gebhart/patrepeval huggingface dataset:
FBW7 Loss Promotes Chromosomal Instability and Tumorigenesis via Cyclin E1/CDK2–Mediated Phosphorylation of CENP-A (2017)

The centromere regulates proper chromosome segregation, and its dysfunction is implicated in chromosomal instability (CIN). However, relatively little is known about how centromere dysfunction occurs in cancer. Here, we define the consequences of phosphorylation by cyclin E1/CDK2 on a conserved Ser18 residue of centromere-associated protein CENP-A, an essential histone H3 variant that specifies centromere identity. Ser18 hyperphosphorylation in cells occurred upon loss of FBW7, a tumor suppressor whose inactivation leads to CIN. This event on CENP-A reduced its centromeric localization, increased CIN, and promoted anchorage-independent growth and xenograft tumor formation. Overall, our results revealed a pathway that cyclin E1/CDK2 activation coupled with FBW7 loss promotes CIN and tumor progression via CENP-A-mediated centromere dysfunction. <i>Cancer Res; 77(18); 4881-93. ©2017 AACR</i>.
Three-dimensional ordered distribution of crystals in turkey tendon collagen fibers. (1989)

The organization of apatite crystals and collagen fibrils in mineralized turkey tendon has been studied by electron microscopy and electron diffraction. To minimize artifactual distortions the tissue was examined, for the first time, as isolated fibrils in an aqueous environment of vitreous ice, as well as in conventionally prepared sections. The electron micrographs show that the plate-shaped apatite crystals are arranged in parallel arrays across the collagen fibrils. This provides direct evidence for highly asymmetric assembly in collagen fibrils, and, indeed, the fibrils were observed to be elongated rather than round in cross-section. There is, furthermore, a pronounced tendency for the layers of crystals to be coherently aligned in adjacent fibrils. These observations may also be important for understanding the mechanical behavior of bone at the molecular level, as such extended, aligned aggregates of flat crystals could develop into natural fracture planes in mature bone.
Glycosylation and biogenesis of a family of serine-rich bacterial adhesins (2009)

Glycosylation of bacterial proteins is an important process for bacterial physiology and pathophysiology. Both O- and N-linked glycan moieties have been identified in bacterial glycoproteins. The N-linked glycosylation pathways are well established in Gram-negative bacteria. However, the O-linked glycosylation pathways are not well defined due to the complex nature of known O-linked glycoproteins in bacteria. In this review, we examine a new family of serine-rich O-linked glycoproteins which are represented by fimbriae-associated adhesin Fap1 of Streptococcus parasanguinis and human platelet-binding protein GspB of Streptococcus gordonii. This family of glycoproteins is conserved in streptococcal and staphylococcal species. A gene cluster coding for glycosyltransferases and accessory Sec proteins has been implicated in the protein glycosylation. A two-step glycosylation model is proposed. Two glycosyltransferases interact with each other and catalyse the first step of the protein glycosylation in the cytoplasm; the cross-talk between glycosylation-associated proteins and accessory Sec components mediates the second step of the protein glycosylation, an emerging mechanism for bacterial O-linked protein glycosylation. Dissecting the molecular mechanism of this conserved biosynthetic pathway offers opportunities to develop new therapeutic strategies targeting this previously unrecognized pathway, as serine-rich glycoproteins have been shown to play a role in bacterial pathogenesis.
Inhibition of allergic responses by CD40 gene silencing (2009)

The present study demonstrates a novel therapeutic use for siRNA in allergy. CD40 siRNA attenuated allergy through inhibition of DC and B cell functions and generation of regulatory T (Treg) cells.
Increased poly(ADP-ribose)polymerase activity in cells infected by human immunodeficiency virus type-1. (1991)

Poly(ADP-ribose)polymerase is a chromatin-bound enzyme which is activated by free DNA ends and is therefore stimulated by a variety of DNA-damaging agents. The enzyme transfers the ADP moiety of NAD to nuclear proteins to create protein-bound ADP-ribose polymers. Under conditions favouring an accelerated poly(ADP-ribose) polymer formation, the enzyme may exhaust cellular NAD pools. At the same time, or shortly thereafter ATP levels drop and cell viability eventually declines. As a series of chemical and physical agents which may play a role in activating latent HIV-1 infection or favouring HIV-1 replication, have a DNA-damaging activity, we investigated the behaviour of poly(ADP-ribose)polymerase activity in various types of HIV-1-infected cells. The results obtained show that HIV-1-infected cells to possess an increased poly(ADP-ribosol)ating activity together with an accentuated fragmentation of cellular DNA which are associated with the time course of HIV-1 replication. These data give circumstantial support to the hypothesis that a NAD-depdendent cellular suicide response to DNA damage, could play a role in the death of HIV-1 infected cells. In this respect, the impared immunocompetence of HIV-1-infected patients could bear some resemblance to immune attribution that sometimes accompanies some inborn errors affecting DNA precursor metabolism and DNA integrity.
Leydig Cell Function in Normal Men: Effect of Age, Life-Style, Residence, Diet, and Activity* (1984)

The decrease of plasma testosterone (T) in old age may be inherent to the aging process or secondary to environmental factors such as stress, minor illness, physical inactivity, etc. We determined plasma T, apparent free T, and gonadotropin levels in healthy men (n = 71), aged 26-90 yr living under identical conditions, i.e. as monks in a monastery. We found a highly significant age-dependent decrease in morning and mean 24-h T and apparent free T levels and a moderate increase in gonadotropin levels; the nycthemeral variation in plasma levels was, however, decreased in the elderly. In a larger group of healthy normal men (n = 302), smokers had higher T levels than nonsmokers in all age groups; values were similar whether older men lived in a geriatric institution or in their home. Diet had no discernable effect on T levels, whereas in young men plasma T levels decreased more in response to stress such as hypoglycemia or myocardial infarction than in elderly subjects. Moderate physical training in men, convalescing from myocardial infarction, did not alter consistently plasma T levels. We conclude that the age-associated decrease in plasma T levels is inherent to the aging process.
Tunable retina encoders for retina implants: why and how (2005)

Current research towards retina implants for partial restoration of vision in blind humans with retinal degenerative dysfunctions focuses on implant and stimulation experiments and technologies. In contrast, our approach takes the availability of an epiretinal multi-electrode neural interface for granted and studies the conditions for successful joint information processing of both retinal prosthesis and brain. Our proposed learning retina encoder (RE) includes information processing modules to simulate the complex mapping operation of parts of the 5-layered neural retina and to provide an iterative, perception-based dialog between RE and human subject. Alternative information processing technologies in the learning RE are being described, which allow an individual optimization of the RE mapping operation by means of iterative tuning with learning algorithms in a dialog between implant wearing subject and RE. The primate visual system is modeled by a retina module (RM) composed of spatio-temporal (ST) filters and a central visual system module (VM). RM performs a mapping 1 of an optical pattern P1 in the physical domain onto a retinal output vector R1(t) in a neural domain, whereas VM performs a mapping 2 of R1(t) in a neural domain onto a visual percept P2 in the perceptual domain. Retinal ganglion cell properties represent non-invertible ST filters in RE, which generate ambiguous output signals. VM generates visual percepts only if the corresponding R1(t) is properly encoded, contains sufficient information, and can be disambiguated. Based on the learning RE and the proposed visual system model, a novel retina encoder (RE*) is proposed, which considers both ambiguity removal and miniature eye movements during fixation. Our simulation results suggest that VM requires miniature eye movements under control of the visual system to retrieve unambiguous patterns P2 corresponding to P1. For retina implant applications, RE* can be tuned to generate optimal ganglion cell codes for epiretinal stimulation.
Inactivation of the Pseudomonas striata broad specificity amino acid racemase by D and L isomers of .beta.-substituted alanines: kinetics, stoichiometry, active site peptide, and mechanistic studies (1984)

Mechanism-based inactivators were used to probe the active site of the broad specificity amino acid racemase from Pseudomonas striata. Kinetic parameters for the inactivation of the racemase with both stereoisomers of beta-fluoroalanine, beta-chloroalanine, and O-acetylserine were determined. By use of 14C-labeled O-acetylserines, the stoichiometry of inactivator binding was found to be one inactivator bound per enzyme subunit. The PLP-dependent enzyme contains one coenzyme per subunit, and after NaB3H4 reduction of the PLP-imine bond, followed by trypsin digestion of the protein, the amino acid sequence of the PLP-binding peptide was determined. Trypsin digestion of the enzyme labeled with either L or D isomer of O-acetylserine and sequencing of the labeled peptide revealed that the inactivators bind to the same lysine residue which binds PLP in native enzyme. The characterization of a PLP adduct released from inactivated enzyme under some conditions is also described. Implications of the formation of this compound with respect to the overall reaction mechanism of inactivation are discussed.
Differential Regulation of Glycogen Synthase Kinase 3β by Insulin and Wnt Signaling (2000)

Glycogen synthase kinase 3beta (GSK3beta) is a key component in many biological processes including insulin and Wnt signaling. Since the activation of each signaling pathway results in a decrease in GSK3beta activity, we examined the specificity of their downstream effects in the same cell type. Insulin induces an increased activity of glycogen synthase but has no influence on the protein level of beta-catenin. In contrast, Wnt increases the cytosolic pool of beta-catenin but not glycogen synthase activity. We found that, unlike insulin, neither the phosphorylation status of the serine9 residue of GSK3beta nor the activity of protein kinase B is regulated by Wnt. Although the decrease in GSK3beta activity is required, GSK3beta may not be the limiting component for Wnt signaling in the cells that we examined. Our results suggest that the axin-conductin complexed GSK3beta may be dedicated to Wnt rather than insulin signaling. Insulin and Wnt pathways regulate GSK3beta through different mechanisms, and therefore lead to distinct downstream events.
Overview of candidate device technologies for storage-class memory (2008)

Storage-class memory (SCM) combines the benefits of a solid-state memory, such as high performance and robustness, with the archival capabilities and low cost of conventional hard-disk magnetic storage. Such a device would require a solid-state nonvolatile memory technology that could be manufactured at an extremely high effective areal density using some combination of sublithographic patterning techniques, multiple bits per cell, and multiple layers of devices. We review the candidate solid-state nonvolatile memory technologies that potentially could be used to construct such an SCM. We discuss evolutionary extensions of conventional flash memory, such as SONOS (silicon-oxide-nitride-oxide-silicon) and nanotraps, as well as a number of revolutionary new memory technologies. We review the capabilities of ferroelectric, magnetic, phase-change, and resistive random-access memories, including perovskites and solid electrolytes, and finally organic and polymeric memory. The potential for practical scaling to ultrahigh effective areal density for each of these candidate technologies is then compared.
Characterization of the chemical and antimicrobial properties of piscicolin 126, a bacteriocin produced by Carnobacterium piscicola JG126 (1996)

A novel peptide bacteriocin produced by the lactic acid bacterium Carnobacterium piscicola JG126 isolated from spoiled ham was purified and characterized. This bacteriocin, designated piscicolin 126, inhibited the growth of several gram-positive bacteria, especially the food-borne pathogen Listeria monocytogenes, but had no effect on the growth of a number of yeasts and gram-negative bacteria. Bactericidal activity was not destroyed by exposure to elevated temperatures at low pH values; however, bactericidal activity was lost at high pH values, especially when high pH values were combined with an elevated temperature. Piscicolin 126 activity was not affected by catalase, lipase, or lysozyme but was destroyed by exposure to a range of proteolytic enzymes. Piscicolin 126 was purified to homogeneity and was found to be a peptide having a molecular weight of 4,416.6 +/- 1.9. A sequence analysis revealed that this compound is a cystibiotic (class IIa) bacteriocin containing 44 amino acid residues and one intrapeptide disulfide ring. Piscicolin 126 has regions of homology with some other bacteriocins obtained from lactic acid bacteria and is most closely related to sakacin P and pediocin PA-1 (levels of identity, 75 and 55%, respectively). Addition of piscicolin 126 to a devilled ham paste test food system inhibited the growth of L. monocytogenes for at least 14 days. Piscicolin 126 was more effective than two commercially available bacteriocin preparations tested in the same system.
Cell Adhesion on a POEGMA-Modified Topographical Surface (2012)

It is well known that adsorbed proteins play a major role in cell adhesion. However, it has also been reported that cells can adhere to a protein-resistant surface. In this work, the behavior of L02 and BEL-7402 cells on a protein-resistant, 3D topographical surface was investigated. The topographical gold nanoparticle layer (GNPL) surfaces were prepared by chemical gold plating, and the topography was described by roughness parameters acquired from a multiscale analysis. Both smooth Au and GNPL surfaces were modified with POEGMA polymer brushes using surface-initiated ATRP. The dry and hydrated thicknesses of POEGMA brushes on both smooth and rough surfaces were measured by AFM using a nanoindentation method. Protein adsorption experiments using (125)I radiolabeling revealed similarly low levels of protein adsorption on smooth and GNPL surfaces modified with POEGMA, thus allowing an investigation of the effects of topography on cell behavior under conditions of minimal protein adsorption. The roles of VN and FN adsorption in both L02 cells and BEL-7402 cells adhesion were investigated using cell culturing with and without a serum supplement. It was found that initial cell adhesion occurred via proteins adsorbed from the cell culture medium, whereas subsequent durable cell adhesion could be attributed to the topographical structure of the surface. Although cell spreading on protein-resistant surfaces was constrained because of the lack of adsorbed proteins, we found that cells adherent to topographical surfaces were more firmly attached and thus were more durable compared to those on smooth surfaces. In general, however, we conclude that topography is more important for cell adhesion on a protein-resistant surface.
Preconcentration and Analysis of Trace Volatile Carbonyl Compounds (2011)

We describe a preconcentration device that may be suitable for quantitative analysis of trace volatile ketones and aldehydes in ambient air as well as in human breath. The approach is based on microreactor chips fabricated from silicon wafers. The microreactors have thousands of micropillars in microfluidic channels for uniformly distributing a gaseous sample flowing through the chips. The surfaces of the micropillars are functionalized with a quaternary ammonium aminooxy salt, [2-(aminooxy)ethyl]-N,N,N-trimethylammonium iodide (ATM), for trapping trace ketones and aldehydes by means of oximation reactions. ATM adducts and unreacted ATM are eluted from the microreactor with less than 40 μL of methanol and directly analyzed by nanospray Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS). Ketones and aldehydes at levels of 1 ppbv have been detected using this microreactor and FTICR-MS system.
In vivo antitumor activity of SU11248, a novel tyrosine kinase inhibitor targeting vascular endothelial growth factor and platelet-derived growth factor receptors: determination of a pharmacokinetic/pharmacodynamic relationship. (2003)

One challenging aspect in the clinical development of molecularly targeted therapies, which represent a new and promising approach to treating cancers, has been the identification of a biologically active dose rather than a maximum tolerated dose. The goal of the present study was to identify a pharmacokinetic/pharmacodynamic relationship in preclinical models that could be used to help guide selection of a clinical dose. SU11248, a novel small molecule receptor tyrosine kinase inhibitor with direct antitumor as well as antiangiogenic activity via targeting the vascular endothelial growth factor (VEGF), platelet-derived growth factor (PDGF), KIT, and FLT3 receptor tyrosine kinases, was used as the pharmacological agent in these studies. In mouse xenograft models, SU11248 exhibited broad and potent antitumor activity causing regression, growth arrest, or substantially reduced growth of various established xenografts derived from human or rat tumor cell lines. To predict the target SU11248 exposure required to achieve antitumor activity in mouse xenograft models, we directly measured target phosphorylation in tumor xenografts before and after SU11248 treatment and correlated this with plasma inhibitor levels. In target modulation studies in vivo, SU11248 selectively inhibited Flk-1/KDR (VEGF receptor 2) and PDGF receptor beta phosphorylation (in a time- and dose-dependent manner) when plasma concentrations of inhibitor reached or exceeded 50-100 ng/ml. Similar results were obtained in a functional assay of VEGF-induced vascular permeability in vivo. Constant inhibition of VEGFR2 and PDGF receptor beta phosphorylation was not required for efficacy; at highly efficacious doses, inhibition was sustained for 12 h of a 24-h dosing interval. The pharmacokinetic/pharmacodynamic relationship established for SU11248 in these preclinical studies has aided in the design, selection, and evaluation of dosing regimens being tested in human trials.
Comparison of the Various Methods Used in Solving Missing Data Problems (2016)

The aim of this study is to compare various methods used in solving missing data problems in terms of the validity and reliability of scale results under some conditions such as missing completely at the random mechanism, normal distribution, unidimensionality, a large sample size and different missing data rates. In the study the PISA 2012 Math Work Ethics Scale results of Turkey sample were used. In the research process estimated values of validity and reliability from original complete and new complete data sets of various methods were compared. The findings reveal that the estimated values of validity and reliability from the new complete data sets of the expectation maximization, regression imputation and multiple imputation methods are the most similar values estimated from the complete data set.
Lamination of polyethylene composite films by ultrasonic welding: Investigation of peel behavior and identification of optimum welding parameters (2013)

Abstract The lamination of different polyethylene (PE) composite films by ultrasonic welding to fabricate peelable seals that open at defined burst pressures is investigated. The sealing time, pressure, and amplitude were varied within the range of 100–400 ms, 50–250 kPa, and 12–24 µm, respectively. T‐peel tests and electron micrographs revealed four different peel regimes, depending on the parameter combination: (I) Interlaminar peeling at low‐peel strength with uniform peeling along a weakly bonded PE lamination layer; (II) transition tearing at intermediate peel strength showing areas of interlaminar peeling and translaminar tearing; (III) translaminar tearing at high‐peel strength showing tears through the entire film; and, (IV) undefined tearing at varying tear strength occurring when vibration effects during welding lead to insufficient contact of the films or high pressures lead to a displacement of PE. This study will allow the systematic adjustment of ultrasonic welding parameters for PE films. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131 , 40291.
Unconventional Repertoire Profile Is Imprinted during Acute Chikungunya Infection for Natural Killer Cells Polarization toward Cytotoxicity (2011)

Chikungunya virus (CHIKV) is a worldwide emerging pathogen. In humans it causes a syndrome characterized by high fever, polyarthritis, and in some cases lethal encephalitis. Growing evidence indicates that the innate immune response plays a role in controlling CHIKV infection. We show here that CHIKV induces major but transient modifications in NK-cell phenotype and function soon after the onset of acute infection. We report a transient clonal expansion of NK cells that coexpress CD94/NKG2C and inhibitory receptors for HLA-C1 alleles and are correlated with the viral load. Functional tests reveal cytolytic capacity driven by NK cells in the absence of exogenous signals and severely impaired IFN-γ production. Collectively these data provide insight into the role of this unique subset of NK cells in controlling CHIKV infection by subset-specific expansion in response to acute infection, followed by a contraction phase after viral clearance.
Absorption of triglycerides with defined or random structure by rats with biliary and pancreatic diversion (1995)

Fat absorption may be compromised by pancreatic or bile insufficiency, resulting in low uptake of essential fatty acid and energy. Using a rat model of malabsorption, we examined the absorption of defined triglycerides with medium-chain fatty acids (MCFA) in the sn-1,3 positions and essential fatty acids in the sn-2 position (MLM) compared to other fats. The thoracic duct was cannulated for collection of lymph, and the common bile and pancreatic duct was cannulated to divert both the pancreatic juice and bile. The rats were given a single bolus of triglyceride as a taurocholate emulsion. Fat absorption was measured from collected lymph samples. The triglycerides administered were a defined triglyceride, MLM [mainly (8:0/10:0)-(18:2n-6)-(8:0/10:0)], a similar triglyceride subjected to chemical randomization, a mixture of medium-chain triglycerides and soybean oil, and soybean oil, respectively. The first three triglycerides had approximately 36 wt% linoleic acid (18:2n-6) content. Administration of defined triglyceride was followed by significantly higher lymphatic level (wt%) of 18:2n-6 (P < 0.01) as well as a relative enhancement in mol% of 18:2n-6 (P < 0.05) compared to the other triglycerides. Lymphatic absorption of MCFA was similar in the three first groups but not as efficient as for long-chain fatty acids. Our results indicate that defined triglycerides thus may provide a means to increase absorption of essential fatty acids in fat malabsorption, such as that seen in cystic fibrosis, or for pre-term infants.