gebhart/patrepeval huggingface dataset:
Probing the TRAP–RNA interaction with nucleoside analogs (1999)

The trp RNA-binding Attenuation Protein (TRAP) from Bacillus subtilis binds a series of GAG and UAG repeats separated by 2-3 nonconserved spacer nucleotides in trp leader mRNA. To identify chemical groups on the RNA required for stability of the TRAP-RNA complex, we introduced several different nucleoside analogs into each pentamer of the RNA sequence 5'-(UAGCC)-3' repeated 11 times and measured their effect on the TRAP-RNA interaction. Deoxyribonucleoside substitutions revealed that a 2'-hydroxyl group (2'-OH) is required only on the guanosine occupying the third residue of the RNA triplets for high-affinity binding to TRAP. The remaining hydroxyl groups are dispensable. Base analog substitutions identified all of the exocyclic functional groups and N1 nitrogens of adenine and guanine in the second and third nucleotides, respectively, of the triplets as being involved in binding TRAP. In contrast, none of the substitutions made in the first residue caused any detectable changes in affinity, indicating that elements of these bases are not necessary for complex formation and stability. Studies using abasic nucleotides in the first residue of the triplets and in the two spacer residues confirmed that the majority of the specificity and stability of the TRAP-RNA complex is provided by the AG dinucleotide of the triplet repeats. In addition to direct effects on binding, we demonstrate that the N7-nitrogen of adenosine and guanosine in UAG triplet and the 2'-OHs of (UAGCC)11 RNA are involved in the formation of an as yet undetermined structure that interferes with TRAP binding.
Nanoscale ultra-thin-body silicon-on-insulator P-MOSFET with a SiGe/Si heterostructure channel (2000)

We report the concept and demonstration of a nanoscale ultra-thin-body silicon on-insulator (SOI) P-channel MOSFET with a Si/sub 1-x/Ge/sub x//Si heterostructure channel. First, a novel lateral solid-phase epitaxy process is employed to form an ultra-thin-body that suppresses the short-channel effects. Negligible threshold voltage roll-off is observed down to a channel length of 50 nm. Second, a selective silicon implant that breaks up the interfacial oxide is shown to facilitate unilateral crystallization to form a single crystalline channel. Third, the incorporation of SiGe in the channel resulted in a 70% enhancement in the drive current.
Amyloid-β peptide induces oligodendrocyte death by activating the neutral sphingomyelinase–ceramide pathway (2004)

Amyloid-beta peptide (Abeta) accumulation in senile plaques, a pathological hallmark of Alzheimer's disease (AD), has been implicated in neuronal degeneration. We have recently demonstrated that Abeta induced oligodendrocyte (OLG) apoptosis, suggesting a role in white matter pathology in AD. Here, we explore the molecular mechanisms involved in Abeta-induced OLG death, examining the potential role of ceramide, a known apoptogenic mediator. Both Abeta and ceramide induced OLG death. In addition, Abeta activated neutral sphingomyelinase (nSMase), but not acidic sphingomyelinase, resulting in increased ceramide generation. Blocking ceramide degradation with N-oleoyl-ethanolamine exacerbated Abeta cytotoxicity; and addition of bacterial sphingomyelinase (mimicking cellular nSMase activity) induced OLG death. Furthermore, nSMase inhibition by 3-O-methyl-sphingomyelin or by gene knockdown using antisense oligonucleotides attenuated Abeta-induced OLG death. Glutathione (GSH) precursors inhibited Abeta activation of nSMase and prevented OLG death, whereas GSH depletors increased nSMase activity and Abeta-induced death. These results suggest that Abeta induces OLG death by activating the nSMase-ceramide cascade via an oxidative mechanism.
OSM-9, A Novel Protein with Structural Similarity to Channels, Is Required for Olfaction, Mechanosensation, and Olfactory Adaptation inCaenorhabditis elegans (1997)

Although cyclic nucleotide-gated channels mediate sensory transduction in olfaction and vision, other forms of sensory transduction are independent of these channels. Caenorhabditis elegans cyclic nucleotide-gated channel mutants respond normally to some olfactory stimuli and to osmotic stimuli, suggesting that these chemosensory responses use an alternative sensory transduction pathway. One gene that may act in this pathway is osm-9, which is required for each of these responses as well as a mechanosensory response to nose touch. osm-9 encodes a protein with ankyrin repeats and multiple predicted transmembrane domains that has limited similarity to the Drosophila phototransduction channels transient receptor potential (TRP) and TRP-like (TRPL). The sequence of OSM-9 and other TRP-like genes reveals a previously unsuspected diversity of mammalian and invertebrate genes in this family. osm-9 is required for the activity of the predicted G-protein-coupled odorant receptor ODR-10, which acts in the AWA olfactory neurons; its similarity to other G-protein-regulated transduction channels suggests that OSM-9 is involved in AWA signaling. osm-9:: GFP fusion genes are expressed in a subset of chemosensory, mechanosensory, and osmosensory neurons. osm-9 also affects olfactory adaptation within neurons that require the cyclic nucleotide-gated channel for olfaction; in these neurons, the gene has a regulatory function and not a primary role in sensory transduction.
Cross-desensitization of receptors for peptide chemoattractants. Characterization of a new form of leukocyte regulation. (1994)

Abstract The formylpeptide (fMLP) and C5a chemoattractants were previously shown to cross-desensitize each other's ability to mobilize Ca2+ in leukocytes but not to affect nonchemoattractant Ca(2+)-mobilizing receptors, and vice versa. Our data show that all receptors studied underwent homologous desensitization. Interestingly, peptide chemoattractants (fMLP, C5a, and IL-8) desensitized each other's Ca(2+)-mobilizing responses, but had no effect on a Ca(2+)-mobilizing purinergic receptor. Lipid chemoattractant receptors (PAF and leukotriene B4) were also desensitized by peptide chemoattractants but not vice versa. In the presence of cytochalasin B, only fMLP and C5a caused the activation of phospholipase D in intact leukocytes and enhanced desensitization of IL-8 and C5a but not fMLP receptors. To measure receptor/G protein interactions, agonist-stimulated GTP gamma S binding to leukocyte membranes was measured. Whereas all peptide receptors underwent homologous desensitization, C5a and IL-8, but not fMLP, receptors were cross-desensitized by other peptide chemoattractants. Furthermore, PMA caused inhibition of C5a- and IL-8- but not fMLP-stimulated GTP gamma S binding. These data suggest that in addition to homologous desensitization, peptide chemoattractant receptors cross-desensitize one another by at least two processes. One can be detected at the level of receptor/G-protein interaction and possibly involves receptor phosphorylation by protein kinase C. The fMLP receptor is resistant to this process. The second process is distal to receptor/G-protein interaction and utilizes an undefined pathway to cross-desensitize the Ca2+ mobilization response to all peptide chemoattractants. We propose that receptor cross-desensitization in leukocytes is orchestrated at several levels by mechanisms with selectivity for types of chemoattractant receptors.
Host Stromal Bradykinin B2 Receptor Signaling Facilitates Tumor-Associated Angiogenesis and Tumor Growth (2004)

We evaluated the significance of the host kallikrein-kinin system in tumor angiogenesis and tumor growth using two rodent models genetically deficient in a kallikrein-kinin system. Inoculation of Walker 256 carcinoma cells into the s.c. tissues of the back of normal Brown Norway Kitasato rats (BN-Ki rats) resulted in the rapid development of solid tumors with marked angiogenesis. By contrast, in kininogen-deficient Brown Norway Katholiek rats (BN-Ka rats), which cannot generate intrinsic bradykinin (BK), the weights of the tumors and the extent of angiogenesis were significantly less than those in BN-Ki rats. Daily administration of B(2) receptor antagonists significantly reduced angiogenesis and tumor weights in BN-Ki rats to levels similar to those in BN-Ka rats but did not do so in BN-Ka rats. Angiogenesis and tumor growth were significantly suppressed in B(2) receptor knockout mice bearing sarcoma 180 compared with their wild-type counterparts. Immunoreactive vascular endothelial growth factor (VEGF) was localized in Walker tumor stroma more extensively in BN-Ki rats than in BN-Ka rats, although immunoreactive B(2) receptor also was detected in the stroma to the same extent in both types of rats. Cultured stromal fibroblasts isolated from BN-Ki rats and BN-Ka rats produced VEGF in response to BK (10(-8)-10(-6) m), and this stimulatory effect of BK was abolished with a B(2) receptor antagonist, Hoe140 (10(-5) m). These results suggest that BK generated from kininogens supplied from the host may facilitate tumor-associated angiogenesis and tumor growth by stimulating stromal B(2) signaling to up-regulate VEGF production mainly in fibroblasts.
A framework for classifying denial of service attacks (2003)

Launching a denial of service (DoS) attack is trivial, but detection and response is a painfully slow and often a manual process. Automatic classification of attacks as single- or multi-source can help focus a response, but current packet-header-based approaches are susceptible to spoofing. This paper introduces a framework for classifying DoS attacks based on header content, and novel techniques such as transient ramp-up behavior and spectral analysis. Although headers are easily forged, we show that characteristics of attack ramp-up and attack spectrum are more difficult to spoof. To evaluate our framework we monitored access links of a regional ISP detecting 80 live attacks. Header analysis identified the number of attackers in 67 attacks, while the remaining 13 attacks were classified based on ramp-up and spectral analysis. We validate our results through monitoring at a second site, controlled experiments, and simulation. We use experiments and simulation to understand the underlying reasons for the characteristics observed. In addition to helping understand attack dynamics, classification mechanisms such as ours are important for the development of realistic models of DoS traffic, can be packaged as an automated tool to aid in rapid response to attacks, and can also be used to estimate the level of DoS activity on the Internet.
The Anti-Inflammatory Effects of Prostaglandins (2009)

Long regarded as proinflammatory molecules, prostaglandins (PGs) also have anti-inflammatory effects. Both prostaglandin D2 (PGD2) and its dehydration end product 15-deoxy-Delta-prostaglandin J2 (15d-PGJ2) seem to play important roles in regulating inflammation, via both receptor-dependent (DP1 and DP2 receptors) and receptor-independent mechanisms. Intracellular effects of PGD2 and 15d-PGJ2 that may suppress inflammation include inhibition of nuclear factor-kappaB (NF-kappaB) by multiple mechanisms (IkappaB kinase inhibition and blockade of NF-kappaB nuclear binding) and activation of peroxisome proliferator-activated receptor-gamma (PPAR-gamma). Prostaglandin F2alpha (PGF2alpha) may also have important anti-inflammatory effects, although current data are limited. In animal models, expression of both PGD and PGF synthases declines during acute inflammation, only to rise again during the resolution phase, suggesting their possible role in resolving inflammation. Prostaglandin E2 (PGE2), the classic model of a proinflammatory lipid mediator, also has anti-inflammatory effects that are both potent and context dependent. Thus, accumulating data suggest that PGs not only participate in initiation, but may also actively contribute to the resolution of inflammation. Indeed, classic inhibitors of PG synthesis such as nonselective and cyclooxygenase-2 (COX-2) selective inhibitors (nonsteroidal anti-inflammatory drugs) may actually prolong inflammation when administered during the resolution phase. These effects may regulate not only tissue inflammation but also vascular disease, possibly shedding light on the controversy surrounding nonsteroidal anti-inflammatory drug use and its relation to myocardial infarction. In this review, we summarize the current understanding of PGs as dichotomous molecules in the inflammatory process.
Accumulation of chlamydial lipopolysaccharide antigen in the plasma membranes of infected cells (1989)

The presence of a chlamydia-specified antigen associated with the plasma membrane of infected cell lines was demonstrated by indirect immunofluorescence staining with a monoclonal antibody, designated 47A2, specific for the chlamydial genus-specific lipopolysaccharide (LPS) antigen. Staining of HeLa, L-929, and McCoy cells infected with the L2 or F serovar of Chlamydia trachomatis was observed either without fixation or following aldehyde fixation and brief drying. The 47A2-reactive antigen appeared to be present on the plasma membrane, on bleb-like structures on the host cell surface, and on proximal processes of neighboring uninfected cells. Antibodies to chlamydial protein antigens such as the major outer membrane protein produced no surface staining under similar conditions. Membrane vesicles elaborated from infected cells were enriched for the 47A2-reactive antigen. Superinfection of chlamydia-infected cells with vesicular stomatitis virus, an enveloped virus which buds from the plasma membrane, allowed purification of progeny virions that were enriched with chlamydial LPS. These results are consistent with the presence of chlamydial LPS in the plasma membranes of infected host cells.
Differential Changes in Heat Shock Protein-, Lipoarabinomannan-, and Purified Protein Derivative-Specific Immunoglobulin G1 and G2 Isotype Responses during BovineMycobacterium aviumsubsp.paratuberculosisInfection (2001)

Bovine paratuberculosis is caused by infection of young calves with Mycobacterium avium subsp. paratuberculosis. In some of the chronically infected cows the long asymptomatic stage (2 to 4 years) is followed by a rapid progression to a clinical stage due to protein-losing enteropathy, which will ultimately be fatal. The current dogma is that in early stages of disease the cell-mediated responses predominate, whereas in the clinical stage of the disease the humoral responses prevail, possibly signaling a switch in immune reactivity related to disease progression. We developed immunoglobulin M (IgM)-, IgA-, and IgG1- and IgG2-isotype-specific enzyme-linked immunosorbent assays for M. avium subsp. paratuberculosis-derived antigens (heat shock proteins of 70 kDa [Hsp70] and 65 kDa [Hsp65], lipoarabinomannan [LAM], and M. avium subsp. paratuberculosis purified protein derivative PPD [PPDP]). The serological responses of cows in different stages of paratuberculosis were used to evaluate the putative shift in immune responsiveness. In the clinical stage the PPDP-specific IgG1 responses were increased compared to those in the asymptomatic stage. However, total IgG1 and IgG2 and the Hsp70-, Hsp65-, and LAM-specific isotype responses were decreased in the clinical stage were decreased compared to those in the asymptomatic stage of disease. Thus, the classical pattern was found only for PPDP antigens and the IgG1 isotype. For other antigens and isotypes and the total IgG levels, the response pattern is different and indicates that there is no uniform association with increased antibody responses during the progression from the asymptomatic stage to the clinical stage of bovine paratuberculosis.
Infection and inflammation as risk factors for myocardial infarction. (1993)

Recent studies have illustrated that in addition to the well known risk factors, such as lipoproteins, smoking, hypertension, there are others that cause atherosclerosis and myocardial infarction. Our knowledge of atherosclerotic lesions has increased. We now know that atherosclerotic changes are due to inflammatory cell infiltration as well as to increases in migration of vascular smooth muscle cells. Endothelial cells play a major role in the pathology of vascular changes. In recent years a new risk factor for coronary artery disease has been discovered: chlamydia pneumonial infections. Herpes class viruses have also been associated with pathology of atherosclerotic lesions. Studies show that dental status and bacterial infections are also related to the risk of myocardial infarction. This review discusses the possible mechanisms of infection and inflammation and whether they are major or modifying risk factors for atherosclerosis and myocardial infarction.
Bacterial Biosensors for Measuring Availability of Environmental Pollutants (2008)

Traditionally, pollution risk assessment is based on the measurement of a pollutant's total concentration in a sample. The toxicity of a given pollutant in the environment, however, is tightly linked to its bioavailability, which may differ significantly from the total amount. Physico-chemical and biological parameters strongly influence pollutant fate in terms of leaching, sequestration and biodegradation. Bacterial sensorreporters, which consist of living micro-organisms genetically engineered to produce specific output in response to target chemicals, offer an interesting alternative to monitoring approaches. Bacterial sensor-reporters detect bioavailable and/or bioaccessible compound fractions in samples. Currently, a variety of environmental pollutants can be targeted by specific biosensor-reporters. Although most of such strains are still confined to the lab, several recent reports have demonstrated utility of bacterial sensing-reporting in the field, with method detection limits in the nanomolar range. This review illustrates the general design principles for bacterial sensor-reporters, presents an overview of the existing biosensor-reporter strains with emphasis on organic compound detection. A specific focus throughout is on the concepts of bioavailability and bioaccessibility, and how bacteria-based sensing-reporting systems can help to improve our basic understanding of the different processes at work.
Like bees around the hive (2009)

We present findings from field trials of MapLens, a mobile augmented reality (AR) map using a magic lens over a paper map. Twenty-six participants used MapLens to play a location-based game in a city centre. Comparisons to a group of 11 users with a standard 2D mobile map uncover phenomena that arise uniquely when interacting with AR features in the wild. The main finding is that AR features facilitate place-making by creating a constant need for referencing to the physical, and in that it allows for ease of bodily configurations for the group, encourages establishment of common ground, and thereby invites discussion, negotiation and public problem-solving. The main potential of AR maps lies in their use as a collaborative tool.
A microsensor for nitrate based on immobilized denitrifying bacteria (1996)

A biosensor for NO(inf3)(sup-) was constructed by attaching a 30- to 70-(mu)m-wide capillary with immobilized denitrifying bacteria in front of an N(inf2)O microsensor. These bacteria reduced O(inf2) so that only bacteria in the very tip of the sensor were exposed to O(inf2) whereas bacteria at a greater depth could carry out the anaerobic process of denitrification. In the presence of acetylene, which inhibits nitrous oxide reductase, bacteria reduced NO(inf3)(sup-) (or NO(inf2)(sup-)) from the surrounding medium to N(inf2)O and the concentration sensed by the N(inf2)O microsensor was directly proportional to the concentration of NO(inf3)(sup-) in the medium. By applying a 250-(mu)m-long capillary in front of the N(inf2)O microsensor, the 90% response time of the biosensor was 50 s. Biosensors may also be made with nitrous oxide-deficient strains so that acetylene inhibition can be omitted.
Cell cycle and apoptosis (2003)

Apoptosis and proliferation are intimately coupled. Some cell cycle regulators can influence both cell division and programmed cell death. The linkage of cell cycle and apoptosis has been recognized for c-Myc, p53, pRb, Ras, PKA, PKC, Bcl-2, NF-kappa B, CDK, cyclins and CKI. This review summarizes the different functions of the proteins presently known to control both apoptosis and cell cycle progression. These proteins can influence apoptosis or proliferation but different variables, including cell type, cellular environment and genetic background, make it difficult to predict the outcome of cell proliferation, cell cycle arrest or cell death. These important decisions of cell proliferation or cell death are likely to be controlled by more than one signal and are necessary to ensure a proper cellular response.
The use of bioreactive probes in protein characterization (1997)

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) has in the past decade found routine use in the biological sciences. With this use has evolved several mass spectrometric-based methods directed at the intricate investigation of biomolecular structure and function. One such methodology involves the enzymatic modification of a protein prior to the mass spectrometric readout of the resulting products. The enzyme-modification/mass spectrometric approach has a definite use in a number of applications, including: the verification/identification of protein sequence, elucidation of post-translational modifications, the investigation of protein higher-order structure, and even the characterization of the modifying enzyme. To avoid the potentials of sample loss and autolytic interferences in the mass spectrum, mass spectrometer targets can be covalently derivatized with enzymes for use in the characterization procedures. The enzymatically active, or bioreactive, probes are used by application of the analyte to the activated surface, followed by application of a suitable MALDI matrix and mass analysis from the surface of the probe. Limited transfer and handling steps eliminate sample losses, and surface-tethered enzymes (and autolytic fragments) are prohibited from interfering with analytical signals in the mass spectra. In addition, the probes are rapid and easy to use. Reviewed here are issues of concern during the manufacture and use of the bioreactive probes, and application of the probes to investigate protein structure and function.
Packet forwarding (1988)

A packet network is viewed as consisting of two major interacting layers: a lower layer responsible for the determination of a set of paths that can be used to carry packet flows, and an upper layer responsible for actually sending the flows over these paths, on a per-packet basis. A systematic review is provided of the various techniques that can be used to perform the actual packet-by-packet routing operation at the upper layer, called the packet forwarding function. The function components of a routing system and its characteristics (responsiveness to changes in network state and degree of centralization) are discussed. Five routing techniques are then examined, namely source, directory, destination, global-path, and channel-link-path routing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The effect of TMS on visual motion sensitivity: an increase in neural noise or a decrease in signal strength? (2011)

The underlying mechanisms of action of transcranial magnetic stimulation (TMS) are still a matter of debate. TMS may impair a subject's performance by increasing neural noise, suppressing the neural signal, or both. Here, we delivered a single pulse of TMS (spTMS) to V5/MT during a motion direction discrimination task while concurrently manipulating the level of noise in the motion stimulus. Our results indicate that spTMS essentially acts by suppressing the strength of the relevant visual signal. We suggest that TMS may induce a pattern of neural activity that complements the ongoing activation elicited by the sensory signal in a manner that partially impoverishes that signal.