gebhart/patrepeval huggingface dataset:
Role of Residues 121 to 124 of Vesicular Stomatitis Virus Matrix Protein in Virus Assembly and Virus-Host Interaction (2006)

The recent solution of the crystal structure of a fragment of the vesicular stomatitis virus matrix (M) protein suggested that amino acids 121 to 124, located on a solvent-exposed loop of the protein, are important for M protein self-association and association with membranes. These residues were mutated from the hydrophobic AVLA sequence to the polar sequence DKQQ. Expression and purification of this mutant from bacteria showed that it was structurally stable and that the mutant M protein had self-association kinetics similar to those of the wild-type M protein. Analysis of the membrane association of M protein in the context of infection with isogenic recombinant viruses showed that both wild-type and mutant M proteins associated with membranes to the same extent. Virus expressing the mutant M protein did show an approximately threefold-lower binding affinity of M protein for nucleocapsid-M complexes. In contrast to the relatively minor effects of the M protein mutation on virus assembly, the mutant virus exhibited growth restriction in MDBK but not BHK cells, a slower induction of apoptosis, and lower viral-protein synthesis. Despite translating less viral protein, the mutant virus produced more viral mRNA, showing that the mutant virus could not effectively promote viral translation. These results demonstrate that the 121-to-124 region of the VSV M protein plays a minor role in virus assembly but is involved in virus-host interactions and VSV replication by augmenting viral-mRNA translation.
On the computational complexity of Ising spin glass models (1982)

In a spin glass with Ising spins, the problems of computing the magnetic partition function and finding a ground state are studied. In a finite two-dimensional lattice these problems can be solved by algorithms that require a number of steps bounded by a polynomial function of the size of the lattice. In contrast to this fact, the same problems are shown to belong to the class of NP-hard problems, both in the two-dimensional case within a magnetic field, and in the three-dimensional case. NP-hardness of a problem suggests that it is very unlikely that a polynomial algorithm could exist to solve it. © 1982 The Japan Society of Applied Physics.
Reductive Cleavage Method for Quantitation of Monolignols and Low‐Abundance Monolignol Conjugates (2018)

As interest in biomass utilization has grown, the manipulation of lignin biosynthesis has received significant attention, such that recent work has demanded more robust lignin analytical methods. As the derivatization followed by reductive cleavage (DFRC) method is particularly effective for structurally characterizing natively acylated lignins, we used an array of synthetic β-ether γ-acylated model compounds to determine theoretical yields for all monolignol conjugates currently known to exist in lignin, and we synthesized a new set of deuterated analogs as internal standards for quantification using GC-MS/MS. Yields of the saturated ester conjugates ranged from 40 to 90 %, and NMR analysis revealed the presence of residual unsaturated conjugates in yields of 20 to 35 %. In contrast to traditional selected-ion-monitoring, we demonstrated the superior sensitivity and accuracy of multiple-reaction-monitoring detection methods, and further highlighted the inadequacy of traditional standards relative to isotopically labeled analogs.
Laguerre-Gaussian beam generated with a multilevel spiral phase plate for high intensity laser pulses (2004)

We investigated an Laguerre-Gaussian (LG) beam that can carry an orbital angular momentum and has a doughnut-shaped intensity pattern. We developed a multilevel spiral phase plate (SPP) that generates an LG beam by applying the wave surface of a spiral structure directly to a Gaussian beam for application to microscopic laser material processing.We experimentally demonstrate, for the first time, that it is possible to generate an LG beam with the multilevel SPP that allows the use in high intensity laser pulses.
Sesquiterpenoids Lactones: Benefits to Plants and People (2013)

Sesquiterpenoids, and specifically sesquiterpene lactones from Asteraceae, may play a highly significant role in human health, both as part of a balanced diet and as pharmaceutical agents, due to their potential for the treatment of cardiovascular disease and cancer. This review highlights the role of sesquiterpene lactones endogenously in the plants that produce them, and explores mechanisms by which they interact in animal and human consumers of these plants. Several mechanisms are proposed for the reduction of inflammation and tumorigenesis at potentially achievable levels in humans. Plants can be classified by their specific array of produced sesquiterpene lactones, showing high levels of translational control. Studies of folk medicines implicate sesquiterpene lactones as the active ingredient in many treatments for other ailments such as diarrhea, burns, influenza, and neurodegradation. In addition to the anti-inflammatory response, sesquiterpene lactones have been found to sensitize tumor cells to conventional drug treatments. This review explores the varied ecological roles of sesquiterpenes in the plant producer, depending upon the plant and the compound. These include allelopathy with other plants, insects, and microbes, thereby causing behavioural or developmental modification to these secondary organisms to the benefit of the sesquiterpenoid producer. Some sesquiterpenoid lactones are antimicrobial, disrupting the cell wall of fungi and invasive bacteria, whereas others protect the plant from environmental stresses that would otherwise cause oxidative damage. Many of the compounds are effective due to their bitter flavor, which has obvious implications for human consumers. The implications of sesquiterpenoid lactone qualities for future crop production are discussed.
C-reactive protein in the differential diagnosis between infection and disease reactivation in SLE. (1981)

Fifty of 197 systemic lupus erythematosus (SLE) sera had 2 + positive C-reactive protein (CRP) determinations by precipitation in capillary tubes. All but 3 of these 50 sera had been taken at the time of infection whereas 80 of the 115 sera taken at the time of SLE activity without infection were negative for CRP. Thirty-two of the 35 CRP positive sera from patients with active lupus were obtained during intercurrent infection. CRP determinations in capillary tubes are clinically useful in distinguishing disease reactivation from intercurrent infection in SLE. These findings confirm a study using the same method for CRP determination. Discrepancy with another study may be due to the use of a different method.
Cohort Profile: The Golestan Cohort Study--a prospective study of oesophageal cancer in northern Iran (2009)

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A Diminished Role for Hydrogen Bonds in Antifreeze Protein Binding to Ice (1997)

The most abundant isoform (HPLC-6) of type I antifreeze protein (AFP1) in winter flounder is a 37-amino-acid-long, alanine-rich, alpha-helical peptide, containing four Thr spaced 11 amino acids apart. It is generally assumed that HPLC-6 binds ice through a hydrogen-bonding match between the Thr and neighboring Asx residues to oxygens atoms on the {2021} plane of the ice lattice. The result is a lowering of the nonequilibrium freezing point below the melting point (thermal hysteresis). HPLC-6, and two variants in which the central two Thr were replaced with either Ser or Val, were synthesized. The Ser variant was virtually inactive, while only a minor loss of activity was observed in the Val variant. CD, ultracentrifugation, and NMR studies indicated no significant structural changes or aggregation of the variants compared to HPLC-6. These results call into question the role of hydrogen bonds and suggest a much more significant role for entropic effects and van der Waals interactions in binding AFP to ice.
Metal-semiconductor contacts (1982)

A review is given of our present knowledge of metal-semiconductor contacts. Topics covered include the factors that determine the height of the Schottky barrier, its current/voltage characteristics, and its capacitance. A short discussion is also given of practical contacts and their application in semiconductor technology, and a comparison is made with p-n junctions.
Power savings analysis of peak-to-average power ratio reduction in OFDM (2004)

Orthogonal frequency division multiplexing (OFDM) has become a popular modulation method in high-speed wireless networks because of its robustness against multipath fading, its simple equalizer structure, and its high bandwidth efficiency. However, in the time domain, the OFDM signal has a large peak-to-average power ratio (PAR), which translates to low power amplifier efficiencies. In this paper we examine and quantify the power savings from PAR reductions. We also relate any power savings to the computational power costs of selected mapping, which is a prominent PAR reduction scheme that results in negligible performance degradation.
Synthesis of 1-Substituted 1, 4-Dihydro-7-[2-(5-nitro-2-furyl) vinyl]-4-oxo-1, 8-naphthyridine Derivatives. I (1969)

In order to test of antimicrobial activity, 1-ethyl-1, 4-dihydro-7-[2-(5-nitro-2-furyl)-vinyl]-4-oxo-1, 8-naphthyridine-3-carboxylic acid (V) which contained nalidixic acid and 5-nitro-2-furaldehyde was prepared and a convenient method for the synthesis of its derivatives was studied.
Membrane Topology of the Yeast Endoplasmic Reticulum-localized Ubiquitin Ligase Doa10 and Comparison with Its Human Ortholog TEB4 (MARCH-VI) (2005)

Quality control machinery in the endoplasmic reticulum (ER) helps ensure that only properly folded and assembled proteins accumulate in the ER or continue along the secretory pathway. Aberrant proteins are retrotranslocated to the cytosol and degraded by the proteasome, a process called ER-associated degradation. Doa10, a transmembrane protein of the ER/nuclear envelope, is one of the primary ubiquitin ligases (E3s) participating in ER-associated degradation in Saccharomyces cerevisiae. Here we report the membrane organization of the 1319-residue Doa10 polypeptide. The topology was determined by fusing a dual-topology reporter after 16 different Doa10 fragments. Our results indicate that Doa10 contains 14 transmembrane helices (TMs). Based on protease digestion of yeast microsomes, both the N-terminal RING-CH domain and the C terminus face the cytosol. Notably, the experimentally derived topology was not predicted correctly by any of the generally available TM prediction algorithms. Bioinformatic analysis and in silico mutagenesis guided the topological studies through problematic regions. The conserved TD domain in Doa10 includes three TMs. These TMs might function in cofactor binding or substrate recognition, or they might be part of a retrotranslocation channel. The Derlins were previously proposed to provide such channels, but we show that the two yeast Derlins are not required for degradation of Doa10 membrane substrates, as was found before for the Sec61 translocon. Finally, we provide evidence that the likely human Doa10 ortholog, TEB4 (MARCH-VI), adopts a topology similar to that of Doa10.
Temperature-Responsive surface for novel co-culture systems of hepatocytes with endothelial cells: 2-D patterned and double layered co-cultures (2000)

We have developed two novel cell co-culture system, without any on cell type combination limitation, utilizing a polymer surface which is temperature-sensitive with respect to its cell adhesion characteristics. One system involves a patterned co-culture of primary hepatocytes with endothelial cells utilizing patterned masked of the electron-beam cured, temperature-responsive polymer, poly (N-isopropylacrylamide) (PIPAAm) by masked electron beam irradiation. Hepatocytes were cultured to confluency at 37 degrees C on these surfaces. When the culture temperature was reduced below 32 degrees C, cells detached from the PIPAAm-grafted areas without any need for trypsin. Endothelial cells were then seeded onto the same surfaces at 37 degrees C. These subsequently seeded endothelial cells adhered only to the now-exposed PIPAAm-grafted domains and could be co-cultured with the hepatocytes initially seeded at 37 degrees C in well-ordered patterns. The other system involves a double layered co-culture obtained by overlaying endothelial cell sheets of the designed shape onto hepatocyte monolayers. The endothelial cells adhered and proliferated on the PIPAAm-grafted surface, as on polystyrene tissue culture dishes at 37 degrees C. By reducing the temperature, confluent monolayers of cells detached from the PIPAAm surfaces without trypsin. Because the recovered cells maintained intact cell-cell junctions together with deposited extracellular matrix, the harvested endothelial cell sheets, with designed shapes, were transferable and readily adhered to hepatocyte monolayers. Stable double layered cell sheets could be co-cultivated. These two co-culture methods enabled long-term co-culture of primary hepatocytes with endothelial cells. Hepatocytes so co-cultured with endothelial cells maintained their differentiated functions, such as albumin synthesis for unexpectedly long periods. These novel two co-culture systems offer promising techniques for basic biologic researches upon intercellular communications, and for the clinical applications of tissue engineered constructs.
Automated liquid chromatography. Synthesis of a broad-spectrum resolving agent and resolution of 1-(1-naphthyl)-2,2,2-trifluoroethanol (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAutomated liquid chromatography. Synthesis of a broad-spectrum resolving agent and resolution of 1-(1-naphthyl)-2,2,2-trifluoroethanolW. H. Pirkle and M. S. HoekstraCite this: J. Org. Chem. 1974, 39, 26, 3904–3906Publication Date (Print):December 1, 1974Publication History Published online1 May 2002Published inissue 1 December 1974https://pubs.acs.org/doi/10.1021/jo00940a023https://doi.org/10.1021/jo00940a023research-articleACS PublicationsRequest reuse permissionsArticle Views479Altmetric-Citations109LEARN 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 optionsGet e-Alertsclose Get e-Alerts
[Recurrent aphthous stomatitis: treatment with colchicine. An open trial of 54 cases]. (2002)

This study, which is the first in size (n=54) and duration of follow-up (4.7 years), showed that colchicine is an efficient preventive treatment of severe aphthous stomatitis for 63 p. 100 of patients after 3 month's treatment and that this improvement was lasting in 37 p. 100 of them. Colchicine should therefore be proposed in first intention in severe recurrent aphthous stomatitis, since it is effective, well tolerated and easy to use.
Selective p38 Activation in Human Non–Small Cell Lung Cancer (2002)

The mitogen-activated protein kinase (MAPK) pathways transmit signals from the cell membrane to the nucleus. Activation of MAPK cascades may play a role in malignant transformation. We hypothesized that enhanced expression of one or more of these pathways would occur in human lung cancers. Using Western blot analysis of tissue homogenates from resected non- small cell lung cancers and matched non-neoplastic lung tissue, we determined that only activated p38 was consistently increased in tumor compared with normal tissue. In vitro kinase assays confirmed that the levels of activated MAPK correlated with the activity of the enzymes, and immunohistochemical analysis confirmed the cellular localization of the activated MAPKs. We incubated a lung cancer cell line in a hypoxic chamber to simulate the hypoxic environment in solid lung tumors, but found no increase in p38 activation. Contrary to our expectations, ERK and JNK, the MAPK pathways traditionally associated with cell growth and perhaps malignant transformation, were not consistently activated in the human lung tumor samples. However, p38, a MAPK usually associated with stress responses, growth arrest, and apoptosis, was activated in all of the human lung cancer samples, suggesting an additional role for this pathway in malignant cell growth or transformation.
Theoretical analysis of antibody targeting of tumor spheroids: importance of dosage for penetration, and affinity for retention. (2003)

The interplay among antibody/antigen binding kinetics, antibody diffusion, and antigen metabolic turnover together determines the depth of penetration of antitumor antibodies into prevascular tumor spheroid cell clumps. A sharp boundary between an outer shell of bound high-affinity antibody and an inner antibody-free core has been previously observed and mathematically modeled and was termed the "binding site barrier." We show here that this process is well described by a simplified shrinking core model wherein binding equilibration is much more rapid than diffusion. This analysis provides the following experimentally testable predictions: (a) the binding site barrier is a moving boundary whose velocity is proportional to the time integral of antibody concentration at the spheroid surface (i.e. plasma antibody AUC); (b) the velocity of this moving boundary is independent of binding affinity, if the affinity is sufficiently high to strongly favor antibody/antigen complex formation at prevailing antibody concentrations; and (c) maximum tumor retention is achieved when the antibody/antigen dissociation rate approaches the rate of antigen metabolic turnover. The consistency of these predictions with published experimental results is demonstrated. The shrinking core model provides a simple analytic relationship predicting the effects of altered antibody pharmacokinetics, antibody molecular weight, antigen turnover rate, antigen expression level, and micrometastasis size on antibody penetration and retention. For example, a formula is provided for predicting the bolus dose necessary to accomplish tumor saturation as a function of antibody and tumor properties. Furthermore, this analysis indicates certain attributes necessary for an optimal tumor targeting agent.
Transforming Growth Factor- and Wound Healing (2006)

Acute and chronic wounds are a source of significant morbidity for patients, and they demand a growing portion of health-care time and finances to be devoted to their care. Transforming growth factor-beta (TGF-beta) has surfaced from abundant research as a key signal in orchestrating wound repair. In beginning this review, we discuss the inflammatory, proliferative, and maturational phases of wound healing. We then focus on TGF-beta by first discussing the pathway from its production to the target cell where Smad proteins execute an intracellular signaling cascade. To review TGF-beta's role in wound healing, we discuss the actions of it individually on keratinocytes, fibroblasts, endothelial cells, and monocytes, which are the major cell types involved in wound repair. From illustrating these cellular actions of TGF-beta, we summarize its multipotent role in the process of wound repair. As a clinical correlation, we also review research dedicated to the involvement of TGF-beta in venous stasis ulcers.
Complex Event Processing using Simple Rule-based Event Correlation Engines for Business Performance Management (2006)

Event correlation is an important component in business performance management. Simple rule-based event correlation engines, like Zurich Correlation Engine (ZCE), usually accept input events that include only name-value pairs. However, when input events are in XML format, the ZCE needs to be adapted to accept complex/structural events. In this paper, we present a model-driven approach to derive solutions for adapting the new type of events, so that the light weight correlation engine can still be used for event monitoring and correlation.
Farnesyltransferase inhibitors reverse altered growth and distribution of actin filaments inTsc-deficient cells via inhibition of both rapamycin-sensitive and -insensitive pathways (2005)

Farnesyltransferase inhibitors (FTI) have been developed as anticancer drugs and are currently being evaluated in clinical trials. In this study, we have examined the effects of FTIs on Tsc-null cells to gain insight into their effects on farnesylated Rheb GTPase. This protein is involved in the activation of mTOR/S6K signaling and is down-regulated by the Tsc1/Tsc2 complex. Both Tsc1(-/-) and Tsc2(-/-) mouse embryonic fibroblasts exhibit constitutive activation of S6K and grow in the absence of serum. Two different FTI compounds, the clinical compound BMS-214662 and the newly described BMS-225975, inhibit the constitutive activation of mTOR/S6K signaling and block serum-free growth of the Tsc-null mouse embryonic fibroblasts. We have also found that Tsc-null mouse embryonic fibroblasts grow under anchorage-independent conditions and that both FTI compounds inhibit this soft agar growth. These FTI effects are similar to those observed with rapamycin. Another interesting phenotype of Tsc-null mouse embryonic fibroblasts is that they are round and contain actin filaments predominantly at the cell periphery. The addition of FTIs, but not rapamycin, led to the reappearance of intracellular actin filaments and reduction of peripheral actin filaments. The ability of FTI to rearrange actin filaments seems to be largely mediated by the inhibition of Rheb protein, as induction of intracellular actin filaments by FTI was much less efficient in Tsc2-null cells expressing Rheb (M184L), a geranylgeranylated mutant Rheb that can bypass farnesylation. These results reveal that FTIs inhibit Rheb, causing two different effects in Tsc-deficient cells, one on growth and the other on actin filament distribution.
Essential role of PDK1 in regulating endothelial cell migration (2007)

The serine/threonine protein kinase phosphoinositide-dependent kinase 1 (PDK1) plays a central role in cellular signaling by phosphorylating members of the AGC family of kinases, including PKB/Akt. We now present evidence showing that PDK1 is essential for the motility of vascular endothelial cells (ECs) and that it is involved in the regulation of their chemotaxis. ECs differentiated from mouse embryonic stem cells lacking PDK1 completely lost their ability to migrate in vitro in response to vascular endothelial growth factor-A (VEGF-A). In addition, PDK1(-/-) embryoid bodies exhibit evident developmental and vascular defects that can be attributed to a reduced cell migration. Moreover, the overexpression of PDK1 increased the EC migration induced by VEGF-A. We propose a model of spatial distribution of PDK1 and Akt in which the synthesis of phosphatidylinositol 3,4,5 triphosphate at plasma membrane by activation of phosphoinositide 3-kinase recruits both proteins at the leading edge of the polarized ECs and promotes cell chemotaxis. These findings establish a mechanism for the spatial localization of PDK1 and its substrate Akt to regulate directional migration.