gebhart/patrepeval huggingface dataset:
<title>MEMS-based interferometric modulator for display applications</title> (1999)

Microelectromechanical Systems or Structures (MEMS) incorporate a set of attributes which make them uniquely suited for an expanding array of applications.The field of displays is one that has been a particular beneficiary of this class of devices. At least one display product has been introduced, and there are numerous products on the verge of being introduced or which are under development. Many segments of displays are experiencing rapid growth. Reflective displays in particular are growing in importance due to their inherent low-power consumption and ambient light performance. Unfortunately, the technical challenges for all these segments are such that traditional solutions, primarily LCD based, are limited in their ultimate performance. These are challenges for which MEMS are well suited, and there are several efforts underway to exploit this fact. One such effort, which is based on a device known as an Interferometric Modulator (IMod), is described here. A brief review of MEMS based display concepts is also included.
Development of Rituximab-Resistant Lymphoma Clones with Altered Cell Signaling and Cross-Resistance to Chemotherapy (2007)

Immunotherapy with rituximab (chimeric anti-CD20 monoclonal antibody, Rituxan), alone or in conjunction with chemotherapy, has significantly improved the treatment outcome of lymphoma patients. Via an elusive mechanism, a subpopulation of patients becomes unresponsive and/or relapses. To recapitulate various aspects of acquired resistance, rituximab-resistant (RR) clones were established from lymphoma lines and compared with parental cells. Surface CD20 expression was diminished in the clones. The clones neither responded to rituximab-mediated growth reduction or complement-dependent cytotoxicity nor underwent apoptosis in response to cross-linked rituximab. Rituximab failed to chemosensitize the RR clones, which exhibited constitutive hyperactivation of the nuclear factor-kappaB and extracellular signal-regulated kinase 1/2 pathways, leading to overexpression of B-cell lymphoma protein 2 (Bcl-2), Bcl-2-related gene (long alternatively spliced variant of Bcl-x gene), and myeloid cell differentiation 1 and higher drug resistance. Unlike parental cells, rituximab neither inhibited the activity of these pathways nor diminished the expression of resistant factors. Pharmacologic inhibitors of the survival pathways or Bcl-2 family members reduced the activity of these pathways, diminished antiapoptotic protein expression, and chemosensitized the RR clones. These novel in vitro results denote that continuous long-term rituximab exposure culminates in RR clones that do not respond to rituximab-mediated effects, have altered cellular signaling dynamics, and exhibit different genetic and phenotypic properties compared with parental cells. The data also reveal that although RR clones exhibit higher resistance to rituximab and cytotoxic drugs, these clones can be chemosensitized following treatment with pharmacologic inhibitors (e.g., dehydroxymethylepoxyquinomicin, bortezomib, PD098059) that target survival/antiapoptotic pathways. The findings also identify intracellular targets for potential molecular therapeutic intervention to increase treatment efficacy. The significance and potential clinical relevance of the findings are discussed.
Porin protein of Neisseria gonorrhoeae: cloning and gene structure. (1987)

The outer membrane porin molecule of Neisseria gonorrhoeae is known as protein I (PI). Among different strains of gonococci there is variability of PI, and two main classes, PIA and PIB, have been recognized. A lambda gt11 bank of gonococcal DNA was screened using monoclonal antibodies directed to a PIB-type porin molecule of N. gonorrhoeae, and three immunoreactive clones were isolated. DNA sequence analysis indicated that each contained only portions of the PI structural gene, but that together they contained the complete gene, and its structure was determined. The DNA sequence predicts a protein of 348 amino acids with a typical 19 amino acid signal peptide. The PI protein resembles Escherichia coli porins in size, lack of long hydrophobic sequences, and absence of cysteine residues. Sequence homologies between PI and the E. coli porins were found, particularly in the 100 N-terminal and the 110 C-terminal amino acids. In addition to the coding sequence of PI, the complementary strand contains a large open reading frame. At the 3' end of the PI gene, immediately following an inverted repeat (probably the transcription terminator), the clone contains an unusual sequence consisting of 31 perfect repeats of the heptamer CTGTTTT. Hybridization analysis suggests that there is a single structural gene for PI and that it is homologous to the gene found in a PIA-bearing strain of gonococcus.
Transcriptional Activation of Dehalorespiration (2006)

Desulfitobacterium dehalogenans can use chlorinated aromatics including polychlorinated biphenyls as electron acceptors in a process called dehalorespiration. Expression of the cpr gene cluster involved in this process is regulated by CprK, which is a member of the CRP/FNR (cAMP-binding protein/fumarate nitrate reduction regulatory protein) family of helix-turn-helix transcriptional regulators. High affinity interaction of the chlorinated aromatic compound with the effector domain of CprK triggers binding of CprK to an upstream target DNA sequence, which leads to transcriptional activation of the cpr gene cluster. When incubated with oxygen or diamide, CprK undergoes inactivation; subsequent treatment with dithiothreitol restores activity. Using mass spectrometry, this study identifies two classes of redox-active thiol groups that form disulfide bonds upon oxidation. Under oxidative conditions, Cys105, which is conserved in FNR and most other CprK homologs, forms an intramolecular disulfide bond with Cys111, whereas an intermolecular disulfide bond is formed between Cys11 and Cys200. SDS-PAGE and site-directed mutagenesis experiments indicate that the Cys11/Cys200 disulfide bond links two CprK subunits in an inactive dimer. Isothermal calorimetry and intrinsic fluorescence quenching studies show that oxidation does not change the affinity of CprK for the effector. Therefore, reversible redox inactivation is manifested at the level of DNA binding. Our studies reveal a strategy for limiting expression of a redox-sensitive pathway by using a thiol-based redox switch in the transcription factor.
The Membrane-Proximal Stem Region of Vesicular Stomatitis Virus G Protein Confers Efficient Virus Assembly (2000)

In this report, we show that the glycoprotein of vesicular stomatitis virus (VSV G) contains within its extracellular membrane-proximal stem (GS) a domain that is required for efficient VSV budding. To determine a minimal sequence in GS that provides for high-level virus assembly, we have generated a series of recombinant DeltaG-VSVs which express chimeric glycoproteins having truncated stem sequences. The recombinant viruses having chimeras with 12 or more membrane-proximal residues of the G stem, and including the G protein transmembrane-cytoplasmic tail domains, produced near-wild-type levels of particles. In contrast, viruses encoding chimeras with shorter or no G-stem sequences produced approximately 10- to 20-fold less. This budding domain when present in chimeric glycoproteins also promoted their incorporation into the VSV envelope. We suggest that the G-stem budding domain promotes virus release by inducing membrane curvature at sites where virus budding occurs or by recruiting condensed nucleocapsids to sites on the plasma membrane which are competent for efficient virus budding.
Degradation of Mutant Proteins, Underlying "Loss of Function" Phenotypes, Plays a Major Role in Genetic Disease (2001)

Many Mendelian monogenic disorders are caused by loss of the function of a single protein. This can result from rapid degradation of the mutant protein by cellular proteases, which reduces the steady-state concentration of the protein within the cell. The susceptibility of a protein to such proteolytic breakdown depends upon its kinetics of monomer folding and oligomer assembly and upon the intrinsic (thermodynamic) stability of its functional native-state conformation. Other cellular proteins, notably molecular chaperones, promote correct protein folding and assembly and thus provide some protection against degradation. An accumulation of recent evidence indicates that premature or accelerated degradation of mutant proteins, provoked by aberrations in their conformation, occurs in various subcellular compartments and represents a significant and prevalent pathogenic mechanism underlying genetic diseases. Inter-individual variability in proteolytic and folding systems can in part explain why "simple monogenic diseases" often display inconsistent genotype-phenotype correlations which show these disorders to be in reality quite complex. Protein folding and degradation may also be modulated artificially using exogenous small molecules. The identification or design of compounds which can interact specifically with particular target proteins, and which in so doing can exert beneficial effects on protein folding, assembly and/or stability, is beginning to open up a new and remarkably promising avenue for the treatment of diverse genetic disorders.
The deconvolution of pyrolysis mass spectra using genetic programming: application to the identification of some Eubacterium species (1998)

Pyrolysis mass spectrometry was used to produce complex biochemical fingerprints of Eubacterium exiguum, E. infirmum, E. tardum and E. timidum. To examine the relationship between these organisms the spectra were clustered by canonical variates analysis, and four clusters, one for each species, were observed. In an earlier study we trained artificial neural networks to identify these clinical isolates successfully; however, the information used by the neural network was not accessible from this so-called 'black box' technique. To allow the deconvolution of such complex spectra (in terms of which masses were important for discrimination) it was necessary to develop a system that itself produces 'rules' that are readily comprehensible. We here exploit the evolutionary computational technique of genetic programming; this rapidly and automatically produced simple mathematical functions that were also able to classify organisms to each of the four bacterial groups correctly and unambiguously. Since the rules used only a very limited set of masses, from a search space some 50 orders of magnitude greater than the dimensionality actually necessary, visual discrimination of the organisms on the basis of these spectral masses alone was also then possible.
Synergy of vaccine strategies to amplify antigen-specific immune responses and antitumor effects. (2001)

Several different vaccine strategies have been evaluated and combined in an attempt to amplify T-cell responses toward induction of antitumor immunity. The model tumor antigen used was carcinoembryonic antigen (CEA). While initial T-cell activation studies were conducted in conventional mice, combined vaccine strategy studies and antitumor studies were conducted in transgenic mice in which CEA is expressed in normal gastrointestinal tissue and CEA protein is found in sera. The studies reported here demonstrate: (a) A recombinant avipox (fowlpox, rF) vector expressing the signal 1 (CEA) and the B7-1 costimulatory molecule transgenes (designated rF-CEA/B7-1) is more potent in inducing CEA-specific T-cell responses than rF-CEA; one administration of recombinant fowlpox vector expressing CEA and three different costimulatory molecule transgenes (B7-1, ICAM-1, LFA-3, designated rF-CEA/TRICOM) was more potent in inducing CEA-specific T-cell responses than four vaccinations with rF-CEA or two vaccinations with rF-CEA/B7-1. Moreover, up to four vaccinations with rF-CEA/TRICOM induced greater CEA-specific T-cell responses with each vaccination. (b) A diversified prime and boost strategy using a prime with a recombinant vaccinia vector expressing CEA and the triad of costimulatory molecules (designated rV-CEA/TRICOM) and a boost with rF-CEA/TRICOM was more potent in inducing CEA-specific T-cell responses than the repeated use of rF-CEA/TRICOM alone. (c) The addition of granulocyte macrophage colony-stimulating factor (GM-CSF) to the rF-CEA or rF-CEA/TRICOM vaccinations via the simultaneous administration of a rF-GM-CSF vector enhanced CEA-specific T-cell responses. These strategies (TRICOM/diversified prime and boost/GM-CSF) were combined to treat CEA-expressing carcinoma liver metastases in CEA-transgenic mice; vaccination was initiated 14 days posttumor transplant. Antitumor effects in terms of survival and CD8(+) and CD4(+) responses specific for CEA were also observed in this CEA-transgenic mouse model. These studies demonstrate that the use of cytokines and diversified prime and boost regimens can be combined with the use of recombinant vectors expressing signal 1 and multiple costimulatory molecules to further amplify T-cell responses toward more effective vaccine strategies.
Differentiation of common benign pigmented skin lesions from melanoma by high-resolution ultrasound (2000)

There are potential clinical benefits if non-invasive methods can be used to diagnose or exclude melanoma.We investigated high-resolution ultrasound (HRU) as a potential non-invasive diagnostic aid for pigmented skin lesions.Using a 20-MHz ultrasound B-scan imaging system interfaced to a computer, we assessed acoustic shadowing and entry echo line enhancement (EEE) for 29 basal cell papillomas (BCPs) and 25 melanomas. Acoustic shadowing was estimated by the dermal echogenicity ratio (DER), comparing mean echogenicity below the lesion with that of adjacent dermis. Histological features were scored independently.DER < 3 correctly distinguished melanoma from BCP with 100% sensitivity and 79% specificity. Specificity increased to 93% if the presence of EEE was included as a discriminator. Shadowing correlated most significantly with histological extent of hyperkeratosis (P < 0.0001). Consequently, this method falsely identified non-keratotic acanthotic BCP (n = 3) as melanoma. Highly significant differences between benign naevi (n = 15) and melanomas (n = 24) were found. The SD of retrolesional echogenicity was higher for naevi than melanomas (P < 0.0001), but such an analysis was poorly specific for the diagnosis of melanoma (30%).Overall, HRU has considerable potential as a high-performance screening tool to assist in the discrimination between BCP, but not benign naevi, and melanoma. In particular, it may be possible to exclude melanoma with 100% certainty in the differentiation of BCP from melanoma.
Computer Simulation of the Responses of Human Motoneurons to Composite 1A EPSPS: Effects of Background Firing Rate (1997)

Two compartmental models of spinal alpha motoneurons were constructed to explore the relationship between background firing rate and response to an excitatory input. The results of these simulations were compared with previous results obtained from human motoneurons and discussed in relation to the current model for repetitively firing human motoneurons. The morphologies and cable parameters of the models were based on two type-identified cat motoneurons previously reported in the literature. Each model included five voltage-dependent channels that were modeled using Hodgkin-Huxley formalism. These included fast Na+ and K+ channels in the initial segment and fast Na+ and K+ channels as well as a slow K+ channel in the soma compartment. The density and rate factors for the slow K+ channel were varied until the models could reproduce single spike AHP parameters for type-identified motoneurons in the cat. Excitatory synaptic conductances were distributed along the equivalent dendrites with the same density described for la synapses from muscle spindles to type-identified cat motoneurons. Simultaneous activation of all synapses on the dendrite resulted in a large compound excitatory postsynaptic potential (EPSP). Brief depolarizing pulses injected into a compartment of the equivalent dendrite resulted in pulse potentials (PPs), which resembled the compound EPSPs. The effects of compound EPSPs and PPs on firing probability of the two motoneuron models were examined during rhythmic firing. Peristimulus time histograms, constructed between the stimulus and the spikes of the model motoneuron, showed excitatory peaks whose integrated time course approximated the time course of the underlying EPSP or PP as has been shown in cat motoneurons. The excitatory peaks were quantified in terms of response probability, and the relationship between background firing rate and response probability was explored. As in real human motoneurons, the models exhibited an inverse relationship between response probability and background firing rate. The biophysical properties responsible for the relationship between response probability and firing rate included the shapes of the membrane voltage trajectories between spikes and nonlinear changes in PP amplitude during the interspike interval at different firing rates. The results from these simulations suggest that the relationship between response probability and background firing rate is an intrinsic feature of motoneurons. The similarity of the results from the models, which were based on the properties of cat motoneurons, and those from human motoneurons suggests that the biophysical properties governing rhythmic firing in human motoneurons are similar to those of the cat.
α1-Antitrypsin inhibits the lethal response to TNF in mice (1996)

alpha1-Antitrypsin, an acute-phase reactant in many species, protects significantly against the lethality induced by TNF or endotoxin in mice. The protection is optimal with a single dose of at least 300 microg i.p. or 100 microg i.v. given 2 h before a lethal challenge, either with a low dose of TNF in the presence of galactosamine or a higher dose of murine TNF alone. Under optimal conditions, the drop in body temperature, the release of liver transaminases, and the increase in clotting time are also inhibited. alpha1-Antitrypsin does not protect against a lethal dose of platelet-activating factor. It is suggested that the protection is due to reduced release of platelet-activating factor.
Targeting alpha-synuclein with a microRNA-embedded silencing vector in the rat substantia nigra: Positive and negative effects (2014)

hSNCA gene silencing with AAV-mir30-hSNCA has positive effects on forelimb behavior and SN DA neurons, which are compromised by inflammation and reduced TH expression, suggesting that AAV2/8-mir30-hSNCA-mediated gene silencing, although promising in vitro, is not a candidate for therapeutic translation for PD.
Cloning and expression of the transhydrogenase gene of Escherichia coli (1985)

Based on the rationale that Escherichia coli cells harboring plasmids containing the pnt gene would contain elevated levels of enzyme, we have isolated three clones bearing the transhydrogenase gene from the Clarke and Carbon colony bank. The three plasmids were subjected to restriction endonuclease analysis. A 10.4-kilobase restriction fragment which overlapped all three plasmids was cloned into the PstI site of plasmid pUC13. Examination of several deletion derivatives of the resulting plasmid and subsequent treatment with exonuclease BAL 31 revealed that enhanced transhydrogenase expression was localized within a 3.05-kilobase segment. This segment was located at 35.4 min in the E. coli genome. Plasmid pDC21 conferred on its host 70-fold overproduction of transhydrogenase. The protein products of plasmids carrying the pnt gene were examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of membranes from cells containing the plasmids. Two polypeptides of molecular weights 50,000 and 47,000 were coded by the 3.05-kilobase fragment of pDC11. Both polypeptides were required for expression of transhydrogenase activity.
Intrinsic Size Parameters for Val, Ile, Leu, Gln, Thr, Phe, and Trp Residues from Ion Mobility Measurements of Polyamino Acid Ions (1999)

The conformations of singly charged ions of eight polyamino acids of varying length [polyalanine (3−23 residues), polyglutamine (2−8 residues), polyisoleucine (2−6 residues), polyleucine (2−9 residues), polyphenylalanine (2−7 residues), polythreonine (8−14 residues), polytryptophan (2−9 residues), and polyvaline (2−7 residues)] have been studied by ion mobility methods and molecular modeling simulations. The average amino acid contributions to cross section for 4−9 residue homopolymers agree with intrinsic size parameters for these residues derived from data for tryptic digest peptides [J. Phys. Chem. B 1999, 103, 1203]. Some variations in residue sizes with changes in oligomer length are apparent for small oligomers and those with polar and aromatic ring side chains. Molecular modeling simulations reveal that all of these homopolymers have roughly spherical (globular) structures. Conformations appear to be influenced by three primary types of interactions: (1) self-solvation of the charge site by backbone carbonyls, a characteristic of all oligomer types; (2) steric hindrance of side chains (leading to efficient ring stacking), a prominent factor for the polyphenylalanine and polytryptophan systems; and (3) hydrogen bonding involving side chains, backbone carbonyls, and the charged residue, apparent in the polyglutamine and polythreonine systems.
The Ultimate Strength of Glass Silica Nanowires (2009)

In the past decade nanowires have attracted an increase interest because of their extraordinary mechanical strength. In fact, material properties in the nanoregime are extremely different from those found in macroscopic samples: few crystalline materials have shown a tensile strength in excess of 10 GPa in the form of nanowires. Still the length of defect-free crystalline nanowires is limited to a few millimeters and the strength of long nanowires is compromised by defects. The strength of glass nanowires is less affected by single defects. In this paper we present the ultimate strength of glass silica nanowires manufactured by a top-down fabrication technique; this is the highest value reported for glass materials. The measured ultimate strength is in excess of 10 GPa and increases for decreasing nanowire diameters. Scanning electron micrographs of the broken fragments showed a fragile rupture.
Cyclooxygenase-1 and -2 expression in rheumatoid synovial tissues. Effects of interleukin-1 beta, phorbol ester, and corticosteroids. (1994)

High levels of immunoreactive cyclooxygenase (Cox; prostaglandin H synthase) are present in synovia from patients with rheumatoid arthritis (RA). We now show that the recently identified inducible isoform of Cox, Cox-2, is expressed in synovia from patients with RA. To further explore modulation of the Cox isoforms in RA synovial tissues, we examined the expression and modulation of Cox-1 and -2 in rheumatoid synovial explant cultures and cultured rheumatoid synovial fibroblast-like cells (synoviocytes). Immunoprecipitation of in vitro labeled proteins and Western blot analysis demonstrated the presence of both Cox-1 and -2 under basal conditions in freshly explanted rheumatoid synovial tissues. De novo synthesis of Cox-2 polypeptide was enhanced by IL-1 beta or PMA, and dramatically suppressed by dexamethasone (dex). Cox-1 expression, under the same conditions, showed only minor variation. Since mRNA for Cox-2 is highly unstable, we examined the regulation of Cox-2 transcripts in cultured rheumatoid synoviocytes. Under basal conditions both Cox-1 and -2 mRNAs were present at low levels, but Cox-2 mRNA was markedly increased by treatment with IL-1 beta or PMA. dex markedly suppressed the induction of Cox-2 mRNA. In sharp contrast, Cox-1 transcripts were not modulated by IL-1 beta or dex. These data suggest that modulation of Cox-2 expression by IL-1 beta and corticosteroids may be an important component of the inflammatory process in synovial tissues from patients with RA.