gebhart/patrepeval huggingface dataset:
Engineering enzymes (2010)

Fundamental research into bioinorganic catalysis of the kind presented at this Faraday Discussion has the potential to turn inspiration drawn from impressive natural energy and chemical transformations into artificial catalyst constructions useful to mankind. Creating bio-inspired artificial constructions requires a level of understanding well beyond simple description of structures and mechanisms of natural enzymes. To be useful, such description must be augmented by a practical sense of structural and energetic engineering tolerances of the mechanism. Significant barriers to achieving an engineering understanding of enzyme mechanisms arise from natural protein complexity. In certain cases we can surmount these barriers to understanding, such as natural electron tunneling, coupling of electron tunneling to light capture and proton exchange as well as simpler bond breaking redox catalysis. Hope for similar solutions of more complex bioinorganic enzymes is indicated in several papers presented in this Discussion. Armed with an engineering understanding of mechanism, the current serious frustrations to successful creation of functional artificial proteins that are rooted in protein complexity can fall away. Here we discuss the genetic and biological roots of protein complexity and show how to dodge and minimize the effects of complexity. In the best-understood cases, artificial enzymes can be designed from scratch using the simplest of protein scaffolds.
Effects of nitrogen, oxygen and air on the magnetic properties of sputtered CoCrTa thin film recording discs (1988)

The effects of partial pressures of oxygen, nitrogen and air on sputtered CoCrTa ternary alloys have been studied relative to their microstructure and magnetic properties. The results show that oxygen affects the crystallinity and orientation of Co ternary alloys more severely than nitrogen or air. The effect of air was intermediate between that of O/sub 2/ and N/sub 2/. Introduction of oxygen results in a very large reduction in coercive force of the films. The coercivity reduction due to nitrogen is moderate, and the effect of air is intermediate between the effects of O/sub 2/ and N/sub 2/. However, no significant change in saturation magnetization values are observed due to the introduction of impurity gases.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Room temperature observation of quantum jumps of single molecule into dark states (1996)

Fluctuations in the room temperature emission rate from single dye molecules which are excited with the near field scanning optical microscope reveal long( .... seconds) and short(-milliseconds) lived dark states.
Low- versus high-fidelity simulations in teaching and assessing clinical skills (2015)

Simulation has been widely used in the education of healthcare workers. In simulation training, there is an approximation to reality in which trainees are supposed to react to problems or conditions as they would under genuine circumstances. The educational value of simulations has been determined to be valuable. Simulation has a significant impact on health care education across the disciplines and in both undergraduate and postgraduate studies. Recent development in technologies permits the reproduction of real-life scenarios with acceptable fidelity, thus profoundly enhancing the learning environment. However, the educational outcomes of high- versus low-fidelity simulations remain controversial. This article aims to review the effectiveness of low- and high-fidelity simulations in teaching and assessing clinical skills.
Response of aerobic and hypoxic cells in a solid tumor to adriamycin and cyclophosphamide and interaction of the drugs with radiation. (1982)

I have assessed the relative sensitivity of aerobic and hypoxic cells to Adriamycin (ADR) and cyclophosphamide (CY) in the drug-sensitive murine 16/C tumor. The end point used was tumor response to subsequent radiation given under aerobic or acutely hypoxic conditions. Delay in tumor growth following 15 gray radiation alone to approximately 0.4 g tumors was about 3 days longer after aerobic than after hypoxic radiation. Prior treatment with CY had little effect on this difference, implying little selectivity of CY for killing aerobic or hypoxic cells, and the effects of CY and radiation were additive. Treatment with ADR abolished the difference in response to aerobic and hypoxic radiation given from 0.5 to 2 hr after the drug, suggesting that most of the cells which survived treatment with ADR were hypoxic. Difference in response to aerobic and hypoxic radiation at 6 to 24 hr after ADR was equal to or greater than that in non-drug-treated mice, implying rapid reoxygenation after ADR. Experiments on small, nonpalpable tumors with a low proportion of hypoxic cells showed that ADR was slightly more effective than against larger tumors and that some aerobic cells were spared by the drug when the hypoxic fraction was small. Misonidazole is known to be selectively toxic for hypoxic cells, and a high dose of misonidazole gave a small increase in antitumor effects of ADR without increased toxicity. My results suggest that ADR (but not CY) may spare hypoxic cells in a solid tumor and are consistent with limited diffusion of ADR from tumor blood vessels.
HOXD13 methylation status is a prognostic indicator in breast cancer. (2015)

Homeobox protein Hox-D13 is encoded by HOXD13 gene which is frequently methylated in cancer and has been recognized as a tumor suppressor in pancreatic cancer. In this study, we examined HOXD13 mRNA expression in 40 pairs of breast cancers and corresponding normal breast tissues. Bisulfite sequencing of HOXD13 promoter was performed in 6 pairs of breast tumors and corresponding normal breast tissues to examine the potential HOXD13 CpG methylated sites. HOXD13 DNA methylation frequency analysis was performed using MethyLight in 196 pairs of breast cancers and corresponding normal breast samples. DNA methylation status and clinico-pathological features were investigated. Kaplan-Meier survival analysis and Cox proportional hazards models were utilized to assess the effect of methylation status on overall survival. We found that 60% (24/40) of breast cancers showed low HOXD13 mRNA expression when compared with corresponding normal breast tissue. The predicted CpG island was located in the -1325 bp to +675 bp region. Next, the -332 bp site in HOXD13 gene promoter was further examined and in 57.7% (113/196) samples methylation was detected at this site. HOXD13 methylation was correlated with larger tumor size (P = 0.004), but not with other clinico-pathological parameters. In addition, patients with methylated -HOXD13 promoter had worse overall survival (OS) (P = 0.005). Based on our results we conclude that HOXD13 methylation is a common event in primary breast cancer and is associated with poor survival of breast cancer patients. HOXD13 methylation could therefore potentially be used as a prognostic factor for breast cancer.
Antispasmodic effects of valeriana compounds: an in-vivo and in-vitro study on the guinea-pig ileum. (1982)

The valepotriates isovaltrate and valtrate, and the essential oil compound valeranone caused a suppression of rhythmic contractions in a closed part of the guinea-pig ileum in-vivo. The same compounds and didrovaltrate relaxed potassium stimulated contractures and inhibited BaCl2 contractions in guinea-pig ileum preparations in-vitro. Guinea-pig stomach fundic strips stimulated by carbachol were also relaxed by these substances. Potassium stimulated smooth muscle cells were also relaxed by the valeriana compounds (10(-5)-10(-4) M) even, when autonomic receptors were blocked by appropriate antagonists. In lower concentrations (10(-6)-10(-5) M), the compounds did not affect the dose-response curves of carbachol and isoprenaline. In some experiments valeranone at 4.10(-6) M produced an increased isoprenaline relaxation of the guinea-pig ileum. Valeranone and didrovaltrate were about equipotent to papaverine in inhibiting BaCl2 contractions. It is concluded that the valeriana compounds probably relax stimulated smooth muscle cells by acting as musculotropic agents and not by interacting with receptors of the autonomic nervous system.
Incidental Radiographic Discovery of a Screw in a Primary Molar: An Unusual Case Report in a 6 Year Old Child (2013)

Dentists often find foreign bodies in the primary dentition of children who habitually place objects in their mouths. The objects are frequently embedded in exposures that result from carious or traumatic lesions or from endodontic procedures that have been left open for drainage. Such bodies are often detected on routine radiographs and, less frequently, during clinical examination. We report a case of a 6-year-old boy who had inadvertently embedded a screw in his mandibular right first primary molar and had forgotten about it until it became symptomatic. The screw was impacted in the exposed pulp chamber due to a large carious lesion in the affected molar. This case report considers the possible medical and dental consequences of placing foreign bodies in the mouth.
STUDIES IN RESPIRATORY PHYSIOLOGY. SECOND SERIES. CHEMISTRY, MECHANICS, AND CIRCULATION OF THE LUNG (1955)

Abstract : The scientific papers compiled in this report on the various aspects of external respiration have been divided into the following groups: Pressure Breathing, Mechanics of Breathing, Pulmonary Circulation, Changes with Acclimatization, Gas Stores of the Body, Alveolar Gas, Alveolar-Arterial Oxygen Difference, Ventilation, Behavior of Gas in Closed Body Cavities. Summary of each of these divisions is found in the section entitled, A Brief Summary of Investigations.
Effect of Heat on Egg White Proteins (2012)

Thermal treatments applied to the egg white cause undesirable modifications of their physicochemical and functional properties. The goal of this study was to acquire some knowledge on the effect of heat on some physico-chemical properties of the albumen while applying different scales (temperature / time). The results show: a sigmoidale evolution with negative slope of the transmittance, an irreversible loss of solubility. Native-Page of protein’s albumen shows the apparition of several bands what denotes diversity of proteins in egg white. The comparison of these profiles dealt to different temperatures /20 min with those unprocessed, shows apparition of new bands and different relative mobility due to the formation of aggregates. Coagulation and/or precipitation of these proteins have been observed around 74°C/20 min.
High-level expression of recombinant protein A in Escherichia coli. (1992)

A high-level expression plasmid pPA-3 was constructed, which yielded up to 20% of soluble cell proteins as recombinant Protein A in E. coli DH5 alpha strain by heat shock induction. The recombinant Protein A contained only the five domains of native Protein A that bind with the Fc part of IgG. The molecular weights of the recombinant Protein A expressed in E. coli were determined to be 33kDa, 32.2kDa, 29.5kDa and 28.6kDa by SDS-PAGE and Western-blotting. The diversity of the molecular weights may be due to proteolysis, and a possible cleavage site is proposed. Some of the protein was purified with coupled human IgG by one-step affinity chromatography. The reactivity of the protein was compared with that of native Protein A and found that this protein could bind with more IgG than native Protein A in equal quantities of proteins.
Rat messenger RNA for the retinal pigment epithelium‐specific protein RPE65 gradually accumulates in two weeks from late embryonic days<sup>1</sup> (1998)

The RPE65 protein appears late during the retinal development. To study the basis for this regulation, the rat RPE65 cDNA was sequenced and the mRNA subsequently quantitated at various stages by competitive RT-PCR. RPE65 mRNA was detected as early as E18 (36 copies/ng of whole eye total RNA). It gradually accumulates up to P12 (27000 copies/ng) at which point it reaches a steady state level. This increase is interrupted for 3 days (P2-P4) during which the levels of mRNA remain stable. This timing and rate of accumulation parallels that of rat and mouse opsin mRNA and suggests that common factors may control the activation of genes in photoreceptors and retinal pigment epithelium cells.
The effects of human body shadowing in RF-based indoor localization (2014)

In radio frequency based indoor human localization systems with body mounted sensors, the human body can cause non-line-of-sight (NLOS) effects which might result in severe range estimation and localization errors. However, previous studies on the impact of the human body only conducted static experiments in controlled environments. We confirm known effects and conduct real-world experiments in a typical indoor human tracking scenario using 2.4 GHz time of flight (TOF) range measurements. We analyze the effect on the raw measurements and on the localization results using the localization algorithms Centroid, NLLS, MD-Min-Max, and Geo-n. The experiment design is focused on incident management, where an infrastructure might only be installed in front of the building. We show that these effects have considerable impact on the localization accuracy of the person.
Secretion of Active Recombinant Phytase from Soybean Cell-Suspension Cultures (1997)

Phytase, an enzyme that degrades the phosphorus storage compound phytate, has the potential to enhance phosphorus availability in animal diets when engineered into soybean (Glycine max) seeds. The phytase gene from Aspergillus niger was inserted into soybean transformation plasmids under control of constitutive and seed-specific promoters, with and without a plant signal sequence. Suspension cultures were used to confirm phytase expression in soybean cells. Phytase mRNA was observed in cultures containing constitutively expressed constructs. Phytase activity was detected in the culture medium from transformants that received constructs containing the plant signal sequence, confirming expectations that the protein would follow the default secretory pathway. Secretion also facilitated characterization of the biochemical properties of recombinant phytase. Soybean-synthesized phytase had a lower molecular mass than did the fungal enzyme. However, deglycosylation of the recombinant and fungal phytase yielded polypeptides of identical molecular mass (49 kD). Temperature and pH optima of the recombinant phytase were indistinguishable from the commercially available fungal phytase. Thermal inactivation studies of the recombinant phytase suggested that the additional protein stability would be required to withstand the elevated temperatures involved in soybean processing.
Rounding techniques for signed binary arithmetic (2002)

This paper is concerned with the derivation of the relationship that exists between the number truncation in two's complement (TC) arithmetic and the corresponding truncation in signed-binary (SB) arithmetic. The resulting relationship is subsequently exploited and applied to the development of a pair of novel techniques for SB rounding. These techniques are then translated into algorithms suitable for two-level logic implementation. Finally, the resulting algorithms are applied to the design and implementation of a high-speed SB-kernel based TC multiply-accumulate arithmetic architecture.
Effects of Calcium Supplementation on Cardiovascular Disease in Postmenopausal Women (2011)

The following is an excerpt from the introduction of the article: In the United States, 53% of the population use dietary supplements. Of the people using supplements, 43% use calcium and 37% use vitamin D. However, 63% of women older than 60 years of age reported using dietary supplements (Park et al., 2009). Calcium supplementation, without co-administered vitamin D, increases the risk of myocardial infarction and cardiovascularrelated diseases among postmenopausal women. On the contrary, calcium supplementation with accompanied vitamin D may not produce similar effects.
Recommender system for contextual advertising in IPTV scenarios (2010)

This paper presents a recommender system for contextual targeted advertisement in Video-on-demand scenarios. The proposal arises from a real case of a Japanese company planning to add advertisement to its On-Demand IPTV services. The advertisements consist of icon or text-based links that may be shown before, during or after the playing of the film the customer has selected to watch. The goal of the company is to maximize the number of times customers follow the links to advertised sites because its revenues depends on this. Since only a small portion of the advertising links can be included in a movie, these must be selected carefully. This work proposes a recommender system for selecting the most appropriate advertisement for a certain customer based on the success the advertisement has had in the past among other customers having similar preferences. The paper describes the proposed method, shows the implementation work done so far and describes the remaining work in order to test it in the real scenario.
Clostridium perfringens BETA2 TOXIN: A POTENTIAL ACCESSORY TOXIN IN GASTROINTESTINAL DISEASES OF HUMANS AND DOMESTIC ANIMALS (2006)

Clostridium perfringens is a Gram-positive, anaerobic, spore-forming, rod-shaped bacterium that causes histotoxic infections and enterotoxaemias in humans and domestic animals. This bacterium owes its pathogenicity to the production of a large arsenal of toxins, including the C. perfringens enterotoxin (CPE) and beta2 toxin (CPB2). Type A, cpe-chromosomal isolates cause human food-poisoning (FP), whereas type A, cpe-plasmid isolates cause human antibiotic associated diarrhea (AAD). Symptoms of AAD are more severe and longer in duration than symptoms of FP. We hypothesized that AAD isolates may produce an accessory toxin, which would contribute to pathogenesis, as an explanation for these symptomatic differences. Consequently, the goal of this dissertation was to determine; 1) whether the recently discovered, plasmid-encoded, CPB2 toxin was produced by AAD isolates, 2) how this toxin functions in vitro, and 3) its role in vivo (in the context of human and animal disease). PCR analysis, pulsed-field gel electrophoresis/Southern blotting, and DNA sequencing determined that the cpb2 gene is preferentially associated with AAD isolates (but not FP isolates), in part, due to its presence on some cpe-encoding plasmids. Sequencing of cpe and cpe/cpb2 plasmids found a large region of plasmid DNA, encoding a conjugal-gene cluster, which appears conserved amongst most C. perfringens virulence plasmids. Subsequent sequencing of a number of cpb2 genes identified two CPB2 variants, both of which are produced (detected using Western blot). Neutral red cytotoxicity assays using purified CPB2 demonstrated that CPB2h1 is more cytotoxic for Caco-2 cells than CPB2h2 and this activity is heat labile. Further in vitro work (using 86Rubidium release assays and osmotic stabilizers) suggested that CPB2 acts by disrupting membrane permeability. In vivo experiments confirmed that our CPB2 preparations also were lethal using a mouse intravenous injection model. However, efforts to develop a more realistic model of pathogenesis (which initiates in the intestines) should be continued to furtheranalyze the role of CPB2 in pathogenesis. Ultimately, the production of CPB2 by most AAD isolates, as opposed to FP isolates, could provide an explanation for the more severe symptoms associated with AAD cases and suggests that CPB2 may be involved in human gastrointestinal disease.
An endogenous A<sub>2B</sub> adenosine receptor coupled to cyclic AMP generation in human embryonic kidney (HEK 293) cells (1997)

1. Cyclic AMP generation by adenosine analogues was examined in human embryonic kidney (HEK 293) cells by use of a [3H]-adenine pre-labelling methodology. 2. Adenosine analogues showed the following rank order of potency (pD2 value): 5'-N-ethylcarboxamidoadenosine (NECA, 5.24)>2-chloroadenosine (4.41) > or = adenosine (4.19)= N6-(2-(4-aminophenyl)-ethylamino)adenosine (APNEA, 4.11). The A2A-selective agonist CGS21680 failed to elicit a significant stimulation of cyclic AMP generation at concentrations below 30 microM. 3. Of these agents, NECA was observed to exhibit the greatest intrinsic activity, while in comparison maximal responses to adenosine (76+/-8% NECA response), 2-chloroadenosine (70+/-6%) and APNEA (40+/-3%) were significantly reduced. 4. Antagonists of the NECA-evoked cyclic AMP generation showed the rank order of apparent affinity (apparent pA2 value): CGS 15943 (7.79)=XAC (7.74)>DPCPX (7.01)=PD115199 (6.93) 8FB-PTP (6.80)>KF 17837 (5.98)>3-propylxanthine (5.13). 5. Agarose gel electrophoresis of the products of the polymerase chain reaction, with cDNA generated from HEK 293 cell total RNA showed virtually identical patterns and nucleotide sizes in comparison with the vector for the full length human brain A2B adenosine receptor. 6. We concluded that HEK 293 cells express an endogenous adenosine receptor coupled to cyclic AMP generation which is of the A2B subtype.
Fluorescence Ratiometry and Fluorescence Lifetime Imaging: Using a Single Molecular Sensor for Dual Mode Imaging of Cellular Viscosity (2011)

Intracellular viscosity strongly influences transportation of mass and signal, interactions between the biomacromolecules, and diffusion of reactive metabolites in live cells. Fluorescent molecular rotors are recently developed reagents used to determine the viscosity in solutions or biological fluid. Due to the complexity of live cells, it is important to carry out the viscosity determinations in multimode for high reliability and accuracy. The first molecular rotor (RY3) capable of dual mode fluorescence imaging (ratiometry imaging and fluorescence lifetime imaging) of intracellular viscosity is reported. RY3 is a pentamethine cyanine dye substituted at the central (meso-) position with an aldehyde group (CHO). In nonviscous media, rotation of the CHO group gives rise to internal conversion by a nonradiative process. The restraining of rotation in viscous or low-temperature media results in strong fluorescence (6-fold increase) and lengthens the fluorescence lifetime (from 200 to 1450 ps). The specially designed molecular sensor has two absorption maxima (λ(abs) 400 and 613 nm in ethanol) and two emission maxima (in blue, λ(em) 456 nm and red, 650 nm in ethanol). However it is only the red emission which is markedly sensitive to viscosity or temperature changes, providing a ratiometric response (12-fold) as well as a large pseudo-Stokes shift (250 nm). A mechanism is proposed, based on quantum chemical calculations and (1)H NMR spectra at low-temperature. Inside cells the viscosity changes, showing some regional differences, can be clearly observed by both ratiometry imaging and fluorescence lifetime imaging (FLIM). Although living cells are complex the correlation observed between the two imaging procedures offers the possibility of previously unavailable reliability and accuracy when determining intracellular viscosity.
Targeted photoporation and transfection in human HepG2 cells by a fiber femtosecond laser at 1554 nm (2008)

We report the transfection of human hepatocarcinoma (HepG2) cells by femtosecond (fs) laser pulses at 1554 nm. It was found that HepG2 cells could be perforated transiently to admit propidium iodide by that laser. This photoporation was safe, as the membrane resealed itself within a short time and no mitochondrial depolarization was detected. The cells were next photoporated in the presence of DNA plasmids for the expression of green fluorescence protein, and about 80% of the exposed cells showed green fluorescence 24 h later. Thus it could be concluded that it is safe and efficient to use fs laser at 1554 nm to transfect foreign molecules into cells under a standard microscope.