gebhart/patrepeval huggingface dataset:
Heterodimeric molecules including nucleic acid bases and 9-aminoacridine. Spectroscopic studies, conformations, and interactions with DNA (1988)

Heterodimeric molecules have been examined in which the 9-amino-6-chloro-2-methoxyacridine ring is linked to the nucleic acid bases adenine, thymine, and guanine by polymethylenic chains (CH2)n of varying length (n = 3, 5, 6). A detailed analysis has been performed, including hypochromism measurement in the UV, chemical shift variations in Fourier transform proton magnetic resonance, and fluorescence emission. All these techniques show that all molecules exist mainly under folded conformations in water in the temperature range 0-90 degrees C, with the acridine and the base rings being stacked one on top of the other. The thermodynamic parameters for the folded in equilibrium unfolded conformational equilibrium were estimated. The geometry of the intramolecular complexes could be determined. (1) All these data give information on the strength and nature of the base-acridine interactions as a function of different parameters such as solvent, temperature, etc. (2) The molecules under study constitute "spectroscopic models" for the drug-base complexes as they occur in DNA. In particular, we show the dramatic influence of the relative orientations of the two stacked chromophores in the complex upon the magnitude of % H, the percent hypochromism. The quenching and enhancement of acridine fluorescence emission induced respectively by guanine and adenine is evidenced and quantitatively estimated. (3) These base-acridine heterodimers bind to DNA to an extent that is inversely proportional to their degree of intramolecular stacking.
Identification of fibroblast growth factor receptor 3 mutations in urine sediment DNA samples complements cytology in bladder tumor detection (2003)

Combining FGFR3 mutation results with cytology in both groups correctly identified tumor presence in 105 of 122 (86%) of patients. The greater sensitivity of FGFR3 mutation detection over cytology in identifying the presence of low-grade, superficial bladder tumors represents a potential new tool to complement standard cytology in screening patients for bladder tumors and recurrent disease.
A Thermally Switchable Latent Ruthenium Olefin Metathesis Catalyst (2008)

The synthesis and characterization of a cis-dichloro sulfur chelated olefin metathesis catalyst is presented. The catalyst was extremely stable at room temperature in solution under ambient conditions and was shown to exhibit a thermo-switchable behavior for ring-closing olefin metathesis of diethyl diallylmalonate, being active at 80 °C and inactive at room temperature.
Phorbol esters and neurotransmitter release: more than just protein kinase C? (2003)

This review focuses on the effects of phorbol esters and the role of phorbol ester receptors in the secretion of neurotransmitter substances. We begin with a brief background on the historical use of phorbol esters as tools to decipher the role of the enzyme protein kinase C in signal transduction cascades. Next, we illustrate the structural differences between active and inactive phorbol esters and the mechanism by which the binding of phorbol to its recognition sites (C1 domains) on a particular protein acts to translocate that protein to the membrane. We then discuss the evidence that the most important nerve terminal receptor for phorbol esters (and their endogenous counterpart diacylglycerol) is likely to be Munc13. Indeed, Munc13 and its invertebrate homologues are the main players in priming the secretory apparatus for its critical function in the exocytosis process.
Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies (2020)

The beginning of 2020 has seen the emergence of COVID-19 outbreak caused by a novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). There is an imminent need to better understand this new virus and to develop ways to control its spread. In this study, we sought to gain insights for vaccine design against SARS-CoV-2 by considering the high genetic similarity between SARS-CoV-2 and SARS-CoV, which caused the outbreak in 2003, and leveraging existing immunological studies of SARS-CoV. By screening the experimentally-determined SARS-CoV-derived B cell and T cell epitopes in the immunogenic structural proteins of SARS-CoV, we identified a set of B cell and T cell epitopes derived from the spike (S) and nucleocapsid (N) proteins that map identically to SARS-CoV-2 proteins. As no mutation has been observed in these identified epitopes among the 120 available SARS-CoV-2 sequences (as of 21 February 2020), immune targeting of these epitopes may potentially offer protection against this novel virus. For the T cell epitopes, we performed a population coverage analysis of the associated MHC alleles and proposed a set of epitopes that is estimated to provide broad coverage globally, as well as in China. Our findings provide a screened set of epitopes that can help guide experimental efforts towards the development of vaccines against SARS-CoV-2.
Parallel In Situ Screening of Remediation Strategies for Improved Decision Making, Remedial Design, and Cost Savings (2013)

Abstract : This report summarizes the development and demonstration of a new tool for remedial design, the in situ microcosm array (ISMA). It may serve potential end users as a general guide on how to utilize the ISMA technology in the design and interpretation of in situ feasibility studies. Before in situ remediation can be implemented at a hazardous waste site, bench-scale or fieldscale feasibility studies are required. These are typically conducted in static batch-bottle microcosms, while an alternative approach, continuous-flow column studies, are rare in the remediation industry. Although scientifically constituting the gold standard approach to studying transport and reaction phenomena in saturated media, column studies are avoided due to a combination of factors including: considerable costs; complexity and difficulty in performing multiple replicates; and the requirement of considerable operator time. Although batch bottle tests may be adequate for qualitative screening of remedial design options, they are generally considered to have poor quantitative predictive power. In contrast, column studies are expected to produce both reliable qualitative and quantitative data, as they create a more realistic reflection of subsurface realities and the associated difficulty of delivering the remedial agent to where the contaminants of concern reside. On the small-scale, the ISMA technology answers this challenge by creating a platform for standardized flow-through sediment column experiments, and thus makes the more sophisticated continuous-flow evaluation method more accessible to the Department of Defense and to the environmental restoration industry.
Autologous Chondrocyte Implantation Using a Bilayer Collagen Membrane: A Preliminary Report (2003)

Matrix-induced autologous chondrocyte implantation offers several advantages with respect to the traditional cultured cell procedure. These include technical simplicity, short operating time, minimal invasiveness, and easier access to difficult sites. It appears to be a reliable method for the repair of deep cartilage defects.
Homologous DNA Pairing Promoted by a 20-Amino Acid Peptide Derived from RecA (1996)

The molecular structure of the Escherichia coli RecA protein in the absence of DNA revealed two disordered or mobile loops that were proposed to be DNA binding sites. A short peptide spanning one of these loops was shown to carry out the key reaction mediated by the whole RecA protein: pairing (targeting) of a single-stranded DNA to its homologous site on a duplex DNA. In the course of the reaction the peptide bound to both substrate DNAs, unstacked the single-stranded DNA, and assumed a beta structure. These events probably recapitulate the underlying molecular pathway or mechanism used by homologous recombination proteins.
Colonic Health: Fermentation and Short Chain Fatty Acids (2006)

Interest has been recently rekindled in short chain fatty acids (SCFAs) with the emergence of prebiotics and probiotics aimed at improving colonic and systemic health. Dietary carbohydrates, specifically resistant starches and dietary fiber, are substrates for fermentation that produce SCFAs, primarily acetate, propionate, and butyrate, as end products. The rate and amount of SCFA production depends on the species and amounts of microflora present in the colon, the substrate source and gut transit time. SCFAs are readily absorbed. Butyrate is the major energy source for colonocytes. Propionate is largely taken up by the liver. Acetate enters the peripheral circulation to be metabolized by peripheral tissues. Specific SCFA may reduce the risk of developing gastrointestinal disorders, cancer, and cardiovascular disease. Acetate is the principal SCFA in the colon, and after absorption it has been shown to increase cholesterol synthesis. However, propionate, a gluconeogenerator, has been shown to inhibit cholesterol synthesis. Therefore, substrates that can decrease the acetate: propionate ratio may reduce serum lipids and possibly cardiovascular disease risk. Butyrate has been studied for its role in nourishing the colonic mucosa and in the prevention of cancer of the colon, by promoting cell differentiation, cell-cycle arrest and apoptosis of transformed colonocytes; inhibiting the enzyme histone deacetylase and decreasing the transformation of primary to secondary bile acids as a result of colonic acidification. Therefore, a greater increase in SCFA production and potentially a greater delivery of SCFA, specifically butyrate, to the distal colon may result in a protective effect. Butyrate irrigation (enema) has also been suggested in the treatment of colitis. More human studies are now needed, especially, given the diverse nature of carbohydrate substrates and the SCFA patterns resulting from their fermentation. Short-term and long-term human studies are particularly required on SCFAs in relation to markers of cancer risk. These studies will be key to the success of dietary recommendations to maximize colonic disease prevention.
Practical quantitative biomedical applications of MALDI-TOF mass spectrometry (2002)

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS) is used to obtain fast and accurate determinations of molecular mass, but quantitative determinations are generally made by other techniques. In this study we illustrate the practical utility of automated MALDI-TOFMS as a tool for quantifying a diverse array of biomolecules covering an extensive molecular weight range, and present in biological extracts and fluids. Growth hormone was measured in rat pituitary tissue; insulin in human pancreatic tissue; homovanillic acid in human urine; and LVV-hemorphin-7, epinephrine and norepinephrine in human adrenal and pheochromocytoma tissues. Internal standards including compounds of similar molecular weight, structural analogs or isotopomers were incorporated into each analysis. We report on the current practical limitations of quantitative MALDI-TOFMS and highlight some of the potential benefits of this technique as a quantitative tool.
Site-specific selfish genes as tools for the control and genetic engineering of natural populations (2003)

Site-specific selfish genes exploit host functions to copy themselves into a defined target DNA sequence, and include homing endonuclease genes, group II introns and some LINE-like transposable elements. If such genes can be engineered to target new host sequences, then they can be used to manipulate natural populations, even if the number of individuals released is a small fraction of the entire population. For example, a genetic load sufficient to eradicate a population can be imposed in fewer than 20 generations, if the target is an essential host gene, the knockout is recessive and the selfish gene has an appropriate promoter. There will be selection for resistance, but several strategies are available for reducing the likelihood of it evolving. These genes may also be used to genetically engineer natural populations, by means of population-wide gene knockouts, gene replacements and genetic transformations. By targeting sex-linked loci just prior to meiosis one may skew the population sex ratio, and by changing the promoter one may limit the spread of the gene to neighbouring populations. The proposed constructs are evolutionarily stable in the face of the mutations most likely to arise during their spread, and strategies are also available for reversing the manipulations.
The Effects of UV Irradiation and Gas Plasma Treatment on Living Mammalian Cells and Bacteria: A Comparative Approach (2004)

Living mammalian cells and bacteria were exposed to irradiation from narrow-band UV lamps and treated with a nonthermal gas plasma (plasma needle). The model systems were: Chinese Hamster Ovary (CHO-K1) cells (fibroblasts) and Escherichia Coli bacteria. UV irradiation can lead to cell death (necrosis) in fibroblasts, but the doses that cause such damage are much higher than those needed to destroy Escherichia Coli. The usage of UV radiation in combination with active oxygen radicals lowers the UV dose sufficient to kill the cells. However, in any case the fibroblasts seem to be fairly resistant to UV radiation and/or radicals. Possibly, the lamps may be used for decontamination of infected wounds. The most important active species in an atmospheric plasma are the radicals; the role of UV is less pronounced. Treatment of CHO-K1 cells with the plasma needle can lead to cell necrosis under extreme conditions, but moderate doses cause only a temporary interruption of cell adhesion. Plasma needle may be used for fine tissue treatment (e.g., controlled cell removal without inflammation) and also for bacterial decontamination.
Approximate is Better than “Exact” for Interval Estimation of Binomial Proportions (1998)

Abstract For interval estimation of a proportion, coverage probabilities tend to be too large for “exact” confidence intervals based on inverting the binomial test and too small for the interval based on inverting the Wald large-sample normal test (i.e., sample proportion ± z-score × estimated standard error). Wilson's suggestion of inverting the related score test with null rather than estimated standard error yields coverage probabilities close to nominal confidence levels, even for very small sample sizes. The 95% score interval has similar behavior as the adjusted Wald interval obtained after adding two “successes” and two “failures” to the sample. In elementary courses, with the score and adjusted Wald methods it is unnecessary to provide students with awkward sample size guidelines.
Properties of the amniotic membrane for potential use in tissue engineering (2008)

An important component of tissue engineering (TE) is the supporting matrix upon which cells and tissues grow, also known as the scaffold. Scaffolds must easily integrate with host tissue and provide an excellent environment for cell growth and differentiation. Most scaffold materials are naturally derived from mammalian tissues. The amniotic membrane (AM) is considered an important potential source for scaffolding material. The AM represents the innermost layer of the placenta and is composed of a single epithelial layer, a thick basement membrane and an avascular stroma. The special structure and biological viability of the AM allows it to be an ideal candidate for creating scaffolds used in TE. Epithelial cells derived from the AM have the advantages of stem cells, yet are a more suitable source of cells for TE than stem cells. The extracellular matrix components of the basement membrane of the AM create an almost native scaffold for cell seeding in TE. In addition, the AM has other biological properties important for TE, including anti-inflammatory, anti-microbial, anti-fibrosis, anti-scarring, as well as reasonable mechanical property and low immunogenicity. In this review, the various properties of the AM are discussed in light of their potential use for TE.
Simulation study on transition mechanisms of microstructures during forming processes of amorphous metals (2001)

For the first time, a molecular dynamics simulation study of 50000 atoms has been performed for the transition mechanisms of the microstructure configurations of liquid metal Al during forming processes of amorphous state by rapid cooling. Not only have various bond-types been researched, but also icosahedra, defective icosahedra and Frank-Kasper polyhedra cluster structures were discussed. A very clear picture of how the metal atoms gather to form clusters and how the clusters evolve further has been obtained. Some discussion corresponding to the microscopic mechanisms of the simulation results was also given. These will give an important enlightenment to understand the forming mechanisms and their microscopic processes of amorphous structures.
Application of computerized tomography to radiation therapy and surgical planning (1983)

Computerized tomography (CT) which permits imaging the internal anatomy in axial cross section, has had a major impact in medicine, primarily in the diagnostic area. The CT scans are also useful in determining the extent of disease which is important in selecting the appropriate therapy. For therapy, the CT scan is becoming important in planning a course of radiation therapy for a cancer patient and to a lesser extent, in planning a surgical reconstruction for some patients. For both of these treatment modalities it would be desirable to have a three-dimensional reconstruction of the internal anatomy. This paper discusses the use of a three-dimensional perspective of the internal anatomy, obtained from multiple CT scans, as a guide to these two therapeutic modalities.
CAPTCHA for Blind People (2007)

Nowadays the Internet users are from different ages and groups. The disabled people also use the Internet. Some websites are especially created for disabled people. Many Internet sites offers services for human users, but unfortunately some computer programs are designed which abuse these services. As a result some systems named CAPTCHA (Completely Automated Public Turing test to tell Computers and Human Apart) have been introduced to tell apart human users and computer software. In this paper, a new CAPTCHA method is introduced which can be used by blind people. In this method a simple mathematical problem is created according to predefined patterns and converted to speech using a Text-To-Speech (TTS) system. Then the sound is played for the user and he/she must enter the answer of the question. Because answering this problem requires recognizing the speech, understanding the problem, and solving the problem, only a human user can answer this question and present computer programs are unable to solve it. In addition, answering the question is easy for blind people, because the question is consists a number of natural language sentences and the answer is a number, which can be entered easily.
Paenibacillus polymyxaantagonizes oomycete plant pathogensPhytophthora palmivoraandPythium aphanidermatum (2009)

Our experiments highlight the need to take biofilm formation and niche exclusion mechanisms into consideration for biocontrol assays performed under natural conditions.
Pancreatic Beta‐Cell Purification by Altering FAD and NAD(P)H Metabolism (2008)

Isolation of primary beta cells from other cells within in the pancreatic islets is of importance for many fields of islet research. However, up to now, no satisfactory method has been developed that gained high numbers of viable beta cells, without considerable alpha-cell contamination. In this study, we investigated whether rat beta cells can be isolated from nonbeta endocrine cells by manipulating the flavin adenine dinucleotide (FAD) and nicotinamide-adenine dinucleotide phosphate (NAD(P)H) autofluorescence. Beta cells were isolated from dispersed islets by flow cytometry, based on their high FAD and NAD(P)H fluorescence. To improve beta cell yield and purity, the cellular FAD and NAD(P)H contents were altered by preincubation in culture media containing varying amounts of D-glucose and amino acids. Manipulation of the cellular FAD and NAD(P)H fluorescence improves beta cell yield and purity after sorting. This method is also a fast and reliable method to measure beta cell functional viability. A conceivable application is assessing beta cell viability before transplantation.
Comparison of different techniques for detection of Gal-GalNAc, an early marker of colonic neoplasia. (1999)

The tumor marker, D-galactose-beta [1-3]-N-acetyl-D-galactosamine (Gal-GalNAc, also known as T-antigen) can be identified by a very simple galactose oxidase-Schiff's (GOS) reaction either on tissues or on rectal mucus samples from patients with colorectal neoplasms. Gal-GalNAc is expressed in the neoplastic mucosa as well as the remote non-neoplastic mucosa. It is, however, not expressed in colonic mucosa of normal subjects. We studied the expression of Gal-GalNAc by GOS reaction, lectin reactivity and immunocytochemistry in 10 normal, .45 precancerous [5 Crohn's disease, 15 ulcerative colitis (5 without dysplasia and 10 with dysplasia), 25 tubular adenomas], and 25 adenocarcinoma cases. Normal mucosa remote from tubular adenoma and adenocarcinoma was also studied. The GOS method was compared with reactivity of the lectin jacalin and immunostaining with antibody to T antigen (Anti-Tag Ab). GOS reaction was negative in all of the 10 normal specimens. Of the 5 Crohn's disease specimens, 2 were positive and 3 negative. In the 5 ulcerative colitis cases without dysplasia, positive reaction was seen in 2 cases and negative in 3. Of the 10 cases of ulcerative colitis with dysplasia, 5 showed positivity in dysplastic areas, and 3 of these were also positive in remote non dysplastic mucosa. Twenty of 25 tubular adenomas yielded a positive reaction in the adenoma, 14 of them showing positivity also in remote mucosa; 3 cases showed a positive reaction only in remote mucosa. Of the 25 adenocarcinomas, 21 showed a positive reaction in the adenocarcinoma as well as the remote mucosa. GOS reaction was intense in well differentiated adenocarcinoma and weak in poorly differentiated adenocarcinoma. Intense reaction was also seen in the intracellular mucus of some aberrant crypts and morphologically normal crypts remote from adenocarcinoma and tubular adenoma. GOS reaction showed an overall sensitivity of 75.7% and specificity of 100% for cancer and precancerous lesions. Jacalin reactivity was slightly more sensitive (84.3%) but less specific (80%) and Tag Ab reactivity even less sensitive (50%) but as specific (100%) for neoplastic and dysplastic mucosa. We conclude that the detection of the carbohydrate moiety Gal-GalNAc varies with the technique used. Compared to other techniques, GOS reaction is extremely simple and has a high degree of sensitivity and specificity. It can be used for detection of this tumor marker in remote non-neoplastic mucosa of patients with neoplasia or at risk of developing neoplasia. It, therefore, could be used as a cost effective screening test in rectal biopsy specimens of such patients.