gebhart/patrepeval huggingface dataset:
&lt;title&gt;Hybridization-triggered fluorescence detection of DNA with minor groove binder-conjugated probes&lt;/title&gt; (2002)

Fluorogenic 2'-deoxynucleotide probes containing a minor groove binding-quencher compound at the 5'-end and a fluorophore at the 3'-end, were recently described. These probes fluoresce upon hybridization to the complementary target. The 5'-MGB-quencher group prevents 5'-nuclease digestion by Taq polymerase during homogeneous amplification. The 5'-MGB-quencher-oligonucleotide-fluor (MGB-Q-ODN-Fl) probes displayed a dynamic range of 7 order of magnitude, with an ultimate sensitivity of better than 5 copies per sample. The high sensitivity and specificity is illustrated by the application of the probes in single nucleotide polymorphism detection, final load determination and gene expression analyses. This paper summarizes new developments in sequence detection, gene expression and SNP analysis using new T<SUB>m</SUB> prediction software to design robust 5'-MGB-Q-ODN-Fl probes. Furthermore, the software is capable of estimating the T<SUB>m</SUB> of probes containing a modified base. Due to G:G self-association, many G-rich probes and primers are poor performers in amplification reactions. The software recognizes such sequences and substitution of G with 6-Amino-1,5-dihydro-pyrazolo(3,4- d)pyrimidin-4-one (PPG) is indicated, when necessary to eliminate G:G self-association. Examples of improved performance of PPG containing primers and probes is demonstrated.
Rational design of hypoallergens applied to the major cat allergen Fel d 1 (2005)

By a rational approach, we have constructed three Fel d 1 hypoallergens with reduced IgE-binding capacities and retained T cell reactivities. This strategy may be applied to any well-characterized allergen to improve immunotherapy for allergic patients.
Thermodynamics of Lipoplex Formation: Relationship between the Lipid Alkyl Tail Length and Thermodynamic Functions (2012)

Abstract The formation of a cationic-lipid/DNA complex (lipoplex), where the lipids that have a quaternary amine headgroup and alkyl tails of various lengths are newly synthesized, was investigated by use of isothermal titration calorimetry (ITC) and small-angle X-ray scattering (SAXS). SAXS showed that all of the samples formed a lamellar structure with DNA sandwiched between the lipid bilayers. For the hexyl tail, ITC showed an exothermic response, while for the nonyl and dodecyl tails, it was endothermic. We propose a lipoplex formation model to explain both SAXS and ITC results.
The role of the mammalian branchpoint sequence in pre-mRNA splicing. (1988)

We show that base substitutions in the mammalian branchpoint sequence (BPS) YNCUGAC dramatically reduce the efficiency of pre-mRNA splicing in vitro and alter 3' splice-site selection in vivo. Contrary to current dogma that an adenine residue at the appropriate distance from the 3' splice site is the primary determinant of lariat formation, we find that many mutations in the BPS virtually abolish splicing even though the position of this adenine is unchanged. Comparison of the analogous single-base changes in the mammalian and yeast BPSs revealed similar relative effects on splicing efficiency. However, in contrast to yeast, mammalian branchpoint mutations that decrease splicing efficiency severely do not prevent spliceosome assembly. Thus, mutations in the mammalian BPS appear to uncouple spliceosome assembly from cleavage at the 5' splice site and lariat formation.
Characterization of the Murine Alpha Interferon Gene Family (2004)

Mouse and human genomes carry more than a dozen genes coding for closely related alpha interferon (IFN-alpha) subtypes. IFN-alpha, as well as IFN-beta, IFN-kappa, IFN-epsilon, and limitin, are thought to bind the same receptor, raising the question of whether different IFN subtypes possess specific functions. As some confusion existed in the identity and characteristics of mouse IFN-alpha subtypes, the availability of data from the mouse genome sequence prompted us to characterize the murine IFN-alpha family. A total of 14 IFN-alpha genes were detected in the mouse genome, in addition to three IFN-alpha pseudogenes. Four IFN-alpha genes (IFN-alpha1, IFN-alpha7/10, IFN-alpha8/6, and IFN-alpha11) exhibited surprising allelic divergence between 129/Sv and C57BL/6 mice. All IFN-alpha subtypes were found to be stable at pH 2 and to exhibit antiviral activity. Interestingly, some IFN subtypes (IFN-alpha4, IFN-alpha11, IFN-alpha12, IFN-beta, and limitin) showed higher biological activity levels than others, whereas IFN-alpha7/10 exhibited lower activity. Most murine IFN-alpha turned out to be N-glycosylated. However, no correlation was found between N-glycosylation and activity. The various IFN-alpha subtypes displayed a good correlation between their antiviral and antiproliferative potencies, suggesting that IFN-alpha subtypes did not diverge primarily to acquire specific biological activities but probably evolved to acquire specific expression patterns. In L929 cells, IFN genes activated in response to poly(I*C) transfection or to viral infection were, however, similar.
Crosslinked chitosan: Its physical properties and the effects of matrix stiffness on chondrocyte cell morphology and proliferation (2005)

Chitosan [beta(1-4)-2 amino-2-deoxy-D-glucose], the natural polyaminosaccharide derived from N-deacetylation of chitin [beta(1-4)-2 acetamide-2-deoxy-D-glucose], has been shown to possess attractive biological and cell interactive properties. Recently chitosan and chitosan analogs have also been shown to support the growth and continued function of chondrocytes. In the present study, chitosan substrates are crosslinked with a functional diepoxide (1,4 butanediol diglycidyl ether) to alter its mechanical property, and the viability and proliferation of the canine articular chondrocytes seeded on the crosslinked surface are further assayed. Of interest is the impact of substrate stiffness on the growth and proliferation of articular canine chondrocytes. Crosslinked scaffolds were also subjected to degradation by chitosanase to examine the impact of crosslinking on enzyme-assisted degradation. The hydrophilicity and compression modulus of the crosslinked surfaces were measured via contact-angle measurements and compression tests, respectively. Scanning electron microscopy (SEM) and fluorescent staining were used to observe the proliferation and morphology of chondrocyte cells on noncrosslinked and crosslinked surfaces. The crosslinked chitosan was found to be nontoxic to chondrocytes and more hydrophilic. Its compression modulus and stiffness increased, which may improve the scaffold resistance to wear and in vivo shrinkage once implanted. The increased stiffness also seemed to serve as an additional mechanical stimulus to promote chondrocyte growth and proliferation. The cell morphology on crosslinked scaffolds seen by SEM and fluorescent stain was the typical chondrocytic rounded shape. The method proposed provides a nontoxic way to increase the mechanical strength of the chitosan scaffolds.
B cell-derived BCGF functions as autocrine growth factor(s) in normal and transformed B lymphocytes. (1986)

This paper demonstrates that B cell lines, as well as normal activated B cells generate and respond to B cell-specific growth factor(s) (BCGF). BCGF derived from B cells (B-BCGF) appears to be distinct from interleukin 1, interleukin 2 (IL 2), B cell stimulatory factor, BCGF-II, interferon-gamma, or transforming growth factor. It acts on activated B cells, but not on resting G0 phase B cells to induce proliferation. B cell lines, immortalized by Epstein-Barr virus, constitutively secrete 10-fold higher level of B-BCGF compared with normal activated B cells, suggesting that an activated autocrine loop might be operating in immortalized B cells. On the basis of our observations, we postulate that B cell clonal expansion may occur, at least in part, through a B-BCGF-dependent autocrine pathway similar to IL 2 effect on T cells.
Dephosphorylation of specific sites in the kinase-specificity sequence domain leads to ubiquitin-mediated degradation of the tyrosine phosphatase STEP (2011)

STEP (striatal-enriched phosphatase) is a non-receptor tyrosine phosphatase that is specifically expressed in the neurons of the central nervous system. STEP regulates the activity of several effector molecules involved in synaptic plasticity and neuronal cell survival, including MAPKs (mitogen-activated protein kinases), Src family kinases and NMDA (N-methyl-D-aspartic acid) receptors. The critical role of STEP in regulating these effectors requires that its activity be tightly regulated. Previous studies have demonstrated that the activity of STEP is regulated through reversible phosphorylation of a serine residue within the KIM (kinase-interacting motif), by cAMP-dependent PKA (protein kinase A). In the present paper we show that STEP is endogenously phosphorylated at two additional sites located within the KISs (kinase-specificity sequences). The basal activity of ERK (extracellular-signal-regulated kinase) and p38 MAPKs plays an important role in the phosphorylation of these two sites. Dephosphorylation of these two sites leads to polyubiquitination and proteolytic degradation of STEP. Conversely, the proteasome inhibitors MG-132 and epoxomicin can stabilize STEP. The active form of STEP is more susceptible to degradation than the inactive form. Taken together the results of the present paper establish that ubiquitin-dependent proteolysis could be a novel mechanism for irreversibly terminating the activity of STEP.
Exfoliated and Restacked MoS<sub>2</sub> and WS<sub>2</sub>:  Ionic or Neutral Species? Encapsulation and Ordering of Hard Electropositive Cations (1999)

The relationship between charge and structure in restacked MS2 (M = Mo, W) has been probed by cation encapsulation and chemical oxidation and characterized by elemental analysis, electron diffraction, X-ray diffraction, and Differential Scanning Calorimetry. Alkali cations have been encapsulated in MoS2 and WS2 without the presence of a co-intercalated counterion, suggesting a negative charge in the 0.15−0.25 electrons per M atom range. Electron diffraction studies show ordering of these cations between the layers. Chemical oxidation with I2 or Br2 results in a change in the structure of restacked MoS2, giving rise to a a × a superlattice, whereas no change is observed in the structure of restacked WS2. Differential Scanning Calorimetry studies show that the irreversible exothermic transition to 2H-MS2 shifts to lower temperature with oxidation. The observed structural distortion and residual negative charge uniquely explain the thermopower measurements, which indicate that restacked MoS2 and WS2 are p-type metallic conductors.
FlyByNight (2008)

Social networking websites are enormously popular, but they present a number of privacy risks to their users, one of the foremost of which being that social network service providers are able to observe and accumulate the information that users transmit through the network. We aim to mitigate this risk by presenting a new architecture for protecting information published through the social networking website, Facebook, through encryption. Our architecture makes a trade-off between security and usability in the interests of minimally affecting users' workflow and maintaining universal accessibility. While active attacks by Facebook could compromise users' privacy, our architecture dramatically raises the cost of such potential compromises and, importantly, places them within a framework for legal privacy protection because they would violate a user's reasonable expectation of privacy. We have built a prototype Facebook application implementing our architecture, addressing some of the limitations of the Facebook platform through proxy cryptography.
A method for the generation of YAC transgenic mice by pronuclear microinjection (1993)

Yeast artificial chromosomes (YACs) represent the latest generation of vectors which have the great advantage of large insert size. The introduction of YACs into mammalian cells and organisms has become an important goal, since it offers the potential to study the control of large and complex transcription units and identify genes by complementation. Microinjection into the nucleus is the most direct and efficient way of delivering YAC DNA into cells, but requires the purification of the YAC from the remaining yeast chromosomes. Here we describe a detailed method for the isolation of pure, intact and highly concentrated YAC DNA. As a model system the murine tyrosinase gene was chosen and four YACs covering this locus were isolated. Introduction by homologous recombination in yeast of sequences permitting YAC amplification greatly facilitated the isolation of YAC DNA at high concentrations. YAC DNA stabilized in a salt and polyamine containing buffer did not compromise the survival of microinjected oocytes and was suitable for the generation of transgenic mice. Applications and benefits of this technique will be discussed.
Pericardial Mesoderm Generates a Population of Coronary Smooth Muscle Cells Migrating into the Heart along with Ingrowth of the Epicardial Organ (1996)

The vascular smooth muscle cells of coronary arteries are distinguished from those of the proximal aorta by a number of structural and functional criteria which may include an increased propensity for atherosclerotic transformation. At present, the source of this variation between smooth muscle subpopulations is uncertain. Whilst smooth muscle of the proximal aorta is thought to be derived from neural crest, the origin of coronary vascular smooth muscle remains uncharacterized. We have previously shown that precursors of the coronary vasculature enter the tubular heart on the same day as the epicardial mantle starts to envelop the myocardium and that coronary vessels form by ingrowth of these migratory precursors and not by outgrowth from the aorta (Mikawa and Fischman, 1992). To study the origin of coronary smooth muscle cells, the proepicardial organ, from which epicardial cells arise, was tagged with either a vital dye (DiI) or replication-defective retroviruses encoding beta-galactosidase. Cellular lineage marking was achieved by either direct targeting of putative vasculogenic cells in the proepicardium in ovo or tagging dissected proepicardial cells in vitro followed by transplantation to stage-matched host embryos. Monitoring of tagged cells during coronary vasculogenesis indicate incorporation of proepicardial-derived cells into three vessel-associated populations; coronary smooth muscle, perivascular connective tissue, and endothelial cells. Immunoconfocal microscopy identified both endothelial and smooth muscle cell populations within the proepicardial organ. The results demonstrate that: (1) the proepicardium contains a progenitor population of coronary smooth muscle cells that migrates into the heart along with ingrowth of the epicardium and (2) prior to the migration, the coronary smooth muscle lineage is established.
The role and control of the glyoxylate cycle in <i>Escherichia coli</i> (1966)

Research Article| April 01 1966 The role and control of the glyoxylate cycle in Escherichia coli HL Kornberg HL Kornberg Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1966) 99 (1): 1–11. https://doi.org/10.1042/bj0990001 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation HL Kornberg; The role and control of the glyoxylate cycle in Escherichia coli. Biochem J 1 April 1966; 99 (1): 1–11. doi: https://doi.org/10.1042/bj0990001 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu nav search search input Search input auto suggest search filter All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1966 The Biochemical Society1966 Article PDF first page preview Close Modal You do not currently have access to this content.
Liver Growth Factor Promotes the Survival of Grafted Neural Stem Cells in a Rat Model of Parkinson's Disease (2012)

Neural stem cells (NSCs) with self-renewal and multilineage potential are considered good candidates for cell replacement of damaged nerve tissue. Several studies have focused on the ability of the neurotrophic factors coadministration to improve the efficiency of grafted NSCs. Liver growth factor (LGF) is an hepatic mitogen that promotes regeneration of damaged tissues, including brain tissue. It has neurogenic activity and has partially restored the nigrostriatal dopaminergic system in an experimental model of Parkinson's disease. Present results demonstrate that in the dopamine- depleted striatum of 6-hydroxydopamine-lesioned rats, grafted NSCs retained their ability to differentiate into neurons, astrocytes, and oligodendrocytes. NSCs also differentiated into microglia/macrophages and endothelial cells. Thus, 23 ± 5.6% of them were inmunoreactive for isolectin IB4, and a small population integrated into blood vessels, showing an endothelial-like morphology. Intrastriatal infusion of LGF promoted the viability of the implants, and favored their differentiation to an endothelial-like phenotype. Moreover, LGF infusion raised the expression of the anti-apoptotic protein Bcl-2 by 3.9 ± 0.9 fold without affecting the levels of the pro-apoptotic protein Bax. Since LGF-treated rats also showed a significant reduction in apomorphine-induced rotational behavior, our results suggest that administration of this factor might be a convenient treatment for Parkinson's disease cell replacement therapies based on NSCs transplantation.
Stem cells in the adult pancreas and liver (2007)

Stem cells are undifferentiated cells that can self-renew and generate specialized (functional) cell types. The remarkable ability of stem cells to differentiate towards functional cells makes them suitable modalities in cellular therapy (which means treating diseases with the body's own cells). Potential targets for cellular therapy include diabetes and liver failure. However, in order for stem cells to be clinically useful, we must learn to identify them and to regulate their differentiation. We will use the intestine as a classical example of a stem cell compartment, and then examine the evidence for the existence of adult stem cells in two endodermally derived organs: pancreas and liver. We will review the characteristics of the putative stem cells in these tissues and the transcription factors controlling their differentiation towards functional cell types.
Effect of overproduction of heat shock chaperones GroESL and DnaK on human procollagenase production in Escherichia coli. (1992)

The effect of overexpression of the heat shock chaperone genes dnaK and groESL on heterologous protein production in Escherichia coli was examined, using a set of related human procollagenase proteins. A diverse range of effects on protein solubility, secretion, and accumulation was observed, and these effects were highly dependent on the particular chaperone/procollagenase pairing involved. Both chaperones caused a large increase in the apparent solubility of a fusion of the LamB signal peptide to procollagenase. GroESL had no effect on the accumulation of mature (secreted) procollagenase, while DnaK suppressed secretion considerably. In the absence of a signal peptide, overexpression of either chaperone resulted in a dramatic increase in both solubility and accumulation of procollagenase. The 10-fold increase in accumulation was associated with an increase in in vivo protein half-life.
Epitopes on foot-and-mouth disease virus outer capsid protein VP1 involved in neutralization and cell attachment (1984)

Foot-and-mouth disease virus structural protein VP1 elicits neutralizing and protective antibody and is probably the viral attachment protein which interacts with cellular receptor sites on cultured cells. To study the relationships between epitopes on the molecule related to neutralization and cell attachment, we tested monoclonal antibodies prepared against type A12 virus, isolated A12 VP1, and a CNBr-generated A12 VP1 fragment for neutralization and effect on viral absorption. The antibodies selected for analysis neutralized viral infectivity with varying efficiencies. One group of antibodies caused a high degree of viral aggregation and inhibited the adsorption of virus to cells by 50 to 70%. A second group of antibodies caused little or no viral aggregation but inhibited the adsorption of virus to cells by 80 to 90%. One antibody, which is specific for the intact virion, caused little viral aggregation and had no effect on the binding of virus to specific cellular receptor sites. Thus, at least three antigenic areas on the surface of foot-and-mouth disease virus which were involved in neutralization were demonstrated. One of the antigenic sites appears to have been responsible for interaction with the cellular receptor sites on the surface of susceptible cells.
Stereoselective Total Synthesis of (-)-α-Eudesmol, a P/Q-Type Calcium Channel Blocker (2001)

Practical and stereoselective total synthesis of (-)-α-eudesmol 1, a P/Q-type calcium channel blocker, has been achieved with the key step being a cyclopropane ring opening accompanying introduction of a hydroxyl group. (+)-Carissone is used as a key intermediate.
Light transport simulation with vertex connection and merging (2012)

Developing robust light transport simulation algorithms that are capable of dealing with arbitrary input scenes remains an elusive challenge. Although efficient global illumination algorithms exist, an acceptable approximation error in a reasonable amount of time is usually only achieved for specific types of input scenes. To address this problem, we present a reformulation of photon mapping as a bidirectional path sampling technique for Monte Carlo light transport simulation. The benefit of our new formulation is twofold. First, it makes it possible, for the first time, to explain in a formal manner the relative efficiency of photon mapping and bidirectional path tracing, which have so far been considered conceptually incompatible solutions to the light transport problem. Second, it allows for a seamless integration of the two methods into a more robust combined rendering algorithm via multiple importance sampling. A progressive version of this algorithm is consistent and efficiently handles a wide variety of lighting conditions, ranging from direct illumination, diffuse and glossy inter-reflections, to specular-diffuse-specular light transport. Our analysis shows that this algorithm inherits the high asymptotic performance from bidirectional path tracing for most light path types, while benefiting from the efficiency of photon mapping for specular-diffuse-specular lighting effects.
Association of chromosome 12p genetic polymorphisms with lung adenocarcinoma risk and prognosis (1997)

The mapping near Kras2 of pulmonary adenoma susceptibility 1 (Pas1), a major locus affecting inherited predisposition to lung cancer in mice prompted us to test the homologous human region (12p12) for association with lung adenocarcinoma, by a population-based study. We genotyped 213 lung adenocarcinoma patients and 219 healthy blood donor subjects for five polymorphic markers mapping in the putative region of interest. Three marker polymorphisms, located in a region spanning approximately 700 kb, were significantly associated with lung adenocarcinoma risk. Furthermore, polymorphisms in KRAS2 and PTHLH loci were also associated with tumor prognosis. These results suggest the existence of a human Pas1 homologous locus on chromosome 12p12.