gebhart/patrepeval huggingface dataset:
Detailed Oligosaccharide Structures of Human Integrin α5β1 Analyzed by a Three‐Dimensional Mapping Technique (1996)

Structures of N-linked oligosaccharides obtained from human integrin alpha 5 beta 1 are described. Integrin alpha 5 beta 1 (4.5 mg) was purified from human placenta and digested using trypsin and chymotrypsin. N-linked oligosaccharides were released from the glycopeptides by digestion with glycoamidase A (from almond). The reducing ends of the oligosaccharides were derivatized with 2-aminopyridine. The pyridylamino-oligosaccharides were separated and these structures were identified by a three-dimensional HPLC mapping technique on three kinds of HPLC columns [Takahashi, N., Nakagawa, H., Fujikawa, K., Kawamura, Y. & Tomiya, N. (1995) Anal. Biochem. 226, 139-146]. Finally, 35 different oligosaccharide structures were identified, 10 of which were neutral, 6 mono-sialyl, 10 di-sialyl, 7 tri-sialyl and 2 tetra-sialyl. The molar ratio of neutral, mono-sialyl, di-sialyl, tri-sialyl and tetra-sialyl oligosaccharides was 20.8%, 24.8%, 27.7%, 18.1% and 8.6%, respectively. High-mannose-type oligosaccharides accounted for only 1.5% of the total. The remaining oligosaccharides were all complex type. The most predominant structure was the diantennary di-alpha-(2,3)-sialyl fucosyl. Major linking of sialic acid was alpha-(2,3)-linkage, and over 50% of all oligosaccharides were fucosylated at the N-acetylglucosamine residue of the reducing end.
Protection of Human Genomic DNA from Mechanical Stress by Reversible Folding Transition (2010)

Be compact, be protected: We show that reversible folding transition allows the protection of human genomic DNA from mechanical stress. By using molecular combing, we established that folded DNA molecules can undergo strong mechanical stress without fragmentation and perfectly recover their initial size and conformation after unfolding. This opens new perspectives for high-throughput DNA mapping and sequencing, large chromosomal rearrangement detection, and high-precision quantification of DNA damage. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Antibodies to liposomal phosphatidylserine and phosphatidic acid (1990)

Polyclonal antisera to phosphatidylserine or phosphatidic acid were induced in rabbits by injecting liposomes containing phosphatidylserine or phosphatidic acid and lipid A. Adsorption of antisera with liposomes containing different phospholipids revealed that some degree of reactivity with one or more phospholipids other than the immunizing phospholipid was often observed. However, cross-reactivity with other phospholipids was not a universal phenomenon, and one antiserum to phosphatidylserine failed to cross-react (i.e., was not adsorbed) with liposomes containing other phospholipids. All of the antisera were inhibited by soluble phosphorylated haptens (e.g., phosphocholine but not choline), but one of the antisera to phosphatidylserine was inhibited both by phosphoserine and by serine alone. Liposomal membrane composition influenced the activity of antiserum to phosphatidylserine. Regardless of whether unsaturated (beef brain) or saturated (dimyristoyl) phosphatidylserine was used in the immunizing liposomes, the antisera reacted more vigorously with liposomes containing unsaturated than saturated phosphatidylserine. We conclude that liposomes containing lipid A can serve as vehicles for stimulating polyclonal antisera to phosphatidylserine and phosphatidic acid. Although cross-reactivity with certain other phospholipids can be observed, sera from selected animals apparently can exhibit a high degree of specific activity to the immunizing phospholipid antigen.
203 EFFECT OF OXYGEN TENSION AND SUBSTRATE ON GROWTH AND DIFFERENTIATION OF MOUSE EMBRYONIC STEM CELLS (2005)

Normally the majority of mammalian cells, including murine embryonic stem (mES) cells, are immersed in a low oxygen environment (hypoxia); however, mES are generally cultured in an atmosphere containing 21% O2 (normoxia). Such conditions may not be the most appropriate for mES propagation. We have tested the effects of hypoxia and culture on either feeder fibroblasts or gelatin substrate on mES cell growth and spontaneous differentiation. Two ES cell lines (R1 129/Sv from the laboratory of A. Nagy and MAR B6D2 F1 generated in our laboratory) were cultured under two different oxygen tensions (5 and 21%), and on two different substrates, 0.1% gelatin or murine embryonic fibroblasts (mEF). Cell cycle, cell proliferation, mRNA expression of pluripotency and differentiation markers, as well as spontaneous differentiation to cardiomyocytes, were monitored. For cell proliferation measurements, mES after 7 days of culture at the different conditions were labeled with 5-(and-6)-carboxyfluorescein diacetate succinimidyl ester, and cultured for up to three more days. Cells were then harvested for flow cytometry analysis every 24 h after labeling (Cell TraceTM CFSE Cell Proliferation Kit; Molecular Probes, Inc., Eugene, OR, USA). For cell cycle analysis, cells grown on mEF under the two different oxygen tensions were fixed after 10 days of culture, and then stained with propidium iodide/Triton-X-100 for flow cytometry analysis (Current Protocols in Cytometry, Chap. 7, 2001). The spontaneous differentiation of embryoid bodies [formed by ES cells in the absence of leukemia inhibitory factor (LIF)] to cardiomyocytes was also monitored. For mRNA expression of pluripotency (Nanog, Oct-3/4, Rex1, GENESIS, FGFR-4, TERF1, Cx43, and GLUT1) and differentiation markers (GATA4, GATA2, AFP, Msx-1, Brachyury, and Myf5), RT-PCR analysis was performed on mES cells from Day 0 to Day 10. Under hypoxia conditions, the proliferation of both types of mES cells was greater than under normoxia, independent of substrate used, and a higher number of apoptotic cells was detected. Moreover, only under normoxia conditions did mES cells lose the expression of pluripotency markers GENESIS and GLUT1. In addition, under lower oxygen tension, the rate of differentiation to beating cardiomyocytes was significantly lower on the feeder layer than that under normoxia (11.9% vs. 28.1%; P = 0.012). The feeder layer supported significantly higher cardiomyocyte formation when compared to 0.1% gelatin at 21% O2 (28.1% vs. 8.3%; P &amp;lt; 0.001). Our results show that normoxia may not be the most appropriate condition for mES cell propagation and that hypoxic culture may be necessary to maintain full pluripotency of mES cells.
Frequency-specific mechanism links human brain networks for spatial attention (2013)

Selective attention allows us to filter out irrelevant information in the environment and focus neural resources on information relevant to our current goals. Functional brain-imaging studies have identified networks of broadly distributed brain regions that are recruited during different attention processes; however, the dynamics by which these networks enable selection are not well understood. Here, we first used functional MRI to localize dorsal and ventral attention networks in human epileptic subjects undergoing seizure monitoring. We subsequently recorded cortical physiology using subdural electrocorticography during a spatial-attention task to study network dynamics. Attention networks become selectively phase-modulated at low frequencies (δ, θ) during the same task epochs in which they are recruited in functional MRI. This mechanism may alter the excitability of task-relevant regions or their effective connectivity. Furthermore, different attention processes (holding vs. shifting attention) are associated with synchrony at different frequencies, which may minimize unnecessary cross-talk between separate neuronal processes.
Theoretical Study of the Electronic Structure of 2,2′-Bisilole in Comparison with 1,1′-Bi-1,3-cyclopentadiene: σ*–π* Conjugation and a Low-Lying LUMO as the Origin of the Unusual Optical Properties of 3,3′,4,4′-Tetraphenyl-2,2′-bisilole (1996)

Abstract The purpose of this work is the theoretical elucidation of the origin of the unusually long UV-vis absorption maximum, λmax = 398 nm, of 3,3′,4,4′-tetraphenyl-2,2′-bisilole, which we have observed recently. Several semiempirical and ab initio calculations have been performed for some model compounds, silole and 2,2′-bisilole, in comparison with their carbon analogs, cyclopentadiene and 1,1′-bi-1,3-cyclopentadiene, respectively. The PM3 calculations indicate that the silole ring has a considerably low-lying LUMO, arising from σ*–π* conjugation between a π-symmetry σ* orbital of the exocyclic σ bonds on silicon and a π* orbital of the butadiene skeleton. Ab initio calculations at the CIS/6-31G* level of theory suggest that the experimental large differences in the absorption maximum in the UV-vis spectra between the bisilole and the bicyclopentadiene derivatives are ascribed also to the low-lying LUMO level of the bisilole compared with the bicyclopentadiene. It is further demonstrated that the σ*–π* conjugation is enhanced by the molecular distortions, twisting and folding, of the bisilole skeleton present in the X-ray structure, resulting in the lowering of the LUMO level. The calculated data are supported by the redox potentials of some representative compounds, as determined by cyclic voltammetry measurements. The σ*–π* conjugation and the low-lying LUMO would thus be the origin of the unusual optical properties of bisilole derivatives.
Effects of duodenal distension on antropyloroduodenal pressures and perception are modified by hyperglycemia (1999)

Marked hyperglycemia (blood glucose approximately 15 mmol/l) affects gastrointestinal motor function and modulates the perception of gastrointestinal sensations. The aims of this study were to evaluate the effects of mild hyperglycemia on the perception of, and motor responses to, duodenal distension. Paired studies were done in nine healthy volunteers, during euglycemia ( approximately 4 mmol/l) and mild hyperglycemia ( approximately 10 mmol/l), in randomized order, using a crossover design. Antropyloroduodenal pressures were recorded with a manometric, sleeve-side hole assembly, and proximal duodenal distensions were performed with a flaccid bag. Intrabag volumes were increased at 4-ml increments from 12 to 48 ml, each distension lasting for 2.5 min and separated by 10 min. Perception of the distensions and sensations of fullness, nausea, and hunger were evaluated. Perceptions of distension (P < 0.001) and fullness (P < 0.05) were greater and hunger less (P < 0.001) during hyperglycemia compared with euglycemia. Proximal duodenal distension stimulated pyloric tone (P < 0.01), isolated pyloric pressure waves (P < 0.01), and duodenal pressure waves (P < 0.01). Compared with euglycemia, hyperglycemia was associated with increases in pyloric tone (P < 0.001), the frequency (P < 0.05) and amplitude (P < 0.01) of isolated pyloric pressure waves, and the frequency of duodenal pressure waves (P < 0.001) in response to duodenal distension. Duodenal compliance was less (P < 0.05) during hyperglycemia compared with euglycemia, but this did not account for the effects of hyperglycemia on perception. We conclude that both the perception of, and stimulation of pyloric and duodenal pressures by, duodenal distension are increased by mild hyperglycemia. These observations are consistent with the concept that the blood glucose concentration plays a role in the regulation of gastrointestinal motility and sensation.
Geometric and photometric constraints: motion and structure from three views (1998)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1998.
Absence of Duplication of Chromosome 21 Genes in Familial and Sporadic Alzheimer's Disease (1987)

The possibility that Alzheimer's disease (AD) is caused by overexpression or duplication of one or more genes on chromosome 21 has been raised by the observation of AD-like neuropathologic changes in individuals with Down syndrome and by the mapping of both the defect for familial AD and the amyloid beta protein gene to this autosome. Possible duplication on chromosome 21 was investigated in both familial and sporadic AD by means of restriction fragment length polymorphisms for the amyloid and SODI loci, as well as for DNA markers in the vicinity of the familial AD defect and in the critical Down syndrome region of chromosome 21. No evidence of increased DNA dosage was observed in either brain or leukocytes of patients with inherited or sporadic forms of AD. Duplication of these regions is therefore not a frequent event in either form of AD. Furthermore, no significant allelic association was detected between AD and any of the loci, including the amyloid and SODI genes, providing no support for the hypothesis that defects in these specific genes are the primary cause of AD.
Levetiracetam inhibits glutamate transmission through presynaptic P/Q‐type calcium channels on the granule cells of the dentate gyrus (2009)

These results suggest that levetiracetam modulated the presynaptic P/Q-type voltage-dependent calcium channel to reduce glutamate release and inhibited the amplitude of EPSC in DG. This effect is most likely to contribute to the anti-epileptic action of levetiracetam in patients.
Total Synthesis of Soraphen A1α (1999)

The convergent synthesis of macrolide soraphen A1α is described starting from glucose (western part) and mannose (eastern part). Mannose was converted into a 2-deoxyribohexapyranoside that could be methylated and reduced stereoselectively. Chain elongation at C-6 was carried out by stereoselective addition of a magnesium acetylide. The two fragments (western and eastern) were assembled by a Julia olefination followed by macrolactonization. The introduction of the methyl group at C-2 of norsoraphen occurred stereoselectively for thermodynamic reasons.
Commercially Available Immunoglobulins Contain Virus Neutralizing Antibodies Against All Major Genotypes of Polyomavirus BK (2015)

Neutralizing antibodies (NAbs) form the basis of immunotherapeutic strategies against many important human viral infections. Accordingly, we studied the prevalence, titer, genotype-specificity, and mechanism of action of anti-polyomavirus BK (BKV) NAbs in commercially available human immune globulin (IG) preparations designed for intravenous (IV) use. Pseudovirions (PsV) of genotypes Ia, Ib2, Ic, II, III, and IV were generated by co-transfecting a reporter plasmid encoding luciferase and expression plasmids containing synthetic codon-modified VP1, VP2, and VP3 capsid protein genes into 293TT cells. NAbs were measured using luminometry. All IG preparations neutralized all BKV genotypes, with mean EC50 titers as high as 254 899 for genotype Ia and 6,666 for genotype IV. Neutralizing titers against genotypes II and III were higher than expected, adding to growing evidence that infections with these genotypes are more common than currently appreciated. Batch to batch variation in different lots of IG was within the limits of experimental error. Antibody mediated virus neutralizing was dose dependent, modestly enhanced by complement, genotype-specific, and achieved without effect on viral aggregation, capsid morphology, elution, or host cell release. IG contains potent NAbs capable of neutralizing all major BKV genotypes. Clinical trials based on sound pharmacokinetic principles are needed to explore prophylactic and therapeutic applications of these anti-viral effects, until effective small molecule inhibitors of BKV replication can be developed.
Positively charged oligonucleotides overcome potassium-mediated inhibition of triplex DNA formation (1996)

The formation of triplex DNA using unmodified, purine-rich oligonucleotides (ODNs) is inhibited by physiologic levels of potassium. Changing negative phosphodiester bonds in a triplex forming oligonucleotide (TFO) to neutral linkages causes a small increase in triplex formation. When phosphodiester bonds in a TFO are converted to positively-charged linkages the formation of triplex DNA increases dramatically. In the absence of KCl, a 17mer TFO containing 11 positively-charged linkages at a concentration of 0.2 microM converts essentially all of a 30 bp target duplex to a triplex. Less than 15% of the target duplex is shifted by 2 microMolar of the unmodified TFO. In 130 mM KCl, triplex formation is undetectable using the unmodified TFO, while triplex formation is nearly complete with 2 microM positively-charged TFO. With increasing potassium, TFOs containing a higher proportion of modified linkages show enhanced triplex formation compared with those less modified. In contrast with unmodified TFOs, triplex formation with more heavily modified TFOs can occur in the absence of divalent cations. We conclude that replacement of phosphodiester bonds with positively-charged phosphoramidate linkages results in more efficient triplex formation, suggesting that these compounds may prove useful for in vivo applications.
Golgi function and dysfunction in the first COG4-deficient CDG type II patient (2009)

The conserved oligomeric Golgi (COG) complex is a hetero-octameric complex essential for normal glycosylation and intra-Golgi transport. An increasing number of congenital disorder of glycosylation type II (CDG-II) mutations are found in COG subunits indicating its importance in glycosylation. We report a new CDG-II patient harbouring a p.R729W missense mutation in COG4 combined with a submicroscopical deletion. The resulting downregulation of COG4 expression additionally affects expression or stability of other lobe A subunits. Despite this, full complex formation was maintained albeit to a lower extent as shown by glycerol gradient centrifugation. Moreover, our data indicate that subunits are present in a cytosolic pool and full complex formation assists tethering preceding membrane fusion. By extending this study to four other known COG-deficient patients, we now present the first comparative analysis on defects in transport, glycosylation and Golgi ultrastructure in these patients. The observed structural and biochemical abnormalities correlate with the severity of the mutation, with the COG4 mutant being the mildest. All together our results indicate that intact COG complexes are required to maintain Golgi dynamics and its associated functions. According to the current CDG nomenclature, this newly identified deficiency is designated CDG-IIj.
TFC selection for MAC scheduling in WCDMA (2003)

Reacting to the evolution of user's needs toward multimedia applications, an important feature of the third generation mobile networks is to support efficiently multiple applications with different quality of service. In the radio access networks of UMTS, RLC/MAC layers are designed to accommodate simultaneously mixed services through establishing multiple bearers. A major issue is the rate adaption of these bearers. In this paper, we examine the scheduling problem in the WCDMA MAC layer and propose five scheduling methods. Our simulation result shows that a load measurement based priority method can achieve better fairness and has better execution time performance than the other four methods.
Fabrication of ordered arrays of silicon nanopillars (1999)

We report the fabrication of ordered arrays of silicon nanopillars via reactive ion etching (RIE). Self-assembled polymer spheres are used as masks for the deposition of hexagonal arrays of Ag islands on a silicon substrate. Following the removal of the polymer spheres, the sample is etched with SF6 and CF4 at 100 W leading to hexagonal arrays of silicon nanopillars. The aspect ratio of the pillars can be influenced by the etching time; maximum aspect ratios of 15:1 have been produced.
Menstrual Reduction With Extended Use of Combination Oral Contraceptive Pills (2001)

In Brief OBJECTIVE To compare a traditional 28-day cycle to an extended 49-day cycle of the 30 μg ethinyl estradiol (E2)/300 μg norgestrel monophasic birth control pill regimen. METHODS Ninety subjects randomized to either 28-day cycles with 21 active pills or 49-day cycles with 42 active pills for a prospective open label trial over four 84-day reference periods or trimesters. Bleeding, pill taking, and symptom diaries were completed. The sample size with 80% power to detect a 40% reduction in bleeding days required 24 subjects in each arm. RESULTS Of the 90 women, 24 subjects (54.5%) on the 28-day cycle and 29 (63%) on the 49-day cycle completed the entire study (P = .41). There were no statistically significant differences between the two groups in demographics or continuation rates. There was a significant reduction in bleeding days in the experimental arm beginning in the first trimester (28-day = 10.9, 49-day = 6.4 mean days of bleeding, P < .001) and continuing to the fourth trimester (28-day = 11.3, 49-day = 5.8 mean days, P = .005). The number of spotting days was similar between both schedules in the first trimester (28-day = 4.8, 49-day = 3.7 mean days, P = .24) and continued into the fourth trimester (28-day = 3.4, 49-day = 2.9 mean days, P = .30). Annual expenditure for hygiene products was significantly less for extended use subjects (28-day = $41.45, 49-day = $17.54 spent, P < .001). CONCLUSION Extension of the 28-day oral contraceptive (OC) cycle to a 49-day cycle resulted in fewer bleeding days and no increase in mean spotting days or bleeding episodes. Extension of a monophasic oral contraceptive regimen from 28-day to 49-day cycles significantly decreases bleeding and hygiene product use without increased spotting.
Template Resolution in XML/HTML. (1998)

This paper describes a framework for applying templates to applications and documents on the Web. The primary motivation is the need of Web application developers to separate program logic from presentation logic. A template is a prototypical document or part thereof. It consists of content in the target language, HTML, XML, or plain text, plus markup specifying variable parts of the document. The Template Markup Language (TML) is an application of XML which defines a generic and flexible set of template markup elements. TRiX (Template Resolution in XML/HTML) is a framework for processing TML. It excels in being highly extensible - both in the types of values variables can take, variables being URLs, and in the set of template elements recognized. Keywords: Templates, Web-based applications, Markup Languages, XML, HTML, Macros, OO Frameworks. 1. Introduction Applications on the World-Wide Web use the Common Gateway Interface or Web server APIs in order to generate content dy...