gebhart/patrepeval huggingface dataset:
Applications of molecular biology in environmental chemistry (1995)

Mutational Spectra and Other Microbiological Processes Monitoring Microbial Pathogens and Indicator Microorganisms in Water Using the Polymerase Chain Reaction and Gene Probe Methods, R.M. Atlas, A.K. Bej, J.L. DiCesare, L.A. Haff, and S. McCarty Allele-Specific Hybridization and Polymerase Chain Reaction (PCR) in Mutation Analysis: The Salmonella Typhimurium his Paradigm, T.A. Cebula Mutational Spectra of the Four Bay Region Diol Epoxides of Benzo[c]Phenanthrene and the Drinking Water Mutagen, MX, Determined with an Improved Set of E. coli lacZ- Mutants, C. Lu, H. Yagi, D.M. Jerin, and A.M. Cheh Assessment of Gene Expression in the Environment: Quantitative mRNA Analysis in Contaminated Soils, J.T. Fleming and G.S. Sayler Biological and Biochemical Evidence of Strand-Specific Repair of DNA Damage Induced in Human Cells by (+/-)-7b,8a-Dihydroxy-9a,10a-Epoxy-7,8,9,10-Tetrahydrobenzo[a]pyrene,V.M. Maher, R.-H. Chen, and J.J. McCormick Molecular Analysis of Frameshift Mutations Induced by Plant-Activated 2-Aminofluorene, M.J. Plewa, M.J. Timme, D. Cortez, S.R. Smith, and E.D. Wagner Identification of Sulfate-Reducing Bacteria by Hydrogenase Gene Probes and Reverse Sample Genome Probing, G. Voordouw, A.J. Telang, T.R. Jack, J. Foght, P.M. Fedorak, and D.W.S. Westlake The Uses and Abuses of Immunological Testing, D.K. Flaherty Human Cytochromes P-450 and Their Roles in Environmentally Based Disease, F.J. Gonzales Biomonitoring and Bioanalytical Chemistry Important Considerations in the Ultratrace Measurement of Volatile Organic Compounds in Blood, D.L. Ashley, M.A. Bonin, F.L. Cardinali, J.M. McCraw, J.V. Wooten, and L.L. Needham Applications of New HPLC/MS Techniques in Human Biomonitoring, W.M. Draper, F.R. Brown, R.A. Bethem, M.J. Miille, and C.E. Becker Measurement of Reductive Dechlorination of Pentachlorophenol by Actinomyces viscosus Strain dechlorini by GC/MS Techniques, F.O. Bryant and H.G. Cutler A Versatile Bioluminescent Reporter System for Organic Pollutant Bioavailability and Biodegradation, A. Heitzer, O.F. Webb, P.M. DiGrazia, and G.S. Sayler Analytical Method for Biomonitoring of Aniline in Urine and Comparison with the Classical Calorimetric Method, R. Orth, G. Spies, R. Nair, and J.M. Wendling Biological Monitoring of Workers Exposed to Triazine Herbicides: I. Determination of Simazine and Its Metabolites in Urine, J.G. Guillot, A. Leblanc, O. Samuel, and J.P. Weber Biological Monitoring of Workers Exposed to Triazine Herbicides: II. Presentation of a Method for the Determination of Hexazinone and Its Main Metabolites in Urine of Exposed Forestry Workers, A. LeBlanc, O. Samuel, J.G. Guillot, and J.P. Weber
Recombinant immunotoxin against B-cell malignancies with no immunogenicity in mice by removal of B-cell epitopes (2011)

Many nonhuman proteins have useful pharmacological activities, but are infrequently effective in humans because of their high immunogenicity. A recombinant immunotoxin (HA22, CAT8015, moxetumomab pasudotox) composed of an anti-CD22 antibody variable fragment fused to PE38, a 38-kDa portion of Pseudomonas exotoxin A, has produced many complete remissions in drug-resistant hairy-cell leukemia when several cycles of the agent can be given, but has much less activity when antibodies develop. We have pursued a strategy to deimmunize recombinant immunotoxins by identifying and removing B-cell epitopes. We previously reported that we could eliminate most B-cell epitopes using a combination of point mutations and deletions. Here we show the location and amino acid composition of all of the B-cell epitopes in the remaining 25-kDa portion of Pseudomonas exotoxin. Using this information, we eliminated these epitopes to produce an immunotoxin (HA22-LR-8M) that is fully cytotoxic against malignant B-cell lines, has high cytotoxic activity against cells directly isolated from patients with chronic lymphocytic leukemia, and has excellent antitumor activity in mice. HA22-LR-8M does not induce antibody formation in mice when given repeatedly by intravenous injection and does not induce a secondary antibody response when given to mice previously exposed to HA22. HA22-LR-8M also has greatly reduced antigenicity when exposed to sera from patients who have produced antibodies to HA22. The properties of HA22-LR-8M make it an excellent candidate for further clinical development.
Granulocyte Macrophage-Colony Stimulating Factor (GM-CSF) Augments Acute Lung Injury via Its Neutrophil Priming Effects (2008)

Granulocyte macrophage-colony stimulating factor (GM-CSF) has immuno-stimulatory effects. We hypothesized that GM-CSF plays an important role both in lipopolysaccharide (LPS)- and hemorrhage-induced acute lung injury (ALI). We also postulated that GM-CSF augments LPS-induced inflammation by priming neutrophils. ALI was induced in GM-CSF-/- or control C57BL mice either by LPS injection or by hemorrhage. Lung inflammation (by lung expression for tumor necrosis factor-alpha (TNF-alpha), macrophage inflammatory protein-2 (MIP-2), interleukin-1beta (IL-1beta), interleukin- 6 (IL-6), and keratinocyte-derived chemokine) and lung injury (by myeloperoxidase and Evans blue dye assay) were evaluated after ALI. Incremental doses of LPS (0, 1, 10, and 100 ng/mL) and GM-CSF (0, 1, 10, and 100 ng/mL) were added to bone marrow neutrophils. The expression of TNF-alpha, MIP-2, and IL-1beta was evaluated with enzyme linked immunosorbent assay. The mRNA expression of three cytokines, and the nuclear translocation of nuclear factor kappa B (NF kappa-B) were evaluated by reverse transcriptase-polymerase chain reaction and electrophoretic mobility shift assay, respectively. GM-CSF -/- mice showed decreased neutrophil infiltration, less leakage, and lower expression of cytokines in the lung after LPS or hemorrhage. GM-CSF augmented LPS-induced protein and mRNA expression of TNF-alpha, MIP-2 and IL-1beta, which was mediated by increased intra-nuclear translocation of NF-kappaB. GM-CSF plays an important role in high-dose LPS and hemorrhage-induced ALI, which appears to be mediated by its priming effect on neutrophils.
Average membrane penetration depth of tryptophan residues of the nicotinic acetylcholine receptor by the parallax method (1991)

The membrane penetration depths of tryptophan residues in the nicotinic acetylcholine receptor from Torpedo californica have been analyzed in reconstituted membranes containing purified receptor and defined lipids. Dioleoylphosphatidylcholine and three spin-labeled phosphatidylcholines with the nitroxide group at three different positions on the fatty acyl chain were used for reconstitution of the receptor. The spin-labeled phospholipids serve as quenchers of tryptophan fluorescence. Differential quenching of the intrinsic fluorescence of the acetylcholine receptor by the spin-labeled phospholipids has been utilized to analyze the average membrane penetration depth of tryptophans by the parallax method [Chattopadhyay, A., & London, E. (1987) Biochemistry 26, 39-45]. Analyses of the quenching data indicate that the tryptophan residues on the average are at a shallow location (10.1 A from the center of the bilayer) in the membrane. In addition, the generally low levels of quenching imply that the majority of tryptophan residues are located in the putative extramembranous region of the receptor. These results are consistent with several proposed models for the tertiary structure of the acetylcholine receptor and are relevant to ongoing analyses of the overall conformation and orientation of the acetylcholine receptor in the membrane.
Fast detection of a (CA)<sub>18</sub> microsatellite repeat in the IgE receptor gene by capillary electrophoresis with laser‐induced flurescence detection (1998)

The optimum separation conditions of polymerase chain reaction (PCR) products have been found for high-speed capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection. DNA fragments obtained after PCR amplification of the region covering the (CA)18 microsatellite repeat in nitron 5 of the gene for FcERIbeta, a high affinity glycoprotein receptor for IgE, located on chromosome 11 (11q13), were analyzed with the aim of investigating the repeat polymorphism. The results of polyacrylamide slab gel electrophoresis (PAGE), agarose gel electrophoresis, CE with absorbance detector and CE with LIF are compared. The CE with LIF proved to shorten analysis time by a factor of 100 when compared to slab gel electrophoresis. CE-LIF utilizes a short capillary with an effective length of 6.3 cm and electric field strength from 100 to 550 V/cm. The respective PCR products of sizes from 116 to 210 base pairs (bp) were analyzed in 3 min.
Highly Crystalline Films of PCPDTBT with Branched Side Chains by Solvent Vapor Crystallization: Influence on Opto‐Electronic Properties (2014)

PCPDTBT, a marginally crystallizable polymer, is crystallized into a new crystal structure using solvent-vapor annealing. Highly ordered areas with three different polymer-chain orientations are identified using TEM/ED, GIWAXS, and polarized Raman spectroscopy. The optical and structural properties differ significantly from films prepared by standard device preparation protocols. Bilayer solar cells, however, show similar performance.
Genome-wide DNA methylation assay reveals novel candidate biomarker genes in cervical cancer (2013)

The oncogenic human papilloma viruses (HPVs) are associated with precancerous cervical lesions and development of cervical cancer. The DNA methylation signatures of the host genome in normal, precancerous and cervical cancer tissue may indicate tissue-specific perturbation in carcinogenesis. The aim of this study was to identify new candidate genes that are differentially methylated in squamous cell carcinoma compared with DNA samples from cervical intraepithelial neoplasia grade 3 (CIN3) and normal cervical scrapes. The Illumina Infinium HumanMethylation450 BeadChip method identifies genome-wide DNA methylation changes in CpG islands, CpG shores and shelves. Our findings showed an extensive differential methylation signature in cervical cancer compared with the CIN3 or normal cervical tissues. The identified candidate biomarker genes for cervical cancer represent several types of mechanisms in the cellular machinery that are epigenetically deregulated by hypermethylation, such as membrane receptors, intracellular signaling and gene transcription. The results also confirm extensive hypomethylation of genes in the immune system in cancer tissues. These insights into the functional role of DNA methylome alterations in cervical cancer could be clinically applicable in diagnostics and prognostics, and may guide the development of new epigenetic therapies.
Human facial feature extraction for face interpretation and recognition (2003)

This paper presents facial features extraction algorithms which can be used for automated visual interpretation and recognition of human faces. It is possible to capture the contours of eye and mouth by deformable template model because of their analytically describable shapes. However, the shapes of eyebrow, nostril and face are difficult to model using a deformable template. They are extracted by using an active contour model, the snake.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Role of CD36 in the formation of non-alcoholic fatty liver disease in mice (2014)

Objective
To investigate the role of cluster of differentiation (CD) 36 in the formation of non-alcoholic fatty liver disease (NAFLD) in mice.


Methods
Twenty specific pathogen free healthy male C57BL/6J mice [8 weeks old, average weight: (18.8±2.3)g] were randomly divided into NAFLD group and control group according to the random number table method with 10 mice in each group. Mice in NAFLD group was fed with high-fat diet for 10 weeks, while mice in control group was fed with normal diet for 10 weeks. The mice were sacrificed after the processing, and samples of cardiac blood and liver tissue were collected. The levels of serum alanine transaminase (ALT), total cholesterol (TC) and triglyceride (TG), levels of TC and TG in liver tissue, pathological changes of liver tissue, expression of CD36 protein and content of its messenger ribonucleic acid (mRNA) in liver tissue of 2 groups were observed. Experimental data of 2 groups were compared using t test.


Results
The level of serum ALT was (49±6)U/L in NAFLD group and (45±7)U/L in control group, where no significant difference was obsersed (t=1.70, P>0.05). The levels of serum TC and TG were (4.42±0.09), (0.45±0.04)mmol/L in NAFLD group and (2.42±0.05), (0.32±0.03)mmol/L in control group respectively. The levels of serum TC and TG in NAFLD group were significantly higher than those in control group (t=21.90, 8.22; P<0.05). The levels of TC and TG in liver tissue were (1.18±0.09), (1.75±0.08)mmol/L in NAFLD group and (0.55±0.06), (1.28±0.06)mmol/L in control group respectively. The levels of TC and TG in liver tissue in NAFLD group were significantly higher than those in control group (t=18.42, 14.86; P<0.05). Obviously fatty degeneration and ballooning degeneration were observed in hepatocytes of NAFLD group, while hepatocytes were normal in morphology and size in control group. The expression of CD36 protein in liver tissue in NAFLD group was significantly stronger than that in control group. The content of CD36 mRNA in liver tissue was 2.75±0.26 in NAFLD group and 1.00±0.08 in control group. The content of CD36 mRNA in liver tissue in NAFLD group was significantly higher than that in control group (t=21.16, P<0.05).


Conclusions
CD36 may play a role in the formation of NAFLD in mice. To decrease its expression can be a new target for the prophylaxis and treatment of NAFLD.


Key words: 
Fatty liver; Mice; Alanine transaminase; Cholesterol; Triglycerides; Antigens,CD36
Lack of Susceptibility to SARS-CoV-2 and MERS-CoV in Poultry (2020)

We challenged chickens, turkeys, ducks, quail, and geese with severe acute respiratory syndrome coronavirus 2 or Middle East respiratory syndrome coronavirus. We observed no disease and detected no virus replication and no serum antibodies. We concluded that poultry are unlikely to serve a role in maintenance of either virus.
The Effect of Fibrin Glue on Skin Grafts in Infected Sites (1992)

Fibrin bonding of skin grafts to wounds is an essential part of the graft-adherence process. Bacteria, in concentrations greater than 10(5)/gm of tissue, are associated with graft failure. Sixty-five rats were randomly divided into three groups, dorsal split-thickness skin grafts were harvested, and the sites were inoculated with Staphylococcus aureus. After incubation, each wound was quantitatively biopsied and treated with saline, fibrin glue with aprotinin, or fibrin glue alone. We found that the addition of commercially available fibrin glue with or without the antifibrinolytic agent aprotinin is capable of restoring graft adherence to normal levels in graft sites infected with greater than 10(5) bacteria/gm of tissue. Fibrin glue may have potential for increasing skin-graft take in the clinical situation where the graft bed is infected.
Brain studies--image co-registration and template creation. (2001)

Image co-registration requires special software, which is usually available for Unix workstations. This work presents two programs running under MS Windows, one for study co-registration and one for template creation. The co-registration can be done by minimising/maximising the count difference, squared difference, shape and mutual information. The quality of the fit can be estimated by evaluating the contours with different tools. The aligned images can be used for template creation. Both programs can be downloaded from http://www.homolka.cz/nm.
The sugar content and the ph of the smoke of cigarette, cigar and pipe tobaccos in relation to lung cancer (1972)

Abstract The risk of lung cancer is greater in cigarette smokers than in cigar or pipe smokers. In Great Britain, which has a very high lung‐cancer death rate, cigarette tobacco (flue‐cured) has a high sugar content (up to 20%) while cigar tobacco (aircured) has a low sugar content (0.5—2%). Determinations of the sugar content of the tobacco and the pH of the smoke of cigarettes from more than 30 countries, and of a number of cigar and pipe tobaccos, have been carried out. The main differences found between the characteristics of cigarette and cigar and pipe tobaccos are: The high sugar content of the popular brands of cigarettes now smoked in many countries, which results in the production of a smoke of acid pH, becoming progressively more acid during the course of smoking, particularly towards the butt‐end of the cigarette when the tar content of the smoke is at its highest; The low sugar content of cigar tobacco and of the air‐dried tobacco used in the cigarettes of certain countries, which gives a smoke of less acid pH becoming progressively more alkaline during the course of smoking; The conditions of smoking in a pipe whereby the smoke from all types of tobacco, with both high and low sugar content, is less acid than that of most cigarettes, and becomes progressively more alkaline during the course of smoking. Since the satisfaction derived from smoking is mainly due to the pharmacological effects of nicotine, it is suggested that the lower lung cancer incidence in cigar and pipe smokers may be related to the fact that nicotine is more readily absorbed in the form of the free base, at alkaline pH, than in the form of a stable salt, at acid pH. To obtain the same degree of “nicotine satisfaction” as in smoking a pipe or cigar, the smoker of cigarettes giving an acid smoke would tend to smoke more, and to encourage more prolonged and extensive contact of the smoke with the mouth and bronchus, and to take the smoke into his lungs, which would thus suffer greater exposure to the “carcinogenic” effects of the smoke than would be the case with cigar or pipe smokers. In preliminary attempts to devise a “safer” cigarette, the addition of substances which give rise to an alkaline vapour at the usual temperature of combustion of cigarettes has been shown to reverse the character of the smoke of high sugar (fluecured) tobacco cigarettes so that it then resembles that of cigars and pipes in becoming progressively more alkaline during the course of smoking.
Characterization of Bacterial Communities in Venous Insufficiency Wounds by Use of Conventional Culture and Molecular Diagnostic Methods (2011)

Microbial infections delay wound healing, but the effect of the composition of the wound microbiome on healing parameters is unknown. To better understand bacterial communities in chronic wounds, we analyzed debridement samples from lower-extremity venous insufficiency ulcers using the following: conventional anaerobic and aerobic bacterial cultures; the Ibis T5000 universal biosensor (Abbott Molecular); and 16S 454 FLX titanium series pyrosequencing (Roche). Wound debridement samples were obtained from 10 patients monitored clinically for at least 6 months, at which point 5 of the 10 sampled wounds had healed. Pyrosequencing data revealed significantly higher bacterial abundance and diversity in wounds that had not healed at 6 months. Additionally, Actinomycetales was increased in wounds that had not healed, and Pseudomonadaceae was increased in wounds that had healed by the 6-month follow-up. Baseline wound surface area, duration, or analysis by Ibis or conventional culture did not reveal significant differences between wounds that healed after 6 months and those that did not. Thus, pyrosequencing identified distinctive baseline characteristics of wounds that did not heal by the 6-month follow-up, furthering our understanding of potentially unique microbiome characteristics of chronic wounds.
Photocontrol of Molecular Orientation of a Photoresponsive Amphiphilic α-Helix in a Lipid Monolayer (1997)

We prepared a photoresponsive polypeptide, Mn = 10 630, composed of two amphiphilic α-helical copolypeptides, poly[(γ-methyl l-glutamate)-co-(l-glutamic acid)], joined by an azobenzene (am.-MAzoM) as a molecular photoreceptor. Dipalmitoylphosphatidylcholine monolayers containing the am.-MAzoM were formed at the air−water interface. We investigated photoinduced changes in the structure of the polypeptide−lipid monolayer systems. The α-helical rod of am.-MAzoM was laid at the air−water interface when the monolayer was in a liquid state. While in the solid condensed monolayer, the polypeptide molecules arranged perpendicular to the membrane (the air−water interface) and formed a bundle by self-association. The bundle of am.-MAzoM could be observed as an intramembranous particle ca. 4 nm in diameter with atomic force microscopy. UV light irradiation induced the destabilization of the bundle structure in the monolayer. This behavior arose from the photoinduced denaturation of the amphiphilic character of the polypeptide owing to a bending of the polypeptide in the main chain by a cis−trans photoisomerization of the azobenzene moiety. After removal of the light, the am.-MAzoM in the solid condensed monolayer returned to the original bundle structure.
Insight on Tafel slopes from a microkinetic analysis of aqueous electrocatalysis for energy conversion (2015)

Microkinetic analyses of aqueous electrochemistry involving gaseous H2 or O2, i.e., hydrogen evolution reaction (HER), hydrogen oxidation reaction (HOR), oxygen reduction reaction (ORR) and oxygen evolution reaction (OER), are revisited. The Tafel slopes used to evaluate the rate determining steps generally assume extreme coverage of the adsorbed species (θ≈0 or ≈1), although, in practice, the slopes are coverage-dependent. We conducted detailed kinetic analyses describing the coverage-dependent Tafel slopes for the aforementioned reactions. Our careful analyses provide a general benchmark for experimentally observed Tafel slopes that can be assigned to specific rate determining steps. The Tafel analysis is a powerful tool for discussing the rate determining steps involved in electrocatalysis, but our study also demonstrated that overly simplified assumptions led to an inaccurate description of the surface electrocatalysis. Additionally, in many studies, Tafel analyses have been performed in conjunction with the Butler-Volmer equation, where its applicability regarding only electron transfer kinetics is often overlooked. Based on the derived kinetic description of the HER/HOR as an example, the limitation of Butler-Volmer expression in electrocatalysis is also discussed in this report.
Attribute2Image: Conditional Image Generation from Visual Attributes (2015)

This paper investigates a novel problem of generating images from visual attributes. We model the image as a composite of foreground and background and develop a layered generative model with disentangled latent variables that can be learned end-to-end using a variational auto-encoder. We experiment with natural images of faces and birds and demonstrate that the proposed models are capable of generating realistic and diverse samples with disentangled latent representations. We use a general energy minimization algorithm for posterior inference of latent variables given novel images. Therefore, the learned generative models show excellent quantitative and visual results in the tasks of attribute-conditioned image reconstruction and completion.
Effect of Intake Pipe on the Volumetric Efficiency of an Internal Combustion Engine (1929)

The writer discusses the phenomena of expansion and compression which alternately take place in the cylinders of four-stroke engines during the induction process at a high mean piston speed due to the inertia and elasticity of the mixture in the intake pipe. The present paper is intended to demonstrate theoretically the existence of a most favorable pipe length for charging.