gebhart/patrepeval huggingface dataset:
Purification and characterization of a human tumor necrosis factor from the LuKII cell line. (1985)

A factor with tumor necrosis factor (TNF) activity produced by the LuKII human lymphoblastoid cell line [designated TNF(LuKII)] was purified sequentially by using controlled-pore glass, lentil lectin-Sepharose, and procion red agarose chromatography, yielding TNF with a specific activity of 1.5 X 10(7) units per mg of protein and an isoelectric point of approximately equal to 6.7. Purified TNF(LuKII) fractionated by NaDodSO4/PAGE under reducing as well as nonreducing conditions was found to contain seven protein bands of Mr 80,000, 70,000, 43,000, 25,000, 23,000, 21,000, and 19,000. The proteins of Mr 80,000 and 70,000 could not be dissociated into lower molecular weight components. Peptide mapping analysis and immunoblotting analysis revealed that the seven protein bands in the purified TNF(LuKII) preparations are related. After fractionation of TNF(LuKII) by NaDodSO4/PAGE under reducing conditions, TNF activity was recovered from the regions of Mr 70,000 and 19,000-25,000. Purified human TNF(LuKII) (i) produces hemorrhagic necrosis of Meth A mouse sarcoma in the standard in vivo mouse TNF assay; (ii) has the same pattern of reactivity as mouse TNF (cytotoxic/cytostatic/no effect) on a panel of human cancer cell lines; and (iii) has its anticellular effect potentiated by interferon, also a feature of mouse TNF.
Über organische Elektronenüberträgersysteme, I. Elektrochemische und spektroskopische Untersuchung bromsubstituierter Triarylamin‐Redoxsysteme (1980)

Abstract Das Redoxverhalten der bromsubstituierten Triarylamine 2 – 7 wurde mit Hilfe der Methode der cyclischen Voltammetrie untersucht. Die Oxidationspotentiale des Redoxpaars Amin/ Radikalkation hängen stark vom Substitutionsgrad in den ortho ‐Positionen ab, wobei zusätzlich zu einem starken elektronischen Effekt ein schwächerer sterischer Einfluß beobachtet wird. Der Einfluß der Substitution auf das zweite Oxidationspotential, Radikalkation/Dikation, ist wesentlich geringer. Die UV/VIS‐Spektren der zugehörigen Radikalkationen sind mit zunehmender ortho ‐Substitution bathochrom verschoben. Zwischen Redoxpotential der Amine und langwelligstem Absorptionsmaximum der Radikalkationen besteht ein linearer Zusammenhang. Redoxpotentiale und UV/VIS‐Spektren gestatten eine partielle Termanalyse der Amine und der zugehörigen Radikalkationen. Die ESR‐Spektren der Radikalkationen zeigen breite unaufgelöste Signale.
Current Understanding of Human Enterovirus D68 (2019)

Human enterovirus D68 (EV-D68), a member of the species <i>Enterovirus D</i> of the <i>Picornaviridae</i> family, was first isolated in 1962 in the United States. EV-D68 infection was only infrequently reported until an outbreak occurred in 2014 in the US; since then, it has continued to increase worldwide. EV-D68 infection leads to severe respiratory illness and has recently been reported to be linked to the development of the neurogenic disease known as acute flaccid myelitis (AFM), mostly in children, seriously endangering public health. Hitherto, treatment options for EV-D68 infections were limited to supportive care, and as yet there are no approved, specific antiviral drugs or vaccines. Research on EV-D68 has mainly focused on its epidemiology, and its virologic characteristics and pathogenesis still need to be further explored. Here, we provide an overview of current research on EV-D68, including the genotypes and genetic characteristics of recent epidemics, the mechanism of infection and virus-host interactions, and its relationship to acute flaccid myelitis (AFM), in order to broaden our understanding of the biological features of EV-D68 and provide a basis for the development of effective antiviral agents.
Probing the Role of the Linker in Ferrocene–ATP Conjugates: Monitoring Protein Kinase Catalyzed Phosphorylations Electrochemically (2011)

The synthesis and electrochemical properties of ferrocene conjugates are presented for the purpose of investigating adenosine 5'-[γ-ferrocenoylalkyl] triphosphate (1 a-4 a, ferrocene (Fc)-ATP) as co-substrates for phosphorylation reactions. Compounds 1 a-4 a were synthesized, purified by HPLC, and characterized by NMR spectroscopy and mass spectrometry. In solution, all Fc-ATP bioconjugates exhibit a reversible one-electron redox process with a half-wave potential (E(1/2)) in the 390-430 mV range, peak separations (ΔE(p)) in the 40-70 mV range, and the peak current ratio (i(pa)/i(pc)) near unity. The peptide-modified surface Glu-Gly-Ile-Tyr-Asp-Val-Pro was used to study the sarcoma-related protein (Src) kinase activity by employing the Fc-ATP bioconjugates as co-substrates. Subsequent kinase-catalyzed transfer of the γ-Fc-phosphate group to the tyrosine residues of the surface-bound peptides was characterized by a formal potential (E°) ≈390 mV (vs. Ag/AgCl). The Fc-coverage, estimated by time-of-flight secondary-ion mass spectrometry (TOF-SIMS) and cyclic voltammetry (CV), suggested validity of Fc-ATP conjugates as kinase co-substrates. Depending on the length of the alkyl spacer of the Fc-ATP conjugate, different current densities were obtained, pointing to a direct correlation between the two. Molecular modeling revealed that the structural constraint imposed by the short alkyl spacer (1 a) causes a steric congestion and negatively affects the outcome of phosphorylation reaction. An optimal analytical response was obtained with the Fc-ATP conjugates with linker lengths longer than six CH(2) groups.
Fairness Under Unawareness: Assessing Disparity When Protected Class Is Unobserved (2018)

Assessing the fairness of a decision making system with respect to a protected class, such as gender or race, is challenging when class membership labels are unavailable. Probabilistic models for predicting the protected class based on observable proxies, such as surname and geolocation for race, are sometimes used to impute these missing labels for compliance assessments. Empirically, these methods are observed to exaggerate disparities, but the reason why is unknown. In this paper, we decompose the biases in estimating outcome disparity via threshold-based imputation into multiple interpretable bias sources, allowing us to explain when over- or underestimation occurs. We also propose an alternative weighted estimator that uses soft classification, and show that its bias arises simply from the conditional covariance of the outcome with the true class membership. Finally, we illustrate our results with numerical simulations and a public dataset of mortgage applications, using geolocation as a proxy for race. We confirm that the bias of threshold-based imputation is generally upward, but its magnitude varies strongly with the threshold chosen. Our new weighted estimator tends to have a negative bias that is much simpler to analyze and reason about.
A compressed sensing technique for OFDM channel estimation in mobile environments: Exploiting channel sparsity for reducing pilots (2008)

We consider the estimation of doubly selective wireless channels within pulse-shaping multicarrier systems (which include OFDM systems as a special case). A new channel estimation technique using the recent methodology of compressed sensing (CS) is proposed. CS-based channel estimation exploits a channel's delay-Doppler sparsity to reduce the number of pilots and, hence, increase spectral efficiency. Simulation results demonstrate a significant reduction of the number of pilots relative to least-squares channel estimation.
Fast Response Photochromic Mesostructures (2000)

Direct photochromism is observed for the mesostructured host–photochromic guest system reported here. Block-copolymer/silica mesostructures were used as hosts for two photochromic dyes, a spirooxazine and a spiropyran. It is shown that the dyes are incorporated predominantly within the hydrophobic occlusions of the mesostructures (see Figure) and exhibit direct photochromism, with very fast response times.
Influence of Hydrocarbon Storage on the Durability of SCR Catalysts (2008)

&lt;div class="htmlview paragraph"&gt;Selective catalytic reduction (SCR) is a technology capable of meeting Tier 2 Bin 5 emissions levels of oxides of nitrogen (NO&lt;sub&gt;X&lt;/sub&gt;) for diesel engines. Base metal zeolite catalysts show the best combination of thermal durability and NO&lt;sub&gt;X&lt;/sub&gt; conversion activity. It is shown in this work that some base metal zeolite catalysts can store high levels of hydrocarbons (HCs). Also, base metal zeolite catalysts can catalyze oxidation of HCs under certain conditions. Oxidation of stored hydrocarbons can lead to permanent catalyst deactivation due to the exotherm generated in the SCR catalyst (over-temperature condition leading to SCR catalyst damage). This paper discusses a laboratory bench test to characterize hydrocarbon storage and burn-off characteristics of several SCR catalyst formulations, as well as engine dynamometer tests showing hydrocarbon storage and exotherm generation. The storage of hydrocarbons is primarily a concern at temperatures below around 200°C, and the oxidation occurs at temperatures around 300°C to 350°C. It is shown that improved SCR formulations have lower HC storage and therefore have much less risk of exotherms based on hydrocarbon storage.&lt;/div&gt;
Quantitative Approach for the Serodiagnosis of Canine Lyme Disease by the Immunoblot Procedure (2000)

Serum samples obtained from healthy, asymptomatic dogs in areas of Wisconsin and northern Illinois where Lyme disease is endemic or nonendemic were assayed for antibodies to Borrelia burgdorferi by enzyme-linked immunosorbent assay (ELISA), and positive results were confirmed by immunoblot assay. We found that 56.9% (562 of 1,077) of the samples were positive by ELISA and 82.0% (461 of 562) were positive by immunoblotting. A logistic regression model was developed to distinguish between nonvaccinated dogs naturally infected with B. burgdorferi from areas where the disease is endemic and dogs from areas where the disease is nonendemic that were vaccinated against Lyme disease. Of the 18 protein bands analyzed, 8 were found to be significantly different (P<0.05) between the two groups. p93, p34, p31, and p28 occurred with increased frequency in vaccinated dogs, while p58, p37, p35, and p30 occurred more frequently in naturally infected dogs. The logistic regression equation obtained was used to determine the probability of natural infection among vaccinated dogs residing in areas where the disease is endemic. Of 125 samples, 87.2% had a very low probability of natural infection and only 2.4% were highly likely to be infected. Logistic regression is a useful method for distinguishing between vaccinated and naturally infected dogs and predicting the serological status of vaccinated dogs from areas where Lyme disease is endemic.
Uptake and metabolic fate of [HisA8,HisB4,GluB10,HisB27]insulin in rat liver in vivo (1998)

Receptor-mediated endocytosis and subsequent endosomal proteolysis of [125I]TyrA14-[HisA8,HisB4,GluB10,HisB27]in sulin ([125I]TyrA14-H2 analogue), an insulin analogue exhibiting a high affinity for the insulin receptor, has been studied in liver parenchymal cells by quantitative subcellular fractionation and compared with that of wild-type [125I]TyrA14-insulin. Whereas the kinetics of uptake of the H2 analogue by liver was not different from that of insulin, the H2 analogue radioactivity after the 2 min peak declined significantly more slowly. A significant retention of the H2 analogue compared with insulin in both plasma membrane and endosomal fractions was observed and corresponded to decreased processing and dissociation of the H2 analogue. Cell-free endosomes preloaded in vivo with radiolabelled ligands and incubated in vitro processed insulin and extraluminally released insulin intermediates at a 2-3-fold higher rate than the H2 analogue. In vitro proteolysis of both non-radiolabelled and monoiodinated molecules by endosomal lysates showed a decreased response to the endosomal proteolytic machinery for the H2 analogue. However, in cross-linking and competition studies the H2 analogue exhibited an affinity for insulin-degrading enzyme identical with that of wild-type insulin. Brij-35-permeabilized endosomes revealed a 2-fold higher rate of dissociation of insulin from internalized receptors compared with the H2 analogue. After the administration of a saturating dose of both ligands, a rapid and reversible ligand-induced translocation of insulin receptor was observed, but without receptor loss. The H2 analogue induced a higher receptor concentration and tyrosine autophosphorylation of the receptor beta subunit in endosomes. Moreover, a prolonged temporal interaction of the in vivo injected H2 analogue with receptor was observed by direct binding assays performed on freshly prepared subcellular fractions. These results indicate that endosomal proteolysis for the H2 analogue is slowed as a result of an increased residence time of the analogue on the insulin receptor and a low affinity of endosomal acidic insulinase for the dissociated H2 molecule.
Localization of Protein Kinases by Anchoring Proteins: a Theme in Signal Transduction (1995)

A fundamental question in signal transduction is how stimulation of a specific protein kinase leads to phosphorylation of particular protein substrates throughout the cell. Recent studies indicate that specific anchoring proteins located at various sites in the cell compartmentalize the kinases to their sites of action. Inhibitors of the interactions between kinases and their anchoring proteins inhibit the functions mediated by the kinases. These data indicate that the location of these anchoring proteins provides some of the specificity of the responses mediated by each kinase and suggest that inhibitors of the interaction between the kinases and their anchoring proteins may be useful as therapeutic agents.
Interferon γ–Inducible Protein-10 (IP-10) and Eotaxin as Biomarkers in Age-Related Macular Degeneration (2010)

IP-10 and eotaxin may be early biomarkers in AMD. The authors hypothesize that the relative balance between levels of IP-10 and eotaxin is critical in regulating the neovascular response.
Influence of Bacillus subtilis phoR on cell wall anionic polymers (1997)

In Bacillus subtilis the Pho regulon is controlled by a sensor and regulator protein pair, PhoR and PhoP, that respond to phosphate concentrations. To facilitate studies of the Pho regulon, a strain with an altered PhoR protein was isolated by in vitro mutagenesis. The mutation in this strain (phoR12) leads to the production of a PhoR sensor kinase that, unlike the wild-type, is functionally active in phosphate-replete conditions. The lesion in PhoR12 was shown to be a single base change that results in an Arg to Ser substitution in a region of PhoR that is highly conserved in histidine sensor kinases. While a phoR-negative mutant was unable to induce the synthesis of cell wall teichuronic acid under phosphate-limited conditions, the phoR12 mutant showed a relative increase in teichuronic acid and a decrease in teichoic acid, even under phosphate-replete conditions. The latter suggests that some or all of the genes required for teichuronic acid synthesis are members of the Pho regulon.
Alteration of the amino terminus of the mature sequence of a periplasmic protein can severely affect protein export in Escherichia coli. (1988)

Escherichia coli alkaline phosphatase, coded for by the phoA gene, is normally translocated across the cytoplasmic membrane into the periplasm with high efficiency. We have constructed a series of derivatives of the phoA gene that code for a wild-type signal sequence but result in altered amino acid sequences at the amino terminus of the mature alkaline phosphatase. Our results suggest that the presence of two positively charged amino acids very early in the mature sequence interferes significantly with protein export. In one case, phoA2AB, the presence of the sequence Arg-Ile-Arg at the amino terminus of alkaline phosphatase results in a 50-times reduction in the export of the protein. By using oligonucleotide-directed mutagenesis, we have constructed mutant derivatives of phoA2AB that are greatly enhanced for export. In all cases, these derivatives reduce the net positive charge in the region. Our results may explain the failure of E. coli to export a number of proteins coded for by artificial constructs and suggest a way to improve export in these cases.
Efficient Bayesian Phase Estimation (2016)

We introduce a new method called rejection filtering that we use to perform adaptive Bayesian phase estimation. Our approach has several advantages: it is classically efficient, easy to implement, achieves Heisenberg limited scaling, resists depolarizing noise, tracks time-dependent eigenstates, recovers from failures, and can be run on a field programmable gate array. It also outperforms existing iterative phase estimation algorithms such as Kitaev's method.
Urethroplasty of Urethral Defect with Longitudinal Tubed Flap of Scrotal Skin after Fournier's Gangrene (Necrotizing Fascitis). (2010)

Purpose: The management of urethral defect represents one of the most challenging clinical problems in uroplastic surgery. Especially for defect after Fournier's Gangrene, optimal management is still a hard problem. During extensive urethral reconstruction, to overcome the poor vascularity due to periurethral scarred tissue and limitation of the choice of local flap, we report our experience with one-stage reconstruction of urethral defect using a longitudinal tubed flap of scrotal skin. Methods: A 72-year-old man with several years of diabetes mellitus history visited for swelling and pain of scrotal area. After diagnosis of Fournier's Gangrene, radical debridement was performed and 6 cm of urethral defect on border of penile-scrotal ventral area was made. Rectangular scrotal skin flap () based on external spermatic fascia was elevated and tubed longitudinally. After transfer the flap to the defect area, end-to-end anastomosis was performed bilaterally. Results: 4 weeks after the operation, the patient started voiding him-self and urethrography showed good fluence of contrast agent. Long term evaluation reveals stable performance characteristics without any complications. Conclusion: We suggest a one-stage reconstruction of extensive urethral defect using a longitudinal tubed flap of scrotal skin. Advantages of this procedures are simple, one-stage reconstruction with the reliable scrotal skin flap based on external spermatic fascial vasculature, and no donor morbidity.
'God' is Norwegian for 'good' (2011)

The Norwegian Humanist Association (Human- Etisk Forbund) hosted IHEU's World Humanist Congress in Oslo, 12-15 August 2011, which my wife and I attended. We were told that there were seventy-eight thousand registered Humanists in Norway, a nation of only 4.9 million people. The Association employs some seventy-five full-time staff, and their Oslo headquarters, Humanist House, is an elegant city building with a staircase spiralling round a column of chandeliers. It is all funded by government as part of a national commitment towards world peace.
Physiological investigations into the resistance of a wild mustard (Sinapis arvensis L.) biotype to auxinic herbicides (1993)

Summary: Résumé: Zusammenfassung Possible mechanism(s) of resistance to auxinic herbicides in wild mustard ( Sinapis arvensis L.) were investigated by characterizing responses of susceptible and resistant biotypes to 2,4‐D, di‐camba or picloram. No differences between bio‐types were observed in absorption, translocation, or metabolism of foliar‐applied radiolabelled herbicides. In contrast, the levels of ethylene production varied between biotypes. The susceptible biotype produced twofold and sixfold more ethylene than the resistant biotype within 4 h and 44 h of herbicide application, respectively. These results suggest that the mechanism of resistance in wild mustard is not due to differences in absorption, translocation, or metabolism. Ethylene production studies imply that resistance to auxinic herbicides may be attributed to altered target site(s) of action. Bases physiologiques de la résistance aux herbicides auxiniques d'un biotype de moutarde des champs (Sinapis arvensis L.) Les mécanismes possibles de la résistance aux herbicides auxiniques chez la moutarde des champs ( Sinapis arvensis L.) ont été recherchés en caractérisant les réponses de biotypes résis‐tants et sensibles au 2,4‐D, au dicamba et au pi‐clorame. Aprés application des herbicides radioactifs sur le feuillage, aucune différence d'absorption, de migration ou de métabolisme n'a été observée. Par contre, la production d'éthylene différait entre les biotypes. Le biotype sensible produisait 2 et 6 fois plus d'éthylène que le biotype sensible, respectivement 4 et 44 heures après l'application d'herbicide. Ces résultats sug‐gèrent que la résistance aux herbicides auxiniques chez la moutarde des champs n'est pas due à des différences d'absorption, de migration ou de métabolisme mais pourrait provenir d'une altération du site d'action. Physiologische Untersuchung der Resistenz eines Acker‐Senf‐(Sinapis arvensis‐) Biotyps gegenüber Wuchsstoffherbiziden Der mögliche Mechanismus der Resistenz gegenüber Wuchsstoffherbiziden beim Acker‐Senf ( Sinapis arvensis L.) wurde unhand der Reaktion von empfindlichen und resistenten Biotypen gegenüber 2,4‐D, Dicamba oder Picloram untersucht. Hinsichtlich Absorption, Translokation oder Metabolismus der auf die Blätter applizierten, radioaktiv markierten Her‐bizide wurden keine Unterschiede beobachtet. Die Ethylenbildung variierte jedoch zwischen den Biotypen. Der empfindliche produzierte in‐nerhalb 4 oder 44 Stunden nach der Herbizid‐applikation 2‐bzw. 6mal mehr Ethylen als der resistente. Aus den Ergebnissen läßt sich schließen, daß beim Acker‐Senf der Resisten‐zmechanismus nicht in der Absorption, der Translokation oder dem Metabolismus liegt, sondern die Ethylenbildung daran beteiligt ist, wo die Wirkorte fur die Wuchsstoffherbizide liegen.
Microenvironmental Regulation of Membrane Type 1 Matrix Metalloproteinase Activity in Ovarian Carcinoma Cells via Collagen-induced EGR1 Expression (2006)

Late stage ovarian cancer is characterized by disseminated intraperitoneal metastasis as secondary lesions anchor in the type I and III collagen-rich submesothelial matrix. Ovarian carcinoma cells preferentially adhere to interstitial collagen, and collagen-induced integrin clustering up-regulates the expression of the transmembrane collagenase membrane type 1 matrix metalloproteinase (MT1-MMP). Collagenolytic activity is important in intraperitoneal metastasis, potentiating invasion through the mesothelial cell layer and colonization of the submesothelial collagen-rich matrix. The objective of this study was to elucidate a potential mechanistic link between collagen adhesion and MT1-MMP expression. Our results indicate that culturing cells on three-dimensional collagen gels, but not thin layer collagen or synthetic three-dimensional hydrogels, results in rapid induction of the transcription factor EGR1. Integrin signaling through a SRC kinase-dependent pathway is necessary for EGR1 induction. Silencing of EGR1 expression using small interfering RNA abrogated collagen-induced MT1-MMP expression and inhibited cellular invasion of three-dimensional collagen gels. These data support a model for intraperitoneal metastasis wherein collagen adhesion and clustering of collagen binding integrins activates integrin-mediated signaling via SRC kinases to induce expression of EGR1, resulting in transcriptional activation of the MT1-MMP promoter and subsequent MT1-MMP-catalyzed collagen invasion. This model highlights the role of unique interactions between ovarian carcinoma cells and interstitial collagens in the ovarian tumor microenvironment in inducing gene expression changes that potentiate intraperitoneal metastatic progression.