gebhart/patrepeval huggingface dataset:
The free radical in pyruvate formate-lyase is located on glycine-734. (1992)

Pyruvate formate-lyase (acetyl-CoA:formate C-acetyltransferase, EC 2.3.1.54) from anaerobic Escherichia coli cells converts pyruvate to acetyl-CoA and formate by a unique homolytic mechanism that involves a free radical harbored in the protein structure. By EPR spectroscopy of selectively 13C-labeled enzyme, the radical (g = 2.0037) has been assigned to carbon-2 of a glycine residue. Estimated hyperfine coupling constants to the central 13C nucleus (A parallel = 4.9 mT and A perpendicular = 0.1 mT) and to 13C nuclei in alpha and beta positions agree with literature data for glycine radical models. N-coupling was verified through uniform 15N-labeling. The large 1H hyperfine splitting (1.5 mT) dominating the EPR spectrum was assigned to the alpha proton, which in the enzyme radical is readily solvent-exchangeable. Oxygen destruction of the radical produced two unique fragments (82 and 3 kDa) of the constituent polypeptide chain. The N-terminal block on the small fragment was identified by mass spectrometry as an oxalyl residue that derives from Gly-734, thus assigning the primary structural glycyl radical position. The carbon-centered radical is probably resonance-stabilized through the adjacent carboxamide groups in the polypeptide main chain and could be comparable energetically with other known protein radicals carrying the unpaired electron in tyrosine or tryptophan residues.
Human Developmental Chondrogenesis as a Basis for Engineering Chondrocytes from Pluripotent Stem Cells (2013)

Joint injury and osteoarthritis affect millions of people worldwide, but attempts to generate articular cartilage using adult stem/progenitor cells have been unsuccessful. We hypothesized that recapitulation of the human developmental chondrogenic program using pluripotent stem cells (PSCs) may represent a superior approach for cartilage restoration. Using laser-capture microdissection followed by microarray analysis, we first defined a surface phenotype (CD166(low/neg)CD146(low/neg)CD73(+)CD44(low)BMPR1B(+)) distinguishing the earliest cartilage committed cells (prechondrocytes) at 5-6 weeks of development. Functional studies confirmed these cells are chondrocyte progenitors. From 12 weeks, only the superficial layers of articular cartilage were enriched in cells with this progenitor phenotype. Isolation of cells with a similar immunophenotype from differentiating human PSCs revealed a population of CD166(low/neg)BMPR1B(+) putative cartilage-committed progenitors. Taken as a whole, these data define a developmental approach for the generation of highly purified functional human chondrocytes from PSCs that could enable substantial progress in cartilage tissue engineering.
En Route to a Motorized Nanocar (2006)

[structure: see text] With the eventual goal of demonstrating a motorized nanocar, the key structure has been synthesized which bears a light-activated unidirectional molecular motor and an oligo(phenylene ethynylene) chassis and axle system with four carboranes to serve as the wheels. Kinetics studies in solution show that the motor indeed rotates upon irradiation with 365 nm light, and the fullerene-free carborane wheel system is an essential design feature for motor operation.
Temporal dynamics of recurrent airway symptoms and cellular random walk (2003)

Asthma is a complex chronic inflammatory disease of the small airways that has dramatically increased in prevalence in industrialized countries during the last decades. Risk factors for adult asthma have been related to the complex array of gene-environment interactions and exposure of the immune system to allergens in early childhood. In genetically predisposed subjects, continuous exposure to environmental agents such as allergens or infections can lead to recurrent airway symptoms characterized by recurrent episodes of airway inflammation and bronchoconstriction with clinical symptoms of cough, dyspnea, or wheezing. In this study, we report that the longterm temporal dynamics of recurrent airway symptoms in a population of unselected infants display a complex intermittent pattern and that the distribution of interepisode intervals follows a power law. We interpret the data by using a model of the dynamics of attack episodes in which an attack is triggered by an avalanche of airway constrictions. We map the dynamics of this model to the known problem of a random walk in the presence of an absorbing boundary in which the walker corresponds to the fluctuations in contractile state of airway smooth muscle cells. These findings may provide new insight into the mechanisms of otherwise unexplained symptom episodes.
Measuring the transient extensional rheology of polyethylene melts using the SER universal testing platform (2005)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Martin Sentmanat, Benjamin N. Wang, Gareth H. McKinley; Measuring the transient extensional rheology of polyethylene melts using the SER universal testing platform. J. Rheol. 1 May 2005; 49 (3): 585–606. https://doi.org/10.1122/1.1896956 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentThe Society of RheologyJournal of Rheology Search Advanced Search |Citation Search
S100P INCREASES PANCREATIC CANCER GROWTH AND INVASION. (2004)

Background: Pancreatic cancer is the most lethal of major cancers. Our previous studies indicated that S100P is highly expressed in pancreatic cancer when compared with normal pancreas and pancreatitis. In the current study, we investigated the role of S100P in pancreatic cancer growth and invasion. Methods: The influence of S100P on pancreatic cancer growth and invasion in vitro and in vivo was evaluated using wild-type and S100P transfected Panc1 cells, which have low endogenous levels, and wild-type and S100P silenced BxPC3 cells, which have high endogenous levels. S100P silencing was accomplished using an SiRNA. Cell proliferation and invasion were analyzed using MTS to estimate cell numbers in vitro. Tumor growth and invasion in vivo were examined using immune compromised mice. Tumor growth was compared between subcutaneous tumors formed from wild-type and S100P expressing Panc-1 cells. Tumor invasion was evaluated by bioluminescence imaging of orthotopically implanted SiRNA silenced and wild-type BxPC3 cells. Results: Expression of S100P stimulated cell proliferation of Panc1 cells in vitro by 164±25% at 96h. Reduction of S100P levels in BxPC3 cells using SiRNA decreased the proliferation rate in vitro by 129±22.5% within 96h. In vitro cell invasion studies indicated that S100P stimulated Panc1 cell invasion by 198±49% and silencing of S100P expression in BxPC3 cells decreased invasion by 221±51% of control. In vivo studies indicated that expression of S100P in Panc1 cells increased tumor volume by 511±140%. Bioluminescence imaging revealed that silencing of S100P expression in BxPC3 cells caused a 10-fold reduction in tumor growth and reduced invasion to liver by 50% (6 vs 3 animals) and to lung by 100% (1 versus 0 animals). Conclusions: These data indicate that S100P expression by pancreatic cancer cells stimulates cancer growth and invasion. Therefore, this molecule may be a useful target for the development of new therapies for this deadly tumor.
Screening for Hypertrophic Cardiomyopathy in Young Athletes (1998)

The results show that hypertrophic cardiomyopathy was an uncommon cause of death in these young competitive athletes and suggest that the identification and disqualification of affected athletes at screening before participation in competitive sports may have prevented sudden death.
Cloning of the Human Cytomegalovirus (HCMV) Genome as an Infectious Bacterial Artificial Chromosome in Escherichia coli : a New Approach for Construction of HCMV Mutants (1999)

We have recently introduced a novel procedure for the construction of herpesvirus mutants that is based on the cloning and mutagenesis of herpesvirus genomes as infectious bacterial artificial chromosomes (BACs) in Escherichia coli (M. Messerle, I. Crnkovic, W. Hammerschmidt, H. Ziegler, and U. H. Koszinowski, Proc. Natl. Acad. Sci. USA 94:14759-14763, 1997). Here we describe the application of this technique to the human cytomegalovirus (HCMV) strain AD169. Since it was not clear whether the terminal and internal repeat sequences of the HCMV genome would give rise to recombination, the stability of the cloned HCMV genome was examined during propagation in E. coli, during mutagenesis, and after transfection in permissive fibroblasts. Interestingly, the HCMV BACs were frozen in defined conformations in E. coli. The transfection of the HCMV BACs into human fibroblasts resulted in the reconstitution of infectious virus and isomerization of the reconstituted genomes. The power of the BAC mutagenesis procedure was exemplarily demonstrated by the disruption of the gpUL37 open reading frame. The transfection of the mutated BAC led to plaque formation, indicating that the gpUL37 gene product is dispensable for growth of HCMV in fibroblasts. The new procedure will considerably speed up the construction of HCMV mutants and facilitate genetic analysis of HCMV functions.
Multifunction optical filter with a Michelson–Gires–Tournois interferometer for wavelength-division-multiplexed network system applications (1998)

We propose using a novel multifunction optical filter with a Michelson-Gires-Tournois interferometer (MGTI) for future smart wavelength-division-multiplexed network system applications. The MGTI filter is a typical Michelson interferometer in which one of its reflecting mirrors is replaced with a Gires-Tournois resonator. One unique feature of this device is that it can function as a channel-passing (CP), a channel-dropping (CD), or a wide-bandpass (BP) filter, depending on the interferometer arm-length difference. Other interesting features are that (1) the linewidths of both the CP and the CD filter are twice as narrow as that of a typical Fabry-Perot filter with similar parameters, (2) theoretical visibility is always unity regardless of the mirror reflectance value, and (3) the BP filter has an excellent boxlike response function. Numerical results showing these characteristics are presented.
CD19 expression levels regulate B lymphocyte development: human CD19 restores normal function in mice lacking endogenous CD19 (1997)

Establishing signal transduction thresholds that regulate B lymphocyte responses to foreign Ags and tolerance to self Ags is critical for humoral immune responses. The effects of altered signaling thresholds in B lymphocytes were examined in CD19-deficient mice and transgenic mice that expressed human CD19 at varying densities. Human CD19 restored normal B cell function and development to CD19-deficient mice when expressed at levels comparable to those of circulating human B cells. While CD19 expression levels were found to be developmentally regulated and tightly controlled in normal mice, two- or threefold changes in cell surface CD19 expression in transgenic mice dramatically affected B cell development, mitogen responses, serum Ig levels, humoral immune responses, and germinal center formation. B cells from mice that overexpressed CD19 also had decreased levels of surface IgM and a cell surface phenotype consistent with increased signaling in these cells. These results suggest that CD19 may serve similar functions in humans and mice and that CD19 defines signaling thresholds in vivo for the Ag receptor as well as other cell surface receptors that regulate B lymphocyte selection, activation, and differentiation.
Functional classification of interferon-stimulated genes identified using microarrays (2001)

Interferons (IFNs) are a family of multifunctional cytokines that activate transcription of subsets of genes. The gene products induced by IFNs are responsible for IFN antiviral, antiproliferative, and immunomodulatory properties. To obtain a more comprehensive list and a better understanding of the genes regulated by IFNs, we compiled data from many experiments, using two different microarray formats. The combined data sets identified >300 IFN-stimulated genes (ISGs). To provide new insight into IFN-induced cellular phenotypes, we assigned these ISGs to functional categories. The data are accessible on the World Wide Web at http://www.lerner.ccf.org/labs/williams/, including functional categories and individual genes listed in a searchable database. The entries are linked to GenBank and Unigene sequence information and other resources. The goal is to eventually compile a comprehensive list of all ISGs. Recognition of the functions of the ISGs and their specific roles in the biological effects of IFNs is leading to a greater appreciation of the many facets of these intriguing and essential cytokines. This review focuses on the functions of the ISGs identified by analyzing the microarray data and focuses particularly on new insights into the protein kinase RNA-regulated (PRKR) protein, which have been made possible with the availability of PRKR-null mice.
Trypanosoma brucei Glycogen Synthase Kinase-3, A Target for Anti-Trypanosomal Drug Development: A Public-Private Partnership to Identify Novel Leads (2011)

We identified potent and selective compounds representing potential attractive starting points for a drug discovery program. Structural analysis of the human and trypanosomal enzymes also revealed hypotheses for further improving selectivity of the compounds.
Protein Glycation Inhibitors from Thyme (Thymus vulgaris) (1995)

Nonenzymatic glycation of bovine serum albumin (BSA) was inhibited in vitro by some extracts of 34 kinds of spices. The methanol extract of thyme (Thymus vulgaris) had the most potent inhibitory activity among them. Chromatographic purification yielded four flavonoids, quercetin (1), eriodictyol (2), 5,6,4'-trihydroxy-7,8,3'-trimethoxyflavone (3), and cirsilineol (4). These known flavonoids suppressed the levels of advanced glycation end products (AGEs) and fructosamines, shown by the measurement of specific fluorescent groups and the reduction of nitroblue tetrazolium (NBT), respectively. The inhibitory activities were compared with those of other structure-related flavonoids and aminoguanidine.
New retrovirus helper cells with almost no nucleotide sequence homology to retrovirus vectors (1989)

We prepared retrovirus packaging cell lines containing gag-pol genes from spleen necrosis virus (expressed from a cytomegalovirus promoter and the simian virus 40 (SV40) polyadenylation sequences) and, on a separate vector, either the env gene from spleen necrosis virus (expressed from the Rous sarcoma virus promoter and the SV40 polyadenylation sequences) or the env gene from amphotropic murine leukemia virus (expressed from a cytomegalovirus promoter and the SV40 polyadenylation sequences). The nucleotide sequences in these packaging cell lines have almost no homology to the retrovirus vectors we used. Retrovirus vectors were produced from these new helper cell lines without any genetic interactions between the vectors and sequences in the helper cells and without transfer of the packaging sequences.
Nanoscale patterning and oxidation of H-passivated Si(100)-2×1 surfaces with an ultrahigh vacuum scanning tunneling microscope (1994)

Nanoscale patterning of the hydrogen terminated Si(100)-2×1 surface has been achieved with an ultrahigh vacuum scanning tunneling microscope. Patterning occurs when electrons field emitted from the probe locally desorb hydrogen, converting the surface into clean silicon. Linewidths of 1 nm on a 3 nm pitch are achieved by this technique. Local chemistry is also demonstrated by the selective oxidation of the patterned areas. During oxidation, the linewidth is preserved and the surrounding H-passivated regions remain unaffected, indicating the potential use of this technique in multistep lithography processes.
RANKL Expression Is Related to the Differentiation State of Human Osteoblasts (2003)

Human osteoblast phenotypes that support osteoclast differentiation and bone formation are not well characterized. Osteoblast differentiation markers were examined in relation to RANKL expression. RANKL expression was induced preferentially in immature cells. These results support an important link between diverse osteoblast functions. Cells of the osteoblast lineage support two apparently distinct functions: bone formation and promotion of osteoclast formation. The aim of this study was to examine the relationship between these phenotypes in human osteoblasts (NHBC), in terms of the pre-osteoblast marker, STRO-1, and the mature osteoblast marker, alkaline phosphatase (AP), and the expression of genes involved in osteoclast formation, RANKL and OPG. The osteotropic stimuli, 1alpha,25(OH)2vitamin D3 (vitD3) and dexamethasone, were found to have profound proliferative and phenotypic effects on NHBCs. VitD3 inhibited NHBC proliferation and increased the percentage of cells expressing STRO-1 over an extended culture period, implying that vitD3 promotes and maintains an immature osteogenic phenotype. Concomitantly, RANKL mRNA expression was upregulated and maintained in NHBC in response to vitD3. Dexamethasone progressively promoted the proliferation of AP-expressing cells, resulting in the overall maturation of the cultures. Dexamethasone had little effect on RANKL mRNA expression and downregulated OPG mRNA expression in a donor-dependent manner. Regression analysis showed that RANKL mRNA expression was associated negatively with the percentage of cells expressing AP (p < 0.01) in vitD3- and dexamethasone-treated NHBCs. In contrast, RANKL mRNA expression was associated positively with the percentage of STRO-1+ cells (p < 0.01). In NHBCs sorted by FACS based on STRO-1 expression (STRO-1bright and STRO-1dim populations), it was found that vitD3 upregulated the expression of RANKL mRNA preferentially in STRO-1bright cells. The results suggest that immature osteoblasts respond to osteotropic factors in a potentially pro-osteoclastogenic manner. Additionally, the dual roles of osteoblasts, in supporting osteoclastogenesis or forming bone, may be performed by the same lineage of cells at different stages of their maturation.
Efficient regular expression evaluation (2008)

Several algorithms and techniques have been proposed recently to accelerate regular expression matching and enable deep packet inspection at line rate. This work aims to provide a comprehensive practical evaluation of existing techniques, extending them and analyzing their compatibility. The study focuses on two hardware architectures: memory-based ASICs and FPGAs.
Label-free in vivo optical imaging of microvasculature and oxygenation level (2008)

The ability to perform high-resolution imaging of microvasculature and its oxygenation is very important in studying early tumor development. Toward this goal, we improved upon our excited state absorption (ESA)-based imaging technique to allow us to not only image hemoglobin directly but also differentiate between oxy- and deoxyhemoglobin in tissue. We demonstrate the separation of arterioles from venules in a live nude mouse ear using our imaging technique.
Time and frequency domain characteristics of polarization-mode dispersion emulators (2001)

We investigate both experimentally and theoretically a new technique to realistically emulate polarization-mode dispersion (PMD). We propose and demonstrate a PMD emulator using rotatable connectors between sections of polarization-maintaining fibers that generates an ensemble of high PMD fiber realizations by randomly rotating the connectors. It is shown that: (1) the DGD of this emulator is Maxwellian-distributed over an ensemble of fiber realizations at any fixed optical frequency; and (2) the frequency autocorrelation function of the PMD emulator resembles that in a real fiber when averaged over an ensemble of fiber realizations. A realistic autocorrelation function is required for proper emulation of higher order PMD and indicates the feasibility of using this emulator for wavelength-division-multiplexing (WDM) systems.
Improved short-channel n-FET performance with virtual extensions (2005)

A method is presented to use electrostatic coupling from a metal of appropriate effective workfunction, separated from the extension region by a thin insulator, to create a "virtual extension" in doped source/drain (S/D) MOSFETs. This electrostatically induced charge layer allows for lower extension doping and increased underlap between the doped extension and the gate, "sharpening" the carrier profile and improving short-channel device performance. In a typical n-channel MOSFET, switching currents in clock-limiting circuit paths are predicted to be 24% higher.
Fgr Deficiency Results in Defective Eosinophil Recruitment to the Lung During Allergic Airway Inflammation (2002)

Using a mouse model of allergic lung inflammation, we found that mice deficient of Fgr, a Src family tyrosine kinase highly expressed in myelomonocytic cells, fail to develop lung eosinophilia in response to repeated challenge with aerosolized OVA. Both tissue and airway eosinophilia were markedly reduced in fgr(-/-) mice, whereas mice with the sole deficiency of Hck, another Src family member, responded normally. Release of allergic mediators, such as histamine, IL-4, RANTES/CCL5, and eotaxin/CCL11, in the airways of OVA-treated animals was equal in wild-type and fgr(-/-) mice. However, lung eosinophilia in Fgr-deficient mice correlated with a defective accumulation of GM-CSF and IL-5 in the airways, whereas secretion of these cytokines by spleen cells in response to OVA was normal. Examination of mRNA expression in whole lung tissue allowed us to detect comparable expression of transcripts for eotaxin/CCL11, macrophage-inflammatory protein-1 alpha/CCL3, macrophage-inflammatory protein-1 beta/CCL4, monocyte chemoattractant protein-1/CCL2, TCA-3/CCL1, IL-4, IL-10, IL-2, IL-3, IL-9, IL-15, and IFN-gamma in OVA-sensitized wild-type and fgr(-/-) mice. In contrast, the increase in IL-5 and IL-13 mRNA expression was lower in fgr(-/-) compared with wild-type mice. These findings suggest that deficiency of Fgr results in a marked reduction of lung eosinophilia and the establishment of a positive feedback loop based on autocrine secretion of eosinophil-active cytokines. These results identify Fgr as a novel pharmacological target to control allergic inflammation.
Temperature-sensitive Mutants of Respiratory Syncytial Virus (1969)

Four conditional-lethal temperature-sensitive mutants of RS virus were detected among the progeny of 454 plaques derived from virus grown in the presence of 10(-4)m 5-fluorouridine. These mutants were stable (reversion frequency, 10(-5.0) or less and failed to produce plaques at 38 or 39 C. Plaquing efficiency was depressed 100-fold or more at 37 C. Variable suppression of growth at the restrictive temperature of 39 C was observed, ranging from 16-fold to complete suppression. The temperature-sensitive defect of three of the mutants appeared to affect functions which were expressed late in the replicative cycle. One of the mutants produced atypical nonsyncytial plaques.