gebhart/patrepeval huggingface dataset:
Temporal Locality in Web Request Streams (2000)

Porphyromonas gingivalis, a keystone pathogen in periodontitis (PD), produces cysteine proteases named gingipains (RgpA, RgpB, and Kgp), which strongly affect the host immune system. The range of action of gingipains is extended by their release as components of outer membrane vesicles, which efficiently diffuse into surrounding gingival tissues. However, away from the anaerobic environment of periodontal pockets, increased oxygen levels lead to oxidation of the catalytic cysteine residues of gingipains, inactivating their proteolytic activity. In this context, the influence of catalytically inactive gingipains on periodontal tissues is of significant interest. Here, we show that proteolytically inactive RgpA induced a proinflammatory response in both gingival keratinocytes and dendritic cells. Inactive RgpA is bound to the cell surface of gingival keratinocytes in the region of lipid rafts, and using affinity chromatography, we identified RgpA-interacting proteins, including epidermal growth factor receptor (EGFR). Next, we showed that EGFR interaction with inactive RgpA stimulated the expression of inflammatory cytokines. The response was mediated via the EGFR-phosphatidylinositol 3-kinase (PI3K)-protein kinase B (AKT) signaling pathway, which when activated in the gingival tissue rich in dendritic cells in the proximity of the alveolar bone, may significantly contribute to bone resorption and the progress of PD. Taken together, these findings broaden our understanding of the biological role of gingipains, which in acting as proinflammatory factors in the gingival tissue, create a favorable milieu for the growth of inflammophilic pathobionts. <b>IMPORTANCE</b> Gingipain cysteine proteases are essential virulence factors of Porphyromonas gingivalis, an oral bacterium implicated in development of periodontitis. Gingipains diffusing from anaerobic periodontal pockets lose proteolytic activity in the oxygenated environment of gingival tissues. We found that despite the loss of activity, gingipains still elicit a strong inflammatory response, which may contribute to the progression of periodontitis and bone resorption. Moreover, we identified the host molecules utilized by the pathogen as receptors for proteolytically inactivated gingipains. The broad distribution of those receptors in human tissue suggests their involvement in systemic diseases associated with periodontal pathogens.
Curvelets, Wave Atoms, and Wave Equations (2006)

We argue that two specific wave packet families---curvelets and wave atoms---provide powerful tools for representing linear systems of hyperbolic differential equations with smooth, time-independent coefficients. In both cases, we prove that the matrix representation of the Green's function is sparse in the sense that the matrix entries decay nearly exponentially fast (i.e., faster than any negative polynomial), and well organized in the sense that the very few nonnegligible entries occur near a few shifted diagonals, whose location is predicted by geometrical optics. This result holds only when the basis elements obey a precise parabolic balance between oscillations and support size, shared by curvelets and wave atoms but not wavelets, Gabor atoms, or any other such transform. A physical interpretation of this result is that curvelets may be viewed as coherent waveforms with enough frequency localization so that they behave like waves but at the same time, with enough spatial localization so that they simultaneously behave like particles. We also provide fast digital implementations of tight frames of curvelets and wave atoms in two dimensions. In both cases the complexity is O(N² log N) flops for N-by-N Cartesian arrays, for forward as well as inverse transforms. Finally, we present a geometric strategy based on wave atoms for the numerical solution of wave equations in smoothly varying, 2D time-independent periodic media. Our algorithm is based on sparsity of the matrix representation of Green's function, as above, and also exploits its low-rank block structure after separation of the spatial indices. As a result, it becomes realistic to accurately build the full matrix exponential using repeated squaring, up to some time which is much larger than the CFL timestep. Once available, the wave atom representation of the Green's function can be used to perform 'upscaled' timestepping. We show numerical examples and prove complexity results based on a priori estimates of sparsity and separation ranks. They beat the O(N^3) bottleneck on an N-by-N grid, for a wide range of physically relevant situations. In practice, the current wave atom solver can become competitive over a pseudospectral method in the regime when the wave equation should be solved several times with different initial conditions, as in reflection seismology.
The solubilization of deoxyhemoglobin S. (1967)

The fundamental defect responsible for sickle-cell disease was recognized by Pauling and his co-workers' as a mutated hemoglobin. A single genetic change2 leads to the synthesis of hemoglobin S which contains a valine residue (instead of glutamic acid') at position 6 of the 13-chain.4-8 Hemoglobin S (Hb S) is thus composed of two normal a-chains and two modified 1-chains and may be written a! A 6v&l 8 In contrast to a normal red blood cell, a sickle cell loses the characteristic biconcave disk shape upon deoxygenation. The distortion in cell shape is caused by gel formation of the deoxyHb S in the cell. The phenomenon may also be observed in stroma-free deoxyHb S solutions.9 Certain hydrocarbons (methane, ethane, and propane) reverse gel formation from deoxyHb S solutions and unsickle sickled cells. On this basis, Murayama'0 proposes hydrophobic bonding as the driving force for the association process. Sickle-cell anemia is a serious disease, its sequellae arising from the abnormal behavior of the sickled cells in the circulation. Individuals afflicted with the disease (perhaps 40,000 in the United States alone) are subject to anemia, recurrent crises, and early death.I Occasional transfusions are the only generally useful supportive measure.12 Drastic techniques like chronic carbon monoxide poisoning,'3 raising the blood pH,'4-'6 oxidation of part of the Hb S to methemoglobin S,17 or supposed inhibition of glucose-6-phosphate dehydrogenase with phenothiazines'8' 19 have little or no clinical value. We have suggested that the introduction of glutamic acid residues into Hb S (a transformation) might diminish the ease of gel formation.a We now report that the solubility of Hb S (Itano2l) can be augmented in the predicted way. Glutamic acid residues can be introduced by reaction of the protein with the Ncarboxyanhydride of glutamic acid.22-24 With a sufficient number of added glutamic acid moieties, the solubility of the modified deoxyHb S exceeds that of deoxyHb A (normal hemoglobin). Methods and Results. -Bloods were drawn from outpatients at Bronx Municipal Hospital Center and Lincoln Hospital, Bronx, New York. All patients were SS and had not been transfused for at least five months. Hb S solutions were prepared from bloods by removal of plasma, washing cells with isotonic buffer, lysis with an equal volume of water, shaking after addition of half a volume of toluene, and separation of the Hb S solutions by centrifugation at 17,000 g. Concentrations were determined spectroscopically with a Cary model 14 spectrophotometer (em8 14,200). All Hb S solutions were maintained at 40 until use. The N-carboxyanhydride of glutamic acid, 1 (NCA 1), was generously supplied by Drs. Ralph Hirschmann and Robert Denkewalter of the Research Laboratories, Merck, Sharp and Dohme, Inc., Rahway, New Jersey. The NCA 1 was transported and stored at -80°. For utilization in the experiments, the stored material
Determination of Dip and Anisotropy from Multi-frequency Tri-axial Induction Measurements (2010)

The tri-axial (or multi-component) induction log is used to measure not only the resistivity anisotropy of an anisotropic formation but also the relative dip of the tool with respect to the formation. When the tri-axial induction log is run at multiple frequencies, multi-frequency focusing can be applied to the measurements. The apparent dip and the apparent anisotropy are algebraically deflned from the frequency-focused tri-axial induction measurements. The apparent dip gives the true dip in thinly bedded formations, but a smaller dip than the true dip in a thick anisotropic bed when the anisotropy is small (the anisotropy efiect). The apparent anisotropy gives the true anisotropy in thick anisotropic formations but is afiected by the shoulder bed anisotropy when the formation is not thick (the shoulder bed efiect).
Pharmacokinetics in Mouse and Comparative Effects of Frondosides in Pancreatic Cancer (2016)

The frondosides are triterpenoid glycosides from the Atlantic sea cucumber Cucumaria frondosa. Frondoside A inhibits growth, invasion, metastases and angiogenesis and induces apoptosis in diverse cancer types, including pancreatic cancer. We compared the growth inhibitory effects of three frondosides and their aglycone and related this to the pharmocokinetics and route of administration. Frondoside A potently inhibited growth of pancreatic cancer cells with an EC50 of ~1 µM. Frondoside B was less potent (EC50 ~2.5 µM). Frondoside C and the aglycone had no effect. At 100 µg/kg, frondoside A administered to CD₂F₁ mice as an i.v. bolus, the Cpmax was 129 nM, Cltb was 6.35 mL/min/m², and half-life was 510 min. With i.p. administration the Cpmax was 18.3 nM, Cltb was 127 mL/min/m² and half-life was 840 min. Oral dosing was ineffective. Frondoside A (100 µg/kg/day i.p.) markedly inhibited growth cancer xenografts in nude mice. The same dose delivered by oral gavage had no effect. No evidence of acute toxicity was seen with frondoside A. Frondoside A is more potent inhibitor of cancer growth than other frondosides. The glycoside component is essential for bioactivity. Frondoside A is only effective when administered systemically. Based on the current and previous studies, frondoside A appears safe and may be valuable in the treatment of cancer.
A survey of the factors that cause the handling mistakes of implantable ventricular assist devices (2018)

保険償還されている植込型補助人工心臓（implantable ventricular assist device：iVAD）を2011/4～2016/12に装着した重症心不全患者109名を対象とし、機器の取り扱い上のミスを引き起こす要因について検討を行った。対象としたミスは、不注意もしくは誤った取り扱いによってポンプが停止した事例およびドライブラインを損傷させた事例とした。統計学的な検討ではFisherの正確検定を用い、p＜0.05で有意差ありとした。
Testing computational prediction of missense mutation phenotypes: Functional characterization of 204 mutations of human cystathionine beta synthase (2010)

Predicting the phenotypes of missense mutations uncovered by large-scale sequencing projects is an important goal in computational biology. High-confidence predictions can be an aid in focusing experimental and association studies on those mutations most likely to be associated with causative relationships between mutation and disease. As an aid in developing these methods further, we have derived a set of random mutations of the enzymatic domains of human cystathionine beta synthase. This enzyme is a dimeric protein that catalyzes the condensation of serine and homocysteine to produce cystathionine. Yeast missing this enzyme cannot grow on medium lacking a source of cysteine, while transfection of functional human CBS into yeast strains missing endogenous enzyme can successfully complement for the missing gene. We used PCR mutagenesis with error-prone Taq polymerase to produce 948 colonies and compared cell growth in the presence or absence of a cysteine source as a measure of CBS function. We were able to infer the phenotypes of 204 single-site mutants, 79 of them deleterious and 125 neutral. This set was used to test the accuracy of six publicly available prediction methods for phenotype prediction of missense mutations: SIFT, PolyPhen, PMut, SNPs3D, PhD-SNP, and nsSNPAnalyzer. The top methods are PolyPhen, SIFT, and nsSNPAnalyzer, which have similar performance. Using kernel discriminant functions, we found that the difference in position-specific scoring matrix values is more predictive than the wild-type PSSM score alone, and that the relative surface area in the biologically relevant complex is more predictive than that of the monomeric proteins.
Molecular marker heterozygosities and genetic distances as correlates of production traits in F1 bovine crosses (2005)

Several studies have investigated the relationship between heterozygosity, genetic distance and production traits. The objective of the present study was to evaluate the influence of the degree of heterozygosity and genetic distance on growth, carcass and reproductive related features in F1 bovine crosses. We tested 10 polymorphic markers in 330 purebred cattle (Nelore, Canchim, Aberdeen Angus and Simental) and 256 crossbred cattle belonging to four crossbred groups. Individual heterozygosities (Hi) and multilocus genetic similarity (Dm) were estimated and used in correlation analysis against individual phenotypic measurements. Significant (p < 0.05) Hi effects occurred for birth weight, 15 to 18 month weight, hot carcass weight and longissimus rib eye area. The extent to which increased heterozygosity (deltaH) in F1 crosses can be predicted from the genetic distance of parental breeds was also investigated using Nei's standard genetic distance (Ds) and standard heterozygosity (Hs). High correlations were found between deltaHi, deltaHs and the Ds of the parental breeds. Our results suggest that heterozygosity of the ten molecular markers used in this study may affect live weight during at least one growth phase. Parental genetic distance was a suitable predictor of the degree of progeny heterozygosity.
HealthGear: Automatic Sleep Apnea Detection and Monitoring with a Mobile Phone (2007)

We present HealthGear, a real-time wearable system for monitoring, visualizing and analyzing physiological signals. HealthGear consists of a set of non-invasive physiological sensors wirelessly connected via Bluetooth to a cell phone which stores, transmits and analyzes the physiological data, and presents it to the user in an intelligible way. In this paper, we focus on an implementation of HealthGear using a blood oximeter to monitor the user’s blood oxygen level and pulse while sleeping. We also describe two different algorithms for automatically detecting sleep apnea events, and illustrate the performance of the overall system in a sleep study with 20 volunteers.
Magnetic Wheeled Robot with High Mobility but only 2 DOF to Control (2008)

In this paper, the mechanical design and calculation of a magnetic wheeled climbing robot is presented. It is able to pass obstacles that previously had only been accessed by robots with more complex mechanisms, but only needs 2 actively controlled DOF. A comparison to other design alternatives and the influence of some core parameters are shown in calculations with simplified 2D models. According to these calculations, a prototype was realized to prove its functionality in real tests. The paper concludes with an outlook on further design improvements and shows possible scenarios for its industrial application in the field of power plant inspection.
Differentiating closed-loop cortical intention from rest: building an asynchronous electrocorticographic BCI (2013)

The results presented here provide valuable insight into the neurophysiology of BCI control as well as important considerations toward the design of an asynchronous BCI system.
Using Colored Cullet for Making Beautiful Glassware (2003)

Eight colored glasses from Fire and Light Originals (FLO) and three container cullet glasses were characterized for the viscosity, density, and thermal expansion, glass transition temperature, dilatometer softening temperature, color chromaticity, Fe(II)/Fe(total) redox ratio, and chemical composition. The results of the characterization were used to evaluate the options for the glass formulation development of colored glasses aimed at increasing the use of recycled container glass cullet. Out of several options considered, the possibility of using clear cullet for FLO’s Citrus colored glass was selected and investigated in this study. It was shown that it is possible to use clear cullet to produce Citrus glass at the cullet oxide ratio of 90 mass% and the final color can be adjusted by controlling the nitrate level and alkali concentrations. From the present study, recommendations for further development efforts are provided to increase the container cullet usage or to replace partially or entirely the clear cullet by the amber cullet.
PRESENCE OF TWO TYPES OF L POLYPEPTIDE CHAINS IN GUINEA PIG 7S IMMUNOGLOBULINS (1966)

Guinea pig 7S immunoglobulins (gamma(1) and gamma(2)) consist of two groups of molecules (K and L) bearing different types of L chains (kappa and lambda). Approximately one-third of the molecules in normal guinea pig gamma(2)-globulin bear the lambda- type of L chains, and all or most of the others bear kappa-chains. kappa- and lambda-chains have similar molecular weights.
Triplet ground state in the dimer bis(pyridine N-oxide)copper(II) nitrate (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTriplet ground state in the dimer bis(pyridine N-oxide)copper(II) nitrateWilliam E. Hatfield, James A. Barnes, David Y. Jeter, Robin Whyman, and Edwin Rudolph Jr. JonesCite this: J. Am. Chem. Soc. 1970, 92, 16, 4982–4984Publication Date (Print):August 1, 1970Publication History Published online1 May 2002Published inissue 1 August 1970https://doi.org/10.1021/ja00719a038RIGHTS & PERMISSIONSArticle Views106Altmetric-Citations55LEARN 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 InReddit PDF (397 KB) Get e-Alerts Get e-Alerts
In situ spectrochemical analysis of solid surfaces by ion beam sputtering (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIn situ spectrochemical analysis of solid surfaces by ion beam sputteringN. H. Tolk, I. S. T. Tsong, and C. W. WhiteCite this: Anal. Chem. 1977, 49, 1, 16A–30APublication Date (Print):January 1, 1977Publication History Published online21 September 2008Published inissue 1 January 1977https://doi.org/10.1021/ac50009a001RIGHTS & PERMISSIONSArticle Views60Altmetric-Citations59LEARN 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 InReddit PDF (2 MB) Get e-Alerts Get e-Alerts
Fractionation of dry bean extracts which increase carbon dioxide egestion in human flatus (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFractionation of dry bean extracts which increase carbon dioxide egestion in human flatusEdwin L. Murphy, Heide Horsley, and Horace K. BurrCite this: J. Agric. Food Chem. 1972, 20, 4, 813–817Publication Date (Print):July 1, 1972Publication History Published online1 May 2002Published inissue 1 July 1972https://pubs.acs.org/doi/10.1021/jf60182a024https://doi.org/10.1021/jf60182a024research-articleACS PublicationsRequest reuse permissionsArticle Views102Altmetric-Citations34LEARN 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
Ab Initio Molecular Dynamics Simulations of Elimination Reactions in Water Solution:  Exploring the Borderline Region between the E1cb and E2 Reaction Mechanisms (2006)

We report a theoretical study, based on ab initio molecular dynamics simulations in water solution, of the mechanism of base-induced beta-elimination reactions in systems activated by the pyridyl ring, with halogen leaving groups. The systems investigated represent borderline cases, where it is uncertain whether the reaction proceeds via a carbanion intermediate (E1cb, A(xh)D(H) + D(N)) or via the concerted loss of a proton and the halide (E2, A(N)D(E)D(N)) upon base attack. Recent theoretical and experimental evidence points toward the lack of a net distinction between the E1cb and E2 reaction paths, which seem to merge smoothly into each other in these borderline cases (Alunni, S.; De Angelis, F.; Ottavi, L.; Papavasileiou, M.; Tarantelli, F. J. Am.Chem. Soc. 2005, 127, 15151-15160). In this study, we explore the dynamics on the potential energy surface for the reaction of 2-(2-fluoroethyl)-1-methyl pyridinium with OH- by means of Car-Parrinello simulations in water solution. Our results indicate that the reaction mechanism effectively evolves through the potential energy region of the carbanion: the carbon-fluoride bond breaks only after the carbon-hydrogen bond, confirming the conclusions of a recently reported study of the potential energy surface for this system.