gebhart/patrepeval huggingface dataset:
Construction and analysis of a detailed three‐dimensional model of the ligand binding domain of the human B cell receptor CD40 (1997)

The interaction between the human B cell receptor CD40 and its ligand on T cells is critical for B cell proliferation and the regulation of humoral immune responses. CD40 is a member of the tumor necrosis factor receptor (TNFR) family. We report here the construction and analysis of a detailed three-dimensional model of the TNFR-homologous extracellular region of CD40. This study provides an example for structure-based model building in the presence of low sequence similarity. The assessment of model quality and sequence-structure compatibility is emphasized, and limitations of the model are discussed. The current CD40 model predicts structural details beyond the backbone level. Features of the CD40 ligand binding site are discussed in conjunction with the results of a previous mutagenesis study. Proteins 27:59–70 © 1997 Wiley-Liss, Inc.
Comparison of immune responses and resistance to brucellosis in mice vaccinated with Brucella abortus 19 or RB51 (1995)

Immune responses and resistance to infection with Brucella abortus 2308 (S2308) were measured in mice following vaccination with B. abortus 19 (S19) or the lipopolysaccharide (LPS) O-antigen-deficient mutant, strain RB51 (SRB51). Live bacteria persisted for 8 weeks in spleens of mice vaccinated with 5 x 10(6) or 5 x 10(8) CFU of SRB51, whereas bacteria persisted for 12 weeks in mice vaccinated with 5 x 10(6) CFU of S19. Mice vaccinated with 5 x 10(6) or 5 x 10(8) CFU of SRB51 had increased resistance to infection with S2308 at 12, 16, and 20 weeks after vaccination, but the resistance was lower than that induced by vaccinating mice with 5 x 10(6) CFU of S19. Spleen cells obtained from mice vaccinated with S19 or SRB51 generally exhibited similar proliferative responses to S2308 bacteria or bacterial proteins (106 to 18 kDa) following challenge of mice with S2308 at 12, 16, or 20 weeks after vaccination. Mice vaccinated with S19 had antibody to S2308 bacteria and S2308 smooth LPS at 4, 8, and 12 weeks after vaccination. In contrast, mice vaccinated with either dose of SRB51 did not produce antibody to S2308 smooth LPS. In addition, only mice vaccinated with the highest dose of SRB51 (5 x 10(8) CFU) had antibody responses to S2308 bacteria, although the responses were lower and less persistent than those in mice vaccinated with S19. Collectively, these results indicate that SRB51-vaccinated mice have similar cell-mediated immune responses to S2308 but lower resistance to infection with S2308 compared with S19-vaccinated mice. The lower resistance in SRB51-vaccinated mice probably resulted from a combination of rapid clearance of SRB51 and an absence of antibodies to S2308 LPS.
Cooling of a single atom in an optical trap inside a resonator (2001)

We present detailed discussions of cooling and trapping mechanisms for an atom in an optical trap inside an optical cavity, as relevant to recent experiments. The interference pattern of cavity QED and trapping fields in space makes the trapping wells, in principle, distinguishable from one another. This adds considerable flexibility to creating effective trapping and cooling conditions and to detection possibilities. Friction and diffusion coefficients are calculated in and beyond the low excitation limit and full three-dimensional simulations of the quasiclassical motion of a Cs atom are performed.
Dissociation equilibrium constant of beta nerve growth factor (1977)

The beta nerve growth factor (NGF) isolated from the high molecular weight 7 S NGF complex from mouse submaxillary gland is a protein of molecular weight 26,500 which contains two noncovalently associated peptide chains. A variety of techniques were employed to determine whether the NGF dimer dissociates at the low concentrations at which it is biologically active. No dissociation was detected in 48 h at low NGF concentrations using the techniques and minimum concentrations which follow: sedimentation equilibrium of NGF at 200 nM and of 125I-NGF at 2.5 nM; gel filtration chromatography of NGF at 5 nM, of 125I-NGF at 5 pM, and of 125I-NGF from which COOH-terminal arginyl residues, or NH2-terminal octapeptide had been cleaved, at 10 pM; and sucrose gradient centrifugation of 125I-NGF at 10 pM. Dissociation of heavily succinylated 125I-NGF was detected by gel filtration chromatography, and the equilibrium dissociation constant for this material is estimated to be 10 pM.
Contribution of the active metabolite M1 to the pharmacological activity of tesofensine in vivo: a pharmacokinetic‐pharmacodynamic modelling approach (2007)

The lower potency of M1 together with approximately 8-fold higher through steady-state concentrations suggest that M1 did contribute to the overall activity of tesofensine in mice.
Hemodynamic changes by recombinant erythropoietin therapy in hemodialyzed patients. (1990)

Recombinant human erythropoietin therapy was given to 15 patients undergoing long-term hemodialysis with normal cardiac function. None of the patients had hypertension before the erythropoietin therapy and had received no antihypertensive agents. Before and after the erythropoietin therapy M-mode and pulsed Doppler echocardiographic studies, measurements of plasma volume by radioiodinated human serum albumin, and measurements of atrial natriuretic factor were carried out. After 6 weeks of erythropoietin therapy, hematocrit increased from 20.0 to 33.0%. Cardiac output, stroke volume, left ventricular diastolic dimensions, and left ventricular wall stress were all significantly decreased. Total peripheral resistance, interventricular septal thickness, and left ventricular posterior wall thickness were significantly increased. In Doppler echocardiographic studies, the mean velocity of aortic ejection flow and left ventricular acceleration time were decreased. The blood volume derived from plasma volume and hematocrit was not changed, whereas plasma atrial natriuretic factor concentration was significantly decreased. These data suggest that recombinant human erythropoietin administration suppressed the hyperdynamic cardiac state that was required to maintain oxygen delivery to the peripheral tissues in severe uremic anemia.
Prospects for Biodiesel as a Byproduct of Wood Pulping - A Review (2006)

Effective utilization of byproducts can affect the profitability of kraft pulping to produce cellulosic fibers from wood. This review considers opportunities to use tall oil components, obtained from kraft pulping, as a source of raw material for biodiesel fuel, or as a source of additives for petrodiesel. Considerable progress has been achieved with respect to converting vegetable oils to diesel fuel, and some of what has been learned appears to have potential application for processing of wood-derived fatty acids and related compounds. Alkaline – catalyzed trans esterification strategies, while seemingly well adapted for relatively pure vegetable oil source materials, may not be the best fit for the processing of tall oil fractions. The promising strategies to consider include acid – catalyzed esterification, enzymatic processes, hydrogenation, and the use of supercritical methanol.
Novel zinc-based fixative for high quality DNA, RNA and protein analysis (2007)

We have developed a reliable, cost-effective and non-toxic fixative to meet the needs of contemporary molecular pathobiology research, particularly in respect of RNA and DNA integrity. The effects of 25 different fixative recipes on the fixed quality of tissues from C57BL/6 mice were investigated. Results from IHC, PCR, RT-PCR, RNA Agilent Bioanalyser and Real-Time PCR showed that a novel zinc-based fixative (Z7) containing zinc trifluoroacetate, zinc chloride and calcium acetate was significantly better than the standard zinc-based fixative (Z2) and neutral buffered formalin (NBF) for DNA, RNA and protein preservation. DNA sequences up to 2.4 kb in length and RNA fragments up to 361 bp in length were successfully amplified from Z7 fixed tissues, as demonstrated by PCR, RT-PCR and Real-Time PCR. Total protein analysis was achieved using 2-D gel electrophoresis. In addition, nucleic acids and proteins were very stable over a 6-14-month period. This improved, non-toxic and economical tissue fixative could be applied for routine use in pathology laboratories to permit subsequent genomic/proteomic studies.
Hairpin Peptide Motif. A New Class of Oligopeptides for Sequence-Specific Recognition in the Minor Groove of Double-Helical DNA (1994)

Peptides which bind in the minor groove of DNA as antiparallel side-by-side dimers can be linked head-to-tail&#13;\nto afford a new class of hairpin oligopeptides with enhanced sequence specificity for DNA. Four hexapeptides were&#13;\nsynthesized wherein the terminal amine and carboxyl groups of tris(N-methylpyrrolecarboxamide) (P3) and&#13;\nN-methylimidazole-2-carboxamide-netropsin (2-ImN), respectively, have been connected with glycine (Gly), β-alanine&#13;\n(βAla), 4-aminobutyric acid (GABA), and 5-aminovaleric acid (Ava) amino acids. The hexapeptide 2-ImN-GABA-P3&#13;\nbinds 5'-TGTTA-3' sites with a binding affinity of 7.6 X 10^7 M^(-1) (10 mM Tris·HCl, 10 mM KCl, 10 mM MgCl_2,&#13;\nand 5 mM CaCl_2 at pH 7.0 and 22 °C). The general and efficient synthetic methodology-for preparation of head-to-tail&#13;\nlinked peptides should allow the design of a new class of hairpin peptides for specific recognition of many different&#13;\nsequences in the minor groove of DNA.&#13;\n
Gold Nanorod−Photosensitizer Complex for Near-Infrared Fluorescence Imaging and Photodynamic/Photothermal Therapy In Vivo (2011)

A gold nanorod (GNR)-photosensitizer complex was developed for noninvasive near-infrared fluorescence imaging and cancer therapy. We showed that (a) fluorescence emission and singlet oxygen generation by AlPcS(4) were quenched after complex formation with GNRs; (b) 4-fold greater intracellular uptake and better in vitro phototoxicity were observed in GNR-AlPcS(4)-treated cells than in free AlPcS(4)-treated cells; and (c) after intravenous injection of the GNR-AlPcS(4) complex, tumor sites were clearly identified on near-infrared fluorescence images as early as 1 h after injection. The tumor-to-background ratio increased over time and was 3.7 at 24 h; tumor growth reduced by 79% with photodynamic therapy (PDT) alone and by 95% with dual photothermal therapy (PTT) and PDT. This novel multifunctional nanomedicine may be useful for near-infrared fluorescence imaging and PTT/PDT in various cancers.
Fall in skin temperature of exercising man. (1992)

Fall in skin temperature during initial muscular work was investigated in ten healthy men. Bicycle exercise was performed at workloads of 50-150 W in a climatic chamber at ambient temperatures of 10-40 degrees C (relative humidity 45-55%). Skin temperatures at seven or eight points over the body surface were measured using thermography and thermocouple recording systems. Sweat rates were significantly higher at 40 degrees C than at 30 degrees C, whereas the fall in skin temperature was almost equal. The reduction of skin temperature during exercise was the same throughout the year, although sweat rate was significantly higher in summer than in winter. In coloured thermographics of the skin temperature distribution during exercise of both 50 and 150 W at 10 or 20 degrees C, the skin temperature began to decline immediately at the onset of the exercise. Increased work intensities reduced skin temperature. The results suggest that fall in skin temperature during initial exercise was not due to increased evaporative cooling but to vasoconstriction, probably caused by non-thermal factors.
Efficient use of side information in multiple-antenna data transmission over fading channels (1998)

We derive performance limits for two closely related communication scenarios involving a wireless system with multiple-element transmitter antenna arrays: a point-to-point system with partial side information at the transmitter, and a broadcast system with multiple receivers. In both cases, ideal beamforming is impossible, leading to an inherently lower achievable performance as the quality of the side information degrades or as the number of receivers increases. Expected signal-to-noise ratio (SNR) and mutual information are both considered as performance measures. In the point-to-point case, we determine when the transmission strategy should use some form of beamforming and when it should not. We also show that, when properly chosen, even a small amount of side information can be quite valuable. For the broadcast scenario with an SNR criterion, we find the efficient frontier of operating points and show that even when the number of receivers is larger than the number of antenna array elements, significant performance improvements can be obtained by tailoring the transmission strategy to the realized channel.
The Limits to Parapatric Speciation: Dobzhansky–Muller Incompatibilities in a Continent–Island Model (2012)

How much gene flow is needed to inhibit speciation by the accumulation of Dobzhansky-Muller incompatibilities (DMIs) in a structured population? Here, we derive these limits in a classical migration-selection model with two haploid or diploid loci and unidirectional gene flow from a continent to an island. We discuss the dependence of the maximum gene-flow rate on ecological factors (exogeneous selection), genetic factors (epistasis, recombination), and the evolutionary history. Extensive analytical and numerical results show the following: (1) The maximum rate of gene flow is limited by exogeneous selection. In particular, maintenance of neutral DMIs is impossible with gene flow. (2) There are two distinct mechanisms that drive DMI evolution in parapatry, selection against immigrants in a heterogeneous environment and selection against hybrids due to the incompatibility. (3) Depending on the mechanism, opposite predictions result concerning the genetic architecture that maximizes the rate of gene flow a DMI can sustain. Selection against immigrants favors evolution of tightly linked DMIs of arbitrary strength, whereas selection against hybrids promotes the evolution of strong unlinked DMIs. In diploids, the fitness of the double heterozygotes is the decisive factor to predict the pattern of DMI stability.
Experimental Observation of Optically Trapped Atoms (1986)

We report the first observation of optically trapped atoms. Sodium atoms cooled below ${10}^{\ensuremath{-}3}$ K in "optical molasses" are captured by a dipole-force optical trap created by a single, strongly focused, Gaussian laser beam tuned several hundred gigahertz below the ${D}_{1}$ resonance transition. We estimate that about 500 atoms are confined in a volume of about ${10}^{3}$ \ensuremath{\mu}${\mathrm{m}}^{3}$ at a density of ${10}^{11}$-${10}^{12}$ ${\mathrm{cm}}^{\ensuremath{-}3}$. Trap lifetimes are limited by background pressure to several seconds. The observed trapping behavior is in good quantitative agreement with theoretical expectations.
Diabetic neuropathy: classification, measurement and treatment (2007)

Patients with 'idiopathic neuropathy' should be screened for evidence of impaired glucose tolerance and considered for lifestyle management. Future trials of potential therapies will benefit from more relevant surrogate endpoints. Those with painful neuropathy should only be prescribed therapies whose efficacy has been confirmed by independent randomized controlled trials.
Vilsmeier-Haack Reagent (Halomethyleneiminium Salt) (2002)

This feature focuses on a reagent chosen by a postgraduate, highlighting the uses and preparation of the reagent in current research 138 Vilsmeier-Haack Reagent (Halomethyleneiminium Salt)
TP53 mutations in familial breast cancer: Functional aspects (2003)

Mutation in p53 (TP53) remains one of the most commonly described genetic events in human neoplasia. The occurrence of mutations is somewhat less common in sporadic breast carcinomas than in other cancers, with an overall frequency of about 20%. There is, however, evidence that p53 is mutated at a significantly higher frequency in breast carcinomas arising in carriers of germ-line BRCA1 and BRCA2 mutations. Some of the p53 mutants identified in BRCA1 and BRCA2 mutation carriers are either previously undescribed or infrequently reported in sporadic human cancers. Functional characterization of such mutants in various systems has revealed that they frequently possess properties not commonly associated with those occurring in sporadic cases: they retain apoptosis-inducing, transactivating, and growth-inhibitory activities similar to the wild-type protein, yet are compromised for transformation suppression and also possess an independent transforming phenotype. The occurrence of such mutants in familial breast cancer implies the operation of distinct selective pressures during tumorigenesis in BRCA-associated breast cancers.
Cloning and nucleotide sequences of the genes encoding triose phosphate isomerase, phosphoglycerate mutase, and enolase from Bacillus subtilis (1994)

The Bacillus subtilis genes tpi, pgm, and eno, encoding triose phosphate isomerase, phosphoglycerate mutase (PGM), and enolase, respectively, have been cloned and sequenced. These genes are the last three in a large putative operon coding for glycolytic enzymes; the operon includes pgk (coding for phosphoglycerate kinase) followed by tpi, pgm, and eno. The triose phosphate isomerase and enolase from B. subtilis are extremely similar to those from all other species, both eukaryotic and prokaryotic. However, B. subtilis PGM bears no resemblance to mammalian, fungal, or gram-negative bacterial PGMs, which are dependent on 2,3-diphosphoglycerate (DPG) for activity. Instead, B. subtilis PGM, which is DPG independent, is very similar to a DPG-independent PGM from a plant species but differs from the latter in the absolute requirement of B. subtilis PGM for Mn2+. The cloned pgm gene has been used to direct up to 25-fold overexpression of PGM in Escherichia coli; this should facilitate purification of large amounts of this novel Mn(2+)-dependent enzyme. Inactivation of pgm plus eno in B. subtilis resulted in extremely slow growth either on plates or in liquid, but growth of these mutants was enhanced by supplementation of media with malate. However, these mutants were asporogenous with or without malate supplementation.
Using feature locality (2011)

Despite the best efforts of software engineers, faults still escape into deployed software. Developers need time to prepare and distribute fixes, and in the interim deployments must either tolerate or avoid failures. Self-adaptive systems, systems that adapt to meet changing requirements in a dynamic environment, have a daunting task if their reconfiguration involves adding or removing functional features, because configurable software is known to suffer from failures that appear only under certain feature combinations.
The anticoagulant mechanism of action of heparin in contact-activated plasma: inhibition of factor X activation (1985)

The effects of heparin on the activation of blood coagulation factors IX and X in contact-activated plasma were determined in the present study. In the presence and absence of 0.5 U/mL heparin, the amounts of factor IX that were cleaved 30 minutes after the addition of calcium and phospholipid to plasma exposed to glass (ie, contact activated) were essentially identical. In the absence of heparin, however, the plasma clotting time was between three and four minutes, while in the presence of heparin, the clotting time was approximately 40 minutes. More factor IXa was inhibited by antithrombin III in the presence of heparin than in its absence, but factor IXa levels sufficient for factor X activation appeared to be present in the heparinized plasma. Neither an increase in factor Xa nor a decrease in factor X was detected, however, in heparinized plasma. We conclude that the step in the intrinsic pathway of coagulation that is inhibited in the presence of heparin is at the level of factor X activation.
PPARγ induces cell cycle withdrawal: inhibition of E2F/DP DNA-binding activity via down-regulation of PP2A (1997)

PPAR gamma is an adipose-selective nuclear hormone receptor that plays a key role in the control of adipocyte differentiation. Previous studies indicated that activation of ectopically expressed PPAR gamma induces differentiation when cells have ceased growth because of confluence. We show here that ligand activation of PPAR gamma is sufficient to induce growth arrest in fibroblasts and SV40 large T-antigen transformed, adipogenic HIB1B cells. Cell cycle withdrawal is accompanied by a decrease in the DNA-binding and transcriptional activity of the E2F/DP complex, which is attributable to an increase in the phosphorylation of these proteins, especially DP-1. This effect is a consequence of decreased expression of the catalytic subunit of the serine-threonine phosphatase PP2A. These data suggest an important role for PP2A in the control of E2F/DP activity and a new mode of cell cycle control in differentiation.
Bromine Chloride: an Alternative to Bromine (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBromine Chloride: an Alternative to BromineJack F. Mills and John A. SchneiderCite this: Ind. Eng. Chem. Prod. Res. Dev. 1973, 12, 3, 160–165Publication Date (Print):September 1, 1973Publication History Published online1 May 2002Published inissue 1 September 1973https://pubs.acs.org/doi/10.1021/i360047a002https://doi.org/10.1021/i360047a002research-articleACS PublicationsRequest reuse permissionsArticle Views353Altmetric-Citations15LEARN 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 options Get e-Alerts
Contrasting effects of mitogenic growth factors on myelination in neuron–oligodendrocyte co‐cultures (2007)

Mitogenic growth factors play an important role in the initial stages of oligodendrocyte development, but their roles in the process of myelination itself remain less well defined. In order to study directly the effects of different growth factors on myelination, we used a purified in vitro co-culture system with dorsal root ganglion neurons and oligodendrocytes. Extensive myelination had occurred in these cultures 14 days after oligodendrocyte precursors (OPCs) were added, with the relationship between neurite density and the percentage of oligodendrocytes forming myelin sheaths providing a robust and straightforward means of quantifying myelination. Addition of soluble neuregulin (Nrg1), a mitogen for oligodendroglial cells that also provides an axonal signal implicated in oligodendrocyte survival, increased myelination. Conversely, the OPC mitogens FGF-2 and PDGF inhibited myelination. The inhibitory effect of these mitogens was reversible, as inhibition of PDGF allowed myelination to proceed. Taken together, these data indicate that different mitogenic growth factors can regulate myelination by oligodendrocytes in addition to their well-described effects on earlier stages of oligodendroglial development. Moreover, the results highlight important differences between the growth factors.