gebhart/patrepeval huggingface dataset:
Eucaryotic DNA Primase Does Not Prefer To Synthesize Primers at Pyrimidine Rich DNA Sequences When Nucleoside Triphosphates Are Present at Concentrations Found in Whole Cells† (1997)

The critical role of NTP concentration in determining where calf thymus DNA primase synthesizes a primer on a DNA template was examined. Varying the concentration of NTPs dramatically altered the template sequences at which primase synthesized primers. At the low NTP concentrations typically used for in vitro experiments (100 microM), primase greatly preferred to synthesize primers at pyrimidine rich DNA sequences. However, when the concentrations of NTPs were increased to levels typically found in whole cells, primers were now synthesized in all regions of the template. Importantly, synthesis of primers in all regions of the DNA template, not just the pyrimidine rich sequences, is the pattern of primer synthesis observed during DNA replication in whole cells. With low concentrations of NTPs (i.e., Vmax/K(M) conditions), primers are only synthesized at the most preferred synthesis sites, namely, those that are pyrimidine rich. In contrast, under conditions of high NTP concentrations, primer synthesis will occur at the first potential synthesis site to which primase binds. Now, the primase x DNA complex will be immediately converted to a primase x DNA x NTP x NTP complex that is poised for primer synthesis.
Synchrotron x-ray spectroscopy studies of valence and magnetic state in europium metal to extreme pressures (2012)

In order to probe the changes in the valence state and magnetic properties of Eu metal under extreme pressure, x-ray absorption near-edge spectroscopy, x-ray magnetic circular dichroism, and synchrotron M\"ossbauer spectroscopy experiments were carried out. The M\"ossbauer isomer shift exhibits anomalous pressure dependence, passing through a maximum near 20 GPa. Density functional theory has been applied to give insight into the pressure-induced changes in both Eu's electronic structure and M\"ossbauer isomer shift. Contrary to previous reports, Eu is found to remain nearly divalent to the highest pressures reached (87 GPa) with magnetic order persisting to at least 50 GPa. These results should lead to a better understanding of the nature of the superconducting state found above 75 GPa and of the sequence of structural phase transitions observed to 92 GPa.
Self-organization of tip-functionalized elongated colloidal particles (2019)

Weakly attractive interactions between the tips of rodlike colloidal particles affect their liquid-crystal phase behavior due to a subtle interplay between enthalpy and entropy. Here we employ molecular dynamics simulations on semiflexible, repulsive bead-spring chains where one of the two end beads attract each other. We calculate the phase diagram as a function of both the volume fraction of the chains and the strength of the attractive potential. We identify a large number of phases that include isotropic, nematic, smectic-A, smectic-B, and crystalline states. For tip attraction energies lower than the thermal energy, our results are qualitatively consistent with experimental findings: We find that an increase of the attraction strength shifts the nematic to smectic-A phase transition to lower volume fractions, with only minor effect on the stability of the other phases. For sufficiently strong tip attraction, the nematic phase disappears completely, in addition leading to the destabilization of the isotropic phase. In order to better understand the underlying physics of these phenomena, we also investigate the clustering of the particles at their attractive tips and the effective molecular field experienced by the particles in the smectic-A phase. Based on these results, we argue that the clustering of the tips only affects the phase stability if lamellar structures ("micelles") are formed. We find that an increase of the attraction strength increases the degree of order in the layered phases. Interestingly, we also find evidence for the existence of an antiferroelectric smectic-A phase transition induced by the interaction between the tips. A simple Maier-Saupe-McMillan model confirms our findings.
Extracellular Vesicles From Steatotic Hepatocytes Provoke Pro-Fibrotic Responses in Stellate Cells. (2020)

Abstract Background and aims High caloric dietary intake is associated with hepatic steatosis and chronic hepatocyte damage leading ultimately to liver fibrosis and cirrhosis with organ failure. Although the pathophysiologic process orchestrating liver fibrosis is not completely clarified, pivotal steps are the activation and transdifferentiation of hepatic stellate cells. In this study, we aim to assess the direct interplay between hepatocytes and hepatic stellate cells under normal and steatotic conditions and hypothesize that extracellular vesicles (EV) isolated from hepatocytes can directly manipulate the phenotype of stellate cells. Methods By high speed centrifugation, EV were isolated from conditioned media of the hepatocellular carcinoma cell line HepG2, under baseline conditions (C-EV) or after induction of steatosis by linoleic and oleic acid for 24 hours (FA-EV). Migration of the stellate cell line TWNT4 towards respective EV as well as sera of NASH patients was investigated using Boyden chambers. TWNT4 phenotype alterations after incubation with EV was determined by qPCR, western blotting and immunofluorescence staining. Results HepG2 cells released more EV after treatment with fatty acids. Chemotactic migration of TWNT4 cells was increased specifically towards FA-EV. Prolonged incubation of TWNT4 cells with FA-EV induce expression of proliferation markers and a myofibroblast-like phenotype. Whereas the expression of the collagen type 1 1 gene did not change after FA-EV-treatment, expression of the myofibroblast markers e.g. -smooth muscle cell actin and TIMP1 were significantly increased. Conclusion We concluded that EV from steatotic HepG2 cells can influence the behavior and phenotype of TWNT4 cells as well as the expression of remodeling markers and guides directed migration. These findings imply EV as operational, intercellular communicators in the pathophysiology of steatosis associated liver fibrosis.
Robust real-time attention-based head-shoulder detection for video surveillance (2013)

Robust head-shoulder detection has widely been utilized in video surveillance applications. However, most state-of-the-art approaches are very time-consuming and unable to effectively handle videos with radical pose and viewpoint changes. In this paper, we introduce a robust and rapid head-shoulder detection method, which is invariant to pose and viewpoint for video surveillance. The proposed method combines an attention-based foreground segmentation module and a multiview head-shoulder detection cascade to achieve high performance in both accuracy and speed. Specifically, the attention-based foreground segmentation module firstly detects not only active regions that involve motions but also static areas where people stand or sit still in video frames. These regions are then provided to a two-layer head-shoulder detection cascade which is composed of a preliminary linear classifier which eliminates most obvious non-head-shoulder windows rapidly, and a set of histogram intersection kernel (HIK) based multi-view classifiers that can precisely detect head-shoulders with different pose and viewpoint. When compared to the leading methods in the challenging PETS 2009 benchmark dataset, our approach obtains highly competitive results in terms of effectiveness and efficiency.
Common ancestry of Escherichia coli pyruvate oxidase and the acetohydroxy acid synthases of the branched-chain amino acid biosynthetic pathway (1988)

A number of enzymes require flavin for their catalytic activity, although the reaction catalyzed involves no redox reaction. The best studied of these enigmatic nonredox flavoproteins are the acetohydroxy acid synthases (AHAS), which catalyze early steps in the synthesis of branched-chain amino acids in bacteria, yeasts, and plants. Previously, work from our laboratory showed strong amino acid sequence homology between these enzymes and Escherichia coli pyruvate oxidase, a classical flavoprotein dehydrogenase that catalyzes the decarboxylation of pyruvate to acetate. We have now shown this homology (i) to also be present in the DNA sequences and (ii) to represent functional homology in that pyruvate oxidase has AHAS activity and a protein consisting of the amino-terminal half of pyruvate oxidase and the carboxy-terminal half of E. coli AHAS I allows native E. coli AHAS I to function without added flavin. The hybrid protein contains tightly bound flavin, which is essential for the flavin substitution activity. These data, together with the sequence homologies and identical cofactors and substrates, led us to propose that the AHAS enzymes are descended from pyruvate oxidase (or a similar protein) and, thus, that the flavin requirement of the AHAS enzymes is a vestigial remnant, which may have been conserved to play a structural rather than a chemical function.
Vasodilator-stimulated phosphoprotein (VASP) phosphorylation provides a biomarker for the action of exisulind and related agents that activate protein kinase G. (2002)

Recent studies provide evidence that exisulind and two potent derivatives, CP461 and CP248, induce apoptosis in colon cancer cells by inhibiting cyclic GMP (cGMP)-specific phosphodiesterases (phosphodiesterases 2 and 5). This causes an increase in intracellular levels of cGMP, thus activating the cGMP-dependent protein kinase G (PKG), which then activates pathways that lead to apoptosis. To further examine this mechanism and to provide a potential in vivo biomarker for activation of this pathway, we examined phosphorylation of the vasodilator-stimulated phosphoprotein (VASP), a ubiquitously expressed endogenous substrate for PKG. We found that VASP was phosphorylated after treating SW480 colon cancer cells with exisulind, CP461, or CP248. CP248-induced VASP phosphorylation was inhibited by a specific PKG inhibitor but not by a protein kinase A inhibitor. The drug 3-(5'-hydroxymethyl-2'-furyl)-benzylindazole and nitric oxide donors that activate cellular guanylyl cyclase and thus increase cellular levels of cGMP also caused VASP phosphorylation. With all of these agents, the phosphorylation of VASP was associated with increased intracellular levels of cGMP and the induction of apoptosis. We also demonstrated direct in vivo phosphorylation of VASP with constitutively activated mutants of PKG. These results suggest that VASP phosphorylation can provide a useful endogenous cellular biomarker for anticancer agents that cause cGMP-mediated apoptosis.
Estimation of Heart Rate from Vocal Frequency Based on Support Vector Machine (2016)

Heart rate (HR) is one of the vital signs used to assess our physical condition; it would be beneficial if HR could easily be obtained without special medical instruments. In this study, a feature of vocal frequency was used to estimate HR, because it can easily be recorded with a common device such as a smartphone. Previous studies proposed that a support vector machine (SVM) that adopted the inner product as the kernel function was efficient for estimating HR to a certain extent. However, these studies did not present the effectiveness of other kernel functions, such as the hyperbolic tangent function. Therefore, this study identified a combination of kernel functions of the kernel ridge regression (KRR). In addition, features of vocal frequency to effectively estimate HR were investigated. To evaluate the effectiveness, experiments were conducted with two subjects. In the experiment, 60 sets of HRs and voice data were measured per subject. To identify the most effective kernel function, four kernel functions (the inner function, Gaussian function, polynomial function, and hyperbolic tangent function) were compared. Moreover, effective features of vocal frequency were selected with the sequential feature selection (SFS) method. As a consequence, the hyperbolic tangent function worked best, and high-frequency components of voice were efficient. However, results of this research indicated that effective vocal spectrum components to estimate HR differ depending on prediction models.
One-Armed Bandit Problems with Covariates (1991)

As does Woodroofe, we consider a Bayesian sequential allocation between two treatments that incorporates a covariate. The goal is to maximize the total discounted expected reward from an infinite population of patients. Although our model is more general than Woodroofe's, we are able to duplicate his main result: The myopic rule is asymptotically optimal.
Modeling the Structure–Activity Relationship of Arbidol Derivatives and Other SARS-CoV-2 Fusion Inhibitors Targeting the S2 Segment of the Spike Protein (2021)

Umifenovir (Arbidol) has been reported to exhibit some degree of efficacy in multiple clinical trials for the treatment of COVID-19 as a monotherapy. It has also demonstrated synergistic inhibition of SARS-CoV-2 with other direct-acting antivirals such as Remdesivir. A computational approach was used to identify the most favorable binding site to the SARS-CoV-2 Spike S2 segment and to perform virtual screening. Compounds selected from modeling were evaluated in a live SARS-CoV-2 infection assay. An Arbidol (ARB) derivative with substitutions at both the C-4 and C-6 positions was found to exhibit a modest improvement in activity and solubility properties in comparison to ARB. However, all of the derivatives were found to only be partial inhibitors, rather than full inhibitors in a virus-induced cytopathic effect-based assay. The binding mode is also corroborated by parallel modeling of a series of oleanolic acid trisaccharide saponin fusion inhibitors shown to bind to the S2 segment. Recently determined experimental structures of the Spike protein allowed atomic resolution modeling of fusion inhibitor binding as a function of pH, and the implications for the molecular mechanism of direct-acting fusion inhibitors targeting the S2 segment are discussed.
Contributing factors to poor functional recovery after delayed nerve repair: prolonged axotomy (1995)

The contribution of prolonged motoneuron axotomy to the poor functional recovery after delayed nerve repair was determined by means of a nerve cross-anastomosis paradigm in the rat. The tibial nerve was axotomized up to 12 months before it was cross-sutured to the distal stump of the freshly cut common peroneal nerve to innervate the freshly denervated tibialis anterior muscle. Three to 17 months later, muscle and motor unit (MU) forces were measured to quantify the number of axons that had successfully regenerated and reinnervated the muscle. The extent of axonal branching was estimated by the innervation ratio (IR) (i.e., the number of muscle fibers innervated by each axon), which was obtained directly by counting muscle fibers in a single glycogen-depleted MU in each muscle and indirectly by calculation. The total number of MUs in each muscle significantly decreased with progression of axotomy and was only 35% of the control when axotomy was prolonged more than 3 months. Concurrently, MU force and IR increased exponentially, with a mean increase of threefold when axotomy was more than 3 months, which largely compensated for the reduction in the number of axons that reinnervated the muscle. Consequently, muscles reinnervated by tibial motor axons that had been axotomized up to 12 months produced as much force as those reinnervated by freshly axotomized tibial motor axons. Muscle weight, size, and muscle fiber size were similar to those after immediate nerve suture. Although prolonged axotomy does not compromise the number of muscle fibers innervated by each axon, it does reduce the capacity of motor axons to regenerate and thus is an important contributing factor to the poor functional recovery in delayed nerve repair.
Increasing Protein at the Expense of Carbohydrate in the Diet Down-Regulates Glucose Utilization as Glucose Sparing Effect in Rats (2011)

High protein (HP) diet could serve as a good strategy against obesity, provoking the changes in energy metabolic pathways. However, those modifications differ during a dietary adaptation. To better understand the mechanisms involved in effect of high protein diet (HP) on limiting adiposity in rats we studied in parallel the gene expression of enzymes involved in protein and energy metabolism and the profiles of nutrients oxidation. Eighty male Wistar rats were fed a normal protein diet (NP, 14% of protein) for one week, then either maintained on NP diet or assigned to a HP diet (50% of protein) for 1, 3, 6 and 14 days. mRNA levels of genes involved in carbohydrate and lipid metabolism were measured in liver, adipose tissues, kidney and muscles by real time PCR. Energy expenditure (EE) and substrate oxidation were measured by indirect calorimetry. Liver glycogen and plasma glucose and hormones were assayed. In liver, HP feeding 1) decreased mRNA encoding glycolysis enzymes (GK, L-PK) and lipogenesis enzymes(ACC, FAS), 2) increased mRNA encoding gluconeogenesis enzymes (PEPCK), 3) first lowered, then restored mRNA encoding glycogen synthesis enzyme (GS), 4) did not change mRNA encoding β-oxidation enzymes (CPT1, ACOX1, βHAD). Few changes were seen in other organs. In parallel, indirect calorimetry confirmed that following HP feeding, glucose oxidation was reduced and fat oxidation was stable, except during the 1(st) day of adaptation where lipid oxidation was increased. Finally, this study showed that plasma insulin was lowered and hepatic glucose uptake was decreased. Taken together, these results demonstrate that following HP feeding, CHO utilization was increased above the increase in carbohydrate intake while lipogenesis was decreased thus giving a potential explanation for the fat lowering effect of HP diets.
Self‐assembled UCST‐Type Micelles as Potential Drug Carriers for Cancer Therapeutics (2015)

A methoxy‐poly(ethylene glycol)‐ block ‐poly(acrylamide‐ co ‐acrylonitrile) (mPEG‐ b ‐P(AAm‐ co ‐AN)) amphiphilic copolymer exhibiting upper critical solution temperature (UCST) behavior is synthesized, and micelles from this copolymer are fabricated. It is found that the thermal responses of these micelles are tunable through balancing the hydrophobic/hydrophilic blocks in the copolymer. The size of the doxorubicin (DOX)‐loaded micelles is dependent on the hydrophobic interaction as well as hydrogen bonding between polymer and drug molecules. As a proof of concept, the drug release behavior is studied in vitro, and the cumulative release of DOX increases at temperature above the UCST of blank micelles. 3‐(4,5‐dimethyl‐thiazol‐2‐yl)‐2,5‐diphenyl tetrazolium bromide (MTT) assays indicate that these polymers are non‐toxic towards human hepatic carcinoma cells (Bel 7402 cells) as well as human embryonic hepatocytes (L02 cells). DOX‐loaded micelles could effectively enter Bel 7402 cells in 2 h, and display much lower half inhibitory concentration compared with free DOX. These micelles may be exploited as a promising drug carrier for cancer therapeutics. image
Effects of Load and Posture on the Recruitment of Trunk Muscles (2002)

Seven male subjects performed 8 cable lifting and hanging tasks, while trunk kinematics and electromyographic data often trunk muscles were obtained. The objectives of the study were to evaluate trunk muscle recruitment and spine loads resulting from performance of this task in different postures and with different load magnitudes. The eight tasks were combinations of four postures (standing, stooping, kneeling on one knee or both knees) and two levels of load (0 N or 100 N load added to existing cable weight). Results indicated that changes in posture and changes in load magnitude both affected muscle co-activation; however, the influence of these variables were quite different in nature. Increased load magnitude resulted in a generalized increase in the co-activation of all trunk muscles, no matter which posture was employed (p &lt; 0.05). Changes in posture significantly affected trunk muscle recruitment patterns (p &lt; 0.05); however, the posture effect typically involved a relatively small subset of trunk muscles. No significant interactions were detected (p &gt; 0.05), indicating that posture and load effects are both independent and additive.
Gas Chromatographic Analysis of Furfural and Hydroxymethyl-furfural in Wine (1979)

Journal Article Gas Chromatographic Analysis of Furfural and Hydroxymethyl-furfural in Wine Get access Jun-ichi Shimizu, Jun-ichi Shimizu Central Research Laboratories, Kikkoman Shoyu Co., Ltd., 399 Noda, Noda-shi, Chiba-ken, Japan Search for other works by this author on: Oxford Academic Google Scholar Masazumi Watanabe Masazumi Watanabe Central Research Laboratories, Kikkoman Shoyu Co., Ltd., 399 Noda, Noda-shi, Chiba-ken, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 43, Issue 6, 1 June 1979, Pages 1365–1366, https://doi.org/10.1080/00021369.1979.10863629 Published: 01 June 1979 Article history Received: 25 January 1979 Published: 01 June 1979
Isothermal Sintering of Spheroidized Cordierite‐Type Glass Powders (1985)

Jagged (ball–milled) glass particles were spheroidized and pressed into compacts which were isothermally sintered in air. Both jagged‐ and spheroidized‐particle compacts showed about the same 0.7 anisotropy of the ratio of axial to diametral shrinkage, but spheroidizing reduced the shrinkage rate. Thus, shrinkage anisotropy is not a simple particle shape effect; it may relate to differences in the axial and radial distributions of particle sizes present in these compacts.
The assignment of the carbon-13 N.M.R. spectra of Westphalen-rearranged steroid olefins with the aid of the lanthanide shift reagent Eu(fod)3 (1977)

Shifts induced by Eu(fod)3 in the 13C N.M.R. spectra of 5-methyl-19-nor- 5ß-cholest-9(10)-en-4ß- and -6ß-ols are used in conjunction with off- resonance proton decoupling and substituent effects to assign the 27 carbon resonances of the rearranged 5-methyl-19-nor-5ß-cholest-9(10)- ene steroid skeleton.
Indirect chemiluminescence by 1,2-dioxetanes. Evaluation of triplet-singlet excitation efficiencies. Long range singlet-singlet energy transfer and an efficient triplet-singlet energy transfer (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIndirect chemiluminescence by 1,2-dioxetanes. Evaluation of triplet-singlet excitation efficiencies. Long range singlet-singlet energy transfer and an efficient triplet-singlet energy transferNicholas J. Turro, Peter Lechtken, Gary Schuster, Jeffrey Orell, Hans C. Steinmetzer, and Waldemar AdamCite this: J. Am. Chem. Soc. 1974, 96, 5, 1627–1629Publication Date (Print):March 1, 1974Publication History Published online1 May 2002Published inissue 1 March 1974https://pubs.acs.org/doi/10.1021/ja00812a076https://doi.org/10.1021/ja00812a076research-articleACS PublicationsRequest reuse permissionsArticle Views242Altmetric-Citations53LEARN 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