Miracle-dz/UniFAR-FTUs huggingface dataset:
The TFG‐TEC oncoprotein induces transcriptional activation of the human β‐enolase gene via chromatin modification of the promoter region

Recurrent chromosome translocations are the hallmark of many human cancers. A proportion of human extraskeletal myxoid chondrosarcomas (EMCs) are associated with the characteristic chromosomal translocation t(3;9)(q11–12;q22), which results in the formation of a chimeric protein in which the N‐terminal domain of the TRK‐fused gene (TFG) is fused to the translocated in extraskeletal chondrosarcoma (TEC; also called CHN, CSMF, MINOR, NOR1, and NR4A3) gene. The oncogenic effect of this translocation may be due to the higher transactivation ability of the TFG‐TEC chimeric protein; however, downstream target genes of TFG‐TEC have not yet been identified. The results presented here, demonstrate that TFG‐TEC activates the human β‐enolase promoter. EMSAs, ChIP assays, and luciferase reporter assays revealed that TFG‐TEC upregulates β‐enolase transcription by binding to two NGFI‐B response element motifs located upstream of the putative transcription start site. In addition, northern blot, quantitative real‐time PCR, and Western blot analyses showed that overexpression of TFG‐TEC up‐regulated β‐enolase mRNA and protein expression in cultured cell lines. Finally, ChIP analyses revealed that TFG‐TEC controls the activity of the endogenous β‐enolase promoter by promoting histone H3 acetylation. Overall, the results presented here indicate that TFG‐TEC triggers a regulatory gene hierarchy implicated in cancer cell metabolism. This finding may aid the development of new therapeutic strategies for the treatment of human EMCs. © 2015 Wiley Periodicals, Inc.
Glycoprotein production for structure analysis with stable, glycosylation mutant CHO cell lines established by fluorescence‐activated cell sorting

Stable mammalian cell lines are excellent tools for the expression of secreted and membrane glycoproteins. However, structural analysis of these molecules is generally hampered by the complexity of N‐linked carbohydrate side chains. Cell lines with mutations are available that result in shorter and more homogenous carbohydrate chains. Here, we use preparative fluorescence‐activated cell sorting (FACS) and site‐specific gene excision to establish high‐yield glycoprotein expression for structural studies with stable clones derived from the well‐established Lec3.2. 8.1 glycosylation mutant of the Chinese hamster ovary (CHO) cell line. We exemplify the strategy by describing novel clones expressing single‐chain hepatocyte growth factor/scatter factor (HGF/SF, a secreted glycoprotein) and a domain of lysosome‐associated membrane protein 3 (LAMP3d). In both cases, stable GFP‐expressing cell lines were established by transfection with a genetic construct including a GFP marker and two rounds of cell sorting after 1 and 2 weeks. The GFP marker was subsequently removed by heterologous expression of Flp recombinase. Production of HGF/SF and LAMP3d was stable over several months. 1.2 mg HGF/SF and 0.9 mg LAMP3d were purified per litre of culture, respectively. Homogenous glycoprotein preparations were amenable to enzymatic deglycosylation under native conditions. Purified and deglycosylated LAMP3d protein was readily crystallized. The combination of FACS and gene excision described here constitutes a robust and fast procedure for maximizing the yield of glycoproteins for structural analysis from glycosylation mutant cell lines.
Evaluation of Methods for Extracting Xylella fastidiosa DNA from the Glassy-Winged Sharpshooter

Abstract The recent spread of the plant pathogenic bacterium Xylella fastidiosa Wells et al. by an invasive vector species, Homalodisca coagulata Say, in southern California has resulted in new epidemics of Pierce’s disease of grapevine. Our goal is to develop an efficient method to detect low titers of X. fastidiosa in H. coagulata that is amenable to large sample sizes for epidemiological studies. Detection of the plant pathogenic bacterium X. fastidiosa in its insect vector is complicated by low titers of bacteria, difficulty in releasing it from the insect mouthparts and foregut, and the presence of substances in the insect that inhibit polymerase chain reaction (PCR). To select the optimal protocol for DNA extraction to be used with PCR, we compared three standard methods and 11 commercially available kits for relative efficiency of X. fastidiosa DNA extraction in the presence of insect tissue. All of the protocols tested were proficient at extracting DNA from pure bacterial culture (1 × 105 cells), and all but one protocol successfully extracted sufficient bacterial DNA in the presence of insect tissue. Three DNA extraction techniques, immunomagnetic separation, the DNeasy Tissue kit (Qiagen, Hercules, CA), and Genomic DNA Purification kit (Fermentus, Hanover, MD), were compared more closely using a dilution series of X. fastidiosa (5,000–0 cells) with and without insect tissue present. The DNeasy Tissue kit was the best kit tested, allowing detection of 5 × 103 X. fastidiosa cells with an insect head background.
Registrar clinical teaching visits--evaluation of an assessment tool.

BACKGROUND External clinical teaching (ECT) visits provide structured feedback to general practice registrars concerning their performance during training. This study sought to evaluate the acceptability to general practice registrars of a quantitative, criterion based, formative assessment tool to be administered during ECT visits. METHODS We used a standardised, validated consultation feedback proforma and set the 1-5 rating at the FRACGP exam standard. An evaluation questionnaire was given to the registrar and returned separately. RESULTS Twenty-six ECT visits were conducted from September 2005 to March 2006. A total of 21 registrar feedback forms were received (response rate 80.1%). Twenty (95%) registrars agreed the form provided useful feedback and was a useful prompt for discussion with their medical educator. Eighty-six percent felt their ratings were fair. DISCUSSION Quantitative formative assessment was well received by the majority of general practice registrars. This tool complements other formative assessment tools used in general practitioner training.
Cultural actors as agents of generating social co-presences within the place: Istanbul’s contemporary art scene

ABSTRACT This paper builds on the designation of cultural actors’ actions as a decisive factor in the emergence of urban patterns of art-driven social co-presences in Istanbul. It contributes to the creative city debate from the perspective of community development by incorporating the contemporary arts into urban social space making efforts. Methodologically, the locations of art organizations in the contemporary arts scene of Istanbul are approached as an urban pattern of art driven social co-presences that resulted from the ‘collective action’ in which a multitude of cultural actors are involved. We find that the clusters of art organizations serve as multidimensional social interactions among artist communities. There are, however, inefficiencies in spreading this interactive networking throughout different social segments. Research findings conclude that the cultural actors as agents of generating social co-presences within the place, are not effectively contributing to the society’s social coherence, particularly in terms of creating links with disadvantageous neighbourhood residents.
The impact of genetic background on neurodegeneration and behavior in seizured mice

We used pilocarpine‐induced seizures in mice to determine the impact of genetic background on the vulnerability of hippocampal neurons and associated changes of behavioral performance. The susceptibility of hippocampal neurons to seizure‐induced cell death paralleled the severity of the seizures and depended on genetic background. Hippocampal neurons in C57BL/6 mice were most resistant to cell death, whereas they were highly vulnerable in FVB/N mice. The degree of neuronal degeneration in F1 hybrid mice obtained by crossing the two strains was at an intermediate level between the parent strains. Two weeks after the severe seizures, performance in a water‐maze place navigation task showed a bimodal distribution. Seventeen of 19 (90%) F1 mice were completely unable to learn while the other two learned reasonably well. Of 28 C57BL/6 mice with similarly severe seizures, six were as strongly impaired as their F1 counterparts (22%). The remaining 22 performed normally, indicating a much lower probability of C57BL/6 mice to be affected. Treated mice showed a deficit of open‐field exploration which was strongly correlated with the impairment in the place navigation task and was again more severe in F1 mice. Our results show that the vulnerability of hippocampal neurons to pilocarpine‐induced seizures, as well as the associated behavioral changes, depended on genetic background. Furthermore, they confirm and extend our earlier finding that a relatively modest reduction of hippocampal cell death can be associated with dramatic changes of behavioral performance and emphasize the importance of tightly‐controlled genetic backgrounds in biological studies.
A Two-Mode Control Scheme With Input Voltage Feed-Forward for the Two-Switch Buck-Boost DC–DC Converter

The two-switch buck-boost (TSBB) converter is suitable for wide input voltage applications. In order to achieve high efficiency over the entire input voltage range, the TSBB converter is operated in buck mode at high input voltage and boost mode at low input voltage. Such operation is called the two-mode control scheme. The objective of this paper is to propose an input voltage feed-forward (IVFF) method to reduce the influence of the input voltage disturbance on the output voltage. The small-signal models of the TSBB converter are built, and based on which, the IVFF functions under different operating modes of the TSBB converter are derived. The IVFF function in boost mode is simplified for easy implementation. The two-mode control scheme with IVFF compensation is then proposed for the TSBB converter, which realizes automatic selections of operating modes and the corresponding IVFF functions. Besides, nearly smooth switching between buck and boost modes is also guaranteed. For exhibiting the advantages of the proposed control scheme clearly, comparisons between the two-mode control with and without IVFF compensation have been presented in this paper, including the output signal of the voltage regulator and input-to-output voltage transfer function. Finally, a 250-500-V input, 360-V output, and 6-kW-rated power prototype is fabricated to validate the effectiveness of the proposed control scheme in the laboratory, and the experimental results show that the TSBB converter has an improved input transient response and high efficiency over the entire input voltage range with this proposed control scheme.
Large-Scale Screening and Identification of Novel Ebola Virus and Marburg Virus Entry Inhibitors

ABSTRACT Filoviruses are highly infectious, and no FDA-approved drug therapy for filovirus infection is available. Most work to find a treatment has involved only a few strains of Ebola virus and testing of relatively small drug libraries or compounds that have shown efficacy against other virus types. Here we report the findings of a high-throughput screening of 319,855 small molecules from the Molecular Libraries Small Molecule Repository library for their activities against Marburg virus and Ebola virus. Nine of the most potent, novel compounds that blocked infection by both viruses were analyzed in detail for their mechanisms of action. The compounds inhibited known key steps in the Ebola virus infection mechanism by blocking either cell surface attachment, macropinocytosis-mediated uptake, or endosomal trafficking. To date, very few specific inhibitors of macropinocytosis have been reported. The 2 novel macropinocytosis inhibitors are more potent inhibitors of Ebola virus infection and less toxic than ethylisopropylamiloride, one commonly accepted macropinocytosis inhibitor. Each compound blocked infection of primary human macrophages, indicating their potential to be developed as new antifiloviral therapies.
A regulatory protein–protein interaction governs glutamate biosynthesis in Bacillus subtilis: the glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC

Glutamate synthesis is the link between carbon and nitrogen metabolism. In Bacillus subtilis, glutamate is exclusively synthesized by the glutamate synthase encoded by the gltAB operon. The glutamate dehydrogenase RocG from B. subtilis is exclusively devoted to glutamate degradation rather than to its synthesis. The expression of the gltAB operon is induced by glucose and ammonium and strongly repressed by arginine. Regulation by glucose and arginine depends on the transcriptional activator protein GltC. The gltAB operon is constitutively expressed in a rocG mutant strain, but the molecular mechanism of negative control of gltAB expression by RocG has so far remained unknown. We studied the role of RocG in the intracellular accumulation of GltC. Furthermore, we considered the possibility that RocG might act as a transcription factor and be able to inhibit the expression of gltAB either by binding to the mRNA or to the promoter region of the gltAB operon. Finally, we asked whether a direct binding of RocG to GltC could be responsible for the inhibition of GltC. The genetic and biochemical data presented here show that the glutamate dehydrogenase RocG is able to bind to and concomitantly inactivate the activator protein GltC. This regulatory mechanism by the bifunctional enzyme RocG allows the tight control of glutamate metabolism by the availability of carbon and nitrogen sources.
Labor Supply Shocks and the Beveridge Curve

The accession of twelve Eastern European countries to the European Union between 2004 and 2007 led to an increase of migrant labour supply in some incumbent countries. By means of a structural VAR with sign restrictions I find that job-related immigration triggered a counter-clockwise outward movement of the Beveridge curve in Austria, a country that was particularly affected due to its geographical exposure and a high wage gap to the accession countries. A regional analysis shows that the prevalence of labour supply shocks abates from east to west. In contrast to standard theory but in line with existing empirical evidence, labour supply shocks are not found to be price dampening, but more likely inflationary. From this it follows that they cannot be properly identified without resorting to some restriction of the unemployment rate.
Inhibition of PPARγ prevents type I diabetic bone marrow adiposity but not bone loss

Diabetes type I is associated with bone loss and increased bone adiposity. Osteoblasts and adipocytes are both derived from mesenchymal stem cells located in the bone marrow, therefore we hypothesized that if we could block adipocyte differentiation we might prevent bone loss in diabetic mice. Control and insulin‐deficient diabetic BALB/c mice were chronically treated with a peroxisomal proliferator‐activated receptor γ (PPARγ) antagonist, bisphenol‐A‐diglycidyl ether (BADGE), to block adipocyte differentiation. Effects on bone density, adiposity, and gene expression were measured. BADGE treatment did not prevent diabetes‐associated hyperglycemia or weight loss, but did prevent diabetes‐induced hyperlipidemia and effectively blocked diabetes type I‐induced bone adiposity. Despite this, BADGE treatment did not prevent diabetes type I suppression of osteoblast markers (runx2 and osteocalcin) and bone loss (as determined by micro‐computed tomography). BADGE did not suppress osteoblast gene expression or bone mineral density in control mice, however, chronic (but not acute) BADGE treatment did suppress osteocalcin expression in osteoblasts in vitro. Taken together, our findings suggest that BADGE treatment is an effective approach to reduce serum triglyceride and free fatty acid levels as well as bone adiposity associated with type I diabetes. The inability of BADGE treatment to prevent bone loss in diabetic mice suggests that marrow adiposity is not linked to bone density status in type I diabetes, but we cannot exclude the possibility of additional BADGE effects on osteoblasts or other bone cells, which could contribute to preventing the rescue of the bone phenotype. J. Cell. Physiol. 209: 967–976, 2006. © 2006 Wiley‐Liss, Inc.
Dynamics of DNA repair suggested by the subcellular localization of Brca1 and Brca2 proteins

The localization of proteins to specific subcellular compartments often reveals clues regarding their biological functions. Although significant progress has been made towards understanding how damaged DNA is repaired, experiments to date have primarily focused on signal transduction pathways that activate DNA repair protein complexes and on how these complexes are assembled. Current evidence suggests that certain DNA repair processes are spatially organized such that aberrant DNA structures can be brought into proximity with DNA repair proteins at fixed sites. Since biochemical evidence suggests that the tumor suppressor proteins, Brca1 and Brca2, may mediate the assembly of protein complexes involved in the repair of damaged DNA, we have performed subcellular fractionation experiments to determine the subnuclear localization of these proteins. The majority of Brca1 and Brca2 proteins were found to interact tightly with the nuclear matrix. Furthermore, within the limits of detection, localization of Brca1 and Brca2 to the nuclear matrix was not altered following treatment of cells with DNA damaging agents that activate homology‐mediated double‐stranded DNA break and transcription‐coupled repair pathways. Our findings suggest that Brca1 and Brca2 may perform their DNA repair‐related functions from positions that are anchored to the nuclear matrix. These data are consistent with proposed models that suggest that components of specific repair complexes residing on the nuclear matrix function to recruit damaged DNA. © 2005 Wiley‐Liss, Inc.
Spectroscopic studies of interaction of chlorobenzylidine with DNA.

Electronic absorbance and fluorescence titrations are used to probe the interaction of chlorobenzylidine with DNA. The binding of chlorobenzylidine to DNA results in hypochromism, a small shift to a longer wavelength in the absorption spectra, and emission quenching in the fluorescence spectra. These spectral characteristics suggest that chlorobenzylidine binds to DNA by an intercalative mode. This conclusion is reinforced by fluorescence polarization measurements. Scatchard plots constructed from fluorescence titration data give a binding constant of 1.3 x 10(5) M(-1) and a binding site size of 10 base pairs. This indicates that chlorobenzylidine has a high affinity with DNA. The intercalative interaction is exothermic with a Van't Hoff enthalpy of -143 kJ/mol. This result is obtained from the temperature dependence of the binding constant. The interaction of chlorobenzylidine with DNA is affected by the pH value of the solution. The binding constant has its maximum at pH 3.0. Upon binding to DNA, the fluorescence from chlorobenzylidine is quenched efficiently by the DNA bases and the fluorescence intensity tends to be constant at high concentrations of DNA when the binding is saturated. The Stern-Volmer quenching constant obtained from the linear quenching plot is 1.6 x 10(4) M(-1) at 25 degrees C. The measurements of the fluorescence lifetime and the dependence of the quenching constant on the temperature indicate that the fluorescence quenching process is static. The fluorescence lifetime of chlorobenzylidine is 1.9 +/- 0.4 ns.
A 500 Mb/s disk drive read channel in 0.25 /spl mu/m CMOS incorporating programmable noise predictive Viterbi detection and trellis coding

The hard disk drive (HDD) market continues its growth of more than 60% per year in area density. Use of higher spindle rotational speeds is also a HDD market trend over recent years. A combination of these two factors require read channel speed increases in excess of 40% annually to keep up with the HDD requirements. To keep pace with areal density curve, read channel speed alone is not enough. Besides data transfer rate, the effective number of user bits per magnetic transition is also increased. Therefore, more sophisticated signal processing and coding schemes are necessary. In fact, 3.5dB signal processing gain over the previous generation extended class IV partial response (EPR4) is measured at user bit density (UBD) of 3.0. The signal processing features of the 500Mb/s device are described.
Weekly Cisplatin-Based Concurrent Chemoradiotherapy for Treatment of Locally Advanced Head and Neck Cancer: a Single Institution Study.

BACKGROUND The organ preservation approach of choice for the treatment of locally advanced head and neck cancers is concurrent chemoradiation with three weekly high doses of cisplatin. Although this is an efficacious treatment policy, it has high acute systemic and mucosal toxicities, which lead to frequent treatment breaks and increased overall treatment time. Hence, the current study was undertaken to evaluate the efficacy of concurrent chemoradiation using 40 mg/m2 weekly cisplatin. MATERIALS AND METHODS This is a single institutional retrospective study including the data of 266 locally advanced head and neck cancer patients who were treated with concurrent chemoradiation using 40 mg/m2 weekly cisplatin from January 2012 to January 2014. A p-value of < 0.05 was taken to be significant statistically for all purposes in the study. RESULTS The mean age of the study patients was 48.8 years. Some 36.1% of the patients had oral cavity primary tumors. The mean overall treatment time was 57.2 days. With a mean follow up of 15.2 months for all study patients and 17.5 months for survivors, 3 year local control, locoregional control and disease free survival were seen in 62.8%, 42.8% and 42.1% of the study patients. Primary tumor site, nodal stage of disease, AJCC stage of the disease and number of cycles of weekly cisplatin demonstrated statistically significant correlations with 3 year local control, locoregional control and disease free survival. CONCLUSIONS Concurrent chemoradiotherapy with moderate dose weekly cisplatin is an efficacious treatment regime for locally advanced head and neck cancers with tolerable toxicity which can be used in developing countries with limited resources.
Role of the N-terminal Epidermal Growth Factor-like Domain of Factor X/Xa*

The functional importance of the N-terminal epidermal growth factor-like domain (EGF-N) of factor X/Xa (FX/Xa) was investigated by constructing an FX mutant in which the exon coding for EGF-N was deleted from FX cDNA. Following expression and purification to homogeneity, the mutant was characterized with respect to its ability to function as a zymogen for either the factor VIIa-tissue factor complex or the factor IXa-factor VIIIa complex and then to function as an enzyme in the prothrombinase complex to catalyze the conversion of prothrombin to thrombin. It was discovered that EGF-N is essential for the recognition and efficient activation of FX by both activators in the presence of the cofactors. On the other hand, the FXa mutant interacted with factor Va with a normal apparent dissociation constant and activated prothrombin with ∼3-fold lower catalytic efficiency in the prothrombinase complex. Surprisingly, the mutant activated prothrombin with ∼12-fold better catalytic efficiency than wild-type FXa in the absence of factor Va. The mutant was inactive in both prothrombin time and activated partial thromboplastin time assays; however, it exhibited a similar specific activity in a one-stage FXa clotting assay. These results suggest that EGF-N of FX is required for the cofactor-dependent zymogen activation by both physiological activators, but it plays no apparent role in FXa recognition of the cofactor in the prothrombinase complex.