gebhart/patrepeval huggingface dataset:
Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli (1992)

Transcription of the Ntr regulon is controlled by the two-component system consisting of the response regulator NRI (NtrC) and the kinase/phosphatase NRII (NtrB), which both phosphorylates and dephosphorylates NRI. Even though in vitro transcription from nitrogen-regulated promoters requires phosphorylated NRI, NRII-independent activation of NRI also occurs in vivo. We show here that this activation likely involves acetyl phosphate; it is eliminated by mutations that reduce synthesis of acetyl phosphate and is elevated by a mutation expected to cause accumulation of acetyl phosphate. With purified components, we investigated the mechanism by which acetyl phosphate stimulates glutamine synthetase synthesis. Acetyl phosphate, carbamyl phosphate, and phosphoramidate but not ATP or phosphoenolpyruvate acted as substrates for the autophosphorylation of NRI in vitro. Phosphorylated NRI produced by this mechanism exhibited the properties associated with NRI phosphorylated by NRII, including the activated ATPase activity of the central domain of NRI and the ability to activate transcription from the nitrogen-regulated glutamine synthetase glnAp2 promoter.
Nonlinear optical microscopy based on double-clad photonic crystal fibers (2005)

We report on a nonlinear optical microscope that adopts double-clad photonic crystal fibers for single-mode illumination delivery and multimode signal collection. It is demonstrated that two-photon fluorescence and second harmonic generation signals can be simultaneously collected in such a microscope with axial resolution of 2.8 microm and 2.5 mum, respectively. The delivery and detection efficiencies of the photonic-crystal-fiber- based microscope are significantly improved by approximately 3 times and 40 times compared with those in the single-mode fiber-optic microscope. The high resolution three-dimensional second harmonic generation images from rat tail tendon demonstrate the effectiveness of the system.
Coupling Reactions of CO2with Neat Epoxides Catalyzed by PPN Salts To Yield Cyclic Carbonates (2005)

The off-the-shelf reagent PPN+Cl- and PPN-manganese carbonylates [PPN]+[Mn(CO)4L]- (L = CO, PPh3) are good catalysts for the coupling reactions of CO2 with neat epoxides without the use of organic solvents to afford cyclic carbonates. PPN salts with weak nucleophilic anions such as PPN+BF4- and PPN+OTf- are, however, inactive for the coupling reactions.
Gender Differences in the Relationship Between Acute Stress Disorder and Posttraumatic Stress Disorder Following Motor Vehicle Accidents (2003)

Peritraumatic dissociation and ASD is a more accurate predictor of PTSD in females than males. This gender difference may be explained in terms of response bias or biological differences in trauma response between males and females.
Gangliosides Activate Cultured Rat Brain Microglia (1999)

Microglia, brain resident macrophages, are activated in brain injuries and several neurodegenerative diseases. However, microglial activators that are produced in the brain are not yet defined. In this study, we showed that gangliosides, sialic acid-containing glycosphingolipids, could be a microglial activator. Gangliosides induced production of nitric oxide (NO) and tumor necrosis factor-alpha (TNF-alpha) and expression of cyclooxygenase-2 (COX-2). The effect of gangliosides on NO release increased dose-dependently in the range of 10-100 microgram/ml; however, the effect decreased at concentrations higher than 200 microgram/ml. Specific types of gangliosides showed differential effects on microglial activation. Similar to gangliosides, GT1b induced production of NO and TNF-alpha and expression of COX-2. However, GM1 and GD1a induced expression of COX-2 but had little effect on NO and TNF-alpha release. The effect of gangliosides and GT1b on NO release was reduced in the presence of neuraminidase, which removes sialic acid residues from gangliosides and GT1b. Gangliosides activated extracellular signal-regulated kinase significantly but activated c-jun N-terminal kinase/stress-activated protein kinase and p38 relatively weakly. The inhibition of extracellular signal-regulated kinase by PD98059 reduced NO release from both gangliosides- and GT1b-treated microglia whereas inhibition of p38 by SB203580 increased it rather slightly. Gangliosides activated NF-kappaB, and N-acetyl cystein, an inhibitor of NF-kappaB, reduced NO release. These results suggest that gangliosides could be a microglial activator that functions via activation of mitogen-activated protein kinase and NF-kappaB.
Xenopus Cdc7 function is dependent on licensing but not on XORC, XCdc6, or CDK activity and is required for XCdc45 loading (2000)

The assembly and disassembly of protein complexes at replication origins play a crucial role in the regulation of chromosomal DNA replication. The sequential binding of the origin recognition complex (ORC), Cdc6, and the minichromosome maintenance (MCM/P1) proteins produces a licensed replication origin. Before the initiation of replication can occur, each licensed origin must be acted upon by S phase-inducing CDKs and the Cdc7 protein kinase. In the present report we describe the role of Xenopus Cdc7 (XCdc7) in DNA replication using cell-free extracts of Xenopus eggs. We show that XCdc7 binds to chromatin during G(1) and S phase. XCdc7 associates with chromatin only once origins have been licensed, but this association does not require the continued presence of XORC or XCdc6 once they have fulfilled their essential role in licensing. Moreover, XCdc7 is required for the subsequent CDK-dependent loading of XCdc45 but is not required for the destabilization of origins that occurs once licensing is complete. Finally, we show that CDK activity is not necessary for XCdc7 to associate with chromatin, induce MCM/P1 phosphorylation, or perform its essential replicative function. From these results we suggest a simple model for the assembly of functional initiation complexes in the Xenopus system.
Rate of complications in scoliosis surgery – a systematic review of the Pub Med literature (2008)

Scoliosis surgery has a varying but high rate of complications. A medical indication for this treatment cannot be established in view of the lack of evidence. The rate of complications may even be higher than reported. Long-term risks of scoliosis surgery have not yet been reported upon in research. Mandatory reporting for all spinal implants in a standardized way using a spreadsheet list of all recognised complications to reveal a 2-year, 5-year, 10-year and 20-year rate of complications should be established. Trials with untreated control groups in the field of scoliosis raise ethical issues, as the control group could be exposed to the risks of undergoing such surgery.
Taxane-Induced Blockade to Nuclear Accumulation of the Androgen Receptor Predicts Clinical Responses in Metastatic Prostate Cancer (2011)

Prostate cancer progression requires active androgen receptor (AR) signaling which occurs following translocation of AR from the cytoplasm to the nucleus. Chemotherapy with taxanes improves survival in patients with castrate resistant prostate cancer (CRPC). Taxanes induce microtubule stabilization, mitotic arrest, and apoptotic cell death, but recent data suggest that taxanes can also affect AR signaling. Here, we report that taxanes inhibit ligand-induced AR nuclear translocation and downstream transcriptional activation of AR target genes such as prostate-specific antigen. AR nuclear translocation was not inhibited in cells with acquired β-tubulin mutations that prevent taxane-induced microtubule stabilization, confirming a role for microtubules in AR trafficking. Upon ligand activation, AR associated with the minus-end-microtubule motor dynein, thereby trafficking on microtubules to translocate to the nucleus. Analysis of circulating tumor cells (CTC) isolated from the peripheral blood of CRPC patients receiving taxane chemotherapy revealed a significant correlation between AR cytoplasmic sequestration and clinical response to therapy. These results indicate that taxanes act in CRPC patients at least in part by inhibiting AR nuclear transport and signaling. Further, they suggest that monitoring AR subcellular localization in the CTCs of CRPC patients might predict clinical responses to taxane chemotherapy.
Broadband silicon optical modulator using a graphene-integrated hybrid plasmonic waveguide (2015)

Graphene is an excellent electronic and photonic material for developing electronic-photonic integrated circuits in Si-based semiconductor devices with ultra wide operational bandwidth. As an extended application, here we propose a broadband silicon optical modulator using a graphene-integrated hybrid plasmonic waveguide, and investigate the optical characteristics numerically at a wavelength of 1.55 μm. The optical device is based on the surface plasmon polariton absorption of graphene. By electrically tuning the graphene's refractive index as low as that of a noble metal, the hybrid plasmonic waveguide supports a strongly confined highly lossy hybrid long-range surface plasmon polariton strip mode, and hence light coupled from an input waveguide experiences significant power attenuation as it propagates along the waveguide. Over the entire C-band from 1.530 to 1.565 μm wavelengths, the on/off extinction ratio is larger than 13.7 dB. This modulator has the potential to play a key role in realizing graphene-Si waveguide-based integrated photonic devices.
Met-Independent Hepatocyte Growth Factor-mediated regulation of cell adhesion in human prostate cancer cells (2006)

We propose that cell surface localized nucleolin protein may function in these cells as a novel HGF receptor. Membrane localized nucleolin binds heparin-bound growth factors (including HGF) and appears upregulated during prostate cancer progression. Antibodies against nucleolin are able to ameliorate the stimulatory effects of HGF on met-negative prostate cancer cells. HGF-nucleolin interactions could be partially responsible for the complexity of HGF responses and met expression reported in the literature.
Presence of oestrogen receptor type beta in human retina (2001)

The coexistence of two oestrogen receptor subtypes in the human ocular posterior segment raises acute questions about their potential physiological role, but offers a perspective for preferential targeting of a specific receptor subtype.
CD4+T Cell Kinetics and Activation in Human Immunodeficiency Virus–Infected Patients Who Remain Viremic Despite Long‐Term Treatment with Protease Inhibitor–Based Therapy (2002)

T cell dynamics were studied in human immunodeficiency virus-infected patients who continued using antiretroviral therapy despite detectable plasma viremia (RNA copies >2500 /mL). CD4(+) cell fractional replacement rates, measured by the deuterated glucose technique, were lower in treated patients with detectable viremia than in untreated patients and were similar to those in patients with undetectable viremia. Cell cycle and activation markers exhibited similar trends. For any level of viremia, CD4(+) cell fractional replacement rates were lower in patients with drug-resistant virus than in patients with wild-type virus, which suggests that the resistant variant was less virulent. Interruption of treatment in patients with drug-resistant viremia resulted in increased CD4(+) cell activation, increased CD4(+) cell turnover, and decreased CD4(+) cell counts. These data indicate that partial virus suppression reduces CD4(+) cell turnover and activation, thereby resulting in sustained CD4(+) cell gains, and that measurements of T cell dynamics may provide an in vivo marker of viral virulence.
Nanoscale Borromean Rings (2004)

The molecular expression of topologically interesting structures represents a formidable challenge for synthetic chemists. The nontrivial link known as the Borromean rings has long been regarded as one of the most ambitious targets in this field. Of ancient provenance, this symbol comprises three interlocked rings in an inseparable union, but cut any one of the rings and the whole assembly unravels into three separate pieces. This Account delineates different strategies that can be applied to the formation of molecules possessing this distinctive topology, culminating with two successful syntheses of such compounds, thus cutting the Gordian knot of topological chemistry.
Electric-Field-Induced Phase Change in Cholesteric Liquid Crystals (1968)

Abstract Optically-negative cholesteric liquid-crystal films can be transformed to an optically-positive state by applying high d-c electric fields. A phase transformation occurs in which the helicoidal cholesteric structure is converted to either a planar smectic, or a linear nematic, structure. The threshhold field for this transformation has been studied as a function of sample thickness, temperature and composition. Bulk fields are responsible for the phenomenon. It is inferred that the compositional dependences are due to size factors and internal molecular dipole moments.
Therapeutic Drug Delivery by Genetically Modified Lactococcus lactis (2006)

Food-grade bacteria have been consumed throughout history without associated pathologies and are, therefore, absolutely safe to ingest. Unexpectedly, Lactococcus lactis (L. lactis), known from cheese production, can be genetically engineered to constantly secrete satisfactory amounts of bioactive cytokines. Both of these features enabled the development of a new kind of topical delivery system: topical and active delivery of therapeutic proteins by genetically modified micro-organisms. The host organism's record inspired the development of applications that target intestinal diseases. In a variety of mouse models, chronic colon inflammation can be successfully treated with (interleukin) IL-10-secreting L. lactis. Trefoil factor (TFF) producer strains have also been shown to be very effective in the treatment of acute colitis. Such novel therapeutic strains are textbook examples of genetically modified (GM) organisms. There are legitimate concerns with regard to the deliberate release of GM micro-organisms. On development of these applications, therefore, we have engineered these bacteria in such a way that biological containment is guaranteed. The essential gene thyA, encoding thymidylate synthase, has been exchanged for IL-10. This makes the GM strain critically dependent on thymidine. Lack of thymidine, for example, resulting from thymidine consumption by thyA-deficient strains-will irreversibly lead to induced "thymidine-less death." This accomplishment has created the possibility of using this strategy for application in human medicine.
A Prospective Study of Dengue Infections in Bangkok (1988)

Dengue infections were prospectively studied among 4- to 16-year-old students at a Bangkok school. Blood samples were obtained from 1,757 students in June 1980, before the dengue season, and in January 1981, after the season, and tested for dengue antibodies by the hemagglutination inhibition method. Classrooms were monitored daily for school absences. Fifty percent of the children had antibodies to, and were presumably immune to, at least 1 dengue serotype by the age of 7 years. Most (90/103, 87%) students who became infected by dengue viruses during the study period were either asymptomatic or minimally symptomatic (absent only 1 day). Most (7/13, 53%) of the symptomatic dengue infections (absent with fever for greater than or equal to 2 days) were clinically recognized as cases of dengue hemorrhagic fever which required hospitalization. None of 47 primary dengue infections required hospitalization, whereas 7 of 56 secondary infections did (P = 0.012). Preexistent dengue immunity, as detected by conventional serologic techniques, was a significant (odds ratio greater than or equal to 6.5) risk factor for development of dengue hemorrhagic fever.
Near infrared and ab initio study of the vibrational modes of isolated silanol on silica (2000)

Near infrared spectroscopy was used to study the vibrational modes of isolated silanol groups in porous silica monoliths that had been heated in acuo at 750°C. A set of bands is assigned to overtone and combination transitions for normal modes involving mainly the SiOH group: the νOH stretching, the νSi–OH stretching, the δOH bending and the τOH torsion around the SiO bond. The spectra of a deuterated sample were also analysed. The wavenumbers for the fundamental transitions were deduced and some anharmonicity coefficients were calculated. The δOH bending is coupled with a symmetric stretching of SiOSi bridges in an (SiO)3SiOH unit. Pairs of bands involving some SiOH bending character (at 4510/4580 cm−1 for combinations with νOH and at 8100/8165 cm−1 for combinations with 2νOH) were extrapolated to fundamental transitions at 760/835 cm−1. This coupling was not observed for the deuterated sample because the δOD absorption at 605 cm−1 is well separated from SiOSi stretching centred at 815 cm−1. The experimental spectra are discussed with the help of ab initio calculations of the vibrational modes of a molecule modelling an isolated silanol group on silica. The contribution of hot transitions at room temperature, from low lying levels such as τOH and its overtones, is also analysed.
Application of Organolithium and Related Reagents in Synthesis. Part 111. Metallation of 2-Methyl- and 4-Methylnicotinic Acids. A Useful Method for Preparation of AZA-Isocoumarins (1992)

Abstract The metallation (LDA/THF) of 2-methyl- and 4-methylnicotinic acids (1) and (2), and the subsequent reaction of the lithiated species (3) and (4) with carbonyl electrophiles as a synthetic route of 5-aza- and 7-aza-isocoumarins (7), (8), (9) and (10), is described. The isocoumarins (9) and (10) appeared to be readily transformable into the corresponding naphthyridines (11) and (12).
Transcriptional characterization of bone morphogenetic proteins (BMPs)‐mediated osteogenic signaling (2003)

Bone formation is presumably a complex and well-orchestrated process of osteoblast lineage-specific differentiation. As members of the TGFbeta superfamily, bone morphogenetic proteins (BMPs) play an important role in regulating osteoblast differentiation and subsequent bone formation. Several BMPs are able to induce de novo bone formation. Although significant progress has recently been made about the transcriptional control of osteoblast differentiation, detailed molecular events underlying the osteogenic process remain to be elucidated. In order to identify potentially important signaling mediators activated by osteogenic BMPs but not by non-osteogenic BMPs, we sought to determine the transcriptional differences between three osteogenic BMPs (i.e., BMP-2, BMP-6, and BMP-9) and two inhibitory/non-osteogenic BMPs (i.e., BMP-3 and BMP-12). Through the microarray analysis of approximately 12,000 genes in pre-osteoblast progenitor cells, we found that expression level of 203 genes (105 up-regulated and 98 down-regulated) was altered >2-fold upon osteogenic BMP stimulation. Gene ontology analysis revealed that osteogenic BMPs, but not inhibitory/non-osteogenic BMPs, activate genes involved in the proliferation of pre-osteoblast progenitor cells towards osteoblastic differentiation, and simultaneously inhibit myoblast-specific gene expression. BMP-regulated expression of the selected target genes was confirmed by RT-PCR, as well as by the CodeLink Bioarray analysis. Our findings are consistent with the notion that osteogenesis and myogenesis are two divergent processes. Further functional characterization of these downstream target genes should provide important insights into the molecular mechanisms behind BMP-mediated bone formation.
TP53 mutations in serous tubal intraepithelial carcinoma and concurrent pelvic high‐grade serous carcinoma—evidence supporting the clonal relationship of the two lesions (2011)

Serous tubal intraepithelial carcinomas (STICs) have been proposed to be the most likely precursor of ovarian, tubal and 'primary peritoneal' (pelvic) high-grade serous carcinoma (HGSC). As somatic mutation of TP53 is the most common molecular genetic change of ovarian HGSC, occurring in more than 95% of cases, we undertook a mutational analysis of 29 pelvic HGSCs that had concurrent STICs to demonstrate the clonal relationship of STICs and HGSCs. In addition, we correlated the mutational data with p53 immunostaining to determine the role of p53 immunoreactivity as a surrogate for TP53 mutations in histological diagnosis. Somatic TP53 mutations were detected in all 29 HGSCs analysed and the identical mutations were detected in 27 of 29 pairs of STICs and concurrent HGSCs. Missense mutations were observed in 61% of STICs and frameshift/splicing junction/nonsense mutations in 39%. Interestingly, there were two HGSCs with two distinctly different TP53 mutations each, but only one of the mutations was detected in the concurrent STICs. Missense mutations were associated with intense and diffuse (≥ 60%) p53 nuclear immunoreactivity, while most of the null mutations were associated with complete loss of p53 staining (p < 0.0001). Overall, this p53 staining pattern yielded a sensitivity of 87% and a specificity of 100% in detecting TP53 missense mutations. In conclusion, the above findings support the clonal relationship of STIC and pelvic HGSC and demonstrate the utility of p53 immunostaining as a surrogate for TP53 mutation in the histological diagnosis of STIC. In this regard, it is important to appreciate the significance of different staining patterns. Specifically, strong diffuse staining correlates with a missense mutation, whereas complete absence of staining correlates with null mutations.
Sulfuric Acid-Functionalized Mesoporous Benzene−Silica with a Molecular-Scale Periodicity in the Walls (2002)

Novel sulfuric acid-functionalized mesoporous benzene-silicas with a molecular-scale periodicity in the walls were derived from the mesoporous benzene-silica possessing mercaptopropyl groups by the oxidative transformation of -SH into -SO3H.
Current knowledge on treatment of chronic hepatitis B in children. (2001)

So far the treatment of chronic hepatitis B has been based on the use of numerous agents, particularly interferon alpha which proved the most effective. Attempts are made to introduce new therapeutic methods (antiviral agents--nucleoside analogues, immunotherapy--anti HBV vaccine, gene therapy) in order to obtain higher percentage of patients with durable inhibition of HBV replication than it is observed after treatment with interferon alpha. The current work has been devoted to the presentation of the experiences with interferon alpha, lamivudine and anti HBV vaccine used in subjects with chronic type B hepatitis, with special reference to paediatric patients.