gebhart/patrepeval huggingface dataset:
Biochemical Insights on Degradation of Arabidopsis DELLA Proteins Gained From a Cell-Free Assay System (2009)

The phytohormone gibberellic acid (GA) regulates diverse aspects of plant growth and development. GA responses are triggered by the degradation of DELLA proteins, which function as repressors in GA signaling pathways. Recent studies in Arabidopsis thaliana and rice (Oryza sativa) have implied that the degradation of DELLA proteins occurred via the ubiquitin-proteasome system. Here, we developed an Arabidopsis cell-free system to recapitulate DELLA protein degradation in vitro. Using this cell-free system, we documented that Lys-29 of ubiquitin is the major site for ubiquitin chain formation to mediate DELLA protein degradation. We also confirmed the specific roles of GA receptors and multisubunit E3 ligase components in regulating DELLA protein degradation. In addition, blocking DELLA degradation with a PP1/PP2A phosphatase inhibitor in our cell-free assay suggested that degradation of DELLA proteins required protein Ser/Thr dephosphorylation activity. Furthermore, our data revealed that the LZ domain of Arabidopsis DELLA proteins is essential for both their stability and activity. Thus, our in vitro degradation system provides biochemical insights into the regulation of DELLA protein degradation. This in vitro assay system could be widely adapted for dissecting cellular signaling pathways in which regulated proteolysis is a key recurrent theme.
Bioelectronic silicon nanowire devices using functional membrane proteins (2009)

Modern means of communication rely on electric fields and currents to carry the flow of information. In contrast, biological systems follow a different paradigm that uses ion gradients and currents, flows of small molecules, and membrane electric potentials. Living organisms use a sophisticated arsenal of membrane receptors, channels, and pumps to control signal transduction to a degree that is unmatched by manmade devices. Electronic circuits that use such biological components could achieve drastically increased functionality; however, this approach requires nearly seamless integration of biological and manmade structures. We present a versatile hybrid platform for such integration that uses shielded nanowires (NWs) that are coated with a continuous lipid bilayer. We show that when shielded silicon NW transistors incorporate transmembrane peptide pores gramicidin A and alamethicin in the lipid bilayer they can achieve ionic to electronic signal transduction by using voltage-gated or chemically gated ion transport through the membrane pores.
A novel solution-stable, water-soluble prodrug type for drugs containing a hydroxyl or an NH-acidic group (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA novel solution-stable, water-soluble prodrug type for drugs containing a hydroxyl or an NH-acidic groupHans Bundgaard, Erik Falch, and Ejvind JensenCite this: J. Med. Chem. 1989, 32, 12, 2503–2507Publication Date (Print):December 1, 1989Publication History Published online1 May 2002Published inissue 1 December 1989https://pubs.acs.org/doi/10.1021/jm00132a001https://doi.org/10.1021/jm00132a001research-articleACS PublicationsRequest reuse permissionsArticle Views793Altmetric-Citations34LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Immunocytochemistry in the diagnosis of malignant melanoma. (1994)

The role of immunocytochemistry in the routine diagnosis of malignant melanoma is reviewed, with particular emphasis on the potential technical and pathological interpretive problems that may occur. Careful evaluation of the appropriate panel of markers is discussed, along with details of cross-reactivity of markers with tumours of non-melanocytic derivation. Future developments in immunocytochemistry within the field of proliferation indices assessments are highlighted.
Salicylic Acid Is a Systemic Signal and an Inducer of Pathogenesis-Related Proteins in Virus-Infected Tobacco (1991)

Nasser Yalpani, Paul Silverman, T. Michael A. Wilson, Daniel A. Kleier, Ilya Raskin, Salicylic Acid Is a Systemic Signal and an Inducer of Pathogenesis-Related Proteins in Virus-Infected Tobacco, The Plant Cell, Vol. 3, No. 8 (Aug., 1991), pp. 809-818
NOD-like receptors in the human upper airways: a potential role in nasal polyposis (2011)

The present study demonstrates the presence of NLRs in several upper airway tissues and highlights a potential role of NLRs in chronic rhinosinusitis with polyps.
PECULIAR IMMUNOBIOLOGY OF BONE MARROW ALLOGRAFTS (1971)

Mice are capable of rejecting H-2-incompatible bone marrow grafts after a single lethal exposure to X-rays. The onset of rejection begins 18-24 hr after transplantation and is completed by 96 hr. Maturation of this type of allograft reactivity does not occur until the 22nd day of life. In adult mice, the resistance to marrow allografts can be weakened by administration of cyclophosphamide or dead cultures of Corynebacterium parvum, but not heterologous anti-thymocyte serum. Sublethal exposures to X-rays 7 or 14 days before transplantation also weaken resistance. There is considerable interstrain variation in the ability of mice to resist allografts, even when H-2 differences between hosts and donor are kept identical. Although H-2 incompatibility is a necessary prerequisite for resistance, additional genetic factors influence the outcome of marrow allografts, presumably by controlling recognition. The regulator genes are determinant specific and the alleles for resistance or responder status appear to be dominant. The responder phenotype is expressed by hemopoietic cells and not by the environment. Accordingly, resistance is conferred to otherwise susceptible mice upon transfer of bone marrow cells but not of serum. The production and differentiation of effector cells for marrow graft rejection are thymus independent. In conclusion, bone marrow allografts elicit a particular transplantation reaction, previously unknown, in irradiated mice. Peculiar features of this reaction are the lack of proliferation of host lymphoid cells, tissue specificity, thymus independence, and regulation by genetic factors which apparently do not affect the fate of other grafts.
Glucokinase Regulatory Protein Genetic Variant Interacts with Omega-3 PUFA to Influence Insulin Resistance and Inflammation in Metabolic Syndrome (2011)

ClinicalTrials.gov NCT00429195.
Designing attentive cell phone using wearable eyecontact sensors (2002)

We present a prototype attentive cell phone that uses a low-cost EyeContact sensor and speech analysis to detect whether its user is in a face-to-face conversation. We discuss how this information can be communicated to callers to allow them to employ basic social rules of interrruption.
Fuzzy summaries in database mining (2002)

The problem of discovery in databases focuses on the issue of extracting knowledge from information contained in a database. We feel that fuzzy logic can provide a powerful tool to aid in this endeavor. In particular we feel that the the idea of a linguistic summary, can be an important vehicle for representing discovered knowledge. We describe some of the salient ideas related to the concept of linguistic summaries.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nucleotide sequence of the gene encoding the viral polymerase of avian pneumovirus (1996)

We report here the nucleotide sequence of the L gene of avian pneumovirus (APV). This is the second pneumovirus L gene and the second avian paramyxovirus L gene, following that of Newcastle disease virus, to be sequenced. The APV L gene is 6099 nucleotides long and encodes a single large ORF of 2004 amino acids. This makes the APV L protein the smallest to be described for any nonsegmented, negative-strand RNA virus. The protein contains six linear non-contiguous domains, a putative ATP-binding site and four polymerase motifs previously described for the L proteins of negative-strand RNA viruses. Phylogenetic analysis of domain III of 14 different L proteins suggests the pneumoviruses to be as distant in evolutionary terms from the other members of the Paramyxoviridae as are the Filoviridae.
Differential Activity of Nivolumab, Pembrolizumab and MPDL3280A according to the Tumor Expression of Programmed Death-Ligand-1 (PD-L1): Sensitivity Analysis of Trials in Melanoma, Lung and Genitourinary Cancers (2015)

Overall, the three antibodies provide a significant differential effect in terms of activity according to PD-L1 expression on tumor cells. The predictive value of PD-L1 on tumor cells seems to be more robust for anti-PD-1 antibody (nivolumab and pembrolizumab), and in the context of advanced melanoma and NSCLC.
Accuracy criterion for ultrashort pulse characterization techniques: application to spectral phase interferometry for direct electric field reconstruction (2002)

We propose a procedure for the comparison of two ultrashort optical pulses based on the root-mean-square field error. This procedure supplies a practical criterion that allows one to test the accuracy of pulse characterization techniques. We apply this procedure to spectral phase interferometry for direct electric field reconstruction (SPIDER), a method that uses shearing interferometry in the frequency domain to measure ultrashort light pulses. Two novel reconstruction algorithms are described in detail, one based on the reconstruction of the spectral phase by concatenation, the other by integration. The range of validity of these algorithms and the influence of noise on the accuracy of the reconstruction are studied using the proposed criterion.
Up-regulation of bone marrow stromal protein 2 (BST2) in breast cancer with bone metastasis (2009)

These results provide novel data indicating the BST2 protein expression is associated with the formation of bone metastases in human breast cancer. We believe that BST2 may be a potential biomarker in breast cancer with bone metastasis.
Global Initiative for Chronic Obstructive Lung Disease (2002)

From the School of Health Related Professions (Dr Gerald); and the Lung Health Center, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham (Dr Gerald, Dr Bailey), Birmingham, Alabama. Address correspondence to: Lynn B. Gerald, PhD, MSPH, University of Alabama at Birmingham, Lung Health Center, NHB 104, 619 19th Street South, Birmingham, AL 35249-7337.
Sample-Audit Tax Assessment for Businesses: What's Fair? (1995)

How should a revenue agency assess a business taxpayer's income on the basis of a sample audit of transactions? The agency would like to maximize revenue while minimizing the risk that the taxpayer will be assessed more than he really owes. The taxpayer reasons that overassessment is worse than underassessment, as far as he is concerned, and therefore the taxpayer might reasonably argue that the lower bound of a one-sided confidence interval should be used by the assessor. The revenue agency might understandably take a different point of view. The revenue agency might argue that overassessment is really no worse than underassessment, from its point of view, so the midpoint of such a confidence interval should be used. In fact, it is this latter position that is currently in use most commonly by state agencies, but such practice is being challenged. The courts will have to make a decision.
Theories of Industrial Transformation (1998)

Many theories have been offered to explain industrial transformation. These include product cycle theory, development theory, dependency/ world system theory and statist theory. Among them, product cycle theory and statist theory have provided a useful way to understand the pattern of industrial transformation in Korea. I argue that product cycle theory and statist theory are useful, but incomplete to explain industrial transformation of Korea. Both theories neglect the effects of domestic politics on industrial transformations. Product cycle theory only reflects the economic mechanism of shifting industrial bases in a country. However, shift of industrial bases reflects domestic politics. Statist theory emphasizes that the national government is important in exercising its control over industrial transformation. However, it overlooks the political origin of the preferences of state incumbents. This chapter suggests coalition theory could fill the gap left by the two theories by examining the interaction between state incumbents and industrial groups.
Asymmetric Synthesis of β2,3‐Amino Acids by InI—Pd(0)‐Promoted Metalation and Addition of Chiral 2‐Vinylaziridines. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
Alkyl bridged complexes of the group 3A and lanthanoid metals as homogeneous ethylene polymerisation catalysts (1978)

The fully characterised group 3A and lanthanoid metal complexes [M(η-C5H4R)2Me]2(M;Y or Er, RH, Me, or SiMe3, and MYb, RH or Me) and [M(η-C5H4R)2Me2AlMe2](MY, Er, Ho, or Yb RH or Me, and MY, RSiMe3) are active homogenous ethylene polymerisation catalysts; they show an intramolecular deactivation process involving abstraction of a cyclopentadinyl hydrogen which is completely suppressed with peralkylated derivatives.
Gene encoding a minor extracellular protease in Bacillus subtilis (1988)

The gene for a minor, extracellular protease has been identified in Bacillus subtilis. The gene (epr) encoded a primary product of 645 amino acids that was partially homologous to both subtilisin (Apr) and the major internal serine protease (ISP-1) of B. subtilis. Deletion analysis indicated that the C-terminal 240 amino acids of Epr were not necessary for activity. This C-terminal region exhibited several unusual features, including a high abundance of lysine residues and the presence of a partially homologous sequence of 44 amino acids that was directly repeated five times. The epr gene mapped near sacA and was not required for growth or sporulation.
Studies on the Biosynthesis of Antibiotics (1986)

In the framework of studies on the biosynthesis of several antibiotics, specifically asukamycin, acarbose, reductiomycin, actinorhodin, and granaticin, a variety of different approaches to biosynthetic problems are illustrated. These include multiple labeling with stable isotopes in conjunction with modern methods of nmr analysis, as illustrated by the development of a new triple-quantum 2D-INADEQUATE experiment for biosynthetic studies, the use of stereochemical probes, as illustrated by the synthesis and stereochemical analysis of chiral [13C, 2H]malonate, and combinations of genetic and chemical approaches, as illustrated by examples of the production of new hybrid antibiotics by genetic engineering.
Extracellular Vpr protein increases cellular permissiveness to human immunodeficiency virus replication and reactivates virus from latency (1995)

The vpr gene product of human immunodeficiency virus (HIV) and simian immunodeficiency virus is a virion-associated regulatory protein that has been shown using vpr mutant viruses to increase virus replication, particularly in monocytes/macrophages. We have previously shown that vpr can directly inhibit cell proliferation and induce cell differentiation, events linked to the control of HIV replication, and also that the replication of a vpr mutant but not that of wild-type HIV type 1 (HIV-1) was compatible with cellular proliferation (D. N. Levy, L. S. Fernandes, W. V. Williams, and D. B. Weiner, Cell 72:541-550, 1993). Here we show that purified recombinant Vpr protein, in concentrations of < 100 pg/ml to 100 ng/ml, increases wild-type HIV-1 replication in newly infected transformed cell lines via a long-lasting increase in cellular permissiveness to HIV replication. The activity of extracellular Vpr protein could be completely inhibited by anti-Vpr antibodies. Extracellular Vpr also induced efficient HIV-1 replication in newly infected resting peripheral blood mononuclear cells. Extracellular Vpr transcomplemented a vpr mutant virus which was deficient in replication in promonocytic cells, restoring full replication competence. In addition, extracellular Vpr reactivated HIV-1 expression in five latently infected cell lines of T-cell, B-cell, and promonocytic origin which normally express very low levels of HIV RNA and protein, indicating an activation of translational or pretranslational events in the virus life cycle. Together, these results describe a novel pathway governing HIV replication and a potential target for the development of anti-HIV therapeutics.
Vascular cell adhesion molecule-Ig fusion protein selectively targets activated α 4-integrin receptors in vivo. Inhibition of autoimmune diabetes in an adoptive transfer model in nonobese diabetic mice (1995)

The alpha 4 beta 1-integrin (CD49d, CD29) constitutively expressed on leukocytes regulates cell migration to inflammatory sites, cell activation, and development through its interactions with two alternate ligands, vascular cell adhesion molecule-1 (VCAM-1; CD106) expressed on cytokine-activated endothelium, dendritic and stromal cells, and the extracellular matrix protein fibronectin. Another alpha 4-integrin receptor, alpha 4 beta 7, expressed on leukocytes also binds VCAM-1 and fibronectin (FN), and controls homing to mucosal tissues through its interactions with mucosal vascular addressin MAdCAM-1. In vitro studies have shown that alpha 4-dependent cell adhesion is regulated by the activation state of the cell and by divalent cations. However, the existence and role of cells with different alpha 4 activation states in vivo have not been defined. Herein we show that a soluble ligand with the two N-terminal domains of human VCAM-1 fused to a human IgG1 constant region, VCAM-Ig, binds selectively to activated alpha 4-receptors on murine cells, such as those induced by Mn2+ in vitro. To determine whether the cells identified by VCAM-Ig were required under physiologic conditions, we assessed its anti-inflammatory effect. We show that VCAM-Ig is not bound to the majority of murine alpha 4+ cells after in vivo administration, yet it significantly delays the onset of adoptively transferred autoimmune diabetes. Thus, soluble VCAM-Ig can modify alpha 4-dependent disease progression, apparently by its selective action on cells with activated alpha 4-integrin receptors, thereby providing evidence for distinct alpha 4 activation states in vivo.
Micromachined piezoresistive cantilever array with integrated resistive microheater for calorimetry and mass detection (2001)

We describe a microcantilever calorimeter consisting of an array of ten cantilevers. Each single cantilever is capable of detecting heat energy with the resolution of 50 nW Hz(−0.5). The device is based on a Si microcantilever coated with a 1 μm thick layer of SiO2 deposited with a 700 nm thick layer of aluminum which forms a resistive microheater. Heat fluxes are monitored by detecting the cantilever deflection (bending) due to the bimaterial structure of the cantilever (dissimilar thermal expansion properties of SiO2 and Al). The resistive microheater serves for calibration of the heat flux and for temperature sensing. In our design a piezoresistive Wheatstone bridge detector is applied for measurements of the cantilever beam deflection. The cantilever displacement detection system enables investigations in ultrahigh vacuum and low temperature conditions. The microcantilevers are manufactured in a one-dimensional array having ten individual microcantilevers which is the first step in the fabrication of an infrared detector array with spatial resolution. The displacement sensitivity versus temperature change of the described sensor array as a function of temperature change is of about 2 nm/K and an estimated resolution limit of temperature detection is ≈10−3 K at 300 K. In order to demonstrate the cantilever bending sensitivity we employ the piezoresistive cantilever array as a picogram microbalance.
A speech packet recovery technique using a model based tree search interpolator (2005)

A new packet interpolation method based on tree searching with an AR metric is presented. Theoretical and simulation results are compared against an MMSE interpolator and an embedded DPCM system with probability of high order packet loss.
Evaluating the ‘Labeled Magnitude Scale’ for Measuring Sensations of Taste and Smell (1996)

The Labeled Magnitude Scale (LMS) is a semantic scale of perceptual intensity characterized by a quasi-logarithmic spacing of its verbal labels. The LMS had previously been shown to yield psychophysical functions equivalent to magnitude estimation (ME) when gustatory, thermal and nociceptive stimuli were presented and rated together, and the upper bound of the LMS was defined as the 'strongest imaginable oral sensation'. The present study compared the LMS to ME within the more limited contexts of taste and smell. In Experiment 1, subjects used both methods to rate either taste intensity produced by sucrose and NaC1 or odor intensity produced by acetic acid and phenyl ethyl alcohol, with the upper bound of the LMS defined as either the 'strongest imaginable taste' or the 'strongest imaginable odor'. The LMS produced psychophysical functions equivalent to those produced by ME. In, Experiment 2 a new group of subjects used both methods to rate the intensity of three different taste qualities, with the upper bound of the LMS defined as the 'strongest imaginable [sweetness, saltiness, or bitterness]'. In all three cases the LMS produced steeper functions than did ME. Experiment 3 tested the hypothesis that the LMS yields data comparable to ME only when the perceptual domain under study includes painful sensations. This hypothesis was supported when the LMS again produced steeper functions that ME after subjects had been explicitly instructed to omit painful sensations (e.g. the 'burn' of hot peppers) from the concept of 'strongest imaginable taste'. We conclude that the LMS can be used to scale sensations of taste and smell when they are broadly defined, but that it should be modified for use in scaling specific taste (and probably odor) qualities. The implications of these results for theoretical issues related to ME, category-ratio scales and the size of the perceptual range in different sensory modalities are discussed.
Smoothing and Adaptive Redistribution for Grids with Irregular Valence and Hanging Nodes. (2004)

We describe some extensions to the grid smoothing scheme described in [1, 2] that deal with the following issues: 1) the clustering e#ect of changing valence in an unstructured grid and, in particular, the choice of the shape and size control weighting both locally and globally; 2) an analysis of the angle bounds achievable through the new smoothing algorithm under shape control; 3) the extension of the approach to 3D with an application to a 3D grid generated by CUBIT; 4) the use of alternative metrics to provide clustering based on an approximate solution; 5) the treatment of constraints on boundaries and at hanging nodes introduced through adaptive refinement applied in conjunction with interior grid smoothing. The results of numerical studies are included to demonstrate the performance of the resulting schemes.