gebhart/patrepeval huggingface dataset:
Evolution of Repeated DNA Sequences by Unequal Crossover (1976)

It is often supposed that highly repetitious DNA's arise only as a result of unusual mechanisms or in response to selective pressure. My arguments and simulations suggest, by contrast, that a pattern of tandem repeats is the natural state of DNA whose sequence is not maintained by selection. The simulations show that periodicities can develop readily from nonreptitious DNA as a result of the random accumulation of random mutations and random homology-dependent unequal crossovers. The lengths of these periodicities, and the patterns of subrepeats within them, would fluctuate in evolution, with the probability of a given pattern being dependent on the unknown exact nature of the crossover mechanism. Qualitatively, then, unequal crossover provides a reasonable and uncontrived explanation for the prevalence of highly repeated sequences in DNA and for the patterns of periodicity they evince.
Production, crystallization and diffraction to atomic resolution of an antibody Fv specific for the blood-group A oligosaccharide antigen (1998)

The histoblood-group ABO carbohydrate antigens are well known as important factors in blood transfusions, but they can also act as receptors for infectious agents and have been implicated in susceptibility to certain carcinomas. A single-chain variable-domain antigen-binding fragment (scFv) gene based on the known sequence of an anti-blood-group-A monoclonal antibody (AC1001) has been synthesized and expressed in Escherichia coli. The purified scFv preparation existed primarily in the monomeric form but also contained large amounts of dimeric and higher oligomeric forms. The corresponding variable-domain antigen-binding fragment (Fv) was generated by cleaving the VL-VH linker with subtilisin, and its activity was demonstrated by surface plasmon resonance with an immobilized bovine serum albumin-A-trisaccharide conjugate (KD = 290 microM). AC1001 Fv crystals grown in the presence of N-acetylgalactosamine diffracted to 0.93 A resolution. This is the first reported example of a crystal of an antibody antigen-binding fragment diffracting to atomic resolution.
The Effects of Tramadol and Morphine on Immune Responses and Pain After Surgery in Cancer Patients (2000)

Recent studies suggest that opioids can have an adverse impact on the immune system. Because surgical stress also induces immune dysfunction, the search for analgesic drugs devoid of immunosuppressive effects is of import. This study compared the effects on immune responses of morphine and of the atypical opioid analgesic, tramadol, given for postoperative pain to gynecological cancer patients. Tramadol and morphine showed comparable analgesic activity; however, tramadol, in contrast to morphine, induced an improvement of postoperative immunosuppression and, therefore, may be preferred to morphine for the treatment of postoperative pain.
A convenient entry into the rhoeadan skeleton. Total synthesis of (±) cis-alpinigenine (1982)

Condensation of 4-bromoisochroman-3-one (8a) with N-methyl-3,4-dimethoxy-β-phenethylamine (7) provides the aminolactone 9a which by diisobutylaluminum hydride reduction followed by polyphosphoric acid mediated cyclization gives the tetracyclic product 10a, thus constituting a convergent, short entry into the rhoeadan alkaloid skeleton. Chromium trioxide oxidation of 10a affords a low yield of the corresponding lactone 11a. A parallel series of reactions starting from 7,8-dimethoxy-4-bromoisochroman-3-one (8b), prepared either via Baeyer–Villiger oxidation of 4,5-dimethoxy-2-indanone (14) or, more conveniently, via benzeneboronic acid assisted condensation of 3-hydroxy-4-methoxyphenylacetic acid (18) with formaldehyde, yields 7,8,12,13-tetramethoxy-3-methylrhoeadan (10b). Oxidation of compound 10b with chromium trioxide gives the corresponding lactone 11b also in low yield. Since 11b has been previously converted into (±)-cis-alpinigenine (11c) and (±)-cis-alpinine(11d), this work constitutes total syntheses of these alkaloids.
Nuclear and Isotopic Techniques for Addressing Nutritional Problems, with Special Reference to Current Applications in Developing Countries (2002)

Nuclear and isotopic techniques are valuable tools in human nutritional research studies. Isotopes, both radioactive and nonradioactive, enable detailed evaluations of nutrient intake, body composition, energy expenditure, status of micronutrients, and nutrient bioavailability. In recent times, isotopic methods have been widely used in a number of coordinated research projects and technical cooperation projects of the International Atomic Energy Agency's Nutrition Programme. The doubly labeled water technique combines the use of the stable isotopes oxygen-18 and hydrogen-2 (deuterium) to measure total energy expenditure in free-living human subjects, and to investigate the magnitude and causes of both undernutrition and the emergence of obesity in developing countries. The deuterium dilution technique is a reliable tool to measure breastmilk intake and thereby infant growth and development. In collaboration with the World Health Organization's Growth Monitoring Program, this technique is being used to generate new data on growth standards for children in developing countries. This technique is also used in the measurement of body composition by the estimation of lean body mass and fat mass in individuals. Stable isotopes of iron and zinc have been successfully used to assess the nutritional impact of several nationwide food supplementation-programs conducted on pregnant and lactating women and children in both industrialized and developing countries. Isotopic techniques are especially suitable for monitoring changes in body composition, energy metabolism, and mineral status (with particular reference to osteoporosis) in the elderly. Nuclear methods have also served to develop models for a physiological reference man in Asia in support of radiological health and safety issues, for establishing elemental composition of foods, and for measurement of pollutants in the environment.
The Application of Transgenic Mice for Therapeutic Antibody Discovery (2012)

In 2006, panitumumab, the first fully human antibody generated from transgenic mice, was approved for clinical use by the US Food and Drug Administration (FDA). Since then, a further seven such antibodies have been approved. In this chapter, we discuss how transgenic mice technologies can provide a powerful platform for creating human therapeutic antibodies.
Integrated optics 4 × 4 switch matrix with digital optical switches (1990)

We report on the first 4 × 4 switch matrix with digital optical switches as switch elements. The matrix is arranged in a tree structure, and comprises 24 switch elements and is pigtailed and packaged.
Double mutant and formaldehyde inactivated TSST-1 as vaccinecandidates (2002)

Up to now there is no treatment for staphylococcal toxic shock
syndrome, a disease mainly induced by toxic shock syndrome
toxin-1(TSST-1). There is great demand in finding means to
control the disease, one of them is the development of an
effective and safe vaccine against TSST-1. In this study we
constructed a series of vaccine candidates and investigated
their biological activity, toxicity, and potential to invoke an
immune response. TSST-1 was isolated from Stahylococcus aureus
supernatants and recombinantly expressed as a N-terminal 6x
histidine-tagged protein in Escherichia coli. In order to
obtain molecules with minimal toxicity we constructed single
mutants (G31R and H135A) and one double mutant (G31R/H135A)
with both residues exchanged. We also detoxified native TSST-1
isolated from S. aureus, and recombinantly expressed TSST-1 by
treatment with formaldehyde. Functional activity of native and
recombinant TSST-1 and grade of inocuity of mutants and toxoids
was determined by investigating mitogenity, T-cell activation,
and cytokine release upon stimulation of human mononuclear
cells with the vaccine candidates. All substances were tested
in a rabbit immunization study. After primary immunization and
three additional boosts all vaccinated animals developed
antibody titers against TSST-1 and were protected against
challenge with a lethal doses of superantigen potentiated with
lipopolysaccharide.
Spinal and bulbar muscular atrophy: a trinucleotide-repeat expansion neurodegenerative disease (1995)

Spinal and bulbar muscular atrophy (SBMA) is an X-linked, adult-onset motor neuronopathy that is caused by expansion of a trinucleotide (CAG) repeat in the androgen-receptor gene. The length of this repeat varies as it is passed down through SBMA families, and correlates inversely with the age of onset of the disease. The motor-neuron degeneration that occurs in this disease is probably caused by a toxic gain of function in the androgen-receptor protein. Subsequent to the identification of the mutation in SBMA, other inherited neurodegenerative diseases have been found to be caused by the expansion of CAG repeats in the coding regions of other genes. Because these diseases probably share a common pathogenesis, investigation of SBMA might help to determine a general mechanism of neuronal degeneration.
Catalytic Alkane Metathesis by Tandem Alkane Dehydrogenation-Olefin Metathesis (2006)

With petroleum supplies dwindling, there is increasing interest in selective methods for transforming other carbon feedstocks into hydrocarbons suitable for transportation fuel. We report the development of highly productive, well-defined, tandem catalytic systems for the metathesis of n-alkanes. Each system comprises one molecular catalyst (a "pincer"-ligated iridium complex) that effects alkane dehydrogenation and olefin hydrogenation, plus a second catalyst (molecular or solid-phase) for olefin metathesis. The systems all show complete selectivity for linear (n-alkane) product. We report one example that achieves selectivity with respect to the distribution of product molecular weights, in which n-decane is the predominant high-molecular-weight product of the metathesis of two moles of n-hexane.
New detector for 1,k codes equalized to class II partial response (1989)

A modified linear canceller is described which approached maximum-likelihood performance for a 1,k RLL code on a PR2 (class II partial response) channel. With white noise, this detector gains 1.8 dB over simple threshold detection. Performance is analyzed both theoretically and through bit-by-bit simulations for a variety of noise colorations and misequalization conditions. The technique is applicable wherever the channel is equalized to a low-pass characteristic as in instrumentation and video tape recording with Miller-squared code or optical recording with a 1,7 code and pulse-width modulation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Endometrial Decidualization: Of Mice and Men (2010)

In murine and human pregnancies, embryos implant by attaching to the luminal epithelium and invading into the stroma of the endometrium. Under the influence of the steroid hormones estrogen and progesterone, the stromal cells surrounding the implanting embryo undergo a remarkable transformation event. This process, known as decidualization, is an essential prerequisite for implantation. It comprises morphogenetic, biochemical, and vascular changes driven by the estrogen and progesterone receptors. The development of mutant mouse models lacking these receptors has firmly established the necessity of steroid signaling for decidualization. Genomic profiling of mouse and human endometrium has uncovered a complex yet highly conserved network of steroid-regulated genes that supports decidualization. To advance our understanding of the mechanisms regulating implantation and better address the clinical challenges of infertility and endometrial diseases such as endometriosis, it is important to integrate the information gained from the mouse and human models.
Chemical genomics identifies compounds affecting Xenopus laevis pigment cell development (1900)

A forward chemical genomic screen was carried out using Xenopus laevis embryos to identify compounds disrupting pigmented cell development, including the retinal pigment epithelial (RPE) layer of the eye and the melanophores (melanocytes). Phenotypes showing changes in cell migration, morphology and pigmentation were observed. The screen also identified compounds affecting other aspects of Xenopus development including general patterning and morphogenesis, eye development and edema formation. Evidence is presented for the molecular targets of three of the compounds identified. Xenopus melanophore and human melanoma cell lines were also utilised in follow-up cell morphology assays. Chemical genomic screens of this type have an important role to play in the identification of novel compounds providing new molecular tools, and biological information, along with identification of new protein targets and leads for potential therapeutic agents.
New solid-phase catalysts for asymmetric synthesis: cross-linked polymers containing a chiral Schiff base-zinc complex (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew solid-phase catalysts for asymmetric synthesis: cross-linked polymers containing a chiral Schiff base-zinc complexShinichi Itsuno, Yoshiki Sakurai, Koichi Ito, Toshihiro Maruyama, Seiichi Nakahama, and J. M. J. FrechetCite this: J. Org. Chem. 1990, 55, 1, 304–310Publication Date (Print):January 1, 1990Publication History Published online1 May 2002Published inissue 1 January 1990https://pubs.acs.org/doi/10.1021/jo00288a051https://doi.org/10.1021/jo00288a051research-articleACS PublicationsRequest reuse permissionsArticle Views1113Altmetric-Citations152LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Effect of compounds with antibacterial activities in human milk on respiratory syncytial virus and cytomegalovirus in vitro (1998)

The effect of some antibacterial compounds present in human milk were tested for antiviral activity against respiratory syncytial virus, Semliki Forest virus and cytomegalovirus. These included the gangliosides GM1, GM2 and GM3, sialyl-lactose, lactoferrin and chondroitin sulphate A, B and C, which were all tested for their ability to inhibit the viruses in cell culture. Of the compounds tested, only the ganglioside GM2, chondroitin sulphate B and lactoferrin inhibited the absorption and growth of respiratory syncytial virus in cell culture, and none inhibited the growth of Semliki Forest virus, indicating that lipid antiviral activity was not associated with any of the gangliosides. While the concentrations of these two compounds required to inhibit respiratory syncytial virus were in excess of those present in human milk, sialyl-lactose concentrations similar to those present in human milk increased the growth of cytomegalovirus. Lactoferrin was confirmed as inhibiting both respiratory syncytial virus and cytomegalovirus growth in culture even when used at lower concentrations than those present in human milk. The antiviral activities of GM2, chondroitin sulphate B and lactoferrin were tested when added to an infant formula. Lactoferrin continued to have antiviral activity against cytomegalovirus, but a lower activity against respiratory syncytial virus; ganglioside GM2 and chondroitin sulphate B still maintained antiviral activity against respiratory syncytial virus.
Close Association between Clearance of Recombinant Human Granulocyte Colony-Stimulating Factor (G-CSF) and G-CSF Receptor on Neutrophils in Cancer Patients (1999)

Recombinant human granulocyte colony-stimulating factor (rhG-CSF) is used to counter chemotherapy-induced neutropenia. Our previous study showed an inverse correlation between serum rhG-CSF levels and the number of circulating neutrophils in cancer patients (H. Takatani, H. Soda, M. Fukuda, M. Watanabe, A. Kinoshita, T. Nakamura, and M. Oka, Antimicrob. Agents Chemother. 40:988-991, 1996). The aim of this study was to clarify the relationship between rhG-CSF clearance and G-CSF receptors on circulating neutrophils. In five cancer patients receiving chemotherapy, a bolus dose of rhG-CSF (5 microg/kg) was injected intravenously during defined phases of posttreatment neutropenia and neutrophilia. Serum rhG-CSF levels were measured by a chemiluminescence enzyme immunoassay and analyzed by moment analysis. G-CSF receptors on neutrophils were detected by flow cytometry with biotinylated rhG-CSF. rhG-CSF clearance was significantly higher at neutrophilia than at neutropenia (1,497 +/- 132 versus 995 +/- 266 ml/h; P < 0.01). The percentage of G-CSF receptor-positive neutrophils, reflecting the number of G-CSF receptors per cell, was low at neutropenia without rhG-CSF therapy (44.5% +/- 22.1%) and high at neutrophilia with rhG-CSF therapy (73. 0% +/- 11.4%; P < 0.01). rhG-CSF clearance closely correlated with the percentage of G-CSF receptor-positive neutrophils (r2 = 0.91; P < 0.0001) and neutrophil count (r2 = 0.72; P < 0.005). Our results indicate that, in cancer patients receiving chemotherapy, rhG-CSF increases the number of G-CSF receptors per cell as well as circulating neutrophil counts, resulting in modulation of its own clearance.
Structure-Specific DNA Binding by Bacteriophage T5 5'->3' Exonuclease (1997)

Phage T5 exonuclease is a 5'-->3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'-end). Oligonucleotides were used to construct duplexes with either blunt ends, 5'-overhangs, 3'-overhangs, a flap or a forked end (pseudo-Y). The binding of T5 exonuclease to various structures was investigated using native electrophoretic mobility shift assays (EMSA) in the absence of the essential divalent metal cofactor. Binding of T5 exonuclease to either blunt-ended duplexes or single-stranded oligonucleotides could not be detected by EMSA. However, duplexes with 5'-overhangs, flaps and pseudo-Y structures showed decreased mobility with added T5 exonuclease. On binding to DNA the wild-type enzyme was rendered partially resistant to proteolysis, yielding a biologically active 31.5 kDa fragment. However, the protein-DNA complex remained susceptible to inactivation by p-hydroxymercuribenzoate (PHMB, a cysteine-specific modifying agent), suggesting that neither cysteine is intimately associated with substrate binding. Replacement of both cysteine residues of the molecule with serine did not greatly alter the catalytic or binding characteristics of the protein but did render it highly resistant to inhibition by PHMB.
The Levels of Serum Vitamin C, Malonyldialdehyde and Erythrocyte Reduced Glutathione in Chronic Obstructive Pulmonary Disease and in Healthy Smokers (2002)

There is an increasing interest in the concept that oxidant/antioxidant imbalance plays a role in the pathogenesis of chronic obstructive pulmonary disease (COPD). However, most of the studies are concentrated on the local antioxidant/oxidant balance. In this study, we investigated the oxidant/antioxidant balance in systemic circulation of patients with COPD. Serum malonyldialdehyde (MDA), vitamin C and erythrocyte reduced glutathione (GSH) were determined in patients during acute exacerbation and during the stable phase of the disease, and compared with age- and sex-matched healthy controls. The levels of serum MDA, vitamin C and erythrocyte GSH were determined according to Yagi, Beutler and Bauer et al., respectively. Serum MDA levels were significantly higher in patients compared to controls, and during acute exacerbation compared to the stable phase. MDA levels in patients with acute exacerbation and in those in stable phase were also higher than in controls. We found significantly decreased levels of erythrocyte GSH and serum vitamin C in patients with acute exacerbation and stable COPD compared to controls. Although smoking caused an increase in oxidative stress in controls, the measured parameters were not affected by smoking in the patient group. In conclusion, there is a systemic oxidant/antioxidant imbalance in COPD, and this imbalance is probably independent of smoking.
[Studies on the extraction of ingredients from Chinese traditional medicine with CO2 supercritical fluid]. (2003)

CO2 supercritical fluid is good at extracing low polarity ingredients, and it shows the evident individurity in extraction of Chinese herb. The technological factors in industrial usage must be thought of all over.
<title>Numerical investigation of the Knudsen-layer, appearing in the laser-induced evaporation of metals</title> (1990)

The non-equilibrium evaporation of metals is increasingly important in recent applications of high intensity power sources such as lasers, electron beams and arc heated plasmas. Powerful jets of evaporated metal arise when cw-lasers or pulsed laser beams are used, especially in surface processing, ablation and sublimation cutting. An exact understanding of the physical conditions in this evaporation jet is essential to control the ablation rate and minimize the energy loss due to evaporation by adjustment of the external process parameters. The ablation jet is maintained by an appropriate supply of newly evaporated particles and in effect sets the boundary conditions for the hydrodynamic or plasma regime that arises. Exact knowledge concerning the metallic vapour that constitutes the plasma which arises in a wide variety of material processing techniques with a high intensity beam allows to predict the ignition behaviour of the plasma vapour. This is a particular advantage since the presence of the plasma can totally change the physical behaviour of the process. In high intensity beam welding processes a narrow keyhole appears filled with metallic vapour whose behaviour does not depart too strongly from equilibrium. The plasma which is detected in the keyhole is important for the energy transfer from the incident beam to the workpiece1, so that in this case the physical conditions in the vapour are of special interest, as they determine the development of the plasma. When a metal surface is heated to a temperature close to the boiling point of the material of which it is composed, a jet of evaporated material originates at the metal surface. Depending on the surface temperature and the external pressure, the evaporation process ranges from a steady state of thermodynamic equilibrium which describes a vapour with constant spatial density and temperature, and no significant net motion, to one involving a strong non-equilibrium process with a velocity up to the local speed of sound. In all but the equilibrium case, however, a thin surface layer, known as the Knudsen layer, forms in the vapour. The transition from a non-equilibrium velocity distribution at the metal surface to a local Maxwell-Boltzmann distribution some few mean free paths above the metal surface occurs in this layer. This non-equilibrium regime is described by Boltzmann's equation which is solved here in the BGK approximation. This is achieved by employing an iteration algorithm for the solution of an equivalent integral equation with suitable boundary conditions. The temperature, density and velocity either in or behind the Knudsen layer are derived together with the velocity distribution function everywhere in the layer.