gebhart/patrepeval huggingface dataset:
Direct Activation of the Fission Yeast PAK Shk1 by the Novel SH3 Domain Protein, Skb5 (1999)

The p21-activated kinase (PAK) homolog Shk1 is essential for cell viability in the fission yeast Schizosaccharomyces pombe. Roles have been established for Shk1 in the regulation of cell morphology, sexual differentiation, and mitosis in S. pombe. In this report, we describe the genetic and molecular characterization of a novel SH3 domain protein, Skb5, identified as a result of a two-hybrid screen for Shk1 interacting proteins. S. pombe cells carrying a deletion of the skb5 gene exhibit no discernible phenotypic defects under normal growth conditions, but when subjected to hypertonic stress, become spheroidal in shape and growth impaired. Both of these defects can be suppressed by overexpression of the Shk1 modulator, Skb1. The growth inhibition that results from overexpression of Shk1 in S. pombe cells is markedly suppressed by a null mutation in the skb5 gene, suggesting that Skb5 contributes positively to the function of Shk1 in vivo. Consistent with this notion, we show that Skb5 stimulates Shk1 catalytic function in S. pombe cells. Furthermore, and perhaps most significantly, we show that bacterially expressed recombinant Skb5 protein directly stimulates the catalytic activity of recombinant Shk1 kinase in vitro. These and additional data described herein demonstrate that Skb5 is a direct activator of Shk1 in fission yeast.
Improved preservation of rat epididymal sperm for high‐resolution low‐voltage scanning electron microscopy (HR‐LVSEM) (1993)

Abstract Various fixation protocols were used in an attempt to improve preservation of rat epididymal sperm for high‐resolution low‐voltage scanning electron microscopy (HR‐LVSEM). Wash solutions and fixatives of different composition and osmolarity were tested. Paraformaldehyde and glutaraldehyde concentrations were varied between 0.5% and 3%. Ruthenium red was tested as an additive in both primary fixation and postfixation, or in postfixation alone. HR‐LVSEM revealed various degrees of ruffing, folding, blebbing, and peeling off of the plasma membrane, as well as holes of different sizes. The plasma membrane overlying the acrosome and the connecting piece proved to be particularly sensitive to varying fixation conditions. Consistent topographical differences were revealed among the different domains over the sperm head. Most of the differences were considered to be artifacts. Their consistency, however, suggests that structural and biochemical differences exist either within the membrane or in the structures subjacent to the membrane. Primary fixation turned out to be less critical than postfixation. Preservation of a smooth plasma membrane without holes could only be achieved when primary fixation in low aldehyde concentrations, with or without ruthenium red, was followed by postfixation with OsO 4 and 1,000 ppm ruthenium red. Examination of thin sections of the same material confirmed that even a considerable number of small holes are difficult to detect in transmission electron microscopy. These results show that with the recent increase in resolution of LVSEM there is need for further effort to improve sample processing. © 1993 Wiley‐Liss, Inc.
Luminescent Silica Nanobeads:  Characterization and Evaluation as Efficient Cytoplasmatic Transporters for T-Lymphocytes (2007)

We report the fabrication and characterization of neutravidin-conjugated silica nanobeads doped with a ruthenium-complex luminophore and functionalized with antihuman CD3, antihuman CD28, and an acid-sensitive polymer. We observed that the nanobeads were readily delivered into Jurkat T leukemia cells by endocytosis, transported into lysosomes and subsequently into the cytoplasm as revealed by pH-sensitive luminescence. Since signs of cytotoxicity were not observed, the reported nanobeads could be an excellent and nontoxic building block for efficient intracellular transporters.
Nano-Bio-Chip Sensor Platform for Examination of Oral Exfoliative Cytology (2010)

Oral cancer is a deadly and disfiguring disease that could greatly benefit from new diagnostic approaches enabling early detection. In this pilot study, we describe a nano-bio-chip (NBC) sensor technique for analysis of oral cancer biomarkers in exfoliative cytology specimens, targeting both biochemical and morphologic changes associated with early oral tumorigenesis. Here, oral lesions from 41 dental patients, along with normal epithelium from 11 healthy volunteers, were sampled using a noninvasive brush biopsy technique. Specimens were enriched, immunolabeled, and imaged in the NBC sensor according to previously established assays for the epidermal growth factor receptor (EGFR) biomarker and cytomorphometry. A total of 51 measurement parameters were extracted using custom image analysis macros, including EGFR labeling intensity, cell and nuclear size, and the nuclear-to-cytoplasmic ratio. Four key parameters were significantly elevated in both dysplastic and malignant lesions relative to healthy oral epithelium, including the nuclear area and diameter (P < 0.0001), the nuclear-to-cytoplasmic ratio (P < 0.0001), and EGFR biomarker expression (P < 0.03). Further examination using logistic regression and receiver operating characteristic curve analyses identified morphologic features as the best predictors of disease (area under the curve < or =0.93) individually, whereas a combination of all features further enhanced discrimination of oral cancer and precancerous conditions (area under the curve, 0.94) with high sensitivity and specificity. Further clinical trials are necessary to validate the regression model and evaluate other potential biomarkers, but this pilot study supports the NBC sensor technique as a promising new diagnostic tool for early detection of oral cancer, which could enhance patient care and survival.
Derivation and Validation of a Simple Perioperative Sleep Apnea Prediction Score (2010)

The P-SAP score predicts diagnosis of OSA with dependable accuracy across mild to severe disease. The elements of the P-SAP score are derived from a typical university hospital surgical population.
E2F-4, a new member of the E2F transcription factor family, interacts with p107. (1994)

The E2F family of transcription factors has been implicated in the regulation of cell proliferation, and E2F-binding sites are present in the promoters of several growth-regulating genes. E2F family members are functionally regulated, in part, by complex formation with one or more members of the nuclear pocket protein family, RB, p107, and p130. Pocket protein regulation of E2F likely contributes to normal cellular growth control. While the three cloned species of E2F, E2F-1, E2F-2, and E2F-3, are known to be targets of RB interaction, no E2F species has yet been shown to be a specific p107 or p130 target. Here, we describe the cloning of a new member of the E2F family, E2F-4, which forms heterodimers with a member(s) of the DP family and, unlike some family members, is present throughout the cell cycle and appears to be a differentially phosphorylated p107-binding partner. p107 binding not only can be linked to the regulation of E2F-4 transcriptional activity, but also to suppression of the ability of E2F-4 to transform an immortalized rodent cell line.
Towards an Agile Infrastructure to Provision Devices, Applications, and Networks: A Service-oriented Approach (2007)

Most industries and organizations use collections of tools, devices, and applications that are growing in complexity. New tools or applications may be acquired and old tools may become obsolete over time. They are often running on a variety of platforms, have different bandwidth and QoS requirements, and in most cases they cannot be accessed through a single point of entry. Moreover, some tools may require specific configurations done by technical experts. To address these issues, we propose an extensible, reliable, and simple software architecture that can hide the complexity of provisioning the network and running the tools. This paper introduces a service-oriented approach for creating an agile infrastructure to provision devices, applications, and their underlying networks. The Eucalyptus prototype is developed as an empirical application to test this approach. Eucalyptus is built on a set of generic fine-grained Web services to manage and configure available resources, where new resources can be custom-built or imported from a third party. They can be integrated into Eucalyptus using a set of Web service-enabled APIs. Our user community consists of architects and industrial designers. Eucalyptus can manage and configure the resources needed by geographically distributed groups of architects who need to collaborate in real time on the design of buildings, in a virtual participatory design studio (PDS). Eucalyptus provides a single point of entry for the architects to access a wide variety of tools: videoconference applications, visualization services, rendering services employing parallel computers, etc. Eucalyptus provides a set of upper layer services for users to provision devices and applications running on high-speed broadband networks, as well as the commercial IP networks.
Regulation of Growth Hormone (GH) Bioactivity by a Recombinant Human GH-Binding Protein* (1990)

The in vitro biological effects of serum GH-binding protein (GHBP) were measured in the mouse 3T3-F442A preadipocyte adipogenesis assay during GH stimulation. Coincubation of increasing concentrations of human (h) GH (0.14-4.5 nM) with 4.2 nM recombinant hGHBP-(1-247) in serum-free medium shifted the hGH dose-response curve to the right over the range 0.14-0.9 nM. When the hGH concentration was fixed at 0.45 nM, a dose-dependent inhibition of GH bioactivity was seen over the range of 0.1-11.3 nM GHBP, with an ED50 of 3 nM. The presence of serum had no effect on the inhibitory properties of GHBP. When 2% pooled human serum was added to incubation medium containing 0.45 nM hGH and GHBP (0.6 nM-5.7 nM), the effect of GHBP was again inhibitory, with an ED50 of 1.2 nM. Two percent serum alone was adipogenic, but at this low serum concentration it is likely that some factor other than GH is responsible. In a homologous receptor assay, the binding of [125I]hGH to IM-9 lymphocytes was inhibited in a dose-dependent manner by increasing concentrations of hGHBP in the physiological range, providing further support for the idea that GHBP can regulate the bioactivity of GH by blocking the binding of free GH to target tissues in vivo. Our results suggest that one function of GHBP is to dampen the biological effects of pulsatile GH secretion by reducing free GH during secretory pulses. This effect combined with an increased half-life of circulating GH would have the effect of flattening the hormone secretory profile at the target tissue level.
Plaque Dissociation of Herpes Simplex Viruses: Biochemical and Biological Characters of the Viral Variants (1975)

Polycaryocytogenic (P) and non-polycaryocytogenic, or aggregating (A), stable variants were selected from a herpes simplex virus type 1 (HSV-1) and from a herpes simplex virus type 2 (HSV-2) which had not been deliberately exposed to known mutagenic agents. The P variant of HSV-1 (Fp) differed from the A variant (Fa) in polypeptides and glycoprotein patterns, but no gross differences were evident between the two variants of HSV-2 (Gp and Ga). Each P variant proved more ‘specific’ than each A variant in immune neutralization tests. At high multiplicity, Gp produced polycaryocytes but Fp did not. Virulence tests in mice showed Fp to be much more virulent than Fa but Ga to be more virulent than Gp. Finally, A and P variants of each type could not be differentiated with respect to thermal resistance of virions, capacity to grow at high temperature, and buoyant density of DNA.
Molecular Cloning and Identification of a Receptor-Type Protein Tyrosine Phosphatase, IA-2, from Human Insulinoma (1994)

A novel 3.6-kb cDNA, IA-2, with a 2,937-bp open reading frame was isolated from a human insulinoma subtraction library (ISL-153). The predicted amino acid sequence and in vitro-translated product of IA-2 cDNA revealed a 979-amino-acid protein with a pI value of 7.09 and a molecular mass of 105,847 daltons. The protein sequence is consistent with a signal peptide, an extracellular domain, a transmembrane region, and an intracellular domain. The extracellular domain contains an unusual cysteine-rich region following the signal peptide. The intracellular cytoplasmic domain of IA-2 possesses highly conserved regions similar to the catalytic domains found in members of the protein tyrosine phosphatase (PTP) family. Northern blot analysis showed that IA-2 mRNA was expressed in five of five freshly isolated human insulinomas, rat and mouse insulinoma cell lines, and enriched normal mouse islets. It also was found in normal human brain, pituitary, pancreas, and brain tumor cell lines, but not in a variety of other normal or tumor tissues. Based on the sequence and expression data, it appears that IA-2 is a new member of the receptor-type PTP family that is expressed in islet and brain tissues.
Crystallisation of Polymorphs:  Thermodynamic Insight into the Role of Solvent (2000)

Dependent on the conditions, crystallisation of polymorphs from solvent may be under kinetic or thermodynamic control. In the latter case the nature of the solvent will be immaterial in respect of the polymorph produced. The conditions under which each of these factors may apply are analysed in detail. The transition point between two dimorphs may not present a sharp divide in which crystallisation above and below the transition temperature produces the high melting and the low melting polymorph, respectively. It is shown that even in those cases where the choice of solvent appears to be critical this may be a secondary effect related to the concentration attainable in that solvent at a certain temperature rather than a specific effect dependent on solvent−solute interaction. A corollary to these considerations is the necessity to determine solubility curves and metastable zone widths in order to be able to control polymorph crystallisation.
Lactobacilli antagonize biological effects of enterohaemorrhagic Escherichia coli in vitro (2008)

Our findings give a rationale basis for the use of specific probiotic strains for the prophylaxis and prevention of intestinal infections due to EHEC.
Intersubband transitions in GaAs-AlxGa1−xAs modulation-doped superlattices (1987)

We have investigated infrared absorptions between electron subbands in GaAs-AlxGa1−xAs modulation-doped superlattices with constant layer thicknesses (70 Å for the GaAs layer and 180 Å for the AlxGa1−xAs layer) and a wide Al concentration range from 0.3 to 0.7. Sharp resonance absorptions from the ground state to the first excited state were detected in all samples. The transition energy increases from 130 to 170 meV as the Al concentration increases. From the observed transition energies (subband spacing) we estimate that the conduction-band discontinuity is around 63% of the difference between the direct band-gap energy of GaAs and that of AlxGa1−xAs in the Al concentration range used here.
Role of spleen tyrosine kinase in the pathogenesis of chronic lymphocytic leukemia (2014)

The antigen-dependent B-cell receptor (BCR) is triggered by binding to external antigens and transmits signals in normal B lymphocytes. Tonic signaling through the BCR plays a crucial role in the pathogenesis and progression of chronic lymphocytic leukemia (CLL). Spleen tyrosine kinase (Syk) is a key component of both BCR signals, and regulates multiple physiological functions of B lymphocytes. Studies have defined enhanced gene expression and protein expression of Syk in CLL cells which are closely related to the status of the immunoglobulin heavy chain variable region genes (IgVH). Recently, abrogating the BCR-induced signaling pathway by Syk inhibitors has represented a novel and active therapeutic approach for CLL. Studies of the correlation between Syk and ZAP-70 expression in CLL cells have brought a new perspective to determining the value of Syk in evaluating the effect of therapy and the prognosis of CLL. Therefore, we here review the role of Syk in the pathogenesis of CLL and provide an update of progress in the clinical development of Syk inhibitors.
An economical class of digital filters for decimation and interpolation (1981)

A class of digital linear phase finite impulse response (FIR) filters for decimation (sampling rate decrease) and interpolation (sampling rate increase) are presented. They require no multipliers and use limited storage making them an economical alternative to conventional implementations for certain applications. A digital filter in this class consists of cascaded ideal integrator stages operating at a high sampling rate and an equal number of comb stages operating at a low sampling rate. Together, a single integrator-comb pair produces a uniform FIR. The number of cascaded integrator-comb pairs is chosen to meet design requirements for aliasing or imaging error. Design procedures and examples are given for both decimation and interpolation filters with the emphasis on frequency response and register width.
Supramolecular hydrogel microcapsules via cucurbit[8]uril host–guest interactions with triggered and UV-controlled molecular permeability (2015)

Host-guest assembly in droplet-based microfluidics opens a new avenue for fabricating supramolecular hydrogel microcapsules with high monodispersity and controlled functionality. In this paper, we demonstrate a single emulsion microdroplet platform to prepare microcapsules with supramolecular hydrogel skins from host molecule cucurbit[8]uril and guest polymer anthracene-functionalized hydroxyethyl cellulose. In contrast to construction of microcapsules from a droplet-in-droplet double emulsion, here the electrostatic attraction between charged polymer and surfactant facilitates formation of defined supramolecular hydrogel skins in a single emulsion. Furthermore, by taking advantage of dynamic interactions and the tunable cross-linked supramolecular hydrogel network, it is possible to prepare microcapsules with triggered and UV-controlled molecular permeability. These could be potentially used in a delivery system for <i>e.g.</i> agrochemicals, nutraceuticals or cosmetics.
Convergence Results for Neural Networks via Electrodynamics (2018)

We study whether a depth two neural network can learn another depth two network using gradient descent. Assuming a linear output node, we show that the question of whether gradient descent converges to the target function is equivalent to the following question in electrodynamics: Given k fixed protons in R^d, and k electrons, each moving due to the attractive force from the protons and repulsive force from the remaining electrons, whether at equilibrium all the electrons will be matched up with the protons, up to a permutation. Under the standard electrical force, this follows from the classic Earnshaw's theorem. In our setting, the force is determined by the activation function and the input distribution. Building on this equivalence, we prove the existence of an activation function such that gradient descent learns at least one of the hidden nodes in the target network. Iterating, we show that gradient descent can be used to learn the entire network one node at a time.
Design, Synthesis, and StructureActivity Relationships for Chimeric Inhibitors of Hsp90 (2006)

Inhibition of the 90 kDa heat shock protein (Hsp90) family of molecular chaperones represents a promising new chemotherapeutic approach toward the treatment of several cancers. Previous studies have demonstrated that the natural products, radicicol and geldanamycin, are potent inhibitors of the Hsp90 N-terminal ATP binding site. The cocrystal structures of these molecules bound to Hsp90 have been determined, and through molecular modeling and superimposition of these ligands, hybrids of radicicol and geldanamycin have been designed. A series of macrocylic chimeras of radicicol and geldanamycin and the corresponding seco-agents have been prepared and evaluated for both antiproliferative activity and their ability to induce Hsp90-dependent client protein degradation.
Time Course of Synthesis and Assembly of Influenza Virus Proteins (1974)

The synthesis of viral polypeptides was analyzed in BHK-21-F cells infected with the WSN strain of influenza virus at various times in the growth cycle. The relative amounts of polypeptides P, HA, NP, and NS did not change markedly between early and late times in the growth cycle; however, there was a progressive increase in the relative amount of the M polypeptide at later time points. In cell fractionation experiments, the patterns of newly synthesized polypeptides associated with various cytoplasmic fractions remained similar throughout the growth cycle except for an increase in polypeptide M in all fractions late in the growth cycle. The HA polypeptide was chased out of cytoplasmic membranes completely 6 h after synthesis, whereas the M polypeptide was not chased effectively from such membranes. Marked differences were found in the incorporation into mature virions of polypeptides synthesized at different times in the growth cycle. Polypeptides P and NP synthesized at early times were incorporated preferentially, whereas M was synthesized and incorporated predominantly late in the growth cycle. The fact that the rates of incorporation of polypeptides into virions differed significantly from their rates of synthesis indicates that different polypeptides were assembled into virions by distinct pathways.
Carbon Dioxide's Liquid-Vapor Coexistence Curve And Critical Properties as Predicted by a Simple Molecular Model (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbon Dioxide's Liquid-Vapor Coexistence Curve And Critical Properties as Predicted by a Simple Molecular ModelJonathan G. Harris and Kwong H. YungCite this: J. Phys. Chem. 1995, 99, 31, 12021–12024Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/j100031a034https://doi.org/10.1021/j100031a034research-articleACS PublicationsRequest reuse permissionsArticle Views6785Altmetric-Citations1213LEARN 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 options Get e-Alerts