gebhart/patrepeval huggingface dataset:
Investigation of Laser Tissue Welding Dynamics via Experiment and Modeling (1997)

An in vitro study of laser tissue welding mediated with a dye-enhanced protein solder was performed. Freshly harvested sections of porcine aorta were used for the experiments. Arteriotomies approximately 4 mm in length were treated using an 805 nm continuous-wave diode laser coupled to a 1-mm diameter fiber. Temperature histories of the surface of the weld site were obtained using a fiberoptic-based infrared thermometer. The experimental effort was complemented by the LATIS (LAser-TISsue) computer code, which numerically simulates the exposure of tissue to near-infrared radiation using coupled Monte Carlo, thermal transport, and mass transport models. Comparison of the experimental and simulated thermal results shows that the inclusion of water transport and evaporative losses in the model is necessary to determine the thermal distributions and hydration state in the tissue. The hydration state of the weld site was correlated with the acute weld strength.
A novel process-based model of microbial growth: self-inhibition in Saccharomyces cerevisiae aerobic fed-batch cultures (2015)

The presented results clarify the dynamics of microbial growth under different feeding conditions and highlight the relevance of the negative feedback by self-produced inhibitory compounds on the maximum cell densities achieved in a bioreactor.
Progress with inactivated poliovirus vaccines derived from the Sabin strains. (2001)

To produce a safe and effective inactivated poliovirus vaccine (IPV), we have developed S-IPV using Vero cells infected with the Sabin strains in a semi-production scale. All production steps including virus culture on microcarrier beads were highly reproducible. Mean recovery percents of infectious viruses or D-antigens during all processes for concentration, purification and inactivation were 30-50% in the three types. The S-IPV potency was adjusted for D-antigen content as determined by in-house ELISA and was comparable to WHO reference IPV derived from the virulent strains in immunogenicity tests in rats. Antibody development in more than 30 seronegative infant volunteers after two shots of S-IPV at four-week interval were 100% without notable adverse reactions. The mean antibody titres (log2) to Sabin 1, 2 and 3 viruses were 11.1, 8.3 and 8.9, respectively. The antibodies neutralized the Mahoney, MEF-1, and Saukett virulent strains with slightly inferior titres to those of the Sabin strains. D-antigens for each type of S-IPV were stable at 4 degrees C without any significant decrease over more than two years.
Determining the optimal PDMS–PDMS bonding technique for microfluidic devices (2008)

A number of polydimethysiloxane (PDMS) bonding techniques have been reported in the literature over the last several years as the focus on multilayer PDMS microfluidic devices has increased. Oxygen plasma bonding, despite cost, additional fabrication time and inconsistent bonding results, has remained a widely used method for bonding PDMS layers. A comparative study of four rapid, inexpensive alternative PDMS–PDMS bonding approaches was undertaken to determine relative bond strength. These include corona discharge, partial curing, cross-linker variation and uncured PDMS adhesive. Partial curing and uncured PDMS adhesive demonstrated a considerable improvement in bond strength and consistency by retaining average bond strengths of over 600 kPa, which was more than double the average bond strength of oxygen plasma. A description of each technique and their performance relative to oxygen plasma bonding is included.
MicroRNA-195 promotes palmitate-induced apoptosis in cardiomyocytes by down-regulating Sirt1 (2011)

This study demonstrates a pro-apoptotic role of miR-195 in cardiomyocytes and identifies Sirt1 as a direct target of miR-195. The effect of miR-195 on apoptosis is mediated through down-regulation of Sirt1 and Bcl-2 and ROS production. Thus, miR-195 may be a new therapeutic target for lipotoxic cardiomyopathy.
The Development of Bidentate P,N Ligands for Asymmetric Catalysis (2004)

Abstract In this review, an attempt is made to systemise the rôle which bidentate phosphinamine (P,N) ligands play in asymmetric catalysis. The ligands will be classified, not by the reaction to which their metal complexes have been applied, but by the nature of their donor atoms. In this manner the development of ligand architectural design can be more easily monitored. The asymmetric transformations to which metal complexes of these ligands have been applied include among others, palladium‐catalysed allylic substitutions, copper‐catalysed 1,4‐additions to enones and rhodium‐catalysed hydroboration of vinylarenes. Excellent enantioselectivities, regioselectivities and reactivities have been achieved in each of these processes.
Terminal Olefin (1-Alkene) Biosynthesis by a Novel P450 Fatty Acid Decarboxylase from Jeotgalicoccus Species (2011)

Terminal olefins (1-alkenes) are natural products that have important industrial applications as both fuels and chemicals. However, their biosynthesis has been largely unexplored. We describe a group of bacteria, Jeotgalicoccus spp., which synthesize terminal olefins, in particular 18-methyl-1-nonadecene and 17-methyl-1-nonadecene. These olefins are derived from intermediates of fatty acid biosynthesis, and the key enzyme in Jeotgalicoccus sp. ATCC 8456 is a terminal olefin-forming fatty acid decarboxylase. This enzyme, Jeotgalicoccus sp. OleT (OleT(JE)), was identified by purification from cell lysates, and its encoding gene was identified from a draft genome sequence of Jeotgalicoccus sp. ATCC 8456 using reverse genetics. Heterologous expression of the identified gene conferred olefin biosynthesis to Escherichia coli. OleT(JE) is a P450 from the cyp152 family, which includes bacterial fatty acid hydroxylases. Some cyp152 P450 enzymes have the ability to decarboxylate and to hydroxylate fatty acids (in α- and/or β-position), suggesting a common reaction intermediate in their catalytic mechanism and specific structural determinants that favor one reaction over the other. The discovery of these terminal olefin-forming P450 enzymes represents a third biosynthetic pathway (in addition to alkane and long-chain olefin biosynthesis) to convert fatty acid intermediates into hydrocarbons. Olefin-forming fatty acid decarboxylation is a novel reaction that can now be added to the catalytic repertoire of the versatile cytochrome P450 enzyme family.
Development of Thermostable Lyophilized Inactivated Polio Vaccine (2014)

This study showed the potential of a highly stable and safe lyophilized polio vaccine, which might be used in developing countries without the need of a cold-chain.
A miniature confocal optical microscope with MEMS gimbal scanner (2004)

We have developed a unique miniature confocal microscope with a MEMS scanner and successfully obtained a real time image. A scanning head including the MEMS scanner, an optical fiber and an aspherical objective lens is precisely and compactly assembled. By employing two reflectors optical design with the lens, an observation of a longitudinal direction was achieved. The mirrors in the scanner Its diameter and length are 3.3 mm and 8 mm, respectively. The lateral resolution of 0.5 /spl mu/m, the depth resolution of 2.9 /spl mu/m, and the field of view of 100/spl times/75 /spl mu/m were achieved.
Post-processing of the recognized speech for web presentation of large audio archive (2012)

This paper deals with a post-processing phase of automatic transcription of spoken documents stored in the large Czech Radio audio archive (containing hundreds of thousands of recordings). The ultimate goal of the project is to transcribe them and to allow public access to their content. In this paper we focus on methods and algorithms for unsupervised post-processing of automatically recognized recordings. The post-processing is adapted for the needs of the web presentation of the archive. Up to now it has been used to process about 60,000 audio documents. We present the overall structure of the system as well as its core modules - speech recognition engine, speaker diarization module and final text processing. Special attention is paid to the punctuation issue. The punctuation accuracy is evaluated and compared to human use. In the final part of the paper we propose further improvements and ideas for the future research.
Stability of Ionic Liquids in Application Conditions (2011)

Ionic liquids have a large variety of applications in nearly all areas of the chemical industries. They are used for example as lubricants, plasticizers, solvents and catalysts for synthesis, matrices for mass spectroscopy, solvents for extraction and in the manufacture of nano-materials, and as electrolytes. There are numerous studies in the corresponding literature concerning the unique properties, preparation methods, and different applications of ionic liquids. Nowadays, researchers try to answer questions concerning the stability of ionic liquids within practical applications. In this review, a general description of the stability and - degradation products of ionic liquids formed under different physicochemical conditions such as high temperature, irradiation, varying electrical current density, oxidizing agents are discussed. The main focus of this paper is on how the structure of ionic liquid cations and anions as well as impurities (e.g. water) influence the stability of ionic liquids in application and in utilization conditions. Additionally, it is also very important to consider the stability of ionic liquids with respect to environmental issues and for the hazard assessment of those compounds. These aspects, as well the possibility to use strongly oxidizing conditions (advanced oxidation processes) to remove ionic liquid structures from wastewaters are discussed within this review.
ChemInform Abstract: Type I Polyketide Biosynthesis in Bacteria (Part A — Erythromycin Biosynthesis) (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Retroviruses and insertional mutagenesis in mice: proviral integration at the Mov 34 locus leads to early embryonic death. (1987)

Thirty-four transgenic mouse strains, each carrying a single proviral insert, were generated by infection of preimplantation and postimplantation embryos with retroviruses. Animals homozygous for proviral integrations were derived for all strains with the exception of Mov 24, where the provirus is inserted on the Y chromosome, and Mov 34. Embryos homozygous at the Mov 34 locus develop normally to the blastocyst stage and die shortly after implantation, indicating that virus integration resulted in a recessive lethal mutation. The provirus and flanking sequences were cloned and the virus was mapped to the 5' side of an abundantly and ubiquitously transcribed gene. Similar to the previously derived Mov 13 mutation, proviral integration at the Mov 34 locus interferes with the expression of the adjacent gene. These and our previous results indicate that of a total of 48 proviral integrations in the germ line, two resulted in transgenic mouse strains with recessive lethal mutations.
Quantification of arsenic, lead, mercury and cadmium in newborn dried blood spots (2013)

Exposures to heavy metals during fetal and perinatal development are of particular concern. Yet, the health impacts of exposures to toxic metals during these early stages of human development are not well understood due to the paucity of in vivo human data. Dried blood spots (DBS), collected by public health departments to screen for inherited metabolic errors and other disorders, are routinely archived and can be used for exposure assessment. Here we report an improved method for quantifying arsenic, lead, mercury and cadmium in newborn DBS to facilitate epidemiologic research on the health effects of early exposures to toxic metals.
Association of Elevated Serum PO4, Ca × PO4 Product, and Parathyroid Hormone with Cardiac Mortality Risk in Chronic Hemodialysis Patients (2001)

Hyperphosphatemia is highly prevalent among patients with end-stage renal disease (ESRD) and is associated with increased mortality risk in hemodialysis (HD) patients. The mechanism through which this mortality risk is mediated is unclear. Data from two national random samples of HD patients (n = 12,833) was used to test the hypothesis that elevated serum PO(4) contributes mainly to cardiac causes of death. During a 2-yr follow-up, the cause-specific relative risk (RR) of death for patients was analyzed separately for several categories of cause of death, including coronary artery disease (CAD), sudden death, and other cardiac causes, cerebrovascular and infection. Cox regression models were fit for each of the eight cause of death categories, adjusting for patient demographics and non-cardiovascular comorbid conditions. Time at risk for each cause-specific model was censored at death that resulted from any of the other causes. Higher mortality risk was seen for patients in the high PO(4) group (>6.5mg/dl) compared with the lower PO(4) group (< or =6.5mg/dl) for death resulting from CAD (RR 1.41; P < 0.0005), sudden death (RR 1.20; P < 0.01), infection (RR 1.20; P < 0.05), and unknown causes (RR 1.25; P < 0.05). Patients in the high PO(4) group also had non-significantly increased RR of death from other cardiac and cerebrovascular causes of death. The RR of sudden death was also strongly associated with elevated Ca x PO(4) product (RR 1.07 per 10 mg(2)/dl(2); P < 0.005) and serum parathyroid hormone levels greater than 495 pg/ml (RR 1.25; P < 0.05). This study identifies strong relationships between elevated serum PO(4), Ca x PO(4) product, and parathyroid hormone and cardiac causes of death in HD patients, especially deaths resulting from CAD and sudden death. More vigorous measures to reduce the prevalence of these factors in HD patients may result in improved survival.
Protection of innate immunity by C5aR antagonist in septic mice (2002)

Innate immune functions are known to be compromised during sepsis, often with lethal consequences. There is also evidence in rats that sepsis is associated with excessive complement activation and generation of the potent anaphylatoxin C5a. In the presence of a cyclic peptide antagonist (C5aRa) to the C5a receptor (C5aR), the binding of murine 125I-C5a to murine neutrophils was reduced, the in vitro chemotactic responses of mouse neutrophils to mouse C5a were markedly diminished, the acquired defect in hydrogen peroxide (H2O2) production of C5a-exposed neutrophils was reversed, and the lung permeability index (extravascular leakage of albumin) in mice after intrapulmonary deposition of IgG immune complexes was markedly diminished. Mice that developed sepsis after cecal ligation/puncture (CLP) and were treated with C5aRa had greatly improved survival rates. These data suggest that C5aRa interferes with neutrophil responses to C5a, preventing C5a-induced compromise of innate immunity during sepsis, with greatly improved survival rates after CLP.
Crystal Structure of the T877A Human Androgen Receptor Ligand-binding Domain Complexed to Cyproterone Acetate Provides Insight for Ligand-induced Conformational Changes and Structure-based Drug Design (2007)

Cyproterone acetate (CPA) is a steroidal antiandrogen used clinically in the treatment of prostate cancer. Compared with steroidal agonists for the androgen receptor (AR) (e.g. dihydrotestosterone, R1881), CPA is bulkier in structure and therefore seemingly incompatible with the binding pockets observed in currently available x-ray crystal structures of the AR ligand-binding domain (LBD). We solved the x-ray crystal structure of the human AR LBD bound to CPA at 1.8A in the T877A variant, a mutation known to increase the agonist activity of CPA and therefore facilitate purification and crystal formation of the receptor.drug complex. The structure demonstrates that bulk from the 17alpha-acetate group of CPA induces movement of the Leu-701 side chain, which results in partial unfolding of the C-terminal end of helix 11 and displacement of the loop between helices 11 and 12 in comparison to all other AR LBD crystal structures published to date. This structural alteration leads to an expansion of the AR binding cavity to include an additional pocket bordered by Leu-701, Leu-704, Ser-778, Met-780, Phe-876, and Leu-880. Further, we found that CPA invokes transcriptional activation in the L701A AR at low nanomolar concentrations similar to the T877A mutant. Analogous mutations in the glucocorticoid receptor (GR) and progesterone receptor were constructed, and we found that CPA was also converted into a potent agonist in the M560A GR. Altogether, these data offer information for structure-based drug design, elucidate flexible regions of the AR LBD, and provide insight as to how CPA antagonizes the AR and GR.
Equilibrium Flexibility of a Rigid Linear Conjugated Polymer (1996)

The unusual electronic and optical properties of many electroluminescent and conducting polymers arise from extended conjugation along the polymer backbone, which can also lead to insolubility, aggregation, and gelation. Synthetic efforts to produce an optimal structure require a balance between the persistence length and the effective conjugation length for the successful implementation of these materials in photonic and electronic devices. In this study, we have investigated the solution properties of a group of poly(phenyleneethynylenes) using a variety of light scattering techniques, including polarized and depolarized intensity measurements, dynamic light scattering, and size exclusion chromatography with a multiangle light scattering detector (SEC/LS). Interpretation of light scattering in the presence of absorption, fluorescence, and optical anisotropy is discussed. The molecular weights determined by light scattering encompassed the range from 10 × 105 to 5 × 106, with the root-mean-square radius of gyration as high as 250 nm. The results may be interpreted with a wormlike chain model to yield a persistence length of about 15 nm, so that these high-M polymers are coil-like in solution, rather than “rigid rods”. This persistence length is still expected to be several times larger than the effective conjugation length.
Construction and sequence of cDNA for rat liver stearyl coenzyme A desaturase. (1986)

Hepatic poly(A+) RNA from rats induced for stearyl-CoA desaturase was used for primer-extension of cDNA coding for stearyl-CoA desaturase. Previously, Northern blot analysis showed that translatable desaturase mRNA is 4,900 nucleotides in length (Thiede, M. A., and Strittmatter, P. (1985) J. Biol. Chem. 260, 14459-14463). Six overlapping cDNAs, ranging from 850 to 1450 bases, were used to compile the 4,689-nucleotide sequence. The cDNA includes a 1,074-base open reading frame coding for 358 amino acids, corresponding to a molecular mass of 41,400 daltons. Positive identification of this open reading frame was accomplished by matching the amino acid sequence of both amino-terminal and cyanogen bromide peptides of the purified enzyme with regions of the sequence deduced from the cDNA. Amino acid composition data from the cDNA compares well with that from the desaturase. The protein contains 62% hydrophobic amino acids. An interesting feature of this mRNA is the 3,500-base 3' noncoding region, which has been localized on a single 3' exon by Southern blot analysis.
Structure of the Chondroitin 4-Sulfate-Protein Linkage Region (1966)

Abstract A disaccharide composed of glucuronic acid and d-galactose has been isolated from chondroitin 4-sulfate and chondroitin 4-sulfate glycopeptides. Its structure has been determined in the following way. (a) Reduction with borohydride demonstrated that galactose constitutes the reducing end of the disaccharide; (b) digestion with β-glucuronidase cleaved the disaccharide into glucuronic acid and galactose, demonstrating a β linkage; (c) periodate oxidation of the disaccharide methylglycoside resulted in no loss of galactose; and (d) oxidation of the disaccharide with lead tetraacetate degraded the galactose moiety to lyxose. This establishes the structure of the disaccharide as 3-O-β-d-glucuronosyl-d-galactose.
Passive immunization of hamsters against disease caused by Clostridium difficile by use of bovine immunoglobulin G concentrate (1991)

Gestating Holstein cows were vaccinated with Clostridium difficile toxoid prepared from the culture filtrate of a strain that produces high levels of toxins A and B and other antigens. A bovine immunoglobulin G (IgG) concentrate was prepared from colostrum collected at parturition. The results of our studies showed that hamsters treated prophylactically with the hyperimmune bovine IgG concentrate were protected against C. difficile disease. These results suggest that orally administered hyperimmune bovine IgG specific for C. difficile culture filtrate may be useful in prophylaxis against C. difficile disease.
Moats and Drawbridges: An Isolation Primitive for Reconfigurable Hardware Based Systems (2007)

Blurring the line between software and hardware, reconfigurable devices strike a balance between the raw high speed of custom silicon and the post-fabrication flexibility of general-purpose processors. While this flexibility is a boon for embedded system developers, who can now rapidly prototype and deploy solutions with performance approaching custom designs, this results in a system development methodology where functionality is stitched together from a variety of "soft IP cores," often provided by multiple vendors with different levels of trust. Unlike traditional software where resources are managed by an operating system, soft IP cores necessarily have very fine grain control over the underlying hardware. To address this problem, the embedded systems community requires novel security primitives which address the realities of modern reconfigurable hardware. We propose an isolation primitive, moats and drawbridges, that are built around four design properties: logical isolation, interconnect traceability, secure reconfigurable broadcast, and configuration scrubbing. Each of these is a fundamental operation with easily understood formal properties, yet maps cleanly and efficiently to a wide variety of reconfigurable devices. We carefully quantify the required overheads on real FPGAs and demonstrate the utility of our methods by applying them to the practical problem of memory protection.
Malignant neoplasms in registered cases of primary immunodeficiency syndrome. (1985)

The occurrence of malignant neoplasms among registered cases of primary immunodeficiency syndrome was studied. A total of 17 malignant tumors occurred in 596 (2.9%) infant patients; two in eight (25%) patients with Chediak-Higashi syndrome, seven in 49 (14.3%) with ataxia-telangiectasia and one in 12 (8.3%) patients with immunodeficiency with hyper-immunoglobulin-M-emia. The overall incidence of malignant tumors in these cases was 200-300 times that in the general population. The incidence in Japan was compared with that in the U.S.A. and in Italy.
Establishment of Stable, Cell-Mediated Immunity that Makes "Susceptible" Mice Resistant to Leishmania major (1992)

Cell-mediated, but not antibody-mediated, immune responses protect humans against certain pathogens that produce chronic diseases such as leishmaniasis. Effective vaccination against such pathogens must therefore produce an immunological "imprint" so that stable, cell-mediated immunity is induced in all individuals after natural infection. BALB/c mice "innately susceptible" to Leishmania major produce antibodies after substantial infection. In the present study, "susceptible" mice injected with a small number of parasites mounted a cell-mediated response and acquired resistance to a larger, normally pathogenic, challenge. This vaccination strategy may be applicable in diseases in which protection is dependent on cell-mediated immunity.