gebhart/patrepeval huggingface dataset:
Versatile low‐viscosity sieving matrices for nondenaturing DNA separations using capillary array electrophoresis (1997)

The high-resolution separation of double-stranded DNA (dsDNA) has important applications in physical mapping strategies and in the analysis of polymerase chain reaction (PCR) products. Although high-resolution separations of dsDNA by capillary electrophoresis (CE) have been reported, pulsed fields were required to achieve complete resolution of DNA fragments beyond 23 kilobase pairs (kbp). Here, we report a single formulation to separate a broad range (80 bp-40 kbp) of DNA fragments without the use of pulsed fields. We used a low-viscosity sieving medium (ca. 5 cP, at 25 degrees C) based on polyethyleneoxide (PEO) to separate DNA fragments up to 40 kbp. The matrix contained a mixture of 0.5% PEO (Mn 10(6)) to separate fragments up to 1.5 kbp, combined with 0.1% PEO (Mn 8 x 10(6)) to separate fragments between 1-40 kbp, within a single run. All PEO matrix formulations tested were compatible with a variety of intercalating dyes and with two different capillary wall coating methods. We obtained a detection limit of 25 fg of a 200 bp DNA quantitation standard using Vistra Green in the matrix. Resolution was best using short injection times (5 s or less) and low field strengths (approximately 100 V/cm). Sample runs were complete in 70 min, and use of the capillary array electrophoresis (CAE) system permitted high-throughput DNA analysis. The size range separated is approximately 10 times greater than with conventional slab gel separations.
Deaminated neuraminic acid-rich glycoprotein of rainbow trout egg vitelline envelope. Occurrence of a novel alpha-2,8-linked oligo(deaminated neuraminic acid) structure in O-linked glycan chains. (1990)

Deaminated neuraminic acid-rich glycoprotein (KDN-gp), first found and isolated from the vitelline envelope of rainbow trout eggs (Inoue, S., Kanamori, A., Kitajima, K., and Inoue, Y. (1988) Biochem. Biophys. Res. Commun. 153, 172-176), has been found to contain a number of O-linked glycan. Oligosaccharides were released by alkaline borohydride treatment of KDN-gp. Following fractionation by DEAE-Sephadex A-25 and thin-layer chromatography, a series of acidic oligosaccharides were obtained and analyzed for their chemical structures. The structure is based on composition analysis, methylation analysis, alkali-catalyzed "peeling" reactions, periodate oxidation, 400-MHz one- and two-dimensional 1H NMR spectroscopy, and molecular secondary ion mass spectrometry. The O-linked oligosaccharides isolated from KDN-gp have been shown to contain a common core trisaccharide Gal beta 1-3GalNAc alpha 1-3GalNAc in which the terminal Gal residue is blocked by a single residue of deaminated neuraminic acid (KDN) and the proximal GalNAc residue is substituted by alpha-2,8-linked oligo(KDN) chains. Structures of KDN-oligosaccharide chains in the glycoprotein are novel and expressed by the following general formula, where n = 0-5, for which data are available. [formula: see text]
Orientation measurements of microsphere doublets and metaphase chromosomes in flow (1986)

Obtaining information about the shape of particles from slit-scan profiles is facilitated if the particles are oriented. Elongated particles orient in the nozzle of flow cytometers, but orientation may be disrupted before the particles get to the point of measurement. We have used our slit-scan flow cytometer to investigate the orientation of microsphere doublets in a liquid jet in air, in flow across a glass surface, and in a 200-microns-square capillary tube as a function of distance from the flow chamber nozzle. Particles were classified as being oriented if there was a centrally located dip in the slit-scan profile. Essentially all the doublets in the jet were oriented, and no disorientation was noted over the distances measured (up to 10 mm from the nozzle). Particle orientation was maintained for 80 microns in flow across a glass surface. In the capillary-type flow chamber, essentially all of the particles were oriented at the tube entrance and for several millimeters into the tube. There then occurred a region where particle tumbling started and progressively fewer doublets met the orientation criteria. The distance to where tumbling began could be estimated by calculating the length required to establish the parabolic flow profile in the tube. Finally, the fraction of oriented particles reached a constant value that did not change with increased distance into the tube. When sample was injected off axis (i.e., halfway between the chamber center and the chamber walls), particle tumbling began closer to the tube entrance.(ABSTRACT TRUNCATED AT 250 WORDS)
Structures and Immunochemical Properties of Oligosaccharides Isolated from Pig Submaxillary Mucins (1968)

Abstract Two immunochemically distinct mucins have been isolated from pig submaxillary glands. The glands were combined according to the ability of aqueous extracts of these glands to inhibit hemagglutination of human type A erythrocytes. Mucin isolated from the glands containing blood group A activity is designated A+ pig submaxillary mucin (A+-PSM), while mucin isolated from the remaining glands is designated A- pig submaxillary mucin (A--PSM). The carbohydrate composition of both mucins is similar and comprises N-acetylgalactosamine, fucose, galactose, and N-glycolylneuraminic acid. Treatment of these mucins with alkaline borohydride resulted in the release of a series of reduced oligosaccharides and the monosaccharide, 2-acetamido-2-deoxy-d-galactitol (N-acetylgalactosaminitol). Conditions are reported which give more than 90% cleavage of the sugar residues from the protein chain. The most complex oligosaccharide (designated oligosaccharide I) was a pentasaccharide, 2-acetamido-2-deoxy-α-d-galactopyranosyl (1 → 3)-[α-l-fucopyranosyl-(1 → 2)]-β-d-galactopyranosyl-(1 → 3)-[N-glycolylneuraminyl-(2 → 6)]-2-acetamido-2-deoxy-d-galactitol. In addition, the following oligosaccharides were isolated (structures are given as related to oligosaccharide I): oligosaccharide II, I minus N-acetylgalactosamine; oligosaccharide III, a disaccharide N-glycolylneuraminyl → N-acetylgalactosaminitol; oligosaccharide IV, I minus N-glycolylneuraminic acid; oligosaccharide V, II minus N-glycolylneuraminic acid. N-Acetylgalactosaminitol (Fraction VI) was the only detectable monosaccharide. Rabbit antiserum to human type A erythrocyte stroma precipitated A+-PSM, but not A--PSM. Oligosaccharides I and IV, found only in A+-PSM, are potent inhibitors of the anti A-A+-PSM precipitation, but oligosaccharides II, III, and V and a monosaccharide (Fraction VI) are completely inactive.
Damage of the outer membrane of enteric gram-negative bacteria by lactoferrin and transferrin (1988)

Many studies have shown that lactoferrin and transferrin have antimicrobial activity against gram-negative bacteria, but a mechanism of action has not been defined. We hypothesized that the iron-binding proteins could affect the gram-negative outer membrane in a manner similar to that of the chelator EDTA. The ability of lactoferrin and transferrin to release radiolabeled lipopolysaccharide (LPS) from a UDP-galactose epimerase-deficient Escherichia coli mutant and from wild-type Salmonella typhimurium strains was tested. Initial studies in barbital-acetate buffer showed that EDTA and lactoferrin cause significant release of LPS from all three strains. Further studies found that LPS release was blocked by iron saturation of lactoferrin, occurred between pH 6 and 7.5, was comparable for bacterial concentrations from 10(4) to 10(7) CFU/ml, and increased with increasing lactoferrin concentrations. Studies using Hanks balanced salt solution lacking calcium and magnesium showed that transferrin also could cause LPS release. Additionally, both lactoferrin and transferrin increased the antibacterial effect of a subinhibitory concentration of rifampin, a drug excluded by the bacterial outer membrane. This work demonstrates that these iron-binding proteins damage the gram-negative outer membrane and alter bacterial outer membrane permeability.
Granulocyte Activation Markers in Induced Sputum: Comparison Between Chronic Obstructive Pulmonary Disease, Asthma, and Normal Subjects (1997)

Airway inflammation is present in asthma and is thought to play a significant part in the development of airflow obstruction. In chronic obstructive pulmonary disease (COPD), neutrophilic inflammation is present in the airway lumen, whereas the submucosa displays a lymphocytic infiltrate. Less is known about the nature and mechanisms of inflammation in COPD than in asthma. Induced sputum allows noninvasive sampling of respiratory tract secretions from patients and control subjects, allowing characterization of cells and measurement of soluble markers. We exploited this technique in order to compare the presence and quantify specific markers of eosinophil and neutrophil activation in subjects with asthma or COPD, and control subjects. Differential cell counts showed significantly higher neutrophil percentages in the patients with COPD compared with other groups, while patients with asthma had higher numbers of eosinophils. The neutrophil markers myeloperoxidase (MPO), from primary granules in neutrophils, and human neutrophil lipocalin (HNL), released from secondary granules, were elevated in patients with asthma and COPD compared with control subjects but markedly more so in COPD. The difference between COPD and asthma was more marked for HNL than for MPO suggesting that HNL may be a better marker for discriminating between these conditions. Concentrations of the eosinophil granule protein, eosinophil cationic protein (ECP), and the eosinophil granule-derived enzyme, eosinophil peroxidase (EPO) were raised in the patients with asthma and those with COPD.
Radiation Chemistry of Polymers for Electronic Applications (1989)

Polymer chemistry and polymer radiation chemistry in particular are key elements of the electronics industry. Polymer materials that undergo radiation induced changes in solubility are used to define the individual elements of integrated circuits. As the demands placed on these materials increases due to increased circuit density and complexity, new materials and chemistry will be required. Many of the new chemistries that are being developed are described in this article.
Nanoelectrochemical Patterning of Monolayer Surfaces: Toward Spatially Defined Self-Assembly of Nanostructures (1999)

Functionalized organic monolayers are excellent candidates for the preparation of templates with selectable surface chemical properties. A versatile self-assembly approach is reported to the in situ chemical generation of spatially defined surface nanostructures (see Figure). The patterning process used allows the nanoscale inscription of chemical information on the surface of functionalized organic monolayers.
Tyrosine phosphatases as a superfamily of tumor suppressors in colorectal cancer. (2011)

Phosphorylation and dephosphorylation processes catalyzed by numerous kinases and phosphorylases are essential for cell homeostasis and may lead to disturbances in a variety of vital cellular pathways, such as cell proliferation and differentiation, and thus to complex diseases including cancer. As over 80 % of all oncogenes encode protein tyrosine kinases (PTKs), protein tyrosine phosphatases (PTPs), which can reverse the effects of tyrosine kinases, are very important tumor suppressors. Alterations in tyrosine kinase and phosphatase genes including point mutations, changes in epigenetic regulation, as well as chromosomal aberrations involving regions critical to these genes, are frequently observed in a variety of cancers. Colorectal cancer (CRC) is one of the most common cancers in humans. CRCs occur in a familial (about 15 % of all cases), hereditary (about 5%) and sporadic (almost 75-80 %) form. As genetic-environmental interrelations play an important role in the susceptibility to sporadic forms of CRCs, many studies are focused on genetic alterations in such tumors. Mutational analysis of the tyrosine phosphatome in CRCs has identified somatic mutations in PTPRG, PTPRT, PTPN3, PTPN13 and PTPN14. The majority of these mutations result in a loss of protein function. Also, alterations in the expression of these genes, such as decreased expression of PTPRR, PTPRO, PTPRG and PTPRD, mediated by epigenetic mechanisms have been observed in a variety of tumors. Since cancer is a social and global problem, there will be a growing number of studies on alterations in the candidate cancer genes, including protein kinases and phosphatases, to determine the origin, biology and potential pathways for targeted anticancer therapy.
Ursolic Acid fromPlantagomajor, a Selective Inhibitor of Cyclooxygenase-2 Catalyzed Prostaglandin Biosynthesis (1998)

A hexane extract of Plantago major was investigated by bioactivity-directed fractionation, using an in vitro cyclooxygenase-2 (COX-2) catalyzed prostaglandin biosynthesis inhibition assay, and resulted in the isolation of ursolic acid (1). This triterpenoid showed a significant COX-2 inhibitory effect, directly on the enzyme activity, with an IC50 value of 130 microM and a COX-2/COX-1 selectivity ratio of 0.6. The structural isomer oleanolic acid (2) was found to be less active than 1, with an IC50 value of 295 microM, but showed a similar selectivity ratio (0.8). Furthermore, no significant inhibition on COX-2 or COX-1 was observed by the triterpenoid, 18beta-glycyrrhetinic acid (3). The direct inhibitory effect of 1 and 2 on COX-2 catalyzed prostaglandin biosynthesis increased with preincubation, indicating a time-dependent inhibition, while the effect on COX-1 was found to be independent of preincubation time.
Tension-Tension Fatigue of Microcellular Polycarbonate: Initial Results (1993)

The fatigue life of microcellular polycarbonate specimens of five different relative densities ranging from 0.52 to 0.97 was measured in tension-tension tests on dumbbell specimens. Fatigue life varied with relative density and maximum nominal cyclic stress. The fatigue life of microcellular polycarbonate with relative foam density of 0.97 exceeded that of solid polycarbonate by over 400 percent. Fatigue life decreased with decreased relative foam density.
Carotid artery intima‐media thickness and brachial artery flow‐mediated vasodilation in asymptomatic Japanese male subjects amongst apolipoprotein E phenotypes (2002)

ApoE4 phenotype was independently associated with an increased risk of carotid atherosclerosis and elevated LDL-cholesterol levels in asymptomatic middle-aged Japanese men.
Detection ofEhrlichia platysDNA in Brown Dog Ticks (Rhipicephalus sanguineus) in Okinawa Island, Japan (2000)

Thirty-two Rhipicephalus sanguineus females collected from eight free-roaming dogs in Okinawa Island, Japan, were examined for ehrlichial DNA by 16S rRNA-based PCR and subsequent sequencing. Partial sequences of Ehrlichia platys 16S rRNA (678 to 679 bp) were detected in three ticks (9.4%) from two dogs. This is the first report of detection of E. platys in Japan, and also the first report of detection in ticks.
First Total Synthesis of an Exceptionally Potent Antitumor Saponin, OSW-1 (1998)

OSW-1 (1), an acylated disaccharide cholestane saponin from Ornithogalum saudersiae with exceptionally potent antitumor activity, was first synthesized from commercially available dehydroisoandrosterone, L-arabinose, and D-xylose in total 27 steps with the longest linear sequence of 14 steps and in 6% yield.
Changing the institutional practice of prolonged mechanical ventilation after coronary artery bypass graft surgery to early extubation. (1999)

Since 1997 some of our cardiac anaesthetists have, whenever possible, extubated the patients early after cardiac surgery to improve their level of comfort, to allow an early return of the cardiopulmonary physiological function, and to help reduce health care costs. After a few months of implementing this practice, an audit was carried out to evaluate the success of early extubation after coronary artery bypass graft (CABG) surgery. Over a 6-month period starting from May 1997, the perioperative data of 110 consecutive patients with good or moderate left ventricular function scheduled for elective CABG were prospectively collected and analysed. The anaesthetic regime was according to the preference of the anaesthetists. Initially consent was obtained from the surgeons when the extubation criteria were fulfilled, but subsequently as the practice became more accepted by the surgeons, extubation was initiated by the anaesthetists. Within 4 hours of admission into the intensive care unit (ICU), 50 (45.5%) of the 110 patients satisfied the early extubation criteria and were extubated. The extubation criteria are described in the article. For the remaining patients, the median duration of mechanical ventilation was 14.3 hours. The profiles of the two groups of patients and the possible reasons for not extubating early are discussed. Forty-five per cent of the patients with moderate to good ventricular function were extubated safely within 4 hours of admission into the ICU after CABG surgery. With gradual acceptance of the practice and a change in mindset amongst all the care givers, more patients can benefit from this practice. This article highlights the challenges associated with changing institutional practices with respect to the postoperative care of cardiac patients.
Cloned Viral Protein Vaccine for Foot-and-Mouth Disease: Responses in Cattle and Swine (1981)

A DNA sequence coding for the immunogenic capsid protein VP 3 of foot-and-mouth disease virus A 12 , prepared from the virion RNA, was ligated to a plasmid designed to express a chimeric protein from the Escherichia coli tryptophan promoter-operator system. When Escherichia coli transformed with this plasmid was grown in tryptophan-depleted media, approximately 17 percent of the total cellular protein was found to be an insoluble and stable chimeric protein. The purified chimeric protein competed equally on a molar basis with VP 3 for specific antibodies to foot-and-mouth disease virus. When inoculated into six cattle and two swine, this protein elicited high levels of neutralizing antibody and protection against challenge with foot-and-mouth disease virus.
Novel Therapeutics for Schizophrenia: Targeting Glycine Modulation of NMDA Glutamate Receptors (2007)

Currently, a major hypothesis for the pathophysiology of schizophrenia proposes that numerous risk factors converge on the N -methyl-D-aspartate (NMDA) receptor for the neurotransmitter glutamate, resulting in neurodevelopmental abnormalities at glutamate synapses and hypofunction of NMDA receptors.This hypothesis was presented in a previous “Trends in Psychopharmacology” column. Novel treatments are now in development that can theoretically boost the function of NMDA receptors by enhancing actions at the glycine co-transmitter site of this receptor complex. Early studies already indicate that this may lead to improvement in negative and cognitive symptoms of schizophrenia, especially when added as augmenting agents to atypical antipsychotics.
Chemical Inducers of Targeted Protein Degradation (2010)

The functions of many cellular proteins have been elucidated by selective gene inactivation and subsequent phenotypic analysis. For example, genetic mutations, gene knock-out generation, and the use of RNA interference to target mRNA for degradation can all result in decreased production of a specific protein, yielding informative cellular phenotypes. However, these techniques each have certain inherent limitations. This minireview focuses on the recent development of new approaches to study protein function at the post-translational level, namely chemical induction of targeted protein degradation.
Regularized image sequence interpolation by fusing low-resolution frames (2003)

This paper presents the feasibility of using different data sets, which correspond to the same scene to get a better resolution and information of the scene than the one obtained using only one data set. We propose a regularized image sequence interpolation algorithm, which can restore high frequency details by fusing low-resolution frames. In order to apply the regularization approach to the interpolation procedure, we use a two-dimensional separable image degradation model for a low resolution imaging system. The proposed algorithm provides a better-interpolated image by fusing low-resolution frames.
Synthesis and Characterization of a New Series of Hydroxy Pyrazolines (2008)

Abstract 3-Phenyl-1-(thiophen-2-yl)prop-2-en-1-one obtained by Claisen–Schmidt condensation of 2-acetyl thiophene with benzaldehyde was converted into 2,3-dibromo-3-phenyl-1-(thiophen-2-yl)propan-1-one, which on treatment with various thiosemicarbazides in the presence of triethylamine in absolute ethanol, yielded the corresponding hydroxy pyrazolines 3a–h. All the compounds were characterized by IR, 1H NMR, and 13C NMR spectra.
Safeguards and pitfalls in minimally invasive mitral valve surgery. (2013)

Minimally invasive mitral valve surgery has been established in many institutions worldwide. Appropriate indications and patient selection for this procedure must be based on a thorough understanding of its limitations and specific pitfalls. Particular risks can be minimized with careful attention to detail when planning and performing the surgery. The following chapter offers a stepwise description of the procedure; we point out particular advantages, discuss our rationale for certain steps, as well as focus on potential dangers of minimally invasive mitral valve surgery. Several graphics have also been provided to illustrate our approach and demonstrate important structural and anatomical concepts of the mitral valve apparatus.
Robust and efficient quantization of speech LSP parameters using structured vector quantizers (1991)

Three robust algorithms based on the recently proposed concept of structured vector quantization have been developed for quantization of speech LSP (line spectrum pair) parameters. The first algorithm exploits interframe correlation of the LSP parameters and requires 24 bits per LSP vector to achieve 1 dB average spectral distortion. The second and third algorithms quantize each LSP vector independently and for 1 dB distortion require 29 and 25 bits per vector, respectively. The last two algorithms result in a considerably smaller fraction of frames with distortions greater than 2 dB as compared to other schemes proposed so far.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparison of antigenic properties among various strains of Treponema hyodysenteriae. (1979)

Agglutinin-absorption and precipitin-absorption studies demonstrated that three strains of Treponema hyodysenteriae isolated from cases of swine dysentery were antigenically different from each other and also from a spirochete isolated from a clinically normal dog. Each of the strains of T. hyodysenteriae also possessed two common antigens.
Colorless optical add/drop using small matrix switch and cyclic AWG (2013)

We describe a new wavelength routing switch architecture that uses small matrix switches and cyclic arrayed-waveguide gratings. This switch enables us to provide colorless add/drop ports in reconfigurable optical add/drop multiplexer nodes.
Cytokine Concentrations in Plasma from Children with Severe and Non-Severe Community Acquired Pneumonia (2015)

ClinicalTrials.gov NCT00148733.