gebhart/patrepeval huggingface dataset:
High-Temperature Fluorescent In Situ Hybridization for Detecting <i>Escherichia coli</i> in Seawater Samples, Using rRNA-Targeted Oligonucleotide Probes and Flow Cytometry (2005)

Fluorescence in situ hybridization (FISH) is a widely used method to detect environmental microorganisms. The standard protocol is typically conducted at a temperature of 46 degrees C and a hybridization time of 2 or 3 h, using the fluorescence signal intensity as the sole parameter to evaluate the performance of FISH. This paper reports our results for optimizing the conditions of FISH using rRNA-targeted oligonucleotide probes and flow cytometry and the application of these protocols to the detection of Escherichia coli in seawater spiked with E.coli culture. We obtained two types of optimized protocols for FISH, which showed rapid results with a hybridization time of less than 30 min, with performance equivalent to or better than the standard protocol in terms of the fluorescence signal intensity and the FISH hybridization efficiency (i.e., the percentage of hybridized cells giving satisfactory fluorescence intensity): (i) one-step FISH (hybridization is conducted at 60 to 75 degrees C for 30 min) and (ii) two-step FISH (pretreatment in a 90 degrees C water bath for 5 min and a hybridizing step at 50 to 55 degrees C for 15 to 20 min). We also found that satisfactory fluorescence signal intensity does not necessarily guarantee satisfactory hybridization efficiency and the tightness of the targeted population when analyzed with a flow cytometer. We subsequently successfully applied the optimized protocols to E. coli-spiked seawater samples, i.e., obtained flow cytometric signatures where the E. coli population was well separated from other particles carrying fluorescence from nonspecific binding to probes or from autofluorescence, and had a good recovery rate of the spiked E. coli cells (90%).
High numerical aperture multicomponent glass fiber (1980)

High-numerical-aperture (N.A. 0.53) multicomponent glass fibers with 20 dB/km optical loss have been obtained. Glass containing BaO is most promising for fabrication of high-N.A. low-loss optical fibers over a wide wavelength region. The BaO-core glass/multicomponent-clad glass fibers show the following notable characteristics: relatively low optical loss in the 0.6-1.3-microm region, small N.A. wavelength dependence, high effective N.A., large bandwidth due to mode coupling, and high coupling efficiency to LED.
Synthetic Studies on Et-743. Assembly of the Pentacyclic Core and a Formal Total Synthesis (2008)

A formal total synthesis of the potent anticancer agent Et-743 is described. The tetrahydroisoquinoline core is stereoselectively constructed using a novel radical cyclization of a glyoxalimine. Further elaboration of this core rapidly accessed the pentacyclic core of Et-743, but a mixture of regiosisomers was obtained in the key Pictet-Spengler ring closure. A known advanced intermediate in the synthesis of Et-743 was intercepted, constituting a formal synthesis of the molecule.
22.3: A 3.4‐inch Reflective Colour Active Matrix Liquid Crystal Display without Polarisers (2002)

Abstract A 3.4″ reflective colour AMLCD was developed using the standard a‐Si:H TFT technology and a vertically aligned dyed cholesteric liquid crystal mixture. Optimised liquid crystal mixture, de‐saturated colour filters and high pixel aperture ratio were achieved in order to demonstrate a high reflectivity with an acceptable contrast ratio in a large viewing cone.
Critical roles of the S3 segment and S3-S4 linker of repeat I in activation of L-type calcium channels. (1994)

Each of the four repeats (or motifs) of voltage-gated ion channels is thought to contain six transmembrane segments (S1-S6). Mutational analyses indicate that S4 functions as a voltage sensor and that the S5, S6, and S5-S6 linker contribute to formation of the ion pore. However, little information exists regarding the functional role(s) of the amino-terminal portion (S1-S3-S4 linker) of the repeats. Here we report that the amino acid composition of the S3 segment of repeat I and the linker connecting S3 and S4 segments of repeat I is critical for the difference in activation kinetics between cardiac and skeletal muscle L-type calcium channels. Mutant dihydropyridine receptors that have the skeletal muscle dihydropyridine receptor sequence in this region activated relatively slowly with the time constant of current activation (tau act) > 5 ms, whereas mutants that have the cardiac counterpart there activated relatively rapidly with tau act < 5 ms. Comparison of these two mutant groups indicates that a total of 11 conservative and 10 nonconservative amino acid changes from skeletal muscle to cardiac dihydropyridine receptor sequence are sufficient to convert activation from slow to fast. These data demonstrate a functional role for this region of voltage-gated ion channels.
Towards evaluating learners' behaviour in a Web-based distance learning environment (2002)

The accessibility of the World Wide Web and the ease of use of the tools to browse the resources on the Web have made this technology extremely popular and the means of choice for distance education. Many sophisticated Web-based learning environments have been developed and are in use around the world. Educators using these environments and tools, however, have very little support to evaluate learners' activities and discriminate between different learner's online behaviours. The authors exploit the existence of Web access logs and advanced data mining techniques to extract useful patterns that can help educators and Web masters evaluate and interpret online course activities in order to assess the learning process, track student actions and measure Web course structure effectiveness.
Characterization and distribution in human tissues of a glycoproteic antigen defined by monoclonal antibody 1BE12 raised against the human breast cancer cell line T47D. (1990)

Spleen cells from inbred Biozzi mice, immunized against the human breast cancer cell line T47D, were fused with murine myeloma SP2O cells to generate monoclonal antibodies. One of these, 1BE12, of IgM isotype, reacted with five of six human breast tumor cell lines, while no binding was detectable with normal lymphocytes, RBC, or fibroblasts. The antigen recognized by monoclonal antibody 1BE12 was localized on the surface of T47D and MCF7 cells and was detected in cell-free supernatants of cultures. The antigen was found also on the surface of milk secretory cells. Immunohistochemical staining of frozen and paraffin-embedded sections of human tissues showed apical polarized reactivity in normal breast glands, while in all breast cancers staining was either cytoplasmic or membranous and heterogeneously distributed. Immunostaining was also observed in some other normal epithelia, including salivary gland, gastroduodenal mucosa, exocrine pancreas, and cervix. The antigen was not detectable in secretory endometrium, whereas proliferative endometrium was strongly stained. Colon carcinoma, and cancers of the bladder and endometrium were strongly reactive. No staining was detected in melanoma, lymphoma, mesothelioma, non-small cell lung carcinoma, and thyroid, renal, and ovarian carcinomas. Lectin absorption of MCF7 membrane extracts reduced 1BE12 binding. A large reduction in 1BE12 reactivity was observed after digestion of T47D and MCF7 membrane extracts with proteases. Treatment with sodium periodate resulted in complete loss of antigenicity, while neuraminidase treatment did not affect 1BE12 binding. These findings suggest that the 1BE12 epitope is expressed on the carbohydrate moiety of a glycoprotein and does not contain sialic acid. Immunoblotting of the perchloric acid-soluble fraction of MCF7 membrane extracts after electrophoresis in 1% agarose detected the antigen as a high molecular weight species (Mr greater than 900,000). The antigen was purified by perchloric acid extraction of MCF7 membrane preparations followed by affinity chromatography on 1BE12 antibody coupled to Sepharose-4B and gel exclusion fast protein liquid chromatography. No reactivity of the purified material was found with monoclonal antibodies directed against human milk fat globule membrane-associated mucins HMFG1 and DF3.
Development of a Scheimpflug slit lamp camera system for quantitative densitometric analysis (1993)

We have developed a computerised video system for accurate quantification of lens opacities from Scheimpflug images. Using a modified Zeiss Scheimpflug camera and Macintosh computer, the system software can warn of improper exposure and can provide immediate results of cataract progression on individual patients. These results are obtained from a novel technique which automatically divides the lens into anatomical regions and computes regional densities in the standard optical density unit. Because of the system's speed, the operator can properly capture and analyse a cataract in seconds, compare results with past patient records and give feedback to the patient on the results of the analysis. The system provides the appropriate data integrity and formats for documenting and monitoring lens opacities. Such a system will be useful in longitudinal studies of cataracts (i.e. for natural history and anti-cataract drug trials).
α‐Caryopteron, ein neues Pyrano‐juglon aus <i>Caryopteris clandonensis</i> (1969)

Abstract Caryopteris clandonsis B UNGE ( Verbenaceae ) enthält in der Wurzelrinde mehrere Farbstoffe, von denen einer, α‐Caryopteron, C 15 H 12 O 4 , kristallisiert und rein erhalten werden konnte. Er wurde als 9‐Hydroxy‐α‐dehydrolapachon (Ia) erkannt, wobei die Lage der Hydroxylgruppe unter Beiziehung der para ‐ ortho ‐Chinonmlagerung nach P ATERNÒ ;‐H OOKER , am Dihydroderivat festgelegt wurde.
Predictive markers in traumatic brain injury: opportunities for a serum biosignature (2013)

The current diagnostic criteria for traumatic brain injury (TBI) are heavily reliant on an accurate clinical history of events. Diagnosis of mild injury relies on one or more of the following: confusion or disorientation, loss of consciousness (LOC) for 30 min or less, post-ictus amnesia for less than 24 h and/or other transient neurological abnormalities and a Glasgow Coma Score (GCS). Given the nature of the condition it is obvious that significant clinical challenges remain to identify in the cases of mild TBI, and additionally to grade more severe forms so that appropriate treatment is received. The lack of clinically useful biomarkers in the serum of TBI patients is a significant barrier to improving their outlook. Discovery of such markers would aid the timely diagnosis of novel and recurrent disease in a minimally invasive manner. A PubMed search was performed to identify studies reporting serum biomarkers in traumatic brain injury. Details regarding the biomarkers analysed, specificity, indications for outcome and statistical significance were recorded. A total of 40 manuscripts reporting 11 biomarkers were identified in the literature. All but a few studies reported statistically significant differences in biomarker expression between groups. We conclude that serum biomarkers of TBI are an effective means for investigating the condition. However, the lack of novel markers identified in this mass of studies highlights the need to adopt new measure of biomarker identification.
A local mesh refinement algorithm for the FDFD method using a polygonal grid (1996)

A local mesh refinement algorithm for the finite-difference method in the frequency domain (FDFD) is presented that is based on polygonal grids. It is applied to a simple test structure for which the propagation parameters were computed with a mode-matching method as a reference. It is shown that the local mesh refinement realized with this polygonal grid significantly improves the accuracy of the propagation constant compared to the conventional FD method based on rectangular meshes.
Degradation of cellulose by basidiomycetous fungi (2008)

Cellulose is the main polymeric component of the plant cell wall, the most abundant polysaccharide on Earth, and an important renewable resource. Basidiomycetous fungi belong to its most potent degraders because many species grow on dead wood or litter, in environment rich in cellulose. Fungal cellulolytic systems differ from the complex cellulolytic systems of bacteria. For the degradation of cellulose, basidiomycetes utilize a set of hydrolytic enzymes typically composed of endoglucanase, cellobiohydrolase and beta-glucosidase. In some species, the absence of cellobiohydrolase is substituted by the production of processive endoglucanases combining the properties of both of these enzymes. In addition, systems producing hydroxyl radicals based on cellobiose dehydrogenase, quinone redox cycling or glycopeptide-based Fenton reaction are involved in the degradation of several plant cell wall components, including cellulose. The complete cellulolytic complex used by a single fungal species is typically composed of more than one of the above mechanisms that contribute to the utilization of cellulose as a source of carbon or energy or degrade it to ensure fast substrate colonization. The efficiency and regulation of cellulose degradation differs among wood-rotting, litter-decomposing, mycorrhizal or plant pathogenic fungi and yeasts due to the different roles of cellulose degradation in the physiology and ecology of the individual groups.
Winter bird assemblages, species richness and relative abundance at a re-vegetated coal mine in the Middelburg district, Mpumalanga province, South Africa : research article (2005)

Winter bird assemblages, species richness and relative abundance were investigated at six 
re-vegetated sites within the Middelburg Coal Mine (Mpumalanga, South Africa) and 
compared with those for a site thought to be representative of un-mined biotope within the 
nearby Witbank Nature Reserve. Age of site since initiation of re-vegetation had little or 
no apparent effect on richness or abundance. Adjacency to currently active mining and 
variation in current land management practices appeared to have much more profound 
effects. Sites surrounded by active mining had lower richness and abundance. Those with 
40% or more land left as fallow and strips of un-mowed grass as well as artificial ponds had 
higher bird richness and abundance.
Disturbance attenuation controller design by Markov parameters (2002)

This paper proposes to design a dynamic controller, which minimizes a class of conflicting quadratic performance indices, by using only the unit-pulse response of the plant. The method does not employ any parametric models such as transfer functions or state-space equations and, hence, shows how to design a controller directly from the input-output data of the plant. We begin by showing how to estimate the unit-pulse response of the system and the statistical data of the noise from the measured unit-pulse responses corrupted by system and measurement noises. With these informations, we design a conflicting-objective compensator which minimizes a given quadratic cost function. A numerical result that helps validate the efficiency of the method is also included.
Disk drive spindle motors and their controls (1996)

Disk drives require very high-precision spindle motors for fast and accurate access of data. As storage capacity and access rate increase, more demands are being made of spindle motors with respect to both electrical and mechanical performances. For error-free operations, spindle motors are required to comply with a host of requirements, such as run-outs, both axial and radial, acoustics, mechanical vibrations, electromagnetic interference, contamination, etc. Compliance to these requirements necessitate careful and novel design techniques and highly sophisticated manufacturing processes. This paper discusses various requirements and specific design issues (electromagnetic design, mechanical design, motor control) for the development of spindle motors suitable for different form-factor drives using permanent magnet brushless DC motors.
Charge-Transfer Complexes of Benzothienobenzothiophene with Tetracyanoquinodimethane and the n-Channel Organic Field-Effect Transistors (2017)

n-Channel organic transistors with excellent air stability are realized on the basis of charge-transfer complexes, (BTBT)(TCNQ), (BTBT)(F2TCNQ), (BSBS)(F2TCNQ), and (BTBT)(F4TCNQ), where BTBT is benzothieno[3,2-b]benzothiophene, BSBS is benzoseleno[3,2-b]benzoselenophene, and FnTCNQ (n = 0, 2, and 4) are fluorinated 7,7,8,8-tetracyanoquinodimethanes. These complexes consist of mixed stacks of essentially neutral molecules, and the transistors are air stable even after several-month storage in ambient conditions.
Dynamically crosslinked materials via recognition of amino acids by cucurbit[8]uril (2013)

Hydrogels, an increasingly important class of material, have physical properties amenable to many potential uses, particularly in the biomedical area. Utilisation of hydrogels, however, relies not only on their mechanical properties but also on a favourable toxicity profile. Self assembly of polymers through naturally occurring and non-toxic units is therefore a very attractive option. The aromatic amino acids phenylalanine and tryptophan are two such molecular units that form 2 : 1 complexes with cucurbit[8]uril (CB[8]) with high binding equilibrium constants (K<sub>eq</sub> up to 10<sup>12</sup> M<sup>-2</sup>). Herein, water soluble styrenic monomers were copolymerised with synthetically derived aromatic amino acid monomers of phenylalanine and tryptophan. The resulting polymers were shown to form dynamic and self-healing physically crosslinked hydrogels via recognition and binding of the amino acids to cucurbit[8]uril.
MrkH, a Novel c-di-GMP-Dependent Transcriptional Activator, Controls Klebsiella pneumoniae Biofilm Formation by Regulating Type 3 Fimbriae Expression (2011)

Klebsiella pneumoniae causes significant morbidity and mortality worldwide, particularly amongst hospitalized individuals. The principle mechanism for pathogenesis in hospital environments involves the formation of biofilms, primarily on implanted medical devices. In this study, we constructed a transposon mutant library in a clinical isolate, K. pneumoniae AJ218, to identify the genes and pathways implicated in biofilm formation. Three mutants severely defective in biofilm formation contained insertions within the mrkABCDF genes encoding the main structural subunit and assembly machinery for type 3 fimbriae. Two other mutants carried insertions within the yfiN and mrkJ genes, which encode GGDEF domain- and EAL domain-containing c-di-GMP turnover enzymes, respectively. The remaining two isolates contained insertions that inactivated the mrkH and mrkI genes, which encode for novel proteins with a c-di-GMP-binding PilZ domain and a LuxR-type transcriptional regulator, respectively. Biochemical and functional assays indicated that the effects of these factors on biofilm formation accompany concomitant changes in type 3 fimbriae expression. We mapped the transcriptional start site of mrkA, demonstrated that MrkH directly activates transcription of the mrkA promoter and showed that MrkH binds strongly to the mrkA regulatory region only in the presence of c-di-GMP. Furthermore, a point mutation in the putative c-di-GMP-binding domain of MrkH completely abolished its function as a transcriptional activator. In vivo analysis of the yfiN and mrkJ genes strongly indicated their c-di-GMP-specific function as diguanylate cyclase and phosphodiesterase, respectively. In addition, in vitro assays showed that purified MrkJ protein has strong c-di-GMP phosphodiesterase activity. These results demonstrate for the first time that c-di-GMP can function as an effector to stimulate the activity of a transcriptional activator, and explain how type 3 fimbriae expression is coordinated with other gene expression programs in K. pneumoniae to promote biofilm formation to implanted medical devices.
Vitamin supplement use and risk for oral and esophageal cancer (1992)

In a hospital-based case-control study, 290 oral cancer cases and 133 esophageal cancer cases were queried as to smoking status, alcohol consumption, and dietary exposures, including vitamin supplement history. Among oral cancer cases, vitamin E use appeared to exert a protective effect. Vitamins C and E had protective effects among esophageal cancer cases. When stratified by smoking status, the protective effect of vitamin C use in esophageal cancer was significant only among current smokers, as was vitamin B use. A reduced risk of oral cancer was correlated with multivitamin use and increasing vegetable consumption, as was vegetable/fruit consumption and vitamin C supplementation. Among esophageal cancer cases, increasing meat consumption and vitamin C use were associated with a significantly reduced cancer risk.
STUDY OF ANAEROBIC TOXICITY ASSAY AND CATION INHIBITION FOR CHEESE PROCESSING WASTE (2002)

Cheese processing waste is a complex of miscellaneous liquid wastes from a cheese plant not includingstandard whey, which is often dried and used for food. During treatment of cheese processing waste(soluble COD > 80,000) using an upflow anaerobic sludge blanket (UASB) reactor in our lab, we foundmethane production decreased with time. The concentration (mg/l) of Na+ and K+ in the failing UASBwas about 5,000 and 1,000, respectively because pH was controlled by adding sodium or potassiumhydroxide buffer. We presumed methane decreased because of cheese processing waste toxicity or cationinhibition. This study was undertaken to learn more about the causes of poor performance in the UASB.The anaerobic toxicity assay (ATA) and cation inhibition (CI) assay with two different starters wereperformed on various dilutions of cheese processing waste and cheese processing waste spiked withcations. Through 62 and 33 days runs for the ATA and CI studies, respectively, the following results werefound: (1) Cheese processing waste was not found to be toxic to both starters. (2) Sodium and potassiumdid not significantly inhibit methane production when municipal waste sludge was used as a starter, but itdid significantly inhibit methane production when pig waste sludge was used. In this case, the inhibitionconcentration of sodium and potassium was 4,887 mg/l and 8,301 mg/l, respectively.
Effects of Chassis Currents on Hearing Aids Compatibility in the Handset (2010)

In this paper, we investigate the effects of the chassis wavemodes on the near-field electromagnetic intensities that contribute to hearing aid compatibility (HAC) tests at two different frequencies, 900 and 1880 MHz. For a comprehensive view, we also examine the far-field properties of the antenna total efficiency and bandwidth. Additionally, we examine the specific absorption rate in relation to the chassis wavemodes. The examined parameters are then related to the HAC. It was found that the chassis wavemodes have a significant effect on the antenna near-field performance, especially at the 900-MHz frequency range. We show that the optimum near-field antenna performance is achieved when the antenna resonant frequency is aligned with the chassis resonant frequency. With this, a decrease of about 50% can be achieved in the peak magnetic field intensity and a 30% decrease in the peak electric field intensity; hence, a better possibility in passing the HAC compliance tests. Moreover, controlling the chassis wavemodes has a similar effect to that of increasing the distance from the HAC scan plane—a rapid decrease in the field intensities can be achieved. Our analyses are done through simulations and these are validated against measurements.