gebhart/patrepeval huggingface dataset:
Phosphorylation of p53 Is Regulated by TPX2-Aurora A in Xenopus Oocytes (2009)

p53 is an important tumor suppressor regulating the cell cycle at multiple stages in higher vertebrates. The p53 gene is frequently deleted or mutated in human cancers, resulting in loss of p53 activity. This leads to centrosome amplification, aneuploidy, and tumorigenesis, three phenotypes also observed after overexpression of the oncogenic kinase Aurora A. Accordingly, recent studies have focused on the relationship between these two proteins. p53 and Aurora A have been reported to interact in mammalian cells, but the function of this interaction remains unclear. We recently reported that Xenopus p53 can inhibit Aurora A activity in vitro but only in the absence of TPX2. Here we investigate the interplay between Xenopus Aurora A, TPX2, and p53 and show that newly synthesized TPX2 is required for nearly all Aurora A activation and for full p53 synthesis and phosphorylation in vivo during oocyte maturation. In vitro, phosphorylation mediated by Aurora A targets serines 129 and 190 within the DNA binding domain of p53. Glutathione S-transferase pull-down studies indicate that the interaction occurs via the p53 transactivation domain and the Aurora A catalytic domain around the T-loop. Our studies suggest that targeting of TPX2 might be an effective strategy for specifically inhibiting the phosphorylation of Aurora A substrates, including p53.
Designing multifunctional quantum dots for bioimaging, detection, and drug delivery (2010)

The emerging field of bionanotechnology aims at revolutionizing biomedical research and clinical practice via introduction of nanoparticle-based tools, expanding capabilities of existing investigative, diagnostic, and therapeutic techniques as well as creating novel instruments and approaches for addressing challenges faced by medicine. Quantum dots (QDs), semiconductor nanoparticles with unique photo-physical properties, have become one of the dominant classes of imaging probes as well as universal platforms for engineering of multifunctional nanodevices. Possessing versatile surface chemistry and superior optical features, QDs have found initial use in a variety of in vitro and in vivo applications. However, careful engineering of QD probes guided by application-specific design criteria is becoming increasingly important for successful transition of this technology from proof-of-concept studies towards real-life clinical applications. This review outlines the major design principles and criteria, from general ones to application-specific, governing the engineering of novel QD probes satisfying the increasing demands and requirements of nanomedicine and discusses the future directions of QD-focused bionanotechnology research (critical review, 201 references).
Dependency models as a basis for analyzing software product platform modularity : a case study in strategic software design rationalization (2006)

The root package node, a special, empty node.
Synthesis of 2-Methyl-(Z)-4-(phenylimino)naphth[2,3-d]oxazol-9-one, a Monoimine Quinone with Selective Cytotoxicity toward Cancer Cells (1994)

A regio and stereospecific synthesis of 2-methyl-(Z)-4-(phenylimino)naphth[2,3-d]oxazol-9-one (1) was achieved by using titanium tetrachloride in methylene chloride in the preparation of the imine. The regiochemistry was assigned by single-crystal X-ray analysis. In vitro tests showed that this diastereomer is selectively active for some solid cancer tumors.
Development of a multiplex methylation-specific PCR as candidate triage test for women with an HPV-positive cervical scrape (2012)

Multiplex qMSP offers a promising approach for high-throughput diagnostic analysis of the methylation status of multiple genes, which after proper design and validation can be equally specific, sensitive and reproducible as its singleplex versions.
G-CSF potently inhibits osteoblast activity and CXCL12 mRNA expression in the bone marrow (2005)

Accumulating evidence indicates that interaction of stromal cell-derived factor 1 (SDF-1/CXCL12 [CXC motif, ligand 12]) with its cognate receptor, CXCR4 (CXC motif, receptor 4), generates signals that regulate hematopoietic progenitor cell (HPC) trafficking in the bone marrow. During granulocyte colony-stimulating factor (G-CSF)-induced HPC mobilization, CXCL12 protein expression in the bone marrow decreases. Herein, we show that in a series of transgenic mice carrying targeted mutations of their G-CSF receptor and displaying markedly different G-CSF-induced HPC mobilization responses, the decrease in bone marrow CXCL12 protein expression closely correlates with the degree of HPC mobilization. G-CSF treatment induced a decrease in bone marrow CXCL12 mRNA that closely mirrored the fall in CXCL12 protein. Cell sorting experiments showed that osteoblasts and to a lesser degree endothelial cells are the major sources of CXCL12 production in the bone marrow. Interestingly, osteoblast activity, as measured by histomorphometry and osteocalcin expression, is strongly down-regulated during G-CSF treatment. However, the G-CSF receptor is not expressed on osteoblasts; accordingly, G-CSF had no direct effect on osteoblast function. Collectively, these data suggest a model in which G-CSF, through an indirect mechanism, potently inhibits osteoblast activity resulting in decreased CXCL12 expression in the bone marrow. The consequent attenuation of CXCR4 signaling ultimately leads to HPC mobilization.
Contract-based load management in federated distributed systems (2004)

This paper focuses on load management in looselycoupled federated distributed systems. We present a distributed mechanism for moving load between autonomous participants using bilateral contracts that are negotiated offline and that set bounded prices for moving load. We show that our mechanism has good incentive properties, efficiently redistributes excess load, and has a low overhead in practice.
A Genetic Method for Determining the Order of Events in a Biological Pathway (1973)

We describe the application of a simple genetic test that indicates the order of events in a morphogenic or biochemical pathway. The test uses temperature-sensitive (ts) and cold-sensitive (cs) mutants, and it orders the times at which the ts and cs defects are expressed.
Influences of Centrifugation on Cells and Tissues in Liposuction Aspirates: Optimized Centrifugation for Lipotransfer and Cell Isolation (2008)

Excessive centrifugation can destroy adipocytes and adipose-derived stem cells, but appropriate centrifugation concentrates them, resulting in enhanced graft take. The authors tentatively recommend 1200 g as an optimized centrifugal force for obtaining good short- and long-term results in adipose transplantation.
Heterocyclic Analogues ofN-(4-(4-(2,3-Dichlorophenyl)piperazin-1-yl)butyl)arylcarboxamides with Functionalized Linking Chains as Novel Dopamine D3 Receptor Ligands:  Potential Substance Abuse Therapeutic Agents (2007)

Dopamine D3 receptor antagonists and partial agonists have been shown to modulate drug-seeking effects induced by cocaine and other abused substances. Compound 6 [PG01037, (N-(4-(4-(2,3-dichlorophenyl)piperazin-1-yl)-trans-but-2-enyl)-4-pyridine-2-ylbenzamide)] and related analogues are currently being evaluated in animal models of drug addiction. In these studies, a discrepancy between in vitro binding affinity, in vivo occupancy, and behavioral potency has been observed. The purpose of this study was to examine (1) modifications of the 2-pyridylphenyl moiety of 6 and (2) hydroxyl, acetyl, and cyclopropyl substitutions on the butylamide linking chain systematically coupled with 2-fluorenylamide or 2-pyridylphenylamide and 2-methoxy- or 2,3-dichloro-substituted phenylpiperazines to measure the impact on binding affinity, D2/D3 selectivity, lipophilicity, and function. In general, these modifications were well tolerated at the human dopamine D3 (hD3) receptor (Ki = 1-5 nM) as measured in competition binding assays. Several analogues showed >100-fold selectivity for dopamine D3 over D2 and D4 receptors. In addition, while all the derivatives with an olefinic linker were antagonists, in quinpirole-stimulated mitogenesis at hD3 receptors, several of the hydroxybutyl-linked analogues (16, 17, 21) showed partial agonist activity. Finally, several structural modifications reduced lipophilicities while retaining the desired binding profile.
A Chromatin Immunoprecipitation Screen Reveals Protein Kinase Cβ as a Direct RUNX1 Target Gene (2004)

RUNX1 (also known as AML1) is a DNA-binding transcription factor that functions as a tumor suppressor and developmental determinant in hematopoietic cells. Target promoters have been identified primarily through the use of differential expression strategies and candidate gene approaches but not biochemical screens. Using a chromatin immunoprecipitation screen, we identified protein kinase Cbeta as a direct RUNX1 target gene and demonstrate that endogenous RUNX1 binds the chromatinized protein kinase Cbeta promoter of U937 cells. A phylogenetically conserved RUNX1-binding site within the PKCbeta promoter binds RUNX1 in electrophoretic mobility shift analyses and confers RUNX1 responsiveness on a heterologous promoter. Changes in RUNX1 activity affect endogenous protein kinase Cbeta expression, and a dominant-negative form of RUNX1 protects U937 cells from apoptotic stimuli previously shown to be dependent on protein kinase Cbeta. This protection can be reversed by the ectopic expression of protein kinase Cbeta. Together these findings demonstrate that protein kinase Cbeta is a direct, downstream target of RUNX1 and links RUNX1 to a myeloid apoptotic pathway.
Impact of natural variation in bacterial F17G adhesins on crystallization behaviour (2005)

Since the introduction of structural genomics, the protein has been recognized as the most important variable in crystallization. Recent strategies to modify a protein to improve crystal quality have included rationally engineered point mutations, truncations, deletions and fusions. Five naturally occurring variants, differing in 1-18 amino acids, of the 177-residue lectin domain of the F17G fimbrial adhesin were expressed and purified in identical ways. For four out of the five variants crystals were obtained, mostly in non-isomorphous space groups, with diffraction limits ranging between 2.4 and 1.1 A resolution. A comparative analysis of the crystal-packing contacts revealed that the variable amino acids are often involved in lattice contacts and a single amino-acid substitution can suffice to radically change crystal packing. A statistical approach proved reliable to estimate the compatibilities of the variant sequences with the observed crystal forms. In conclusion, natural variation, universally present within prokaryotic species, is a valuable genetic resource that can be favourably employed to enhance the crystallization success rate with considerably less effort than other strategies.
Depth-resolved imaging of capillary networks in retina and choroid using ultrahigh sensitive optical microangiography (2010)

We demonstrate the depth-resolved and detailed ocular perfusion maps within retina and choroid can be obtained from an ultrahigh sensitive optical microangiography (OMAG). As opposed to the conventional OMAG, we apply the OMAG algorithm along the slow scanning axis to achieve the ultrahigh sensitive imaging to the slow flows within capillaries. We use an 840 nm system operating at an imaging rate of 400 frames/s that requires 3 s to complete one 3D scan of approximately 3 x 3 mm(2) area on retina. We show the superior imaging performance of OMAG to provide functional images of capillary level microcirculation at different land-marked depths within retina and choroid that correlate well with the standard retinal pathology.
Cloning and characterization of Pseudomonas aeruginosa fliF, necessary for flagellar assembly and bacterial adherence to mucin (1996)

Pseudomonas aeruginosa adheres to the mucosal surfaces of the lungs. This process appears to be mediated by nonpilus adhesins which bind to mucin. To find this nonpilus adhesin(s), mutagenesis of a nonpiliated mutant of P. aeruginosa with transposon Tn5G, followed by a screen for mucin adhesion, was used to isolate a series of mutants unable to adhere to mucin. All of these mutants were also found to be defective in motility. One such mutant, PAK-RR20, is characterized here. The site of the transposon insertion in PAK-RR20 was localized to a gene which is homologous to the fliF gene of other organisms and was flanked by other motility-related genes, fliE and fliG. Both adhesion and motility defects in PAK-RR20 were complemented by providing the fliF gene in trans. Since complementation could have been due to the presence of an internal promoter in the fliF gene or in the Tn5G transposon, which allowed the transcription of the downstream genes, another chromosomal mutant of the fliF gene was constructed by insertional inactivation with an antibiotic resistance cassette. This mutant was also nonmotile and nonadhesive. However, the two defects in this new mutant could not be complemented by the fliF gene in trans, consistent with the interpretation that there is no internal fliF promoter but possibly a functional promoter in the Tn5G transposon. The complete nucleotide sequences of the fliE and fliF genes and a partial nucleotide sequence of the fliG gene of P. aeruginosa were determined. Control of the promoter upstream of the fliE gene was analyzed by construction of a fliE-lacZ fusion and the introduction of this construct into strains of P. aeruginosa with mutations in several regulatory genes. Beta-Galactosidase expression measurements indicated that the fliE promoter does not utilize RpoF (sigma(28)) or RpoN (sigma(54)) sigma factors. The characterization of this gene as being responsible for the loss of adhesion indicates that basal body structures are probably important for localization of the adhesin.
On the Physical Origin of Blue-Shifted Hydrogen Bonds (2002)

For blue-shifted hydrogen-bonded systems, the hydrogen stretching frequency increases rather than decreases on complexation. In computations at various levels of theory, the blue-shift in the archetypical system, F(3)C-H.FH, is reproduced at the Hartree-Fock level, indicating that electron correlation is not the primary cause. Calculations also demonstrate that a blue-shift does not require either a carbon center or the absence of a lone pair on the proton donor, because F(3)Si-H.OH(2), F(2)NH.FH, F(2)PH.NH(3), and F(2)PH.OH(2) have substantial blue-shifts. Orbital interactions are shown to lengthen the X-H bond and lower its vibrational frequency, and thus cannot be the source of the blue-shift. In the F(3)CH.FH system, the charge redistribution in F(3)CH can be reproduced very well by replacing the FH with a simple dipole, which suggests that the interactions are predominantly electrostatic. When modeled with a point charge for the proton acceptor, attractive electrostatic interactions elongate the F(3)C-H, while repulsive interactions shorten it. At the equilibrium geometry of a hydrogen-bonded complex, the electrostatic attraction between the dipole moments of the proton donor and proton acceptor must be balanced by the Pauli repulsion between the two fragments. In the absence of orbital interactions that cause bond elongation, this repulsive interaction leads to compression of the X-H bond and a blue-shift in its vibrational frequency.
Replantation of 400 avulsed permanent incisors. 2. Factors related to pulpal healing (1995)

Four hundred avulsed and replanted permanent teeth were examined for pulpal healing. In 110 teeth, the apical foramen was either open or half-open. In 16 teeth, the pulps were extirpated prophylactically. Thus, pulpal revascularization was considered possible in 94 teeth. Revascularization occurred in 32 teeth (34%). Pulp necrosis could usually be demonstrated after 3 weeks. Positive pulpal sensibility and radiographis signs of pulp canal obliteration were usually observed after 6 months. The effect of various clinical factors was examined, such as sex, age, type of tooth replanted, stage of root formation, type and length of extra-alveolar storage, clinical contamination of the root surface, type of cleansing procedure of the root surface, type and length of splinting and the use of antibiotics. Finally, the width of the apical foramen and the length of the root canal were measured on radiographs taken at the time of injury. A multivariate statistical analysis revealed that pulpal revascularization was more frequent in teeth with shorter distances from the apical foramen to the pulp horns. Furthermore, that wet storage (saliva and/or saline) for more than 5 min decreased the chance of pulpal revascularization; whereas dry extraalveolar storage had a monotonous effect on pulpal revascularization, i.e. decreasing chance of revasculatization with increasing length of the extraalveolar dry storage. Based on these findings, immediate replantation after brief cleansing in either tap water or saline is recommended.
Multimodal flexible cystoscopy for creating co-registered panoramas of the bladder urothelium (2012)

Bladder cancer is the most expensive cancer to treat due to the high rate of recurrence. Though white light cystoscopy is the gold standard for bladder cancer surveillance, the advent of fluorescence biomarkers provides an opportunity to improve sensitivity for early detection and reduced recurrence resulting from more accurate excision. Ideally, fluorescence information could be combined with standard reflectance images to provide multimodal views of the bladder wall. The scanning fiber endoscope (SFE) of 1.2mm in diameter is able to acquire wide-field multimodal video from a bladder phantom with fluorescence cancer "hot-spots". The SFE generates images by scanning red, green, and blue (RGB) laser light and detects the backscatter signal for reflectance video of 500-line resolution at 30 frames per second. We imaged a bladder phantom with painted vessels and mimicked fluorescent lesions by applying green fluorescent microspheres to the surface. By eliminating the green laser illumination, simultaneous reflectance and fluorescence images can be acquired at the same field of view, resolution, and frame rate. Moreover, the multimodal SFE is combined with a robotic steering mechanism and image stitching software as part of a fully automated bladder surveillance system. Using this system, the SFE can be reliably articulated over the entire 360&deg; bladder surface. Acquired images can then be stitched into a multimodal 3D panorama of the bladder using software developed in our laboratory. In each panorama, the fluorescence images are exactly co-registered with RGB reflectance.
The bioactive phospholipid lysophosphatidic acid is released from activated platelets (1993)

Lysophosphatidic acid (LPA) is a water-soluble phospholipid with hormone-like and growth-factor-like activities. LPA activates a putative G-protein-coupled receptor in responsive cells, but the natural source of exogenous LPA is unknown. Here we show that LPA is present in mammalian serum in an active form (bound to albumin) at concentrations of 1-5 microM, but is not detectable in platelet-poor plasma, suggesting that LPA is produced during blood clotting. We find that thrombin activation of platelets prelabelled with [32P]Pi results in the rapid release of newly formed [32P]LPA into the extracellular environment. We conclude that LPA is a novel platelet-derived lipid mediator that may play a role in inflammatory and proliferative responses to injury.
Expression, crystallization and preliminary X-ray diffraction analysis of human paired Ig-like type 2 receptor α (PILRα) (2007)

Human paired immunoglobulin-like (Ig-like) type 2 receptor alpha (PILRalpha) is a type I membrane protein that is mainly expressed in immune-related cells such as monocytes, granulocytes and dendritic cells. PILRalpha can suppress the functions of such immune cells because it has the immunoreceptor tyrosine-based inhibitory motif (ITIM) in the intracellular region, which recruits the phosphatase Src homology-2 (SH2) domain-containing protein tyrosine phosphatase 2 (SHP-2) to inhibit phosphorylations induced by activation signals. The extracellular region of human PILRalpha comprises one immunoglobulin superfamily V-set domain and a stalk region. The V-set domain (residues 13-131) of human PILRalpha was overexpressed in Escherichia coli as inclusion bodies, refolded by rapid dilution and purified. The PILRalpha protein was successfully crystallized at 293 K using the sitting-drop vapour-diffusion method. The crystals diffracted to 1.3 A resolution at SPring-8 BL41XU; they belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 40.4, b = 45.0, c = 56.9 A, and contain one molecule per asymmetric unit.
Adaptive channel estimator for an HF radio link (1989)

A simple estimator designed for a 2400-b/s modem is a development of the conventional gradient estimator and uses a polynomial filter that gives a prediction of the channel response. A description is given of new estimators that are developments of the simple estimator but make no use of any knowledge of the number of different paths. The new estimators have performances intermediate between those of the simple and improved estimators, but are only a little more complex than the simple estimator. The new estimators are studied for a particular QPSK modem that operates at 4800 b/s over voiceband HF radio links. Results of computer simulation tests are presented, comparing the accuracies of the channel estimates given by different estimators, and hence suggesting the most suitable of these.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Androgen Receptor Corepressor-19 kDa (ARR19), a Leucine-Rich Protein that Represses the Transcriptional Activity of Androgen Receptor through Recruitment of Histone Deacetylase (2003)

Androgen receptor (AR) that mediates androgen action is a crucial factor in male reproductive functions. Here, we report a novel AR corepressor ARR19 (androgen receptor corepressor-19 kDa), which has been isolated as a putative androgen-induced gene from murine testis. ARR19 encoding a leucine-rich protein is expressed only in male reproductive organs such as testis and prostate. ARR19 expression in the testis is developmentally regulated. Functional analysis conducted by the transient transfection of mammalian cells shows that ARR19 represses AR transactivation in a dose-dependent manner. Furthermore, yeast two-hybrid and glutathione S-transferase pull-down analyses reveal that ARR19 directly associates with AR through the N-terminal and leucine zipper-containing regions of ARR19 and the DNA binding-hinge domain of AR. Interestingly, ARR19 localized in the cytoplasmic compartment cotranslocates into the nucleus with AR upon androgen exposure. The ARR19 repression of AR transactivation is through the recruitment of histone deacetylase 4 (HDAC4) by ARR19. Overexpression of HDAC4 further inhibits the ARR19-repressed AR transactivation. In addition, ARR19 directly interacts with HDAC4 in vitro. Furthermore, DNA-protein complex immunoprecipitation assays reveal that HDAC4 is recruited to an androgen-regulated promoter through ARR19. Taken together, the results suggest that ARR19 may act as an AR corepressor in vivo and play an important role in male reproductive functions.