gebhart/patrepeval huggingface dataset:
Toward Tailoring the Specificity of the S<sub>1</sub> Pocket of Subtilisin <i>B. lentus</i>:  Chemical Modification of Mutant Enzymes as a Strategy for Removing Specificity Limitations (1999)

In both protein chemistry studies and organic synthesis applications, it is desirable to have available a toolbox of inexpensive proteases with high selectivity and diverse substrate preferences. Toward this goal, we have generated a series of chemically modified mutant enzymes (CMMs) of subtilisin B. lentus (SBL) possessing expanded S(1) pocket specificity. Wild-type SBL shows a marked preference for substrates with large hydrophobic P(1) residues, such as the large Phe P(1) residue of the standard suc-AAPF-pNA substrate. To confer more universal P(1) specificity on S(1), a strategy of chemical modification in combination with site-directed mutagenesis was applied. For example, WT-SBL does not readily accept small uncharged P(1) residues such as the -CH(3) side chain of alanine. Accordingly, with a view to creating a S(1) pocket that would be of reduced volume providing a better fit for small P(1) side chains, a large cyclohexyl group was introduced by the CMM approach at position S166C with the aim of partially filling up the S(1) pocket. The S166C-S-CH(2)-c-C(6)H(11) CMM thus created showed a 2-fold improvement in k(cat)/K(M) with the suc-AAPA-pNA substrate and a 51-fold improvement in suc-AAPA-pNA/suc-AAPF-pNA selectivity relative to WT-SBL. Furthermore, WT-SBL does not readily accept positively or negatively charged P(1) residues. Therefore, to improve SBL's specificity toward positively and negatively charged P(1) residues, we applied the CMM methodology to introduce complementary negatively and positively charged groups, respectively, at position S166C in S(1). A series of mono-, di-, and trinegatively charged CMMs were generated and all showed improved k(cat)/K(M)s with the positively charged P(1) residue containing substrate, suc-AAPR-pNA. Furthermore, virtually arithmetic improvements in k(cat)/K(M) were exhibited with increasing number of negative charges on the S166C-R side chain. These increases culminated in a 9-fold improvement in k(cat)/K(M) for the suc-AAPR-pNA substrate and a 61-fold improvement in suc-AAPR-pNA/suc-AAPF-pNA selectivity compared to WT-SBL for the trinegatively charged S166C-S-CH(2)CH(2)C(COO(-))(3) CMM. Conversely, the positively charged S166C-S-CH(2)CH(2)NH(3)(+) CMM generated showed a 19-fold improvement in k(cat)/K(M) for the suc-AAPE-pNA substrate and a 54-fold improvement in suc-AAPE-pNA/suc-AAPF-pNA selectivity relative to WT-SBL.
Model-based mediation with domain maps (2002)

Proposes an extension to current view-based mediator systems called "model-based mediation", in which views are defined and executed at the level of conceptual models (CMs) rather than at the structural level. Structural integration and lifting of data to the conceptual level is "pushed down" from the mediator to wrappers which, in our system, export the classes, associations, constraints and query capabilities of a source. Another novel feature of our architecture is the use of domain maps - semantic nets of concepts and relationships that are used to mediate across sources from multiple worlds (i.e. whose data are related in indirect and often complex ways). As part of registering a source's CM with the mediator, the wrapper creates a "semantic index" of its data into the domain map. We show that these indexes not only semantically correlate the multiple-worlds data, and thereby support the definition of the integrated CM, but they are also useful during query processing, for example, to select relevant sources. A first prototype of the system has been implemented for a complex neuroscience mediation problem.
Fanconi Anemia Proteins Localize to Chromatin and the Nuclear Matrix in a DNA Damage- and Cell Cycle-regulated Manner (2001)

Fanconi anemia (FA) is a genetic disease characterized by congenital defects, bone marrow failure, and cancer susceptibility. Cells from patients with FA exhibit genomic instability and hypersensitivity to DNA cross linking agents such as mitomycin C. Despite the identification of seven complementation groups and the cloning of six genes, the function of the encoded gene products remains elusive. The FancA (Fanconi anemia complementation group A), FancC, and FancG proteins have been detected within a nuclear complex, but no change in level, binding, or localization has been reported as a result of drug treatment or cell cycle. We show that in immunofluorescence studies, FancA appears as a non-nucleolar nuclear protein that is excluded from condensed, mitotic chromosomes. Biochemical fractionation reveals that the FA proteins are found in nuclear matrix and chromatin and that treatment with mitomycin C results in increase of the FA proteins in nuclear matrix and chromatin fractions. This induction occurs in wild-type cells and mutant FA-D (Fanconi complementation group D) cells but not in mutant FA-A cells. Immunoprecipitation of FancA protein in chromatin demonstrates the coprecipitation of FancA, FancC, and FancG, showing that the FA proteins move together as a complex. Also, fractionation of mitotic cells confirms the lack of FA proteins in chromatin or the nuclear matrix. Furthermore, phosphorylation of FancG was found to be temporally correlated with exit of the FA complex from chromosomes at mitosis. Taken together, these findings suggest a role for FA proteins in chromatin and nuclear matrix.
541. The synthesis of some new phenols (1961)

R. E. Dean, A. Midgley, E. N. White and D. McNeil, J. Chem. Soc., 1961, 2773 DOI: 10.1039/JR9610002773
MobiCom 2011 poster (2012)

poster Share on MobiCom 2011 poster: AirTrack: locating non-WiFi interferers using commodity WiFi hardware Authors: Ashish Patro Computer Sciences Department, University of Wisconsin Madison Computer Sciences Department, University of Wisconsin MadisonView Profile , Shravan Rayanchu Computer Sciences Department, University of Wisconsin Madison Computer Sciences Department, University of Wisconsin MadisonView Profile , Suman Banerjee Computer Sciences Department, University of Wisconsin Madison Computer Sciences Department, University of Wisconsin MadisonView Profile Authors Info & Claims ACM SIGMOBILE Mobile Computing and Communications ReviewVolume 15Issue 4October 2011 pp 52–54https://doi.org/10.1145/2169077.2169088Online:27 March 2012Publication History 3citation219DownloadsMetricsTotal Citations3Total Downloads219Last 12 Months9Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Hypersomnia after head–neck trauma (2000)

A systematic approach is required when dealing with patients complaining of hypersomnia following a head-neck trauma.
The global regulator CsrA of Escherichia coli is a specific mRNA-binding protein (1997)

The csrA gene encodes a global regulatory protein which facilitates glgC mRNA decay in vivo. A purified recombinant CsrA protein was found to inhibit in vitro glg (glycogen biosynthesis) gene expression posttranscriptionally and bind specifically to a glgC runoff transcript without causing its decay. Our results provide further insight into the mechanism by which CsrA functions as an mRNA decay factor.
A Prospective Randomized Study in 100 Consecutive Patients Undergoing Major Liver Resection With Versus Without Ischemic Preconditioning (2003)

This study establishes ischemic preconditioning as a protective strategy against hepatic ischemia in humans. The strategy is particularly effective in young patients requiring a prolonged period of inflow occlusion, and in the presence of steatosis, and is possibly related to preservation of ATP content in liver tissue. Other strategies are needed in older patients.
Interactive mesh dragging with adaptive remeshing technique (2002)

We propose a 3D mesh dragging method useful for intuitive, efficient geometric modeling of free form polygonal models. With our method, the user can drag a part of a triangular mesh and change its position and orientation. This method is based on an adaptive remeshing procedure which evaluates the deformation of faces by dragging and properly modifies them by deleting or splitting with local topological operations. Therefore the mesh is automatically adjusted for dragging, and irregularity caused by dragging onto the mesh is no longer a concern. In addition, this method is local to the dragged portion, so its computation is efficient. We describe our adaptive remeshing method and demonstrate some dragging examples.
Anti-adult T‑cell leukemia/lymphoma activity of cerdulatinib, a dual SYK/JAK kinase inhibitor (2018)

Adult T‑cell leukemia/lymphoma (ATLL) constitutes an aggressive malignancy caused by human T‑cell leukemia virus type 1 (HTLV‑1) that is resistant to available chemotherapeutics. The constitutive activation of Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling is an important feature of ATLL, and spleen tyrosine kinase (SYK) is overexpressed in HTLV‑1-transformed T‑cell lines. In this study, we evaluated the effects of SYK- (PRT060318) or JAK- (JAK inhibitor 1) selective inhibitors and the dual SYK/JAK inhibitor, cerdulatinib, on the viability of HTLV‑1-transformed and ATLL-derived T‑cell lines. Cell proliferation, viability, cell cycle, apoptosis and intracellular signaling cascades were analyzed by the water-soluble tetrazolium-8 assay, flow cytometry and western blot analysis. HTLV‑1-infected T‑cell lines were sensitive to both SYK-selective and pan-JAK inhibitors, whereas cerdulatinib more potently suppressed cell proliferation and reduced cell viability than either of these agents alone. By contrast, the cytotoxic effects of cerdulatinib on uninfected T‑cell lines and peripheral blood mononuclear cells from a healthy donor were less pronounced. Cerdulatinib induced cell cycle arrest in the G2/M phase, which was associated with a decreased cyclin-dependent kinase 1 and cyclin B1, and an increased p21 and p27 expression. Hoechst staining revealed chromatin condensation and nuclear fragmentation in the cells treated with cerdulatinib, and an increased fraction of apoptotic APO2.7-stained cells was detected by flow cytometry. This corresponded to the activation of caspase-8, -9 and -3, and decreased levels of the anti-apoptotic factors, Bcl-xL, survivin, X-linked inhibitor of apoptosis (XIAP) and c‑FLIP. The cerdulatinib-induced decrease in cell viability was partly reversed by the caspase inhibitor, z‑VAD‑FMK. These anti-ATLL effects were associated with the suppression of SYK and JAK/STAT signaling, along with that of the downstream factors, AKT, ERK, activator protein‑1 and nuclear factor-κB. Finally, oral dosing with cerdulatinib lowered the tumor burden in a murine model of ATLL. Thus, our findings indicate that the simultaneous inhibition of therapeutically relevant targets, such as SYK and JAK is a more effective approach than single-agent therapy for the treatment of ATLL.
Study of modified polypropylene nonwoven cloth. I. graft copolymerization of 4-vinylpyridine onto polypropylene nonwoven cloth by preirradiation method (2000)

Polypropylene (PP) nonwoven cloth was grafted with 4-vinylpyridine (4-VP) by a preirradiation method. The effects of preirradiation conditions on the mechanical properties of preirradiated PP nonwoven cloth and the percentage of grafting (Pg) of 4-VP onto the preirradiated PP nonwoven cloth were systematically investigated. The results indicated that the mechanical properties of preirradiated PP nonwoven cloth decreased with increasing irradiation dose and that the Pg was greatly affected by the concentration of monomer, irradiation dose, grafting reaction temperature, and the addition of inhibitor and inorganic acid in the grafting reaction system. The grafted nonwoven cloth samples were characterized using IR spectroscopy and SEM. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 77: 1861–1868, 2000
[The impact of PDTC on circulating tumor cells of laryngocarcinoma in nude mice model]. (2011)

PDTC can reduce the incidence of CTC in the laryngocarcinoma nude mouse model, its role may benefit from PDTC reduced the ability of laryngocarcinoma metastasis, which may be as PDTC inhibit NF-kappaB activity, thus make VEGF-C and the expression of MMP-9 down, reducing angiogenesis and reduce tumor invasion of the larynx.
Synthesis of dl-3-Isobutyroxy-β-ionone and dl-Dehydrovomifoliol (1973)

3-Isobutyroxy-β-ionone (III) is the proposed structure of quiesone, the naturally occurring inhibitor of the germination of Peronospora tabacina conidia. This was synthesized as a racemate and shown to possess qualitatively identical biological activity as quiesone itself. Employing an intermediate of this synthesis, dl-dehydrovomifoliol (VII) was also synthesized.
Molecular mapping of point mutations in the period gene that stop or speed up biological clocks in Drosophila melanogaster. (1987)

The pero1 and the pers mutations in Drosophila melanogaster, which seem to eliminate or speed up, respectively, the clocks underlying biological rhythmicity, were mapped to single nucleotides. Chimeric DNA fragments consisting of well-defined wild-type plus mutant DNA subsegments were constructed, introduced into flies by germ-line transformation, and assayed for biological activity. These experiments localized both pero1 and pers to a 1.7-kilobase DNA fragment that is mostly coding DNA. Sequencing of this subsegment from each mutant showed that pero1 is completely accounted for by a nonsense mutation in the third coding exon of a 4.5-kilobase RNA transcribed from this locus. The pers mutation is also a single nucleotide substitution, in the fourth coding exon, which results in a serine-to-asparagine substitution in the per gene protein product. The functional significance of these changes is discussed with reference to the phenotypes of the two mutations.
An object-oriented approach to federated databases (2002)

Work on object-oriented database and programming technology has resulted in a number of important and powerful concepts and mechanisms, not only essential for modeling and implementing next generation database systems, but also useful for designing and constructing a network of distributed, autonomous databases (e.g. a federated database architecture). By applying the concept of 'object' to database level, many of the associated mechanisms can be adopted and extended naturally, so as to accommodate the desired sharing and exchange of information among databases. The authors describe such an 'object-oriented' approach towards federating a collection of decentralized, heterogeneous databases, and examines several issues that must be addressed within such an environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Estimation of Water Contents of Polymer Electrolytes from <sup>1</sup>H NMR Peak of Confined Water (2009)

Water molecules confined in perfluorinated ionomer membranes which are widely used for polymer electrolyte fuel cells, presented apparently a single 1H NMR peak in hydrated states because of the rapid exchange among the water molecules at the distinct segments of the polymer. The peak shifts to the lower field with decreasing the water content due to the decrease of the fraction of the bulk water molecules which present a peak at higher field. The chemical shifts were found to be well correlated with the peak area. The water peak for MEA (Membrane Electrode Assembly) showed also similar behaviors to the membranes. From the relationship between the chemical shift and the peak area of the confined water peak we demonstrated the potential that the chemical shift could be utilized to estimate the water content in the hydrated membranes and MEA.
Unplanned Shutdown Plus Lack of Knowledge Equals Incidents (2010)

This chapter contains sections titled: Introduction Scrubber Packing Failure Hydrogen Peroxide Decomposition in a Filter Neutralization Reaction Overpressurizes Vessel Conclusions
The NDV-3A vaccine protects mice from multidrug resistant Candida auris infection (2019)

Candida auris is an emerging, multi-drug resistant, health care-associated fungal pathogen. Its predominant prevalence in hospitals and nursing homes indicates its ability to adhere to and colonize the skin, or persist in an environment outside the host-a trait unique from other Candida species. Besides being associated globally with life-threatening disseminated infections, C. auris also poses significant clinical challenges due to its ability to adhere to polymeric surfaces and form highly drug-resistant biofilms. Here, we performed bioinformatic studies to identify the presence of adhesin proteins in C. auris, with sequence as well as 3-D structural homologies to the major adhesin/invasin of C. albicans, Als3. Anti-Als3p antibodies generated by vaccinating mice with NDV-3A (a vaccine based on the N-terminus of Als3 protein formulated with alum) recognized C. auris in vitro, blocked its ability to form biofilms and enhanced macrophage-mediated killing of the fungus. Furthermore, NDV-3A vaccination induced significant levels of C. auris cross-reactive humoral and cellular immune responses, and protected immunosuppressed mice from lethal C. auris disseminated infection, compared to the control alum-vaccinated mice. The mechanism of protection is attributed to anti-Als3p antibodies and CD4+ T helper cells activating tissue macrophages. Finally, NDV-3A potentiated the protective efficacy of the antifungal drug micafungin, against C. auris candidemia. Identification of Als3-like adhesins in C. auris makes it a target for immunotherapeutic strategies using NDV-3A, a vaccine with known efficacy against other Candida species and safety as well as efficacy in clinical trials. Considering that C. auris can be resistant to almost all classes of antifungal drugs, such an approach has profound clinical relevance.
A comparison of the specificity of phosphatidylcholine synthesis by human fetal lung maintained in either organ or organotypic culture (1988)

Human fetal lung (14-18 weeks gestation) was maintained in either organ or organotypic culture. By 4 days in organ culture or 14 days in organotypic culture, epithelial cells within both culture systems exhibited well-developed apical microvilli and possessed numerous intracellular lamellar bodies characteristic of surfactant phospholipid stores. However, analysis of the pattern of synthesis of individual molecular species of phosphatidylcholine by [14C]choline incorporation and reversed-phase h.p.l.c. showed that this apparent maturation was not paralleled by an increased synthesis of the dipalmitoyl species in either culture system. By contrast, the fractional synthesis of dipalmitoyl phosphatidylcholine, expressed as a percentage of total [14C]choline incorporation, decreased with time in both organ and organotypic culture. Moreover, these fractions were not significantly different from those measured in parallel monolayer cultures of mixed human fetal lung cells that displayed mainly fibroblast morphology. These results suggest that the synthesis pattern of phosphatidylcholine species by lung cells in culture is determined principally by their incubation conditions and not by their state of apparent maturation.
Signaling network architecture and transaction protocols to support realtime connection rerouting in ATM/B-ISDNs (2002)

In future B-ISDN and PCN environments, an increasing number of network control services, such as dynamic multiparty conferences, mobile call handoff, etc., will require realtime connection rerouting services not currently supported by the B-ISDN signaling network architecture based on the SS7 CCS network and its transaction protocols (TCAP). To support these services, we propose a novel signaling network architecture employing the following new signaling transport protocols in the signaling ATM adaptation layer: (1) associated-CCS employing source-routing unicast and multicast to provide fast distributed signaling transport for realtime distributed transactions, and (2) inband signaling required for synchronization data transport, and the following new transaction protocols in the TCAP layer: (1) robust fast reservation of communication resources, and (2) packet-ordering synchronization to minimize traffic descriptions.
Ivermectin Promotes Peripheral Nerve Regeneration during Wound Healing (2018)

Peripheral nerves have the capacity to regenerate due to the presence of neuroprotective glia of the peripheral nervous system, Schwann cells. Upon peripheral nerve injury, Schwann cells create a permissive microenvironment for neuronal regrowth by taking up cytotoxic glutamate and secreting neurotrophic signaling molecules. Impaired peripheral nerve repair is often caused by a defective Schwann cell response after injury, and there is a critical need to develop new strategies to enhance nerve regeneration, especially in organisms with restricted regenerative potential, such as humans. One approach is to explore mechanisms in lower organisms, in which nerve repair is much more efficient. A recent study demonstrated that the antiparasitic drug, ivermectin, caused hyperinnervation of primordial eye tissue in <i>Xenopus laevis</i> tadpoles. Our study aimed to examine the role of ivermectin in mammalian nerve repair. We performed in vitro assays utilizing human induced neural stem cells (hiNSCs) in co-culture with human dermal fibroblasts (hDFs) and found that ivermectin-treated hDFs promote hiNSC proliferation and migration. We also characterized the effects of ivermectin on hDFs and found that ivermectin causes hDFs to uptake extracellular glutamate, secrete glial cell-derived neurotrophic factor, develop an elongated bipolar morphology, and express glial fibrillary acidic protein. Finally, in a corresponding in vivo model, we found that localized ivermectin treatment in a dermal wound site induced the upregulation of both glial and neuronal markers upon healing. Taken together, we demonstrate that ivermectin promotes peripheral nerve regeneration by inducing fibroblasts to adopt a glia-like phenotype.
March 82nd, 1859 (1859)

assumed a feminine appearance ; but birds, on the contrary, when the function of the ovary was destroyed, put on the male character.
Query performance prediction for IR (2012)

The goal of this tutorial is to expose participants to current research on query performance prediction. Participants will become familiar with state-of-the-art performance prediction methods, with common evaluation methodologies of prediction quality, and with potential applications that can utilize performance predictors. In addition, some open issues and challenges in the field will be discussed.
The Evolving Legacy of Japanese American Internment Redress: Next Steps We Can (and Should) Take (2012)

for Law and Equality's conference on Gordon Hirabayashi's life and contributions to civil liberties is both timely and significant.It is timely because Gordon recently passed on, and he was a man of extraordinary conviction and quiet courage.In challenging the United States government and its mass racial internment, he stood tall not only for Japanese Americans but for all Americans.It is significant because the issues his challenge raised-the role of the judiciary in protecting civil liberties during times of national distress and, later, the importance of redress for deep injustice-live on today in the