gebhart/patrepeval huggingface dataset:
Diazotrophic Growth Allows Azotobacter vinelandii To Overcome the Deleterious Effects of a glnE Deletion (2017)

Overcoming the inhibitory effects of excess environmental ammonium on nitrogenase synthesis or activity and preventing ammonium assimilation have been considered strategies to increase the amount of fixed nitrogen transferred from bacterial to plant partners in associative or symbiotic plant-diazotroph relationships. The GlnE adenylyltransferase/adenylyl-removing enzyme catalyzes reversible adenylylation of glutamine synthetase (GS), thereby affecting the posttranslational regulation of ammonium assimilation that is critical for the appropriate coordination of carbon and nitrogen assimilation. Since GS is key to the sole ammonium assimilation pathway of <i>Azotobacter vinelandii</i>, attempts to obtain deletion mutants in the gene encoding GS (<i>glnA</i>) have been unsuccessful. We have generated a <i>glnE</i> deletion strain, thus preventing posttranslational regulation of GS. The resultant strain containing constitutively active GS is unable to grow well on ammonium-containing medium, as previously observed in other organisms, and can be cultured only at low ammonium concentrations. This phenotype is caused by the lack of downregulation of GS activity, resulting in high intracellular glutamine levels and severe perturbation of the ratio of glutamine to 2-oxoglutarate under excess-nitrogen conditions. Interestingly, the mutant can grow diazotrophically at rates comparable to those of the wild type. This observation suggests that the control of nitrogen fixation-specific gene expression at the transcriptional level in response to 2-oxoglutarate via NifA is sufficiently tight to alone regulate ammonium production at levels appropriate for optimal carbon and nitrogen balance.<b>IMPORTANCE</b> In this study, the characterization of the <i>glnE</i> knockout mutant of the model diazotroph <i>Azotobacter vinelandii</i> provides significant insights into the integration of the regulatory mechanisms of ammonium production and ammonium assimilation during nitrogen fixation. The work reveals the profound fidelity of nitrogen fixation regulation in providing ammonium sufficient for maximal growth but constraining energetically costly excess production. A detailed fundamental understanding of the interplay between the regulation of ammonium production and assimilation is of paramount importance in exploiting existing and potentially engineering new plant-diazotroph relationships for improved agriculture.
Chromogenic Cross-Linker for the Characterization of Protein Structure by Infrared Multiphoton Dissociation Mass Spectrometry (2008)

We have developed a new IR chromogenic cross-linker (IRCX) to aid in rapidly distinguishing cross-linked peptides from unmodified species in complex mixtures. By incorporating a phosphate functional group into the cross-linker, one can take advantage of its unique IR absorption properties, affording selective infrared multiphoton dissociation (IRMPD) of the cross-linked peptides. In a mock mixture of unmodified peptides and IRCX-cross-linked peptides (intramolecularly and intermolecularly cross-linked), only the peptides containing the IRCX modification were shown to dissociate upon exposure to 50 ms of 10.6-microm radiation. LC-IRMPD-MS proved to be an effective method to distinguish the cross-linked peptides in a tryptic digest of IRCX-cross-linked ubiquitin. A total of four intermolecular cross-links and two dead-end modifications were identified using IRCX and LC-IRMPD-MS. IRMPD of these cross-linked peptides resulted in secondary dissociation of all primary fragment ions containing the chromophore, producing a series of unmodified b- or y-type ions that allowed the cross-linked peptides to be sequenced without the need for collision-induced dissociation.
Analysis of genes under the downstream control of the t(8;21) fusion protein AML1-MTG8: overexpression of the TIS11b(ERF-1, cMG1) gene induces myeloid cell proliferation in response to G-CSF (2000)

The AML1-MTG8 fusion transcription factor generated by t(8;21) translocation is thought to dysregulate genes that are crucial for normal differentiation and proliferation of hematopoietic progenitors to cause acute myelogenous leukemia (AML). Although AML1-MTG8 has been shown to repress the transcription of AML1 targets, none of the known targets of AML1 are probably responsible for AML1-MTG8-mediated leukemogenesis. In this study, 24 genes under the downstream control of AML1-MTG8 were isolated by using a differential display technique. Analysis with deletion mutants of AML1-MTG8 demonstrated that the regulation of the majority of these genes requires the region of 51 residues (488-538) containing the Nervy homology region 2 (NHR2), through which AML1-MTG8 interacts with MTGR1. Among the 24 genes identified, 10 were considered to be genes under the control of AML1, because their expression was altered by AML1b or AML1a or both. However, the other 14 genes were not affected by either AML1b or AML1a, suggesting the possibility that AML1-MTG8 regulates a number of specific target genes that are not normally regulated by AML1. Furthermore, an up-regulated gene, TIS11b (ERF-1,cMG1), was highly expressed in t(8;21) leukemic cells, and the overexpression of TIS11b induced myeloid cell proliferation in response to granulocyte colony-stimulating factor. These results suggest that the high-level expression of TIS11b contributes to AML1-MTG8-mediated leukemogenesis.
Left Ventricular Electromechanical Mapping to Assess Efficacy of phVEGF 165 Gene Transfer for Therapeutic Angiogenesis in Chronic Myocardial Ischemia (2000)

The results of EMM constitute objective evidence that phVEGF(165) GTx augments perfusion of ischemic myocardium. These findings, together with reduction in the size of the defects documented at rest by serial single-photon emission CT-sestamibi imaging, suggest that phVEGF(165) GTx may successfully rescue foci of hibernating myocardium.
Carnitine--metabolism and functions (1983)

Carnitine was detected at the beginning of this century, but it was nearly forgotten among biochemists until its importance in fatty acid metabolism was established 50 years later. In the last 30 years, interest in the metabolism and functions of carnitine has steadily increased. Carnitine is synthesized in most eucaryotic organisms, although a few insects (and most likely some newborn animals) require it as a nutritional factor (vitamin BT). Carnitine biosynthesis is initiated by methylation of lysine. The trimethyllysine formed is subsequently converted to butyrobetaine in all tissues; the butyrobetaine is finally hydroxylated to carnitine in the liver and, in some animals, in the kidneys (see Fig. 1). It is released from these tissues and is then actively taken up by all other tissues. The turnover of carnitine in the body is slow, and the regulation of its synthesis is still incompletely understood. Microorganisms (e.g., in the intestine) can metabolize carnitine to trimethylamine, dehydrocarnitine (beta-keto-gamma-trimethylaminobutyric acid), betaine, and possibly to trimethylaminoacetone. In some insects carnitine can be converted to methylcholine, presumably with trimethylaminoacetone as an intermediate (see Fig. 3). In mammals the unphysiological isomer (+) carnitine is converted to trimethylaminoacetone. The natural isomer (-)carnitine is excreted unchanged in the urine, and it is still uncertain if it is degraded in mammalian tissues at all (Fig. 2). The only firmly established function of carnitine is its function as a carrier of activated fatty acids and activated acetate across the inner mitochondrial membrane. Two acyl-CoA:carnitine acyltransferases with overlapping chain-length specificities have been isolated: one acetyltransferase taking part in the transport of acetyl and short-chain acyl groups and one palmitoyltransferase taking part in the transport of long-chain acyl groups. An additional octanoyltransferase has been isolated from liver peroxisomes. Although a carnitine translocase that allows carnitine and acylcarnitine to penetrate the inner mitochondrial membrane has been deduced from functional studies (see Fig. 5), this translocase has not been isolated as a protein separate from the acyltransferases. Carnitine acetyltransferase and carnitine octanoyltransferase are also found in the peroxisomes. In these organelles the enzymes may be important in the transfer of acyl groups, which are produced by the peroxisomal beta-oxidation enzymes, to the mitochondria for oxidation in the citric acid cycle. The carnitine-dependent transport of activated fatty acids across the mitochondrial membrane is a regulated process. Malonyl-CoA inh
MxiD, an outer membrane protein necessary for the secretion of the Shigella flexneri Ipa invasins (1993)

Summary The invasive phenotype of Shigella flexneri is conferred by a 220 kb virulence plasmid, pWR100, that encodes both the Ipa proteins, which are involved in the entry process, and factors which are required for the export and correct localization of the Ipa proteins. We have characterized the mxiD gene, whose expression, like that of the ipa operon, is regulated by temperature. After inactivation of mxiD , the mutant strain was unable to invade HeLa cells and to provoke keratoconjunctivitis in guinea‐pigs. Analysis of culture supernatants indicated that wild‐type S. flexneri secretes about nine polypeptides and that secretion of several of these, including IpaA, IpaB, and IpaC, is abolished in the mxiD mutant. Examination of the membrane proteins of the wild‐type and mxiD strains suggested that MxiD is an outer membrane protein. Amino acid sequence comparison revealed that MxiD is homologous to the YscC protein of Yersinia enterocolitica and to the C ‐terminal region of the PulD protein of Klebsiella pneumoniae. Both YscC and PulD are involved in extracellular protein secretion. These results indicate that MxiD is an essential component of the Ipa secretion apparatus.
Type-Restricted Neutralization of Molecular Clones of Human Immunodeficiency Virus (1988)

In a study of the immunologic significance of the genetic diversity present within single isolates of human immunodeficiency virus type 1 (HIV-1), the neutralization of viruses derived from molecular clones of the HIV-1 strain HTLV-IIIB by an extensive panel of sera was compared. Sera from HIV-1-infected patients and from goats immunized with polyacrylamide gel-purified HIV-1 envelope glycoprotein (gp120), native gp120, or gp120-derived recombinant peptides, showed marked heterogeneity in neutralizing activity against these closely related viruses. The change of a single amino acid residue in gp120 may account for such "clonal restriction" of neutralizing activity.
The properties of citrate transport catalyzed by CitP of Lactococcus lactis ssp. lactis biovar diacetylactis (1996)

Citrate uptake in Lactococcus lactis ssp. lactis biovar diacetylactis (L. diacetylactis) is catalysed by a secondary citrate carrier, the citrate permease P (CitP). In this report the mechanism of citrate uptake was investigated in resting cells of L. diacetylactis. The results presented reveal that the pH gradient (ΔpH) and the membrane potential (ΔΨ) are driving forces for citrate uptake. Moreover, it seems that CitP activity requires neither Na+ nor Mg2+ cations.
Handbook of Pharmaceutical Excipients (1994)

Since 1986, the Handbook of Pharmaceutical Excipients has been the essential reference for those involved in the development, production, control, or regulation of pharmaceutical preparations. Published jointly by the American Pharmacists Association and the Pharmaceutical Press, a division of the Royal Pharmaceutical Society of Great Britain, London, UK, this new edition is a comprehensive guide to the uses, properties, and safety of pharmaceutical excipients.
Constitutive macropinocytosis allows TAP‐dependent major histocompatibility compex class I presentation of exogenous soluble antigen by bone marrow‐derived dendritic cells (1997)

Dendritic cells expanded from mouse bone marrow (BMDC) with granulocyte/macrophage-colony-stimulating factor have potent T cell-stimulatory properties both in vitro and in vivo. This has been well documented for major histocompatibility complex (MHC) class II-restricted responses, and more recently using peptide-loaded and protein-pulsed DC for CD8 responses following adoptive transfer in mice. An unresolved question concerns the capacity of BMDC to present exogenous antigen on MHC class I molecules, an unconventional mode of MHC class I loading for which there is now considerable evidence, particularly in macrophages. Here, we show that BMDC exhibit high levels of macropinocytosis driven by constitutive membrane ruffling activity. Up to one-third of actively ruffling and macropinocytosing BMDC transferred pinocytosed horseradish peroxidase into the cytosol following a 15-min pulse, suggesting that they might be capable of presenting exogenous soluble antigen on MHC class I molecules. We show that BMDC presented exogenous ovalbumin to a T cell hybridoma more effectively, more rapidly, and at lower exogenous antigen concentrations than BM macrophages on a cell-for-cell basis. Presentation was TAP dependent, brefeldin A sensitive, and blocked by inhibitors of proteasomal processing, demonstrating use of the classical MHC class I pathway. Although effective presentation of exogenous antigen by BMDC occurred in the absence of agents which stimulate macropinocytosis, treatment with phorbol myristate acetate (PMA) enhanced both pinocytosis and MHC class I presentation by BMDC. Finally, PMA-stimulated BMDC exposed to exogenous ovalbumin in vitro were able to prime an antigen-specific cytotoxic T lymphocyte response following adoptive transfer in vivo.
Flt‐3 Ligand, in Combination with Bovine Granulocyte–Macrophage Colony‐Stimulating Factor and Interleukin‐4, Promotes the Growth of Bovine Bone Marrow Derived Dendritic Cells (2000)

Culture of bone marrow precursor cells with cytokines, including granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin-4 (IL-4) and the tyrosine kinase receptor binding proteins Flt-3 ligand (Flt-3L) and stem-cell factor (SCF), has previously been shown, in both mouse and human, to result in the generation of large numbers of dendritic cells. We extend these findings to bovine dendritic cells. Culture of bovine bone marrow cells with GM-CSF, IL-4 and either Flt-3L or SCF enhanced the generation of low buoyant-density dendritic cells. However, only the addition of Flt-3L to cells cultured with GM-CSF and IL-4 was shown to increase the number of dendritic cells and induce the differentiation of dendritic cells with potent capacity to stimulate allogeneic T cells and resting CD4+ memory T cells. The effective ability to stimulate T cells was associated with the expression of major histocompatibility complex (MHC) class II molecules and CD80/86 by dendritic cells. Bovine bone marrow derived dendritic cells appeared to be exclusively of myeloid origin because they expressed the myeloid-related antigens CD14, MyD-1 and CD11b.
Arginine 206 of the C5a Receptor Is Critical for Ligand Recognition and Receptor Activation by C-terminal Hexapeptide Analogs (1995)

C5a is a 74-amino-acid glycoprotein whose receptor is a member of the rhodopsin superfamily. While antagonists have been generated to many of these receptors, similar efforts directed at family members whose natural ligands are proteins have met with little success. The recent development of hexapeptide analogs of C5a has allowed us to begin elucidation of the molecular events that lead to activation by combining a structure/activity study of the ligand with receptor mutagenesis. Removal of the hexapeptide's C-terminal arginine reduces affinity by 100-fold and eliminates the ability of the ligand to activate the receptor. Both the guanidino side chain and the free carboxyl of the arginine participate in the interaction. The guanidino group makes the energy-yielding contact with the receptor, while the free carboxylate negates "electrostatic" interference with Arg-206 of the receptor. It is the apparent movement Arg-206 induced by this set of interactions that is responsible for activation, since conversion of Arg-206 to alanine eliminates the agonist activity of the hexapeptides. Surprisingly, activation is a nearly energy-neutral event and may reflect the binding process rather than the final resting site of the ligand.
Sensor synaesthesia (2011)

We explore techniques for hand-held devices that leverage the multimodal combination of touch and motion. Hybrid touch + motion gestures exhibit interaction properties that combine the strengths of multi-touch with those of motion-sensing. This affords touch-enhanced motion gestures, such as one-handed zooming by holding one's thumb on the screen while tilting a device. We also consider the reverse perspective, that of motion-enhanced touch, which uses motion sensors to probe what happens underneath the surface of touch. Touching the screen induces secondary accelerations and angular velocities in the sensors. For example, our prototype uses motion sensors to distinguish gently swiping a finger on the screen from 'Sdrags with a hard onset' - to enable more expressive touch interactions.
Insulin Stimulates Postsynaptic Density-95 Protein Translation via the Phosphoinositide 3-Kinase-Akt-Mammalian Target of Rapamycin Signaling Pathway (2005)

Insulin receptors are highly enriched at neuronal synapses, but whose function remains unclear. Here we present evidence that brief incubations of rat hippocampal slices with insulin resulted in an increased protein expression of dendritic scaffolding protein postsynaptic density-95 (PSD-95) in area CA1. This insulin-induced increase in the PSD-95 protein expression was inhibited by the tyrosine kinase inhibitor, AG1024, phosphatidylinositol 3-kinase (PI3K) inhibitors, LY294002 and wortmannin, translational inhibitors, anisomycin and rapamycin, but not by LY303511 (an inactive analogue of LY294002), and transcriptional inhibitor, actinomycin D, suggesting that insulin regulates the translation of PSD-95 by activating the receptor tyrosine kinase-PI3K-mammalian target of rapamycin (mTOR) signaling pathway. A similar insulin-induced increase in the PSD-95 protein expression was detected after stimulation of the synaptic fractions isolated from the hippocampal neurons. Furthermore, insulin treatment did not affect the PSD-95 mRNA levels. In agreement, insulin rapidly induced the phosphorylation of 3-phosphoinositide-dependent protein kinase-1 (PDK1), protein kinase B (Akt), and mTOR, effects that were prevented by the AG1024 and LY294002. We also show that insulin stimulated the phosphorylation of 4E-binding protein 1 (4E-BP1) and p70S6 kinase (p70S6K) in a mTOR-dependent manner. Finally, we demonstrate the constitutive expression of PSD-95 mRNA in the synaptic fractions isolated from hippocampal neurons. Taken together, these findings suggest that activation of the PI3K-Akt-mTOR signaling pathway is essential for the insulin-induced up-regulation of local PSD-95 protein synthesis in neuronal dendrites and indicate a new molecular mechanism that may contribute to the modulation of synaptic function by insulin in hippocampal area CA1.
Route optimization and location updates for mobile hosts (2002)

Mobile hosts in a wireless network can move from one location to another while communicating with other hosts. A challenge is to provide seamless network access for mobile hosts and, at the same time, to retain compatibility with existing network protocols and applications. This paper addresses the issue of route optimization in IP mobility support that provides mobile handoff and "triangle" routing to mobile hosts through their home agents. We combine IP mobility support with hierarchical dynamic routing protocols OSPF and BGP. Existing mechanisms of authentication, incremental route propagation, and address aggregation can be used for efficient and secure propagation of location updates of mobile hosts. The geographical locality of consecutive mobile handoffs fits well with hierarchical dynamic routing protocols. No changes are required on fixed hosts or on routers that do not handle mobile hosts directly.
Solution Synthesis Approach to Colloidal Cesium Lead Halide Perovskite Nanoplatelets with Monolayer-Level Thickness Control (2016)

We report a colloidal synthesis approach to CsPbBr3 nanoplatelets (NPLs). The nucleation and growth of the platelets, which takes place at room temperature, is triggered by the injection of acetone in a mixture of precursors that would remain unreactive otherwise. The low growth temperature enables the control of the plate thickness, which can be precisely tuned from 3 to 5 monolayers. The strong two-dimensional confinement of the carriers at such small vertical sizes is responsible for a narrow PL, strong excitonic absorption, and a blue shift of the optical band gap by more than 0.47 eV compared to that of bulk CsPbBr3. We also show that the composition of the NPLs can be varied all the way to CsPbBr3 or CsPbI3 by anion exchange, with preservation of the size and shape of the starting particles. The blue fluorescent CsPbCl3 NPLs represent a new member of the scarcely populated group of blue-emitting colloidal nanocrystals. The exciton dynamics were found to be independent of the extent of 2D confinement in these platelets, and this was supported by band structure calculations.
Stapedectomy complications (1976)

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Differential expression of SPARC and thrombospondin 1 in wound repair: immunolocalization and in situ hybridization. (1993)

SPARC and thrombospondin 1 (TSP-1) are secreted glycoproteins expressed by similar types of cells in culture and in tissues. To compare these two proteins in vivo, we analyzed the differential expression of SPARC and TSP-1 during wound repair. Full-thickness incision wounds were made in rats and biopsied at 12 hr-14 days. Antibodies against SPARC revealed an increased proportion of immunoreactive fibroblastic cells at the wound edge at 3 days with maximal numbers at 7 days. In situ hybridization for SPARC produced results consistent with those of immunohistochemistry. With combined immunohistochemistry and in situ hybridization, some of the macrophages at the wound edge expressed SPARC mRNA. In contrast, immunoreactivity for TSP-1 was extracellular; expression at the wound edge was noted at 12 hr and was maximal at 1-2 days. TSP-1 mRNA was found in the thrombus, but not at the wound edge. In conclusion, SPARC and TSP-1 have contrasting roles during wound healing. SPARC expression from the middle through late stages of repair was consistent with its previously proposed functions in remodeling; in contrast, the transient expression of TSP-1 early in repair might facilitate the action of other proteins in recruitment and/or proliferation of cells in the healing wound.
All-silicon nonlinear transmission line integrated into a Si/SiGe heterostructure bipolar transistor process (2002)

Summary form only given. Nonlinear Transmission Lines (NLTL) have been fabricated so far on GaAs substrates only. Recently, we were able to demonstrate a working nonlinear transmission line for the first time on high resistivity silicon proving the applicability of the NLTL concept to silicon millimeter wave integrated circuits (SIMMWICs). We have significantly improved our previous results by integrating the NLTL into a Si/SiGe Heterostructure Bipolar Transistor (HBT) process. The falltime of 74 ps of a 4 GHz sine wave was compressed to 12 ps, 4 V amplitude at the output of the NLTL.