gebhart/patrepeval huggingface dataset:
Characterization of a Nucleus-Encoded Chitinase from the Yeast Kluyveromyces lactis (2005)

Endogenous proteins secreted from Kluyveromyces lactis were screened for their ability to bind to or to hydrolyze chitin. This analysis resulted in identification of a nucleus-encoded extracellular chitinase (KlCts1p) with a chitinolytic activity distinct from that of the plasmid-encoded killer toxin alpha-subunit. Sequence analysis of cloned KlCTS1 indicated that it encodes a 551-amino-acid chitinase having a secretion signal peptide, an amino-terminal family 18 chitinase catalytic domain, a serine-threonine-rich domain, and a carboxy-terminal type 2 chitin-binding domain. The association of purified KlCts1p with chitin is stable in the presence of high salt concentrations and pH 3 to 10 buffers; however, complete dissociation and release of fully active KlCts1p occur in 20 mM NaOH. Similarly, secreted human serum albumin harboring a carboxy-terminal fusion with the chitin-binding domain derived from KlCts1p also dissociates from chitin in 20 mM NaOH, demonstrating the domain's potential utility as an affinity tag for reversible chitin immobilization or purification of alkaliphilic or alkali-tolerant recombinant fusion proteins. Finally, haploid K. lactis cells harboring a cts1 null mutation are viable but exhibit a cell separation defect, suggesting that KlCts1p is required for normal cytokinesis, probably by facilitating the degradation of septum-localized chitin.
Temporal Relation Between Ischemic Episodes and Activation of the Coagulation System in Unstable Angina (1996)

Our study demonstrates that patients with active unstable angina develop frequent bursts of thrombin production not necessarily associated with ischemic episodes and that, conversely, some ischemic episodes are not associated with evidence of thrombin activation.
Two metal‐binding sites in a lead ribozyme bound to competitively by Pb2+ and Mg2+ (1998)

We reported recently that a lead ribozyme with modified bases cleaved at an additional site at high Pb2+ concentrations (>0.1 mM), and that the cleavage at a canonical site was enhanced nearly fourfold at the optimum combination of Pb2+ and Mg2+ concentrations [Kim, M. H., Katahira, M., Sugiyama, T. & Uesugi, S. (1997) J. Biochem. (Tokyo) 122, 1062-1067]. Here we have identified two metal-binding sites (sites 1 and 2) of the lead ribozyme at the residue level by NMR. Both sites are located in an asymmetric internal loop of the lead ribozyme. Site 1 is composed of residues of an enzyme strand and site 2 of residues of a substrate strand. The two sites are bound to competitively by Pb2+ and Mg2+. It was revealed that at certain Pb2+ and Mg2+ concentrations, site 1 is occupied by Pb2+ and site 2 is occupied by Mg2+. The dependency of the cleavage at the canonical and other sites on the Pb2+ and Mg2+ concentrations is interpreted by considering the species of metal ions bound to the two sites. It is suggested that the addition of the two metal ions produces similar and different effects on the structure of the lead ribozyme, and the two metal ions have a synergistic effect on the structure.
Architectural considerations for mobile mesh networking (2002)

Mobile communications is central to many military operations and is necessary to communicate simultaneously with multiple warfighters engaged in a common task. This paper describes the problem of routing and resource reservation in mobile mesh networks and presents architectural recommendations necessary for Internet protocols to operate effectively in these environments. A "mobile mesh" network is an autonomous system of mobile routers connected by wireless links, the union of which form an arbitrary graph. The routers are free to move randomly; thus, the network's wireless topology may change rapidly and unpredictably.
Hyperammonaemia does not impair brain function in the absence of net glutamine synthesis (1991)

1. It has been established that chronic hyperammonaemia, whether caused by portacaval shunting or other means, leads to a variety of metabolic changes, including a depression in the cerebral metabolic rate of glucose (CMRGlc) increased permeability of the blood-brain barrier to neutral amino acids, and an increase in the brain content of aromatic amino acids. The preceding paper [Jessy, DeJoseph & Hawkins (1991) Biochem. J. 277, 693-696] showed that the depression in CMRGlc caused by hyperammonaemia correlated more closely with glutamine, a metabolite of ammonia, than with ammonia itself. This suggested that ammonia (NH3 and NH4+) was without effect. The present experiments address the question whether ammonia, in the absence of net glutamine synthesis, induces any of the metabolic symptoms of cerebral dysfunction associated with hyperammonaemia. 2. Small doses of methionine sulphoximine, an inhibitor of glutamine synthetase, were used to raise the plasma ammonia levels of normal rats without increasing the brain glutamine content. These hyperammonaemic rats, with plasma and brain ammonia levels equivalent to those known to depress brain function, behaved normally over 48 h. There was no depression of cerebral energy metabolism (i.e. the rate of glucose consumption). Contents of key intermediary metabolites and high-energy phosphates were normal. Neutral amino acid transport (tryptophan and leucine) and the brain contents of aromatic amino acids were unchanged. 3. The data suggest that ammonia is without effect at concentrations less than 1 mumol/ml if it is not converted into glutamine. The deleterious effect of chronic hyperammonaemia seems to begin with the synthesis of glutamine.
Recursive Neural Networks Can Learn Logical Semantics (2015)

Tree-structured recursive neural networks (TreeRNNs) for sentence meaning have been successful for many applications, but it remains an open question whether the fixed-length representations that they learn can support tasks as demanding as logical deduction. We pursue this question by evaluating whether two such modelsplain TreeRNNs and tree-structured neural tensor networks (TreeRNTNs)-can correctly learn to identify logical relationships such as entailment and contradiction using these representations. In our first set of experiments, we generate artificial data from a logical grammar and use it to evaluate the models' ability to learn to handle basic relational reasoning, recursive structures, and quantification. We then evaluate the models on the more natural SICK challenge data. Both models perform competitively on the SICK data and generalize well in all three experiments on simulated data, suggesting that they can learn suitable representations for logical inference in natural language.
Genetic Analysis Of Extracellular Toxins Of Staphylococcus Aureus (1989)

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and ...Read More
Using the Vacuum Dressing Alternative for Difficult Wounds (1994)

ixty-one-year-old Joan Cooper, originally admitted for a mitral valve replacement, developed a bleeding duodenal ulcer during her stay. While performing resection for the ulcer, surgeons discovered and drained several intra-abdominal abscesses. Ms. Cooper was left with a large, draining abdominal wound. At first, a normal saline, wet-to-dry dressing was applied, but it couldn't control the heavy drainage. Surrounding skin became irritated and painful. Experiences like this can leave you and your patient feeling frustrated, but don't despair-there's a solution. A vacuum dressing system can put you in control of large, draining wounds that don't respond well to traditional measures. And since it remains in place for three to five days, it costs about $1,200 per week less than conventional dressings that need to be changed four to six times a day. We found that the vacuum dressing not only hastened Ms. Cooper's healing and made her more comfortable, but also required less nursing time so her nurse was better able to attend to Ms. Cooper's other needs. Here's what you need to know to apply the vacuum dressing and manage these difficult wounds.
Human monocytes augment invasiveness and proteolytic activity of inflammatory breast cancer (2008)

Inflammatory breast cancer (IBC) is the most aggressive form of breast cancer, and here, we examined in vitro the interactions between the human IBC cell line SUM149 and U937 human naive monocytes. We found an altered morphology, enhanced invasiveness and proteolytic activity of SUM149 cells when cultured with U937 cells or in U937-conditioned media (U937-CM). Increases in expression and activity of the cysteine protease cathepsin B and expression of caveolin-1 were also detected in SUM149 cells grown in U937-CM, thus suggesting a contribution of these proteins to the augmented invasion through and proteolysis of the extracellular matrix by the IBC cells.
Mechanisms of MYC stabilization in human malignancies (2008)

MYC is a pleiotropic transcription factor that has been linked to a diverse range of cellular functions, such as cell cycle regulation, proliferation, growth, differentiation and metabolism. Not surprisingly, aberrant MYC signaling has been observed in human cancers and MYC has been demonstrated to promote cell transformation and tumor progression. Here we discuss recent discoveries that have expanded our knowledge of MYC protein stability. In particular we focus on mechanisms that might explain the increased stability of MYC often observed in human cancers and cell lines. We also summarize our recent characterization of Cancerous inhibitor of PP2A (CIP2A(/KIAA1524)) as a protein that inhibits PP2A-mediated MYC dephosphorylation and proteolytic degradation. Finally, we discuss the potential relevance of mechanisms that regulate MYC stability for tumor formation in the context of cancer therapy.
Floating body cell (FBC) memory for 16-nm technology with low variation on thin silicon and 10-nm BOX (2008)

A scaled planar FBC technology with undoped-body is demonstrated featuring 10-nm BOX, 25-nm SOI, high-k and metal gate. Good agreement on retention window characteristics between measured data and simulations is achieved at multiple temperatures and illustrates Shockley-Read-Hall (SRH) recombination and generation dominated loss mechanism during hold condition. Optimization of Source-Drain (SD) and TIP implants are critical for achieving the balance between long retention time and large memory signal. For a minimum 3-muA sensing window, worst-case disturb retention of 25 ms is shown in scaled devices with 55 nm gate-length (L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> ) and 65 nm width (W). FBC scaling is predicted to be feasible at 16-nm technology node, enabling memory cell sizes much smaller than 6T-SRAM.
Differential proliferative responses in subsets of human CD28+cells delineated by BB27 mAb (1994)

We report the identification of a novel 140 kDa disulfide-linked dimer expressed by a subset of peripheral blood T lymphocytes. This molecule, which is recognized by mAb BB27, is also detected on cells of the myelomonocytic lineage. In the T cell lineage, its expression is positively modulated after lymphocyte activation. A series of double-labeling experiments revealed that BB27 mAb identifies new CD4 and CD8 cell subsets different from those defined by CD45RA, CD45RO, CD26, CD29, CD31, and CD38. Finally, BB27 mAb also subdivides the CD28 subset. Of the utmost interest is the finding that a proliferative response to CD28 mAb and phorbol myristate acetate stimulation is exclusively obtained in the CD28+BB27+ cell subset, whereas the CD28+BB27- subset fails to proliferate.
Structural Action Recognition in Body Sensor Networks: Distributed Classification Based on String Matching (2009)

Mobile sensor-based systems are emerging as promising platforms for healthcare monitoring. An important goal of these systems is to extract physiological information about the subject wearing the network. Such information can be used for life logging, quality of life measures, fall detection, extraction of contextual information, and many other applications. Data collected by these sensor nodes are overwhelming, and hence, an efficient data processing technique is essential. In this paper, we present a system using inexpensive, off-the-shelf inertial sensor nodes that constructs motion transcripts from biomedical signals and identifies movements by taking collaboration between the nodes into consideration. Transcripts are built of motion primitives and aim to reduce the complexity of the original data. We then label each primitive with a unique symbol and generate a sequence of symbols, known as motion template, representing a particular action. This model leads to a distributed algorithm for action recognition using edit distance with respect to motion templates. The algorithm reduces the number of active nodes during every classification decision. We present our results using data collected from five normal subjects performing transitional movements. The results clearly illustrate the effectiveness of our framework. In particular, we obtain a classification accuracy of 84.13% with only one sensor node involved in the classification process.
The Agonist-Induced Phosphorylation of the Rat Follitropin Receptor Maps to the First and Third Intracellular Loops (1998)

Previous results from this laboratory have shown that the rat FSH receptor (rFSHR) becomes phosphorylated on S/T residues upon stimulation of transfected cells with human (h)FSH and that a truncation of the C-terminal tail that removes 12 of the 25 intracellular S/T residues does not affect phosphorylation. Based on the results of phosphopeptide-mapping experiments we analyzed three new mutants. rFSHR-1L and rFSHR-3L were constructed by mutating the S/T residues in the first intracellular loop or the third intracellular loop, respectively. rFSHR-(3L+CT) was constructed by mutating all the S/T residues in the third loop as well as S624, the only C-terminal tail residue that was not previously eliminated as a potential phosphorylation site. All mutants were biologically active. The agonist-induced phosphorylation of rFSHR-3L and rFSHR-(3L+CT) were partially reduced, while that of rFSHR-1L was almost completely lost. The agonist-induced uncoupling of rFSHR-1L and rFSHR-3L are retarded to about the same extent, while the agonist-induced internalization is retarded only in rFSHR-1L. Four major conclusions can be made from the present studies: 1) the phosphorylated rFSHR is a common molecular intermediate in agonist-induced uncoupling and internalization; 2) agonist-induced phosphorylation of the rFSHR maps to the first and third intracellular loops; 3) the phosphorylation of the third intracellular loop facilitates agonist-induced uncoupling but is not necessary for agonist-induced internalization; 4) agonist-induced internalization is facilitated by phosphorylation but it is not known if only the first loop, only the third loop, or both the first and third loops need to be phosphorylated for this response.
Reciprocal T H 17 and Regulatory T Cell Differentiation Mediated by Retinoic Acid (2007)

The cytokine transforming growth factor-beta (TGF-beta) converts naïve T cells into regulatory T (Treg) cells that prevent autoimmunity. However, in the presence of interleukin-6 (IL-6), TGF-beta has also been found to promote the differentiation of naïve T lymphocytes into proinflammatory IL-17 cytokine-producing T helper 17 (T(H)17) cells, which promote autoimmunity and inflammation. This raises the question of how TGF-beta can generate such distinct outcomes. We identified the vitamin A metabolite retinoic acid as a key regulator of TGF-beta-dependent immune responses, capable of inhibiting the IL-6-driven induction of proinflammatory T(H)17 cells and promoting anti-inflammatory Treg cell differentiation. These findings indicate that a common metabolite can regulate the balance between pro- and anti-inflammatory immunity.
The localization of KpsC, S and T, and KfiA, C and D proteins involved in the biosynthesis of the Escherichia coli K5 capsular polysaccharide: evidence for a membrane-bound complex (1998)

Biosynthesis of the Escherichia coli K5 polysaccharide requires the KfiA, KfiB, KfiC and KfiD proteins. The subsequent transport of the polysaccharide onto the cell surface requires the KpsC, KpsD, KpsE, KpsM, KpsS and KpsT proteins, which are conserved between different group II capsular polysaccharides. The KfiA and KfiC, together with the KpsC, KpsS and KpsT proteins, were purified and polyclonal antisera to each protein generated. These antisera, together with one previously generated (by others) against the purified KfiD protein, were used in Western blot analysis to locate the corresponding proteins within the cell. Analysis of membrane fractions revealed that KfiA (involved in initiation of polysaccharide synthesis), KfiC (K5 glycosyl transferase) and the KfiD protein (UDP-glucose dehydrogenase) were associated with the inner membrane. The KpsC, KpsS, and KpsT proteins involved in polysaccharide transport were associated with the inner membrane and this membrane association occurred in the absence of any other capsule-related proteins. The effect of mutations in individual kps genes on the localization of each protein was determined. Mutations in the kpsC, kpsM, kpsS and kpsT genes resulted in a loss of membrane targeting for KfiA and KfiC, suggesting some form of hetero-oligomeric membrane-bound biosynthetic complex. Osmotic shock caused the release of KfiA, KfiC, KpsC and KpsS from the inner membrane into the periplasm, suggesting that the polysaccharide biosynthetic complex may be associated with sites of adhesion between the inner and outer membrane.
Regulatory mechanisms of monofunctional and bifunctional anticarcinogenic enzyme inducers in murine liver. (1988)

Anticarcinogenic enzyme inducers are of two types: (a) bifunctional inducers [2,3,7,8-tetrachlorodibenzo-p-dioxin, polycyclic aromatics, azo dyes, beta-naphthoflavone] that elevate both Phase II enzymes [e.g., glutathione S-transferases, UDP-glucuronosyltransferases, and NAD(P)H:(quinone-acceptor) oxidoreductase] and certain Phase I enzymes [e.g., aryl hydrocarbon hydroxylase (AHH)]; and (b) monofunctional inducers [e.g., diphenols, thiocarbamates, 1,2-dithiol-3-thiones, isothiocyanates] that elevate primarily Phase II enzymes without significantly affecting AHH. Since Phase I enzymes such as AHH may activate precarcinogens to ultimate carcinogens whereas Phase II enzyme induction suffices to achieve chemoprotection, an understanding of the molecular mechanisms that regulate these enzymes is critical for devising methods for chemoprotection. We report a systematic analysis of the inductions of aryl hydrocarbon hydroxylase (AHH) and NAD(P)H:quinone reductase (QR) by seven monofunctional and eight bifunctional inducers, singly or in combination, in a murine hepatoma cell line (Hepa 1c1c7) and two mutants defective in either Ah (Aryl hydrocarbon) receptor function (BPrc1) or in AHH expression (c1). We have also examined such inductions in genetically defined mouse strains with high affinity (C57BL/6J) and low affinity (DBA/2J) Ah receptors. The combination of our earlier model for the induction of Phase I and Phase II enzymes (H. J. Prochaska, M. J. De Long, and P. Talalay, Proc. Natl. Acad. Sci. USA, 82: 8232, 1985) with mechanism(s) for autoregulation of AHH (O. Hankinson, R. D. Anderson, B. W. Birren, F. Sander, M. Negishi, and D. W. Nebert, J. Biol. Chem., 260: 1790, 1985) is compatible with our results. Thus, induction of QR by monofunctional inducers does not depend on a competent Ah receptor or AHH activity and appears to involve an electrophilic chemical signal. In contrast, bifunctional inducers require competent Ah receptors to induce both AHH and QR, although the latter process appears to be regulated by more than one mechanism. It is our view that bifunctional inducers bind to the Ah receptor thereby enhancing transcription of genes encoding both AHH and QR. Metabolizable bifunctional inducers are then converted by the induced AHH to products that resemble monofunctional inducers and are capable of generating the aforementioned chemical signal. The existence of mechanism(s) for AHH autoregulation that also affect Phase II enzyme expression would account for the high basal activities of QR in the AHH-defective mutant (c1).
Crystalline 1H‐1,2,3‐Triazol‐5‐ylidenes: New Stable Mesoionic Carbenes (MICs) (2010)

Click makes MICs: A short modular synthesis allows the preparation of novel stable heterocycles that feature a lone pair of electrons on a carbon center. The donor properties of these mesoionic compounds are greater than those of classical N-heterocyclic carbenes; they are accessible by deprotonation of the corresponding conjugate acids using comparatively mild bases.
Ralstonia eutropha H16 in progress: Applications beside PHAs and establishment as production platform by advanced genetic tools (2017)

Ralstonia eutropha strain H16 is a Gram-negative non-pathogenic betaproteobacterium ubiquitously found in soils and has been the subject of intensive research for more than 50 years. Due to its remarkable metabolically versatility, it utilizes a broad range of renewable heterotrophic resources. The substrate utilization range can be further extended by metabolic engineering as genetic tools are available. It has become the best studied "Knallgas" bacterium capable of chemolithoautotrophic growth with hydrogen as the electron donor and carbon dioxide as the carbon source. It also serves as a model organism to study the metabolism of poly(β-hydroxybutyrate), a polyester which is accumulated within the cells for storage of both carbon and energy. Thermoplastic and biodegradable properties of this polyhydroxyalkanoate (PHA) have attracted much biotechnical interest as a replacement for fossil resource-based plastics. The first applications of R. eutropha aimed at chemolithoautotrophic production of single cell protein (SCP) for food and feed and the synthesis of various PHAs. The complete annotated genome is available allowing systematic biology approaches together with data provided by available omics studies. Besides PHAs, novel biopolymers of 2-hydroxyalkanoates and polythioesters or cyanophycin as well as chemicals such as alcohols, alkanes, alkenes, and further interesting value added chemicals significantly recently extended the range of products synthesized by R. eutropha. High cell density cultivations can be performed without too much effort and the available repertoire of genetic tools is rapidly growing. Altogether, this qualifies R. eutropha strain H16 to become a production platform strain for a large spectrum of products.
Microtubules in Dendritic Spine Development (2008)

It is generally believed that only the actin cytoskeleton resides in dendritic spines and controls spine morphology and plasticity. Here, we report that microtubules (MTs) are present in spines and that shRNA knockdown of the MT plus-end-binding protein EB3 significantly reduces spine formation. Furthermore, stabilization and inhibition of MTs by low doses of taxol and nocodazole enhance and impair spine formation elicited by BDNF (brain-derived neurotrophic factor), respectively. Therefore, MTs play an important role in the control and regulation of dendritic spine development and plasticity.