gebhart/patrepeval huggingface dataset:
Interaction between ROCK II and Nucleophosmin/B23 in the Regulation of Centrosome Duplication (2006)

Nucleophosmin (NPM)/B23 has been implicated in the regulation of centrosome duplication. NPM/B23 localizes between two centrioles in the unduplicated centrosome. Upon phosphorylation on Thr(199) by cyclin-dependent kinase 2 (CDK2)/cyclin E, the majority of centrosomal NPM/B23 dissociates from centrosomes, but some NPM/B23 phosphorylated on Thr(199) remains at centrosomes. It has been shown that Thr(199) phosphorylation of NPM/B23 is critical for the physical separation of the paired centrioles, an initial event of the centrosome duplication process. Here, we identified ROCK II kinase, an effector of Rho small GTPase, as a protein that localizes to centrosomes and physically interacts with NPM/B23. Expression of the constitutively active form of ROCK II promotes centrosome duplication, while down-regulation of ROCK II expression results in the suppression of centrosome duplication, especially delaying the initiation of centrosome duplication during the cell cycle. Moreover, ROCK II regulates centrosome duplication in its kinase and centrosome localization activity-dependent manner. We further found that ROCK II kinase activity is significantly enhanced by binding to NPM/B23 and that NPM/B23 acquires a higher binding affinity to ROCK II upon phosphorylation on Thr(199). Moreover, physical interaction between ROCK II and NPM/B23 in vivo occurs in association with CDK2/cyclin E activation and the emergence of Thr(199)-phosphorylated NPM/B23. All these findings point to ROCK II as the effector of the CDK2/cyclin E-NPM/B23 pathway in the regulation of centrosome duplication.
Immunologic Adjuvants for Modern Vaccine Formulations (1995)

Optimization of the immunogenicity of many new-generation vaccine formulations, including combination vaccines, will require the use of immunologic adjuvants other than the aluminum compounds in today's licensed vaccines. The selection of adjuvants for use in vaccine formulation may be as critical as the choice of the vaccine antigens themselves in providing optimal efficacy for the target populations, vaccine compliance, and cost. Adjuvants have diverse mechanisms of action and must be selected for use based on the immune responses desired for a particular candidate vaccine. Recent advances in the number and variety of adjuvants available for clinical evaluation coupled with the increased understanding of their mechanisms of action encourage the inclusion of adjuvants as part of rational vaccine design. Finally, the proposed standardized methods to evaluate adjuvant safety should be implemented for human candidate vaccines formulated with novel adjuvants.
Gene expression of forkhead transcription factors in the normal and diseased human prostate (2009)

OBJECTIVE To assess the expression of forkhead transcription factors (FOX) in normal prostate and prostate diseases, as since the first FOX was identified, its family members have been implicated in a variety of cellular processes, including embryonic development and disease. MATERIAL AND METHODS We analysed a set of 12 different FOX genes by quantitative reverse transcription-polymerase chain reaction in prostate zones, prostate cancer, lymph node metastases, benign prostatic hyperplasia (BPH), xenografts and several prostate cell lines. RESULTS There were striking differences among the expression of various FOX family members; most prominent were the high expression of FOXF1 and FOXF2 in the normal prostate transition zone and BPH, and their decreased expression in prostate cancer. Interestingly, although the FOXF genes are stroma-specific, some of the androgen-independent prostate cancer xenografts uniquely express these two genes. FOXD1 and FOXD2 were more highly expressed in prostate cancer and lymph node metastases. FOXA1 and FOXC1 have an opposite expression pattern for androgen-dependent growth of prostate cancer cell lines and xenografts. CONCLUSIONS Various members of the FOX family are differentially expressed in the zones of the normal prostate and in benign and malignant outgrowths. The expression profiles of FOXF1 and FOXF2 suggest a role in epithelial to mesenchymal transition, while FOXA1 and FOXC1 expression is linked to androgen-associated growth status of cancer.
Rapid Deceleration-Driven Wetting Transition during Pendant Drop Deposition on Superhydrophobic Surfaces (2011)

A hitherto unknown mechanism for wetting transition is reported. When a pendant drop settles upon deposition, there is a virtual "collision" where its center of gravity undergoes rapid deceleration. This induces a high water hammer-type pressure that causes wetting transition. A new phase diagram shows that both large and small droplets can transition to wetted states due to the new deceleration driven and the previously known Laplace mechanisms, respectively. It is explained how the attainment of a nonwetted Cassie-Baxter state is more restrictive than previously known.
On‐demand three‐dimensional freeform fabrication of multi‐layered hydrogel scaffold with fluidic channels (2009)

One of the challenges in tissue engineering is to provide adequate supplies of oxygen and nutrients to cells within the engineered tissue construct. Soft-lithographic techniques have allowed the generation of hydrogel scaffolds containing a network of fluidic channels, but at the cost of complicated and often time-consuming manufacturing steps. We report a three-dimensional (3D) direct printing technique to construct hydrogel scaffolds containing fluidic channels. Cells can also be printed on to and embedded in the scaffold with this technique. Collagen hydrogel precursor was printed and subsequently crosslinked via nebulized sodium bicarbonate solution. A heated gelatin solution, which served as a sacrificial element for the fluidic channels, was printed between the collagen layers. The process was repeated layer-by-layer to form a 3D hydrogel block. The printed hydrogel block was heated to 37 degrees C, which allowed the gelatin to be selectively liquefied and drained, generating a hollow channel within the collagen scaffold. The dermal fibroblasts grown in a scaffold containing fluidic channels showed significantly elevated cell viability compared to the ones without any channels. The on-demand capability to print fluidic channel structures and cells in a 3D hydrogel scaffold offers flexibility in generating perfusable 3D artificial tissue composites.
Characterization of highly repetitive sequences ofArabidopsis thaliana (1988)

We have analyzed three classes of highly repetitive DNA sequences of Arabidopsis thaliana, composed of tamdemly repeated units of 180 bp, 500 bp, and 160 bp, respectively. The three families comprise approximately 2% of the Arabidopsis genome and are the major component of the highly repetitive DNA. The 500-bp element arose by duplication of one half of a 180-bp ancestor and insertion of a foreign segment between the two duplicated parts followed by amplification. The repeat elements contain occasionally palindromes and other motifs but none are significantly conserved. There is no significant similarity with previously published repetitive elements. Heterogeneity between monomers ranges from 6% to 17%. Monomers derived from different clusters in the genome are more diverged than monomers of the same array.
Orexins/Hypocretins Acting at Gi Protein-Coupled OX2 Receptors Inhibit Cyclic AMP Synthesis in the Primary Neuronal Cultures (2011)

Orexins A and B are newly discovered neuropeptides with pleiotropic activity. They signal through two G protein-coupled receptors: OX(1) and OX(2). In this study, we examined the expression of orexin receptors and effects of the receptors' activation on cyclic AMP formation in the primary neuronal cell cultures from rat cerebral cortex. Both types of orexin receptors were expressed in rat cortical neurons; the level of OX(2)R was markedly higher compared to OX(1)R. Orexin A (an agonist of OX(1)R and OX(2)R) and [Ala(11)-D-Leu(15)]orexin B (a selective agonist of OX(2)R) did not affect basal cyclic AMP formation in the primary neuronal cell cultures. Both peptides (0.001-1 μM) inhibited, in a concentration-dependent manner and IC(50) values in low nanomolar range, the increase in the nucleotide production evoked by forskolin (1 μM; a direct activator of adenylyl cyclase), pituitary adenylate cyclase-activating polypeptide (PACAP27; 0.1 μM), and vasoactive intestinal peptide (VIP; 3 μM). Effects of orexin A on forskolin-, PACAP27-, and VIP-stimulated cyclic AMP synthesis were blocked by TCS OX2 29 (a selective antagonist of OX(2)R), and unaffected by SB 408124 (a selective antagonist of OX(1)R). Pretreatment of neuronal cell cultures with pertussis toxin (PTX) abolished the inhibitory action of orexin A on forskolin- and PACAP-stimulated cyclic AMP accumulation. It is suggested that in cultured rat cortical neurons orexins, acting at OX(2) receptors coupled to PTX-sensitive G(i) protein, inhibit cyclic AMP synthesis.
Conversion of Si to epitaxial SiC by reaction with C2H2 (1974)

The growth of β-SiC films on Si by reaction of a Si single crystal with C2H2 has been studied for the conditions 10−7 ≤PC2H2≤5×10−4 Torr, 800≤T≤1100°C, in both high- and ultrahigh-vacuum chambers. At C2H2 pressures below approximately 10−5 Torr, linear growth kinetics were observed over the temperature range investigated and the reaction probability was determined as 0.02–0.03. In this pressure range growth occurs by the diffusion of Si through porous defects incorporated in the growing film. We have studied in detail the structure of defected films formed under various growth conditions by scanning electron microscopy, scanning transmission electron microscopy, and transmission electron microscopy. We conclude that the occurrence of defects is intrinsic to the mechanism of film growth. The predominant defect type consists of a shallow (∼ 2000 Å) pit in the Si substrate, over which the growing SiC assumes a porous polycrystalline morphology. The number and areal densities of these defects are proportional to the C2H2 partial pressure and the SiC film thickness, respectively. The defects act as sources of Si for reaction, and film growth occurs via diffusion of Si from the substrate through the porous overgrowth to the epitaxial SiC/vacuum interface, where reaction occurs. For C2H2 pressures exceeding approximately 10−5 Torr the porous defects are sealed off at an early stage in the growth and further reaction is virtually arrested due to the extremely small bulk and/or grain boundary diffusivity for Si in SiC over the experimental temperature range. No significant effect on growth rate due to the type of vacuum system used was found.
Increased soluble serum markers caspase‐cleaved cytokeratin‐18, histones, and ST2 indicate apoptotic turnover and chronic immune response in COPD (2009)

Our results indicate a systemic release of apoptosis-specific proteins as markers for increased cellular turnover accompanied by progression of COPD. Furthermore, soluble ST2 seems to have a critical role in the anti-inflammatory regulatory mechanism at early stages of the disease.
Early intervention with a small molecule inhibitor for tumor nefosis factor-α prevents cognitive deficits in a triple transgenic mouse model of Alzheimer’s disease (2012)

These results suggest that modulation of tumor necrosis factor-α with small molecule inhibitors is safe and effective with potential for the long-term prevention and treatment of Alzheimer's disease.
Genomic profiling identifies common HPV-associated chromosomal alterations in squamous cell carcinomas of cervix and head and neck (2009)

In this study hrHPV-specific, organ-specific, and pan-SCC chromosomal alterations were identified. The existence of hrHPV-specific alterations in SCCs of different anatomical origin, suggests that these alterations are crucial for hrHPV-mediated carcinogenesis.
THIN FILM OXIDATIVE AGING AND LOW TEMPERATURE PERFORMANCE GRADING USING SMALL PLATE DYNAMIC SHEAR RHEOMETRY: AN ALTERNATIVE TO STANDARD RTFO, PAV, AND BBR (2012)

This report describes progress towards development of a new thin film (300 μm) short- and long-term aging test suggested as an alternative to the standard rolling thin film oven (RTFO) and pressure aging vessel (PAV) tests. The new test, referred to as the Simple Aging Test (SAT), can be applied to neat and modified bitumens, and emulsion residues. Before the Strategic Highway Research Program, there was considerable interest in static thin film aging. However, the RTFO test was adopted for short term aging because of the large amount of aged asphalt needed for the Bending Beam Rheometer (BBR) test. Since the adoption of the RTFO, it has been found problematic for aging highly modified binders. In the case of warm mix binders, RTFO testing at lower temperature to simulate a “warm” plant may limit rolling needed to uniformly age the material. Recent development of a 4-mm dia. parallel-plate dynamic shear rheometer (DSR) technique allows DSR tests to -40°C, requires only 25 mg of binder, and can estimate BBR m-value and creep stiffness. By combining this new DSR technique with the SAT, the low and intermediate temperature rheology of short and long-term aged bitumens can be determined. Also, there is sufficient aged material to perform high temperature DSR using 25 mm plates. The SAT eliminates the “rolling” issue for polymer modified and warm mix asphalts. The SAT time and temperature equivalent to reach the same aging as the standard RTFO and PAV are reported for several bitumens.
Overexpression of DNA polymerase β in cell results in a mutator phenotype and a decreased sensitivity to anticancer drugs (1998)

DNA polymerase beta (pol beta) is the most error prone of all known eukaryotic DNA polymerases tested in vitro. Here, we show that cells overexpressing pol beta cDNA have acquired a spontaneous mutator phenotype. By measuring the appearance of mutational events using three independent assays, we found that genetic instability increased in the cell lines that overexpressed pol beta. In addition, these cells displayed a decreased sensitivity to cancer chemotherapeutic, bifunctional, DNA-damaging agents such as cisplatin, melphalan, and mechlorethamine, resulting in enhanced mutagenesis compared with control cells. By using cell-free extracts and modified DNA substrates, we present data in support of error-prone translesion replication as one of the key determinants of tolerance phenotype. These results have implications for the potential role of pol beta overexpression in cancer predisposition and tumor progression during chemotherapy.
Murine herpesvirus 68 is genetically related to the gammaherpesviruses Epstein-Barr virus and herpesvirus saimiri (1990)

Short nucleotide sequence analysis of seven restriction fragments of murine herpesvirus 68 (MHV-68) DNA has been undertaken and used to determine the overall genome organization and relatedness of this virus to other well characterized representatives of the alpha-, beta- and gammaherpesvirus subgroups. Nine genes have been identified which encode amino acid sequences with greater similarity to proteins of the gammaherpesvirus Epstein-Barr virus (EBV) than to the homologous products of the alphaherpesviruses varicella-zoster virus and herpes simples virus type 1 or the betaherpesvirus human cytomegalovirus. In addition, the genome organization of MHV-68 is shown to have an overall collinearity with that of the gammaherpesviruses EBV and herpesvirus saimiri. In common with these viruses, dinucleotide frequency analysis of MHV-68 coding sequences reveals a marked reduction in CpG dinucleotide frequency thus implicating a dividing cell population as the site of latency in vivo.
Towards Heat-stable Oxytocin Formulations: Analysis of Degradation Kinetics and Identification of Degradation Products (2009)

Multiple degradation products of oxytocin have been identified unequivocally, including various deamidated species, intramolecular oligosulfides and covalent aggregates. The strongly pH dependent degradation can be described by the Arrhenius equation.
A repetitive peptide of Leishmania can activate T helper type 2 cells and enhance disease progression. (1990)

Leishmaniasis provides a biologically relevant model to analyze the heterogeneity of CD4+ T cells and may lead to answering the major question of the mechanism for the preferential induction of T helper type 1 (Th1) and Th2 cells. Using synthetic peptides corresponding to the tandemly repeating regions of Leishmania proteins, we have identified an epitope that can preferentially induce the disease-exacerbating Th2 cells in susceptible BALB/c mice. Lymph node cells from BALB/c mice immunized subcutaneously with the octamer (p183) of the repeating 10-mer peptide EAEEAARLQA proliferated strongly against the peptide as well as the soluble antigen extract (SolAg) of Leishmania major. The proliferative T cells are CD4+, major histocompatibility complex class II restricted, and secrete interleukin 4 (IL-4) but little or no IL-2 and interferon gamma when stimulated with the peptide in vitro. T cells from BALB/c mice with progressive disease, but not from BALB/c mice cured of the infection, recognized this epitope. BALB/c mice injected subcutaneously with p183 developed significantly exacerbated disease when subsequently challenged with L. major. Furthermore, subcutaneous injection with p183 prevented the subsequent induction of resistance against L. major by intravenous immunization with soluble antigen. The T cell response to p183 is H-2d restricted. Immunization of the genetically resistant B10.D2 mice with p183 also produced strong T cell responses and exacerbated disease when challenged with L. major.
A supersensitive immunofluorometric assay for rat luteinizing hormone. (1993)

We have developed an immunofluorometric assay (IFMA) for rat (r) LH, which is based on two monoclonal antibodies, one to bovine and the other to human LH. Signal detection occurs by time-resolved fluorescence evoked by a europium label (Delfia, Wallac). The method is fast in comparison to the standard RIA with the NIDDK reagents (4 h vs. 3 days). The sensitivity of the IFMA assay (0.75 pg/tube; NIDDK rLH RP-2) is over 30-fold higher than that of the NIDDK RIA (usual detection limit, 20-30 pg/tube). Using 25-microliters serum samples, the sensitivity of IFMA is 0.03 micrograms/liter; with 100-microliters samples, it is 0.0075 micrograms/liter. The cross-reactivity of the IFMA assay is 0.3% with rFSH, 3% with rTSH, and less than 0.05% with rGH, rPRL, and the rat alpha-subunit. A linear correlation between IFMA and RIA values is seen at serum levels above 0.4 micrograms/liter. Below this level, only IFMA is able to detect concentration differences between samples. In practice, this means that only IFMA is able to provide meaningful measurements of suppressed levels of serum LH. The correlation coefficient between IFMA and the mouse interstitial cell in vitro bioassay for LH in randomly selected rat pituitary homogenates was 0.93 (n = 47). The serum concentration of LH determined by IFMA is 0.57 +/- 0.10 micrograms/liter in intact adult male rats (mean +/- SEM; n = 12) and 0.41 +/- 0.10 micrograms/liter (n = 10) in randomly cycling females. The level in hypophysectomized rat serum is 0.035 +/- 0.0033 micrograms/liter (n = 8), if the limit of sensitivity (0.03 microgram/liter) is assigned to unmeasurable levels. One-week treatment of male rats with 2-cm Silastic implants containing testosterone suppressed serum LH, measured by IFMA, from 0.56 +/- 0.057 to 0.086 +/- 0.057 micrograms/liter (P < 0.01). The suppression of LH measured in the same samples by RIA was lower, from 0.73 +/- 0.057 to 0.44 +/- 0.048 micrograms/liter (P < 0.01). A 5-day starvation of intact male rats suppressed serum LH from 0.57 +/- 0.10 to 0.30 +/- 0.05 microgram/liter by IFMA (P < 0.01), whereas the decrease determined by RIA was not significant (0.80 +/- 0.07 vs. 0.66 +/- 0.13 micrograms/liter).(ABSTRACT TRUNCATED AT 400 WORDS)
Expression of functional factor VIII in primary human skin fibroblasts after retrovirus-mediated gene transfer. (1990)

We have developed a retroviral-vector system for the transfer and expression of a cloned blood clotting factor VIII cDNA. Since inclusion of the complete cDNA into existing vectors is precluded by its large size, we deleted most codons for the B-domain, which is also excised during in vivo maturation of factor VIII. When inserted into the retroviral vector M5-neoR (Laker, C., Stocking, C., Bergholtz, V., Hess, N., DeLamarter, J. F., and Ostertag, W. (1987) Proc. Natl. Acad. Sci. U. S. A. 84, 8458-8462), the sequence was shown to be efficiently expressed in murine fibroblast cell lines, as well as in primary human skin fibroblasts. Upon infection of murine fibroblast cell lines, clones containing only a single copy of the integrated vector-provirus secreted up to 125 milliunits of factor VIII antigen/10(6) cells/day. Equivalent amounts were found in a factor VIII activity assay, which signifies that the factor VIII protein secreted by the infected fibroblasts is fully functional. Primary human skin fibroblasts infected with the vector virus secreted up to 30 milliunits/10(6) cells/day.
A Streptomyces avermitilis gene encoding a 4-hydroxyphenylpyruvic acid dioxygenase-like protein that directs the production of homogentisic acid and an ochronotic pigment in Escherichia coli (1994)

A 1.5-kb genomic fragment isolated from Streptomyces avermitilis that directs the synthesis of a brown pigment in Escherichia coli was characterized. Since pigment production in recombinant E. coli was enhanced by the addition of tyrosine to the medium, it had been inferred that the cloned DNA might be associated with melanin biosynthesis. Hybridization studies, however, showed that the pigment gene isolated from S. avermitilis was unrelated to the Streptomyces antibioticus melC2 determinant, which is the prototype of melanin genes in Streptomyces spp. Sequence analysis of the 1.5-kb DNA that caused pigment production revealed a single open reading frame encoding a protein of 41.6 kDa (380 amino acids) that resembled several prokaryotic and eukaryotic 4-hydroxyphenylpyruvate dioxygenases (HPDs). When this open reading frame was overexpressed in E. coli, a protein of about 41 kDa was detected. This E. coli clone produced homogentisic acid (HGA), which is the expected product of the oxidation of 4-hydroxyphenylpyruvate catalyzed by an HPD, and also a brown pigment with characteristics similar to the pigment observed in the urine of alkaptonuric patients. Alkaptonuria is a genetic disease in which inability to metabolize HGA leads to increasing concentrations of this acid in urine, followed by oxidation and polymerization of HGA to an ochronotic pigment. Similarly, the production of ochronotic-like pigment in the recombinant E. coli clone overexpressing the S. avermitilis gene encoding HPD is likely to be due to the spontaneous oxidation and polymerization of the HGA accumulated in the medium by this clone.