gebhart/patrepeval huggingface dataset:
Epidermal Growth Factor and Fibroblast Growth Factor-2 Have Different Effects on Neural Progenitors in the Adult Rat Brain (1997)

Neurons and glia are generated throughout adulthood from proliferating cells in two regions of the rat brain, the subventricular zone (SVZ) and the hippocampus. This study shows that exogenous basic fibroblast growth factor (FGF-2) and epidermal growth factor (EGF) have differential and site-specific effects on progenitor cells in vivo . Both growth factors expanded the SVZ progenitor population after 2 weeks of intracerebroventricular administration, but only FGF-2 induced an increase in the number of newborn cells, most prominently neurons, in the olfactory bulb, the normal destination for neuronal progenitors migrating from the SVZ. EGF, on the other hand, reduced the total number of newborn neurons reaching the olfactory bulb and substantially enhanced the generation of astrocytes in the olfactory bulb. Moreover, EGF increased the number of newborn cells in the striatum either by migration of SVZ cells or by stimulation of local progenitor cells. No evidence of neuronal differentiation of newborn striatal cells was found by three-dimensional confocal analysis, although many of these newborn cells were associated closely with striatal neurons. The proliferation of hippocampal progenitors was not affected by either growth factor. However, EGF increased the number of newborn glia and reduced the number of newborn neurons, similar to the effects seen in the olfactory bulb. These findings may be useful for elucidating the in vivo role of growth factors in neurogenesis in the adult CNS and may aid development of neuronal replacement strategies after brain damage.
Translation Initiation at the CUU Codon Is Mediated by the Internal Ribosome Entry Site of an Insect Picorna-Like Virus In Vitro (1999)

AUG-unrelated translation initiation was found in an insect picorna-like virus, Plautia stali intestine virus (PSIV). The positive-strand RNA genome of the virus contains two nonoverlapping open reading frames (ORFs). The capsid protein gene is located in the 3'-proximal ORF and lacks an AUG initiation codon. We examined the translation mechanism and the initiation codon of the capsid protein gene by using various dicistronic and monocistronic RNAs in vitro. The capsid protein gene was translated cap independently in the presence of the upstream cistron, indicating that the gene is translated by internal ribosome entry. Deletion analysis showed that the internal ribosome entry site (IRES) consisted of approximately 250 bases and that its 3' boundary extended slightly into the capsid-coding region. The initiation codon for the IRES-mediated translation was identified as the CUU codon, which is located just upstream of the 5' terminus of the capsid-coding region by site-directed mutagenesis. In vitro translation assays of monocistronic RNAs lacking the 5' part of the IRES showed that this CUU codon was not recognized by scanning ribosomes. This suggests that the PSIV IRES can effectively direct translation initiation without stable codon-anticodon pairing between the initiation codon and the initiator methionyl-tRNA.
Localized Surface Plasmon Resonance Spectroscopy of Single Silver Nanocubes (2005)

In this work, we use dark-field microscopy to observe a new plasmon resonance effect for a single silver nanocube in which the plasmon line shape has two distinct peaks when the particles are located on a glass substrate. The dependence of the resonance on nanocube size and shape is characterized, and it is found that the bluer peak has a higher figure of merit for chemical sensing applications than that for other particle shapes that have been studied previously. Comparison of the measured results with finite difference time domain (FDTD) electrodynamics calculations enables us to confirm the accuracy of our spectral assignments.
Liposomal delivery of nucleic acid-based anticancer therapeutics: BP-100-1.01 (2014)

To further improve the clinical potential of nucleic acid cancer drugs, we predict research on the next generation of lipid nanoparticles will focus on: i) enhancing nucleic acid delivery to poorly vascularized tumors, as well as tumors behind the blood-brain barrier; and ii) improving the accessibility of nucleic acids to the cytoplasm by enhancing endosomal escape of nucleic acids and/or reducing exocytosis of nucleic acids to the external milieu.
Spatial learning for navigation in dynamic environments (1996)

This article describes techniques that have been developed for spatial learning in dynamic environments and a mobile robot system, ELDEN, that integrates these techniques for exploration and navigation. In this research, we introduce the concept of adaptive place networks, incrementally-constructed spatial representations that incorporate variable-confidence links to model uncertainty about topological adjacency. These networks guide the robot's navigation while constantly adapting to any topological changes that are encountered. ELDEN integrates these networks with a reactive controller that is robust to transient changes in the environment and a relocalization system that uses evidence grids to recalibrate dead reckoning.
Efficient event-driven simulation of spiking neural networks (2002)

Abstract:- We present a general event-driven algorithm for the efficient simulation of spiking neural networks. We focus in this paper on its application to self-organizing maps. Standard event-driven approaches to simulation can significantly reduce computational time, but only when network activity is relatively low. In this article, we propose several strategies to manage efficiently, large numbers of spiking events. The simulation scales well with the increase of the neural activity and is more biologically plausible than competing methods. Key-Words:- Event-driven simulation, spiking neurons, self-organizing maps. 1.
The NFIII/OCT-1 binding site stimulates adenovirus DNA replication in vivo and is functionally redundant with adjacent sequences (1993)

The inverted terminal repeat (ITR) of adenovirus type 5 (Ad5) is 103 bp in length and contains the origin of DNA replication. Cellular transcription factors NFI/CTF and NFIII/OCT-1 bind to sites within the ITR and participate in the initiation of viral DNA replication in vitro. The ITR also contains multiple copies of two conserved sequence motifs that bind the cellular transcription factors SP1 and ATF. We have analyzed a series of viruses that carry deletions at the left terminus of Ad5. A virus carrying a deletion of the NFIII/OCT-1, SP1, and ATF sites within the ITR (mutant dl309-44/107) was wild type for virus growth. However, the deletion of these elements in addition to sequences immediately flanking the ITR (mutant dl309-44/195) resulted in a virus that grew poorly. The analysis of growth parameters of these and other mutants demonstrate that the NFIII/OCT-1 and adjacent SP1 sites augment the accumulation of viral DNA following infection. The function of these elements was most evident in coinfections with a wild-type virus, suggesting that these sites enhance the ability of a limiting trans-acting factor(s), that stimulates viral DNA replication, to interact with the ITR. The results of these analyses indicate functional redundancy between different transcription elements at the left terminus of the Ad5 genome and demonstrate that the NFIII/OCT-1 site and adjacent SP1 site, previously thought to be nonessential for adenovirus growth, play a role in viral DNA replication in vivo.
Conservation of sequences adjacent to the telomeric C4A2repeats of ciliate macronuclear ribosomal RNA gene molecules (1986)

We sequenced and compared the telomeric regions of linear rDNAs from vegetative macronuclei of several ciliates in the suborder Tetrahymenina. All telomeres consisted of tandemly repeated C4A2 sequences, including the 5' telomere of the 11 kb rDNA from developing macronuclei of Tetrahymena thermophila. Our sequence of the 11 kb 5' telomeric region shows that each one of a previously described pair of inverted repeats flanking the micronuclear rDNA (Yao et al., Mol. Cell. Biol. 5: 1260-1267, 1985) is 29 bp away from the positions to which telomeric C4A2 repeats are joined to the ends of excised 11 kb rDNA. In general we found that the macronuclear rDNA sequences adjacent to C4A2 repeats are not highly conserved. However, in the non-palindromic rDNA of Glaucoma, we identified a single copy of a conserved sequence, repeated in inverted orientation in Tetrahymena spp., which all form palindromic rDNAs. We propose that this sequence is required for a step in rDNA excision common to both Tetrahymena and Glaucoma.
Heteroatom-Controlled Kinetics of Switchable Polyoxometalate Frameworks (2009)

The framework materials [W(72)Mn(II/III)(12)O(268)X(7)](52-/40-) undergo heteroatom (X)-controlled reversible SC-SC redox reactions whereby the Ge-templated framework reduction is fast and reoxidation is slow. The opposite trend is set for the Si-templated framework, and these processes can be followed optically, spectroscopically and crystallographically.
Assessment of High-Frequency Performance Potential of Carbon Nanotube Transistors (2005)

Self-consistent quantum simulations are used to explore the high-frequency performance potential of carbon nantube field-effect transistors (CNTFETs). The cutoff frequency expected for a recently reported CNT Schottky-barrier FET is well below the performance limit, due to the large parasitic capacitance between electrodes. We show that using an array of parallel nanotubes as the transistor channel reduces parasitic capacitance per tube. Increasing tube density gives a large improvement of high-frequency performance when tubes are widely spaced and parasitic capacitance dominates but only a small improvement when the tube spacing is small and intrinsic gate capacitance dominates. Alternatively, using quasi-one-dimensional nanowires as source and drain contacts should significantly reduce parasitic capacitance and improve high-frequency performance. Ballistic CNTFETs should outperform ballistic Si MOSFETs in terms of the high-frequency performance limit because of their larger band-structure-limited velocity.
The influence of extravascular lung water on cardiac output measurements using thoracic impedance cardiography (1998)

The purpose of this study was to investigate the influence of pulmonary oedema as measured with the double indicator dilution technique on the accuracy of cardiac output (CO) measurement using thoracic impedance cardiography (TIC) compared with thermodilution in thirteen sepsis patients. Differences in the Kubicek and Sramek-Bernstein equation with respect to pulmonary oedema were explored theoretically and experimentally. From a parallel two cylinder model a hypothesis can be derived that CO determined with the Kubicek equation is oedema independent, whereas CO determined using the Sramek-Bernstein equation is oedema dependent. Experimentally, CO determined using Kubicek's equation correlated better with thermodilution CO (r = 0.75) than CO determined with the Sramek-Bernstein equation (r = 0.25). The effect of oedema on the accuracy of TIC was investigated by comparing the differences in the CO of impedance and thermodilution to the extravascular lung water index. For the Kubicek equation the difference was not influenced by oedema (r = 0.04, p = 0.84), whereas for the Sramek-Bernstein equation the difference was affected by oedema (r = 0.39, p = 0.05). Thus, the effects of pulmonary oedema on the accuracy of TIC measurements can better be understood with the parallel cylinder model. Moreover, the Kubicek equation still holds when pulmonary oedema is present, in contrast to the Sramek-Bernstein equation.
Bioinformatic and expression analysis of the putative gliotoxin biosynthetic gene cluster ofAspergillus fumigatus (2005)

Gliotoxin is a secondary metabolite produced by several fungi including the opportunistic animal pathogen Aspergillus fumigatus. It is a member of the epipolythiodioxopiperazine (ETP) class of toxins characterised by a disulphide bridged cyclic dipeptide. A putative cluster of 12 genes involved in gliotoxin biosynthesis has been identified in A. fumigatus by a comparative genomics approach based on homology to genes from the sirodesmin (another ETP) biosynthetic gene cluster of Leptosphaeria maculans. The physical limits of the cluster in A. fumigatus have been defined by bioinformatics and by identifying the genes that are co-regulated and whose timing of expression correlates with the production of gliotoxin in culture.
Acute hematomas: effects of deoxygenation, hematocrit, and fibrin-clot formation and retraction on T2 shortening. (1990)

Acute hematomas can appear hypointense on T2-weighted magnetic resonance (MR) images at field strengths as low as 0.35 T. Using Raman spectroscopy to measure blood oxygenation and taking T2 measurements at 2.1 and 9.4 T, the authors examined the relaxation mechanisms acting during deoxygenation, increases in hematocrit, and fibrin-clot formation and retraction. Individual contributions to overall T2 from deoxyhemoglobin and the interactions of water with protein hydration layers in hemoglobin, plasma proteins, and fibrin were measured. Overall T2 values estimated by summing individual relaxation rates were in reasonable agreement with the T2 values of clotted blood. Results suggest that deoxygenation may be most important in T2 shortening, followed by increased hematocrit. T2 shortening from fibrin polymerization was minimal at the field strengths used. Effects of deoxygenation and increasing hematocrit are more sensitive to field strength than fibrin T2 shortening. Effects of fibrin may be more significant at middle and low field strengths.
MDM2 and Promyelocytic Leukemia Antagonize Each Other through Their Direct Interaction with p53 (2003)

p53 can be regulated through post-translational modifications and through interactions with positive and negative regulatory factors. MDM2 binding inhibits p53 and promotes its degradation by the proteasome, whereas promyelocytic leukemia (PML) activates p53 by recruiting it to multiprotein complexes termed PML-nuclear bodies. We reported previously an in vivo and in vitro interaction between PML and MDM2 that is independent of p53. In the current study, we investigated whether interaction between MDM2 and PML can indirectly affect p53 activity. Increasing amounts of MDM2 inhibited p53 activation by PML but could not inhibit PML-mediated activation of a p53 fusion protein that lacked the MDM2-binding domain. Conversely, increasing amounts of PML could overcome p53 inhibition by MDM2 but could not overcome MDM2-mediated inhibition of a p53 fusion protein that lacked the PML-binding domain. These results demonstrate that MDM2 and PML can antagonize each other through their direct interaction with p53 and suggest the combined effects of MDM2 and PML on p53 function are determined by the relative level of each protein. Furthermore, these results imply that interactions between MDM2 and PML by themselves have little or no effect on p53 activity.
Finding available bandwidth in multihop mobile wireless networks (2002)

This paper proposes a new method for finding the available bandwidth of a path in multihop mobile wireless networks. The proposed method finds the link with the minimum current bandwidth and increases its bandwidth. This process is repeated until the bandwidth of the link with the smallest current bandwidth cannot be increased. Then the available bandwidth of the path is found to be the minimum of the current bandwidths of the links along the path. Extensive simulations are performed to compare the performance of the proposed method and that of the method which calculates the path bandwidth hop by hop. Our simulation results show that using the proposed method in a multihop mobile wireless network produces significantly lower call blocking ratio than the method which calculates the path bandwidth hop by hop.
Production of antigen-specific human monoclonal antibodies from in vitro-primed human splenocytes (1991)

We have developed culture conditions for human lymphocytes that support primary in vitro immune responses to protein Ag of either human or nonhuman origin. We now show that these primed B cells can be efficiently immortalized by fusion with a heterohybrid fusion partner to generate human, Ag-specific IgM or IgG antibody-producing heterohybridomas at a rate of 17 to 50 hybrids/10(6) lymphocytes fused. Approximately 50% of the Ig-secreting clones were stable with respect to Ig secretion. Levels of secretion attained with terminal cultures ranged from less than 1 to 100 micrograms/ml. Fusions of cells between 2 and 5 days after initiation of in vitro exposure to Ag produced more Ag-reactive and Ag-specific antibodies than fusions at 1 day or fusions performed after 5 days. Ag-reactive hybrids could be isolated at frequencies of 3 to 10%, depending on antigenicity of the immunogen. Foreign proteins, horse spleen ferritin, and a murine monoclonal Ig, induced higher percentages of Ag-reactive mAb than immunization with the human-derived ferritin. Ag-reactive IgG mAb were produced at relatively high frequency, depending on immunization conditions and the nature of the Ag. The strategy for identification of the best hybrids included early elimination of unstable hybridomas and of hybridomas producing broadly cross-reactive antibody, followed by evaluation of units of Ag reactivity/micrograms Ig. Ferritin-specific mAb selected according to these criteria showed immunocytochemical reactivity with ferritin-containing tissues and apparent affinities in the range of 10(7) to 10(8)/mol.
Oxytocin Modulates Glutamatergic Synaptic Transmission between Cultured Neonatal Spinal Cord Dorsal Horn Neurons (1998)

The functional characteristics of binding sites for the neuropeptide oxytocin (OT) detected by radioautography in laminae I and II of the dorsal horn (DH) and on cultured neonatal DH neurons were studied on the latter using perforated patch-clamp recordings. The neurons were identified by their spike discharge properties and on the basis of the presence of met-enkephalin-like and glutamate decarboxylase-like immunoreactivities. OT (100 nM) never induced any membrane current at a holding potential of -60 mV but increased the frequency of spontaneously occurring AMPA receptor-mediated EPSCs or the mean amplitude of electrically evoked EPSCs in a subset (35%) of neurons. The frequency of miniature EPSCs (m-EPSCs) recorded in the presence of 0.5 microM tetrodotoxin was also increased by OT (100 nM) without any change in their mean amplitude, indicating an action at a site close to the presynaptic terminal. The decay kinetics of any type of EPSC were never modified by OT. The effect of OT was reproduced by [Thr4, Gly7]-OT (100 nM), a selective OT receptor agonist, and blocked by d(CH2)5-[Tyr(Me)2,Thr4,Tyr-NH29]-ornithine vasotocin (100 nM), a specific OT receptor antagonist. Reducing the extracellular Ca2+ concentration from 2.5 to 0.3 mM in the presence of Cd2+ (100 microM) reversibly blocked the effect of OT on m-EPSCs. The OT receptors described here may represent the substrate for modulatory actions of descending hypothalamo-spinal OT-containing pathways on the nociceptive system.
Suppression of in vitro Epstein-Barr virus infection. A new role for adult human T lymphocytes. (1977)

Studies have been performed on in vitro infection by Epstein-Barr virus (EBV) of subpopulations of human lymphocytes. B cells of adult peripheral or fetal cord blood transform with equal efficiency, whether assayed by DNA synthesis induction or by outgrowth of transformed lymphocytes. In contrast, unfractionated adult lymphocytes transform much less efficiently than those from fetal cord. Reconstitution experiments of different cell preparations indicated that this difference was due to a suppression of B-cell proliferation by adult Ig-negative lymphocytes which fetal Ig-negative lymphocytes were unable to perform. Separation of Ig-negative lymphocytes into various subpopulations revealed that the suppression was performed by T cells. Macrophages and null cells play little or no role in suppression. The relevance of this phenomenon to infection and recovery from EBV infection during and after infectious mononucleosis is discussed.
siRNA and shRNA as Anticancer Agents in a Cervical Cancer Model (2008)

We describe the protocols of using siRNAs, or shRNAs delivered by a lentiviral vector, as a means to silence cancer-causing genes. We use cervical cancer as a model to demonstrate the inhibition of the human papillomavirus (HPV) oncogenes E6 and E7 in cervical cancer cells by RNAi and inhibition of the cell growth in vitro and tumor growth in mouse models. The protocols include methods on siRNA and shRNA design, production of lentiviral-vectored shRNA, transfection or transduction of cervical cancer cells with siRNA or shRNA, and detection of the inhibitory effects of siRNA or shRNA both in vitro and in vitro.
The panoply of αβT cells in the skin (2014)

Skin protects body from continual attack by microbial pathogens and environmental factors. Such barrier function of skin is achieved by multiple components including immune system, which is mainly regulated by lymphocytes. T lymphocytes (T cells) that express T cell receptor (TCR) α and β chains (αβT cells) control the strength and the type of immune response. CD4T cell population consists of helper T (Th) cell-subsets and immunosuppressive regulatory T (Treg) cells. Th1 cells produce IFN-γ and protect against intracellular pathogens. Th2 cells produce IL-4 family cytokines and participate in allergic skin diseases, including atopic dermatitis (AD). Th17 cells secrete IL-17, recruit granulocytes to fight against extracellular microorganisms, and play a role in psoriasis and AD. Th22 cells produce IL-22 that activates epithelial cells and mediates acanthosis in psoriasis and AD. On the other hand, Foxp3+ Treg cells attenuate immune responses partly via TGF-β or IL-10. Tissue resident memory T (Trm) cells in the skin-most of which are epidermal CD8T cells-constitute the first line of the defense against repeated infections. CD8 T cells are also engaged in psoriasis, lichen planus, and drug eruptions. Skin harbors innate-like αβT cells such as natural killer T (NKT) cells as well, whose function is not fully revealed. Understanding these αβT cells helps to comprehend skin diseases.
Tears (and Acting) in Shakespeare (1995)

Did Shakespeare's actors actually cry on stage?And if so, how did they manage to do it?And what might that say about the emotional "realism" of the acting in Shakespeare's company?Characters shed tears throughout the canon; moreover, they do it while being observed by other characters.The words "weep" and "tears" appear more than 600 times in the plays, almost always in reference to someone sobbing in front of someone else: Othello, for example, weeps when he confronts Desdemona ("Am I the motive of these tears, my Lord?" she asks [4.1.43]); 1 Menenius sobs before Coriolanus ("Thy tears are saltier than a younger man's," says Marcius [4.1.22]);and Romeo wails in the Friar's cell ("There on the ground, with his own tears made drunk" complains the Friar [3.3.83]).Often the sobbing is before a larger public: Claudio has "wash'd" Hero's foulness "with tears" in front of the whole wedding party (Ado 4.1.153-54);and Enobarbus.weeps openly amidst Antony's brigade of also-sobbing soldiers ("Look, they weep, And I, an ass, am onion-eyed" [A&C 4.2.34]).Sometimes the weeping is contagious, as in the ubiquitous lachrymosity of Titus Andronicus: Titus: . . .behold our cheeks how they are stain'd, like meadows yet not dry, with miry slime left on them by a flood? . . .Lucius: Sweet father, cease your tears; for