gebhart/patrepeval huggingface dataset:
An Inhibitory Fragment Derived from Protein Kinase Cε Prevents Enhancement of Nerve Growth Factor Responses by Ethanol and Phorbol Esters (1997)

We have studied nerve growth factor (NGF)-induced differentiation of PC12 cells to identify PKC isozymes important for neuronal differentiation. Previous work showed that tumor-promoting phorbol esters and ethanol enhance NGF-induced mitogen-activated protein (MAP) kinase activation and neurite outgrowth by a PKC-dependent mechanism. Ethanol also increases expression of PKCdelta and PKCepsilon, suggesting that one these isozymes regulates responses to NGF. To examine this possibility, we established PC12 cell lines that express a fragment encoding the first variable domain of PKCepsilon (amino acids 2-144), which acts as an isozyme-specific inhibitor of PKCepsilon in cardiac myocytes. Phorbol ester-stimulated translocation of PKCepsilon was markedly reduced in these PC12 cell lines. In addition, phorbol ester and ethanol did not enhance NGF-induced MAP kinase activation or neurite outgrowth in these cells. In contrast, phorbol ester and ethanol increased neurite outgrowth and MAP kinase phosphorylation in cells expressing a fragment derived from the first variable domain of PKCdelta. These results demonstrate that PKCepsilon mediates enhancement of NGF-induced signaling and neurite outgrowth by phorbol esters and ethanol in PC12 cells.
Serum Levels of Melatonin and Oxidative Stress Markers and Correlation between Them in Infertile Men (2013)

It is concluded that melatonin could be involved in infertility. In other word, melatonin treatment and antioxidant-rich nutrition could help fertility by combating oxidative stress.
Influence of Pressure on Silicon Nanowire Growth Kinetics (2008)

Si nanowire growth kinetics was studied, and the growth rate was shown to be highly sensitive to SiH4 precursor pressures, changing from a second-order dependence at low pressures to first-order and then independent at high pressures. Molecular collisions of SiH4 with He carrier gas account for this finding. The second- and first-order correlation was explained by the unimolecular reaction model and the saturated growth rate was due to the Langmuir adsorption limit. Our results suggest that precursor pressures must be controlled carefully for desired growth kinetics.
Spatial Photorelease of Oligonucleotides, Using a Safety-Catch Photolabile Linker (2006)

[reaction: see text] We report the development of a safety-catch photolabile linker that allows the light-directed synthesis and spatially selective photorelease of oligonucleotides from microarrays. The linker remains stable to light during DNA synthesis, and is activated for photorelease after acidic hydrolysis. We demonstrate that the photoreleased oligonucleotides can be amplified by PCR to produce double stranded DNA. The advantages offered by this linker could aid the development of an automated gene synthesis platform.
Design of a Two Degree-of-Freedom Ankle-Foot Orthosis for Robotic Rehabilitation (2005)

An ankle-foot orthosis (AFO) is commonly used to help subjects with weakness of ankle dorsiflexor muscles due to peripheral or central nervous system disorders. Both these disorders are due to the weakness of the tibialis anterior muscle which results in lack of dorsiflexion assist moment. The deformity and muscle weakness of one joint in the lower extremity influences the stability of the adjacent joints, thereby requiring compensatory adaptations. We present an innovative ankle-foot orthosis (AFO) that was designed to allow two degree-of-freedom motion while serving to maintain proper foot position for subjects. The prototype AFO would introduce greater functionality over currently marketed devices by means of its inversion-eversion degree-of-freedom in addition to flexion/extension. The flexion/extension is controlled with the help of an actuator and inversion/eversion with a spring and a damper.
Hendra Virus Vaccine, a One Health Approach to Protecting Horse, Human, and Environmental Health (2014)

In recent years, the emergence of several highly pathogenic zoonotic diseases in humans has led to a renewed emphasis on the interconnectedness of human, animal, and environmental health, otherwise known as One Health. For example, Hendra virus (HeV), a zoonotic paramyxovirus, was discovered in 1994, and since then, infections have occurred in 7 humans, each of whom had a strong epidemiologic link to similarly affected horses. As a consequence of these outbreaks, eradication of bat populations was discussed, despite their crucial environmental roles in pollination and reduction of the insect population. We describe the development and evaluation of a vaccine for horses with the potential for breaking the chain of HeV transmission from bats to horses to humans, thereby protecting horse, human, and environmental health. The HeV vaccine for horses is a key example of a One Health approach to the control of human disease.
Modeling and performance analysis of IP traffic with multi-class QoS in mobile ad hoc networks. (2004)

This thesis focuses primarily on modeling and performance analysis of IP traffic with multi-class QoS in MANETs.
Homologous, homeologous, and illegitimate repair of double-strand breaks during transformation of a wild-type strain and a rad52 mutant strain of Saccharomyces cerevisiae. (1994)

Different modes of in vivo repair of double-strand breaks (DSBs) have been described for various organisms: the recombinational DSB repair (DSBR) mode, the single-strand annealing (SSA) mode, and end-to-end joining. To investigate these modes of DSB repair in Saccharomyces cerevisiae, we have examined the fate of in vitro linearized replicative plasmids during transformation with respect to several parameters. We found that (i) the efficiencies of both intramolecular and intermolecular linear plasmid DSB repair are homology dependent (according to the amount of DNA used during transformation [100 ng or less], recombination between similar but not identical [homeologous] P450s sequences sharing 73% identity is 2- to 18-fold lower than recombination between identical sequences); (ii) the RAD52 gene product is not essential for intramolecular recombination between homologous and homeologous direct repeats (as in the wild-type strain, recombination occurs with respect to the overall alignment of the parental sequences); (iii) in contrast, the RAD52 gene product is required for intermolecular interactions (the rare transformants which are obtained contain plasmids resulting from deletion-forming intramolecular events involving little or no sequence homology); (iv) similarly, sequencing data revealed examples of intramolecular joining within the few terminal nucleotides of the transforming DNA upon transformation with a linear plasmid with no repeat in the wild-type strain. The recombinant junctions of the rare illegitimate events obtained with S. cerevisiae are very similar to those observed in the repair of DSB in mammalian cells. Together, these and previous results suggest the existence of alternative modes for DSB repair during transformation which differ in their efficiencies and in the structure of their products. We discuss the implications of these results with respect to the existence of alternative pathways and the role of the RAD52 gene product.
Identification and Characterization of Inhibitors of Multidrug Resistance Efflux Pumps in Pseudomonas aeruginosa : Novel Agents for Combination Therapy (2001)

Whole-cell assays were implemented to search for efflux pump inhibitors (EPIs) of the three multidrug resistance efflux pumps (MexAB-OprM, MexCD-OprJ, MexEF-OprN) that contribute to fluoroquinolone resistance in clinical isolates of Pseudomonas aeruginosa. Secondary assays were developed to identify lead compounds with exquisite activities as inhibitors. A broad-spectrum EPI which is active against all three known Mex efflux pumps from P. aeruginosa and their close Escherichia coli efflux pump homolog (AcrAB-TolC) was discovered. When this compound, MC-207,110, was used, the intrinsic resistance of P. aeruginosa to fluoroquinolones was decreased significantly (eightfold for levofloxacin). Acquired resistance due to the overexpression of efflux pumps was also decreased (32- to 64-fold reduction in the MIC of levofloxacin). Similarly, 32- to 64-fold reductions in MICs in the presence of MC-207,110 were observed for strains with overexpressed efflux pumps and various target mutations that confer resistance to levofloxacin (e.g., gyrA and parC). We also compared the frequencies of emergence of levofloxacin-resistant variants in the wild-type strain at four times the MIC of levofloxacin (1 microg/ml) when it was used either alone or in combination with EPI. In the case of levofloxacin alone, the frequency was approximately 10(-7) CFU/ml. In contrast, with an EPI, the frequency was below the level of detection (<10(-11)). In summary, we have demonstrated that inhibition of efflux pumps (i) decreased the level of intrinsic resistance significantly, (ii) reversed acquired resistance, and (iii) resulted in a decreased frequency of emergence of P. aeruginosa strains that are highly resistant to fluoroquinolones.
Sustained effects of nonallele‐specific Huntingtin silencing (2009)

These data indicate that the coincident silencing of the wild-type and mutant htt may be considered as a therapeutic tool for HD.
The host response to cancer virotherapy. (2008)

Clinical trials of oncolytic viruses (OVs) for cancers have revealed that these agents are well tolerated. However, clear-cut evidence of efficacy has been elusive. Although investigators are attempting to generate more efficacious OVs, a fundamental issue continues to limit the efficacy of cancer virotherapy - the response of the host to the ongoing viral infection. This response occurs at the level of intracellular tumor defenses to the viral infection, extracellular stromal reactions to the propagating virus, and, importantly, active host defenses consisting of innate immune as well as inflammatory angiogenic responses. The combination of these host responses severely limits and curtails tumor cell infection and viral replication, thus limiting anticancer efficacy. We believe that such host responses have to be circumvented, at least temporarily or partially, or both, in order to fulfill the promising anticancer effects of these agents.
Long-Term Survival of Chondrocytes in an Osteochondral Articular Cartilage Allograft. A Case Report* (1996)

CONVERY, F. RICHARD M.D.†; AKESON, WAYNE H. M.D.†; AMIEL, DAVID PH.D.†; MEYERS, MARVIN H. M.D.†; MONOSOV, ANNA PH.D.†, SAN DIEGO, CALIFORNIA Author Information
Design and demonstration of an optical true-time-delay device based on an octic-style white cell (2006)

A methodology for designing an octic-style optical true-time-delay (TTD) device based on the White cell (WC) is investigated. The octic cell is a "polynomial" cell, one of the two classes of TTD White cells. This octic cell is designed to produce a maximum of 6399 delays in 17 bounces, with a unit delay of 3 ps. Glass blocks are used for short delays, white lens trains are used for the longer delays. The octic cell is designed to use a microelectromechanical tip/tilt micromirror array to direct light beams into various delay paths.
Conserved epitopes of influenza A virus inducing protective immunity and their prospects for universal vaccine development (2010)

Influenza A viruses belong to the best studied viruses, however no effective prevention against influenza infection has been developed. The emerging of still new escape variants of influenza A viruses causing epidemics and periodic worldwide pandemics represents a threat for human population. Therefore, current, hot task of influenza virus research is to look for a way how to get us closer to a universal vaccine. Combination of chosen conserved antigens inducing cross-protective antibody response with epitopes activating also cross-protective cytotoxic T-cells would offer an attractive strategy for improving protection against drift variants of seasonal influenza viruses and reduces the impact of future pandemic strains. Antigenically conserved fusion-active subunit of hemagglutinin (HA2 gp) and ectodomain of matrix protein 2 (eM2) are promising candidates for preparation of broadly protective HA2- or eM2-based vaccine that may aid in pandemic preparedness. Overall protective effect could be achieved by contribution of epitopes recognized by cytotoxic T-lymphocytes (CTL) that have been studied extensively to reach much broader control of influenza infection. In this review we present the state-of-art in this field. We describe known adaptive immune mechanisms mediated by influenza specific B- and T-cells involved in the anti-influenza immune defense together with the contribution of innate immunity. We discuss the mechanisms of neutralization of influenza infection mediated by antibodies, the role of CTL in viral elimination and new approaches to develop epitope based vaccine inducing cross-protective influenza virus-specific immune response.
Inhibition of Lung Metastasis by Synthetic and Recombinant Fragments of Human Fibronectin with Functional Domains (1990)

We have investigated the antimetastatic effect of synthetic or recombinant peptides containing the functional domains of fibronectin on experimental and spontaneous lung metastases of murine tumor cells. CS1 peptide which is present within type III homology connecting segment (IIICS) as well as C-274 (cell-binding domain) were able to inhibit experimental lung metastasis when co-injected intravenously (iv) with B16-BL6 melanoma cells, while H-271 (heparin-binding domain) could not. In the spontaneous metastasis model, multiple iv administrations of CS1 or C-274 after surgical excision of primary tumors caused a significant reduction of metastatic colonies in the lung. Both CS1 and C-274 significantly inhibited cell adhesion and migration to fibronectin-coated substrates when added freely in solution. CS1 peptide also inhibited the cell adhesion and migration to laminin-coated substrates, but C-274 did not. H-271 did not have any inhibitory effect on cell adhesion or migration to either of the substrates. Similarly, CS1 inhibited tumor invasion to both Matrigel/fibronectin- and Matrigel/laminin-coated filters, whereas C-274 inhibited the invasion to only Matrigel/fibronectin-coated filter. These results indicate that CS1 peptide of fibronectin, lacking the Arg-Gly-Asp-containing domain, actively inhibits tumor metastases in spontaneous and experimental metastasis models. The use of such a peptide might offer a promising therapeutic approach for combatting or preventing cancer metastasis.
Ponder over Advanced Metering Infrastructure and Future Power Grid (2010)

The smart grid is the future direction of modern power grid. As an important component of smart grid, Advanced Metering Infrastructure (AMI) will trigger deep changes in future power system. In the paper, the definition, function and some closely related to AMI, such as electricity pricing mechanism, renewable sources of energy generation, consumer's energy storage devices, users' data acquisition system are introduced, and the influences of AMI on future power system are discussed, too. Finally, suggestions are provided for the research and construction of AMI in China.
Amyloid β Peptide of Alzheimer’s Disease Downregulates Bcl-2 and Upregulates Bax Expression in Human Neurons (1996)

Neuronal apoptosis is a suspected cause of neurodegeneration in Alzheimer’s disease (AD). Increased levels of amyloid β peptide (Aβ) induce neuronal apoptosis in vitro and in vivo . The underlying molecular mechanism of Aβ neurotoxicity is not clear. The normal concentration of Aβ in cerebrospinal fluid is 4 n m . We treated human neuron primary cultures with 100 n m amyloid β peptides Aβ 1–40 and Aβ 1–42 and the control reverse peptide Aβ 40–1 . We find that although little neuronal apoptosis is induced by either peptide after 3 d of treatment, Aβ 1–42 provokes a rapid and sustained downregulation of a key anti-apoptotic protein, bcl-2, whereas it increases levels of bax, a protein known to promote cell death. In contrast, the Aβ 1–40 downregulation of bcl-2 is gradual, although the levels are equivalent to those of Aβ 1–42 -treated neurons by 72 hr of treatment. Aβ 1–40 does not upregulate bax levels. The control, reverse peptide Aβ 40–1 , does not affect either bcl-2 or bax protein levels. In addition, we found that the Aβ 1–40 - and Aβ 1–42 - but not Aβ 40–1 -treated neurons had increased vulnerability to low levels of oxidative stress. Therefore, we propose that although high physiological amounts of Aβ are not sufficient to induce apoptosis, Aβ depletes the neurons of one of its anti-apoptotic mechanisms. We hypothesize that increased Aβ in individuals renders the neurons vulnerable to age-dependent stress and neurodegeneration.
Patient Perspectives Regarding the Value of Total Skin Electron Beam Therapy for Cutaneous T-Cell Lymphoma/Mycosis Fungoides (2009)

TSEBT is perceived by patients to be a successful treatment. TSEBT is thought to be a difficult treatment to undergo and recover from compared with other treatments.
A Close Association of the Ganglioside-specific Sialidase Neu3 with Caveolin in Membrane Microdomains (2002)

The ganglioside-specific sialidase Neu3 has been suggested to play essential roles in regulation of cell surface functions because of its major localization in the plasma membrane and strict substrate preference for gangliosides involved in signal transduction. Here we show that human Neu3 sialidase is enriched in caveolae microdomains and closely associates with caveolin like other caveolin-binding signaling molecules. Using HeLa cells and Neu3-transfected COS-1 cells, endogenous and exogenous Neu3 was found to co-concentrate caveolin-1 in low density Triton X-100-insoluble membrane fractions on sucrose density gradients of the respective cell extracts, as assessed by enzyme activity assays and immunoblotting with a monoclonal antibody to human Neu3. The presence of a putative caveolin-binding motif within Neu3 prompted us to determine whether Neu3 binds to caveolin-1. In transfectants expressing a polyhistidine-tagged form of Neu3, caveolin-1 co-eluted with Neu3 on affinity column chromatography. A mutation with a single amino acid change in the caveolin-binding motif led to inhibition of recruitment of the sialidase to the microdomain, accompanied by reduction of the enzyme activity. Neu3 also failed to associate with caveolin-enriched microdomains by cholesterol depletion with beta-cyclodextrin (with concomitant decrease of the sialidase activity), whereas Neu3 was activated by increased caveolin-1 expression. The tight association of Neu3 with caveolin-1 was supported further by co-immunoprecipitation of Neu3 by anti-caveolin-1 antibody. These results strongly suggest that Neu3 functions as a caveolin-related signaling molecule within caveolin-rich microdomains.
Branched Cationic Peptides for Gene Delivery: Role of Type and Number of Cationic Residues in Formation and in Vitro Activity of DNA Polyplexes (1999)

To examine the suitability of synthetic peptides as DNA-binding and -compacting agents for receptor-mediated gene delivery, we have synthesized and characterized a series of branched oligocationic peptides that differ in the number and type (lysine, arginine, ornithine) of cationic amino acids in the DNA-binding moiety. The peptides were designed as branched molecules to provide a coupling site via a spacer for the attachment of effectors at a flexible distance from the DNA-binding moiety. This design provides torsional flexibility in the peptide backbone of the DNA-binding moiety to maximize cation-DNA phosphate interactions and also minimizes the potential for interference by the effector with DNA binding. The branched peptides bind DNA with affinities that increase with the number of cationic groups. The peptides compact DNA into microparticulate structures as judged by an ethidium bromide displacement assay, dynamic light scattering, and electron microscopy. In general, differences in DNA binding and compaction owing to variation in the cationic side chain were modest, with the rank order being arginyl > lysyl approximately ornithyl. Incorporation of tryptophans into the DNA-binding moiety had no major effect on apparent binding affinity but clearly reduced the DNA-compacting potency of the peptides. Compared with polylysine, the peptides and their DNA complexes are weak activators of the complement system. Complement activation by an octaarginyl peptide was stronger than that induced by an octalysyl peptide. The microparticulate peptide-DNA complexes are suitable for receptor-mediated gene delivery as evidenced by transferrinfection of K562 cells in the presence of chloroquine. The results obtained in gene delivery in vitro suggest that a minimum chain length of six to eight cationic amino acids is required to compact DNA into structures active in receptor-mediated gene delivery.
Dissection of B cell differentiation during primary immune responses in mice with altered CD40 signals (2002)

CD40 is essential for efficient humoral immune responses. CD40 has two cytoplasmic domains required for binding of tumor necrosis factor receptor-associated factors (TRAF). The TRAF6-binding site is within the membrane proximal cytoplasmic (Cmp) region, while a PXQXT motif in the membrane distal cytoplasmic (Cmd) region needs to engage TRAF2/3/5. To dissect CD40 signals necessary for B cell differentiation, we generated transgenic mice expressing wild-type and mutant human CD40 (hCD40) molecules in a mouse CD40-deficient (mCD40(-/-)) background. The B cell-specific expression of hCD40 in mCD40(-/-) mice resulted in T-dependent antibody responses including germinal center (GC) formation. Mutant hCD40 molecules that carry either a point mutation of the TRAF2/3/5-binding site or a deletion of the Cmd region rescued extrafollicular B cell differentiation but not GC formation. A mutant hCD40 that comprises of only the TRAF2/3/5-binding site in the cytoplasmic region also rescued low but significant titers of antigen-specific IgG1 without GC formation. These results demonstrated that two distinct signals either from the Cmp or from the Cmd region induced the extrafollicular B cell differentiation and Ig class switching; however, GC formation required both. We conclude that combinations of these two signals determine which of the extrafollicular or the follicular (GC) differentiation pathway B cells enter.
Estimation of effective temperatures in quantum annealers for sampling applications: A case study with possible applications in deep learning (2016)

An increase in the efficiency of sampling from Boltzmann distributions would have a significant impact on deep learning and other machine-learning applications. Recently, quantum annealers have been proposed as a potential candidate to speed up this task, but several limitations still bar these state-of-the-art technologies from being used effectively. One of the main limitations is that, while the device may indeed sample from a Boltzmann-like distribution, quantum dynamical arguments suggest it will do so with an instance-dependent effective temperature, different from its physical temperature. Unless this unknown temperature can be unveiled, it might not be possible to effectively use a quantum annealer for Boltzmann sampling. In this work, we propose a strategy to overcome this challenge with a simple effective-temperature estimation algorithm. We provide a systematic study assessing the impact of the effective temperatures in the learning of a special class of a restricted Boltzmann machine embedded on quantum hardware, which can serve as a building block for deep-learning architectures. We also provide a comparison to $k$-step contrastive divergence (CD-$k$) with $k$ up to 100. Although assuming a suitable fixed effective temperature also allows us to outperform one-step contrastive divergence (CD-1), only when using an instance-dependent effective temperature do we find a performance close to that of CD-100 for the case studied here.