced with a sample containing a mixture of many different bacterial species, whose genome has not necessarily been sequenced beforehand. In the simpler case of the analysis of 16S ribosomal RNA metagenomic data, for which databases of reference sequences are known, we survey the computational challenges to be solved in order to be able to characterize and quantify a sample. In particular, we examine two aspects: how the necessary adoption of new tools geared towards high-throughput analysis impacts the quality of the results, and how good is the performance of various established methods to assign sequence reads to microbial species, with and without taking taxonomic information into account.
Infrastructure for Data Processing in Large-Scale Interconnected Sensor Networks (2007)

With the price of wireless sensor technologies diminishing rapidly we can expect large numbers of autonomous sensor networks being deployed in the near future. These sensor networks will typically not remain isolated but the need of interconnecting them on the network level to enable integrated data processing will arise, thus realizing the vision of a global "sensor Internet." This requires a flexible middleware layer which abstracts from the underlying, heterogeneous sensor network technologies and supports fast and simple deployment and addition of new platforms, facilitates efficient distributed query processing and combination of sensor data, provides support for sensor mobility, and enables the dynamic adaption of the system configuration during runtime with minimal (zero-programming) effort. This paper describes the global sensor networks (GSN) middleware which addresses these goals. We present GSN's conceptual model, abstractions, and architecture, and demonstrate the efficiency of the implementation through experiments with typical high-load application profiles. The GSN implementation is available from http://gsn.sourceforge.net/.
Φ-Sensitivity for LTGC Engines: Understanding the Fundamentals and Tailoring Fuel Blends to Maximize This Property (2019)

<div class="section abstract"><div class="htmlview paragraph">Φ-sensitivity is a fuel characteristic that has important benefits for the operation and control of low-temperature gasoline combustion (LTGC) engines. A fuel is φ-sensitive if its autoignition reactivity varies with the fuel/air equivalence ratio (φ). Thus, multiple-injection strategies can be used to create a φ-distribution that leads to several benefits. First, the φ-distribution causes a sequential autoignition that reduces the maximum heat release rate. This allows higher loads without knock and/or advanced combustion timing for higher efficiencies. Second, combustion phasing can be controlled by adjusting the fuel-injection strategy. Finally, experiments show that intermediate-temperature heat release (ITHR) increases with φ-sensitivity, increasing the allowable combustion retard and improving stability.</div><div class="htmlview paragraph">A detailed mechanism was applied using CHEMKIN to understand the chemistry responsible for φ-sensitivity. For fuels with NTC behavior, φ-sensitivity is greatest in the NTC region due to enhanced ITHR reactions, which explains the experimental correlation between φ-sensitivity and ITHR. Under engine conditions, higher intake pressure means lower intake temperature to balance the reactivity, and both effects increase the φ-sensitivity. However, φ-sensitivity remains almost constant if decreased oxygen concentration is used to control the reactivity increase with intake-pressure boost because pressure and oxygen have opposite effects. Finally, for fuels without an NTC region, φ-sensitivity is lower and almost constant as operating conditions vary.</div><div class="htmlview paragraph">The potential of designing fuel blends that increase the φ-sensitivity compared to RD5-87 (regular E10 gasoline), while maintaining high RON and octane-sensitivity, was investigated. Higher φ-sensitivity and higher RON than RD5-87 can be reached with a 5-component blend that meets U.S. regulations. The fuel mixture is composed of a combination of 1-hexene, n-pentane, iso-octane, p-xylene and iso-butanol (which was recently approved for gasoline in the U.S.). This study shows that it is possible to have both high φ-sensitivity and high RON with high octane-sensitivity.</div></div>
Hemin inhibits ubiquitin-dependent proteolysis in both a higher plant and yeast (1988)

In eukaryotes, a major route for ATP-dependent protein breakdown proceeds through covalent intermediates of target proteins destined for degradation and the highly conserved, 76 amino acid protein ubiquitin. In rabbit reticulocytes, it has been shown that hemin effectively inhibits this pathway by blocking the catabolism of ubiquitin-protein conjugates [KI = 25 microM (Haas, A. L., & Rose, I. A. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 6845-6848)]. Here, we demonstrate that hemin is also an effective inhibitor of the ubiquitin-dependent proteolytic pathway in both a higher plant, oats (Avena sativa), and yeast (Saccharomyces cerevisiae). Hemin inhibits all stages of the pathway in vitro, including ATP-dependent formation of ubiquitin-protein conjugates, disassembly of conjugates by ubiquitin-protein lyase(s) (or isopeptidases), and degradation of ubiquitin-protein conjugates by ATP-dependent protease(s). Using ubiquitin-125I-lysozyme conjugates synthesized in vitro as substrates, we determined the specific effects of hemin on the rates of disassembly and degradation separately. The concentration of hemin required for half-maximal inhibition of both processes was identical in each species, approximately 60 microM in oats and approximately 50 microM in yeast. Similar inhibitory effects were observed when two hemin analogues, mesoheme or protoporphyrin IX, were employed. These results demonstrate that the effect of hemin on ubiquitin-dependent proteolysis is not restricted to erythroid cells and as a result hemin may be a useful tool in studies of this pathway in all eukaryotic cells. These results also question models where hemin serves as a specific negative modulator of proteolysis in erythroid cells.
Improved Performance of Bayesian Solutions for Inverse Electrocardiography Using Multiple Information Sources (2006)

The usual goal in inverse electrocardiography (ECG) is to reconstruct cardiac electrical sources from body surface potentials and a mathematical model that relates the sources to the measurements. Due to attenuation and smoothing that occurs in the thorax, the inverse ECG problem is ill-posed and imposition of a priori constraints is needed to combat this ill-posedness. When the problem is posed in terms of reconstructing heart surface potentials, solutions have not yet achieved clinical utility; limitations include the limited availability of good a priori information about the solution and the lack of a "good" error metric. We describe an approach that combines body surface measurements and standard forward models with two additional information sources: statistical prior information about epicardial potential distributions and sparse simultaneous measurements of epicardial potentials made with multielectrode coronary venous catheters. We employ a Bayesian methodology which offers a general way to incorporate these information sources and additionally provides statistical performance analysis tools. In a simulation study, we first compare solutions using one or more of these information sources. Then, we study the effects of varying the number of sparse epicardial potential measurements on reconstruction accuracy. To evaluate accuracy, we used the Bayesian error covariance as well as traditional error metrics such as relative error. Our results show that including even sparsely sampled information from coronary venous catheters can substantially improve the reconstruction of epicardial potential distributions and that a Bayesian framework provides a feasible approach to using this information. Moreover, computing the Bayesian error standard deviations offers a means to indicate confidence in the results even in the absence of validation data.