gebhart/patrepeval huggingface dataset:
Alternate-Strand Triplex Formation:  Modulation of Binding to Matched and Mismatched Duplexes by Sequence Choice in the Pu-Pu-Py Block (1996)

In double-stranded DNA, tandem blocks of purines (Pu) and pyrimidines (Py) can form triplexes by pairing with oligonucleotides which also consist of blocks of purines and pyrimidines, using both Py.Pu.Py (Y-type) and Pu.Pu.Py (R-type) pairing motifs in a scheme called "alternate-strand recognition," or ASR [Jayasena, S. D., & Johnston, B. H. (1992) Biochemistry 31, 320-327; Beal P. A., & Dervan, P. B. (1992) J. Am. Chem. Soc. 114, 1470-1478]. We investigated the relative contributions of the Py.Pu.Py and Pu.Pu.Py blocks in the 16-bp duplex sequence 5'-AAGGAGAATTCCCTCT-3' paired with the third-strand oligonucleotides 5'-TTCCTCTTXXGGGZGZ-3' (XZ-16), where X and Z are either T or A and C is 5-methylcytosine, using chemical footprinting and get electrophoretic mobility shift measurements. We found that the left-hand, pyrimidine half (Y-block) of the third strand (TTCCTCTT, Y-8) forms a Py.Pu.Py triplex as detected by both dimethyl sulfate (DMS) probing and a gel-shift assay; in contrast, the triplex formed by the right-hand half alone (R-block) with X = T (TTGGGTGT, R-8) is not detectable under the conditions tested. However, when tethered to the Y-block (i.e., as XZ-16), the R-block contributes greatly increased specificity of target recognition and confers protection from DMS onto the duplex even under conditions unfavorable for Pu-Pu-Py triplexes (lack of divalent cations). In general, the 16-mer (XZ-16) can bind with apparent strength either greater or lesser than Y-8, depending on whether X and Z are A or T. The order of apparent binding strength, as measured by the target duplex concentration necessary to cause retardation of the third strand during gel electrophoresis, is TT-16 approximately AT-16 > Y-8 > AA-16 > TA-16. Chemical probing experiments showed that both halves of the triplex form even for AA-16, which binds with less apparent binding strength than the pyrimidine block alone (Y-8). The presence of the right half of the 16-mers, although detracting from affinity in cases of AA-16 and TA-16, provides strong specificity for the correct target compared to a target incapable of forming the Pu.Pu.Py part of the triplex. We discuss possible explanations for these observations in terms of alternate oligonucleotide conformations and suggest practical applications of affinity modulation by A-to-T replacements.
An efficiency-enhanced auto-reconfigurable 2x/3x SC charge pump for transcutaneous power transmission (2009)

An auto-reconfigurable 2x/3x switched-capacitor charge pump (SC-CP) for transcutaneous power transmission is presented in this paper. The proposed SC-CP can automatically configure its own voltage conversion ratio by adaptive control circuitry for maintaining high efficiencies of the DC/DC regulator under coupling variations. An adaptive deadtime control is developed to improve the efficiency of the proposed SCCP by minimizing the shoot-through current. Implemented in a standard 0.35-mum n-well CMOS process, the proposed SC-CP achieves peak power efficiencies of 95% (2x) and 92% (3x). The efficiency of the DC/DC regulator with the proposed SC-CP is improved by >25%, compared to that using the conventional 3x SC-CP, when the input voltage varies from 1.6 V to 2.4 V.
Comparative experiments on large vocabulary speech recognition (2002)

We describe recent changes to the BYBLOS system's training and recognition algorithms and report on numerous experiments in large vocabulary speech recognition. In earlier work, we performed five key experiments that were designed to answer questions related to different training scenarios. We investigated (1) the effect of varying the number of training speakers if the total amount of training data remains constant, (2) data pooling versus model averaging for generating speaker-independent (SI) HMMs, (3) the benefit of doubling the acoustic training data, (4) SI versus SD performance when the SI training data is twelve times greater, (5) the effect of cross-domain training for both the acoustic and language models. Our recent work was focused on four specific problem areas sharing the common thread that the test condition exposes the recognizer to phenomena not observed in the training data. Here we investigated (1) words outside the vocabulary, (2) spoken language effects due to subject variability and spontaneous dictation, (3) non-native dialects of the language, and (4) new microphones not used in training.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Die Möglichkeit der flächenunabhängigen Tonografie und Tonometrie (1987)

A method of simultaneous measurement of intraocular pressure and volume displacement is reported. An electronic pressure sensor (diameter 3 mm) was positioned in the centre of the base of a transparent applanation body (diameter 9 mm). The corneal applanation area could be changed by different applanation forces and was measured photographically. In isolated human and porcine eyes, sensor signal and intraocularly measured pressure were related linearly and independently of the applanation area. In human eyes in situ, the rigidity coefficient decreased with increasing pressure. Adhesive forces and stiffness of the cornea obviously only falsify tonometry at the margin of the applanation area.
A comparison of men's and women's professional basketball injuries (1982)

Injuries sustained by male and female professional basketball teams were compared. Injuries from two consecutive seasons were coded, and computer-based cross-tabulations comparing sex, body part, and type of injury were performed. The women's injury frequency was 1.6 times that of men. The body part most frequently injured on both teams was the ankle. Women sustained significantly more knee and thigh injuries as well as sprains, strains, and contusions. Men had significantly more muscle spasms. Other injuries occurred in similar patterns in both sexes. Alterations in training programs are suggested with emphasis on women's strengthening and men's flexibility.
Block Annotation: Better Image Annotation for Semantic Segmentation with Sub-Image Decomposition (2020)

Image datasets with high-quality pixel-level annotations are valuable for semantic segmentation: labelling every pixel in an image ensures that rare classes and small objects are annotated. However, full-image annotations are expensive, with experts spending up to 90 minutes per image. We propose block sub-image annotation as a replacement for full-image annotation. Despite the attention cost of frequent task switching, we find that block annotations can be crowdsourced at higher quality compared to full-image annotation with equal monetary cost using existing annotation tools developed for full-image annotation. Surprisingly, we find that 50% pixels annotated with blocks allows semantic segmentation to achieve equivalent performance to 100% pixels annotated. Furthermore, as little as 12% of pixels annotated allows performance as high as 98% of the performance with dense annotation. In weakly-supervised settings, block annotation outperforms existing methods by 3-4% (absolute) given equivalent annotation time. To recover the necessary global structure for applications such as characterizing spatial context and affordance relationships, we propose an effective method to inpaint block-annotated images with high-quality labels without additional human effort. As such, fewer annotations can also be used for these applications compared to full-image annotation.
Different regions of synaptic vesicle membrane regulate VAMP2 conformation for the SNARE assembly (2020)

Vesicle associated membrane protein 2 (VAMP2/synaptobrevin2), a core SNARE protein residing on synaptic vesicles (SVs), forms helix bundles with syntaxin-1 and SNAP25 for the SNARE assembly. Prior to the SNARE assembly, the structure of VAMP2 is unclear. Here, by using in-cell NMR spectroscopy, we describe the dynamic membrane association of VAMP2 SNARE motif in mammalian cells, and the structural change of VAMP2 upon the change of intracellular lipid environment. We analyze the lipid compositions of the SV membrane by mass-spectrometry-based lipidomic profiling, and further reveal that VAMP2 forms distinctive conformations in different membrane regions. In contrast to the non-raft region, the membrane region of cholesterol-rich lipid raft markedly weakens the membrane association of VAMP2 SNARE motif, which releases the SNARE motif and facilitates the SNARE assembly. Our work reveals the regulation of different membrane regions on VAMP2 structure and sheds light on the spatial regulation of SNARE assembly.
Low-Cost Coincidence-Counting Electronics for Quantum Optics (2007)

We have built and tested a multi-order coincidence-counting circuit that has higher count rates and lower cost than widely-used time-to-amplitude-converters. This is attractive for experimenters, especially in places where cost is a serious issue.
Role-play in English Language Teaching (2009)

Role-play is an effective technique to animate the teaching and learning atmosphere, arouse the interests of learners, and make the language acquisition impressive. So this research will mainly focus on how to apply it successfully and take the most advantage of it in English class. The outcome shows there are four crucial factors for its success: the topic chosen should be real and relevant; the teacher need 'feed-in' the appropriate language; correct errors in a proper way; some of teachers role are facilitator, spectator or participant. Incorporating role-play into the classroom adds variety, a change of pace and opportunities for a lot of language production and also a lot of fun!
Th17-type cytokines, IL-6 and TNF-α synergistically activate STAT3 and NF-kB to promote colorectal cancer cell growth (2014)

Colorectal cancers (CRCs) often show a dense infiltrate of cytokine-producing immune/inflammatory cells. The exact contribution of each immune cell subset and cytokine in the activation of the intracellular pathways sustaining CRC cell growth is not understood. Herein, we isolate tumor-infiltrating leukocytes (TILs) and lamina propria mononuclear cells (LPMCs) from the tumor area and the macroscopically unaffected, adjacent, colonic mucosa of patients who underwent resection for sporadic CRC and show that the culture supernatants of TILs, but not of LPMCs, potently enhance the growth of human CRC cell lines through the activation of the oncogenic transcription factors signal transducer and activator of transcription 3 (STAT3) and nuclear factor-kappa B (NF-kB). Characterization of immune cell complexity of TILs and LPMCs reveals no differences in the percentages of T cells, natural killer T cells, natural killer (NK) cells, macrophages and B cells. However, T cells from TILs show a functional switch compared with those from LPMCs to produce large amounts of T helper type 17 (Th17)-related cytokines (that is, interleukin-17A (IL-17A), IL-17F, IL-21 and IL-22), tumor necrosis factor-α (TNF-α) and IL-6. Individual neutralization of IL-17A, IL-17F, IL-21, IL-22, TNF-α or IL-6 does not change TIL-derived supernatant-driven STAT3 and NF-kB activation, as well as their proproliferative effect in CRC cells. In contrast, simultaneous neutralization of both IL-17A and TNF-α, which abrogates NF-kB signaling, and IL-22 and IL-6, which abrogates STAT3 signaling, reduces the mitogenic effect of supernatants in CRC cells. IL-17A, IL-21, IL-22, TNF-α and IL-6 are also produced in excess in the early colonic lesions in a mouse model of sporadic CRC, associated with enhanced STAT3/NF-kB activation. Mice therapeutically given BP-1-102, an orally bioavailable compound targeting STAT3/NF-kB activation and cross-talk, exhibit reduced colon tumorigenesis and diminished expression of STAT3/NF-kB-activating cytokines in the neoplastic areas. These data suggest that strategies aimed at the cotargeting of STAT3/NF-kB activation and interaction between them might represent an attractive and novel approach to combat CRC.
Transgenic Mice to Study the Role of Dopamine Receptors in Cardiovascular Function (1997)

Dopamine, an intrarenal regulator of sodium transport, is important in the pathogenesis of hypertension. The transduction of D1-like receptors in renal proximal tubules is defective in animal models of genetic hypertension. The defect is associated with an impaired regulation of proximal tubular sodium transport and cosegregates with hypertension in rats. Moreover, mice lacking one or both D1A receptor alleles develop hypertension. Extrasynaptic D3 receptors in renal tubules and juxtaglomerular cells may also regulate renal sodium transport and renin secretion while presynaptic D3 receptors may act as autoreceptors to inhibit neural norepinephrine release. Mice lacking one or both D3 alleles have elevated systolic blood pressure and developed diastolic hypertension. Although basal urine flow, sodium excretion, and glomerular filtration rate are similar, mice homozygous to the D3 receptor have an impaired ability to excrete an acute saline load compared to heterozygous and wild type mice. These studies suggest that abnormalities in dopamine receptor genes or their regulation may lead to the development of hypertension via different pathogenetic mechanisms.
Deformation of ionic polymer gels by electric fields (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDeformation of ionic polymer gels by electric fieldsMasao Doi, Mitsuhiro Matsumoto, and Yoshiharu HiroseCite this: Macromolecules 1992, 25, 20, 5504–5511Publication Date (Print):September 1, 1992Publication History Published online1 May 2002Published inissue 1 September 1992https://pubs.acs.org/doi/10.1021/ma00046a058https://doi.org/10.1021/ma00046a058research-articleACS PublicationsRequest reuse permissionsArticle Views1459Altmetric-Citations180LEARN 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
Ring Closure Mediated by Intramolecular Hydrogen Transfer in the Decomposition of a Push−Pull Nitroaromatic:  TATB (2000)

Using gradient-corrected density functional theory, we have investigated various competing mechanisms involved in the early stages of the decomposition of a “push−pull” (containing both electron-donating and -withdrawing groups) aromatic (1,3,5-triamino-2,4,6-trinitrobeznene, TATB), and particularly how hydrogen transfer affects the competition between ring closure and single bond scission. On the basis of the obtained energetics, we found several previously suggested mechanisms to be energetically disfavored. These mechanisms include direct N−H, N−O, C−NH2 bond dissociation, carbon ring cleavage, and the production of NO2-1 anion. Our results indicate that the rate-limiting step is ring closure mediated by intramolecular hydrogen transfer. This mechanism is predicted to have a barrier height of 47.5 kcal/mol. The hydrogen motion forms a biradical state which we suggest is the precursor to further decomposition products, such as benzofurazans.
An Easy‐to‐Machine Electrochemical Flow Microreactor: Efficient Synthesis of Isoindolinone and Flow Functionalization (2017)

Flow electrochemistry is an efficient methodology to generate radical intermediates. An electrochemical flow microreactor has been designed and manufactured to improve the efficiency of electrochemical flow reactions. With this device only little or no supporting electrolytes are needed, making processes less costly and enabling easier purification. This is demonstrated by the facile synthesis of amidyl radicals used in intramolecular hydroaminations to produce isoindolinones. The combination with inline mass spectrometry facilitates a much easier combination of chemical steps in a single flow process.
Glycogen Phosphorylase, the Product of the <i>glgP</i> Gene, Catalyzes Glycogen Breakdown by Removing Glucose Units from the Nonreducing Ends in <i>Escherichia coli</i> (2006)

To understand the biological function of bacterial glycogen phosphorylase (GlgP), we have produced and characterized Escherichia coli cells with null or altered glgP expression. glgP deletion mutants (DeltaglgP) totally lacked glycogen phosphorylase activity, indicating that all the enzymatic activity is dependent upon the glgP product. Moderate increases of glycogen phosphorylase activity were accompanied by marked reductions of the intracellular glycogen levels in cells cultured in the presence of glucose. In turn, both glycogen content and rates of glycogen accumulation in DeltaglgP cells were severalfold higher than those of wild-type cells. These defects correlated with the presence of longer external chains in the polysaccharide accumulated by DeltaglgP cells. The overall results thus show that GlgP catalyzes glycogen breakdown and affects glycogen structure by removing glucose units from the polysaccharide outer chains in E. coli.
Ceramic Nuclear Fuels in the System UO <sub>2</sub> ‐ZrO <sub>2</sub> ‐CaO (1963)

Potential nuclear fuels in the system UO 2 ‐ZrO 2 ‐CaO were investigated. Cubic fluorite‐type solid solutions, as indicated by X‐ray diffraction patterns, were formed by sintering U 3 O 8 ‐CaO‐stabilized ZrO 2 compacts in either air or hydrogen. A continuous solid solution was found between urania and stabilized zirconia after sintering in hydrogen at 1750°C. Sintering in air produced a limited solid‐solution region in the stabilized zirconia portion of the system at 1450°C. Results on phase identification, oxidation behavior, and water corrosion are presented.
Effect of illumination on switching process in PbTiO<sub>3</sub>crystals (1994)

Abstract The effect of photoassisted domain switching depending on irradiating light was found in PbTiO3 crystals.
Preliminary Study of the Protective Effect of the Calcium Channel Blocker, Nifedipine, on Adriamycin-Induced Tissue Injury (1991)

The effect of nifedipine, an oral calcium-channel blocker, on adriamycin-induced wound healing was studied. Nifedipine was administered to animals prior to treating with adriamycin. The healing strengths of cecal, fascial, and skin anatomoses were measured. Animals treated with adriamycin alone had significant decreases in healing strength compared to controls: for cecum at postoperative days (POD) 7 and 14; for skin at PODs 14, 21, and 28; for fascia at POD 28. Overall, nifedipine reduced the impact of adriamycin injury on the strength of healing incisional anastomoses. Nifedipine also appeared to protect collagen synthesis at anastomotic sites from adriamycin-induced impairment.
ChemInform Abstract: The Selective Functionalization of Saturated Hydrocarbons. Part 33. Further Reactions which Take Place in the Fe(II)‐Fe(IV) Manifold. (1996)

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.
Isolation and primary structure of a novel chromogranin A‐derived peptide, WE‐14, from a human midgut carcinoid tumour (1992)

The primary structure of a novel human chromogranin A-derived tetradecapeptide, WE-14, possessing N-terminal tryptophanyl (W) and C-terminal glutamyl (E) residues was isolated from a hepatic metastasis of an human ileal carcinoid tumour. Human and bovine WE-14 are structurally identical, while rat, mouse and porcine analogues exhibit 93% homology. WE-14 is flanked by paired basic residues (KR) in all known chromogranin A sequences.
An Arabidopsis chloroplast‐targeted Hsp101 homologue, APG6, has an essential role in chloroplast development as well as heat‐stress response (2006)

Analysis of albino or pale-green (apg) mutants is important for identifying nuclear genes responsible for chloroplast development and pigment synthesis. We have identified 38 apg mutants by screening 11 000 Arabidopsis Ds-tagged lines. One mutant, apg6, contains a Ds insertion in a gene encoding APG6 (ClpB3), a homologue of the heat-shock protein Hsp101 (ClpB1). We isolated somatic revertants and identified two Ds-tagged and one T-DNA-tagged mutant alleles of apg6. All three alleles gave the same pale-green phenotype. These results suggest that APG6 is important for chloroplast development. The APG6 protein contains a transit peptide and is localized in chloroplasts. The plastids of apg6 pale-green cells were smaller than those of the wild type, and contained undeveloped thylakoid membranes. APG6 mRNA accumulated in response to heat shock in various organs, but not in response to other abiotic stresses. Under normal conditions, APG6 is constitutively expressed in the root tips, the organ boundary region, the reproductive tissues of mature plants where plastids exist as proplastids, and slightly in the stems and leaves. In addition, constitutive overexpression of APG6 in transgenic plants inhibited chloroplast development and resulted in a mild pale-green phenotype. The amounts of chloroplast proteins related to photosynthesis were markedly decreased in apg6 mutants. These results suggest that APG6 functions as a molecular chaperone involved in plastid differentiation mediating internal thylakoid membrane formation and conferring thermotolerance to chloroplasts during heat stress. The APG6 protein is not only involved in heat-stress response in chloroplasts, but is also essential for chloroplast development.
Hyaluronan mediates sperm motility by enhancing phosphorylation of proteins including hyaluronan binding protein. (1995)

The present study was carried out to explore the mechanisms underlying hyaluronan-induced sperm motility. We demonstrate for the first time the enhanced cellular protein phosphorylation in hyaluronic acid stimulated cauda spermatozoa. Labeling of spermatozoa with [Pi] orthophosphoric acid yielded a wide range of labeled phosphoproteins in presence of hyaluronan. Under these experimental conditions, we further show tyrosine specific phosphorylation of proteins. In addition, this is also the first report showing enhanced phosphorylation of 34 kDa hyaluronan binding protein in response to hyaluronan. The role of 34 kDa hyaluronan binding protein in hyaluronan-induced spermatozoa is supported by elevated production of inositol triphosphate accompanied by increased phosphorylation in Triton X-100 insoluble cytoskeletal proteins. The evidence strongly suggests the biological importance of hyaluronan binding protein phosphorylation in the transduction of signals resulting from the interaction of hyaluronate with the sperm surface.