Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced phosphorylation of the C‐terminal domain of RNA polymerase II upon serum stimulation of quiescent cells: possible involvement of MAP kinases.

The largest subunit of RNA polymerase (RNAP) II contains at it C‐terminus an unusual domain comprising tandem repeats of the consensus sequence Tyr‐Ser‐Pro‐Thr‐Ser‐Pro‐Ser. This C‐terminal domain (CTD) can undergo phosphorylation at multiple sites giving rise to a form of the enzyme designated RNAP IIO. The unphosphorylated form is designated RNAP IIA. The largest subunits of RNAPs IIO and IIA are designated IIo and IIa, respectively. In quiescent NIH 3T3 fibroblasts, subunits IIo and IIa are present in comparable amounts. Upon serum stimulation, the amount of subunit IIo increases markedly and remains elevated for several hours. The increase of subunit IIo also occurs in transcription‐inhibited cells and, therefore, is not a consequence of serum‐activated transcription. This observation suggests that serum stimulation activates a CTD kinase and/or inhibits a CTD phosphatase. This hypothesis is supported by the finding that serum stimulates phosphorylation of a beta‐galactosidase‐CTD fusion protein expressed in these cells. Furthermore, an enhanced CTD kinase activity was discovered in lysates from serum‐stimulated fibroblasts and was found to copurify with MAP kinases on a Mono Q column and to bind to anti‐MAP kinase antibodies. The idea that MAP kinases phosphorylate the CTD in vivo is supported by the observation that subunit IIa, but not subunit IIb which lacks the CTD, is phosphorylated at multiple sites by purified MAP kinase. Consequently, the MAP kinases are a new class of CTD kinases which appear to be involved in the phosphorylation of RNAP II following serum stimulation. This phosphorylation may contribute to the transcriptional activation of serum‐stimulated genes.
Pharmacological therapy for glaucoma: a review.

For some time the medical treatment of glaucoma has consisted of topical beta-blockers, adrenergic agents, miotics and oral carbonic anhydrase inhibitors (CAIs). However, the therapeutic arsenal available for the medical treatment of glaucoma has recently extended with new classes of ocular hypotensive agents i.e. prostaglandins, local CAIs and alpha2-adrenergic agents. Beta-blockers are still the mainstay in glaucoma treatment and are first line drugs. However, even if they are applied once daily, as with timolol in gel forming solution and levobunolol, the possible cardiopulmonary adverse effects of beta-blockers remain a cause for concern. When monotherapy with beta-blockers is ineffective in reducing intraocular pressure (IOP) or is hampered by adverse effects, a change of monotherapy to prostaglandins, local CAIs, alpha2-adrenergic agonists (brimonidine) or to dipivalyl epinephrine is advised. Prostaglandins, local CAIs and alpha2-adrenergic agonists, such as brimonidine, may in time become first line drugs because they reduce IOP effectively and until now systemic adverse effects have rarely been reported with these agents. The development of a pro-drug of either a local CAI or an alpha2-adrenergic agonist with a sustained and continuous effect on IOP level, which could be applied once a day is suggested. Because of these new developments, miotics, i.e. pilocarpine and carbachol, are recommended as second or third line drugs. The cholinesterase inhibitors are considered third line drugs as better agents with fewer local and systemic adverse effects have become available. Oral CAIs may be used temporarily in patients with elevated IOPs e.g. postsurgery or post-laser, or continuously in patients with glaucoma resistant to other treatment. Combining ocular hypotensive drugs is indicated when the target pressure for an individual patient cannot be reached with monotherapy. Combination therapy of beta-blockers is additive with prostaglandins, topical CAIs and miotics. Prostaglandins such as latanoprost can be combined with beta-blockers, adrenergic agents, local CAIs and miotics. Combinations with brimonidine or local CAIs need further investigation. Treatment of glaucoma with the new ocular hypotensive agents, either in monotherapy or combination therapy, may provide lower IOPs and delay or postpone the need for surgery.
[Determination of cartilage thickness in the ankle joint. an MRT (1.5)-anatomical comparative study].

PURPOSE The aim of this study was to evaluate the accuracy of MRI in the measurement of cartilage thickness of the ankle joint in comparison to pathologic and histologic specimens. PATIENTS AND METHODS The ankle joints of four fresh cadaver feet were imaged on a 1.5T MR-unit in the coronal plane. Standard T1-weighted spin echo (SE) and a T1-weighted 3D-GE (FLASH-3D) sequence with fat saturation were applied. Following MR imaging, the talus was explanted and cut parallel to the MR images for macroscopic evaluation and histologic specimens were prepared. MRI measurements of the cartilage thickness of the talus were carried out in two ways: without and with consideration of a transition zone of intermediate signal intensity between hyperintense cartilage and hypointense cortical bone. The data were compared with the anatomic specimens as the gold standard expressing the difference as a percentage value. On histologic specimens thickness of deep calcified cartilage layer was measured. RESULTS Measurements without the transition zone showed a mean underestimation of talus cartilage thickness of 46.8% (41.3-52.1) for T1-SE and 47.5% (43.1-52.1) for fat saturated FLASH-3D images. Considering the transition zone the mean values were 25.0% (23.1-26.2) and 14.1% (6.7-21.5). The histologic specimens showed a three-fold increase of thickness of deep calcified cartilage layer. CONCLUSIONS Measurements of the cartilage layer of the ankle joint on MR images are only accurate if the transition zone (calcified cartilage layer) is considered and the optimal pulse sequence (FLASH-3D-fat-sat) is applied.
Limited Heat-Shock Protein 72 Induction in Caco-2 Cells by L-Glutamine

Background/Aims:L-Glutamine (L-gln) is a conditionally essential amino acid which is consumed by certain tissues like the intestine in large amounts as energy source during critical illness. Apart from nutritive action, recent data suggest a link to heat-shock protein (hsp) induction. We investigated the effect of L-gln on hsp72 expression in the intestinal cell line Caco-2 under basal and heat-shock conditions and compared it with related amino acids. Methods: Total cellular protein was extracted and separated by SDS-PAGE. Immunoblots were performed with anti-hsp72 followed by chemiluminescence detection and densitometric scanning. Results: Following heat shock, hsp72 protein expression increased by 72 and 53% at 2 and 4 mmol/l L-gln, respectively, compared to heat shock alone (p < 0.05). Under basal conditions a limited increase occurred only at 8 mmol/l L-gln (p < 0.01). Levels remained unaffected when related amino acids including alanine, glutamate or glycine were supplemented under basal and heat-shock conditions. Similarly, the nonmetabolizable glutamine analogue DON or the toxic metabolite L-pyroglutamate did not induce hsp72. Conclusion: We conclude that the glutamine-mediated effect may be specifically attributed to the metabolic action of L-gln.
ASSESSING THE IMPACT OF LIQUIDITY REFORMS ON ECONOMIC GROWTH OF NIGERIA

The study assesses the impact of bank liquidity reform on the economy of Nigeria with annual time series data from 1986 to 2013. There are mixed and conflicting conclusions indicating that the effect of bank liquidity reforms on economic growth has not yet been resolved. Thus, there is the need to further examine the effect of liquidity on the economic growth of Nigeria. The present study improves on the previous ones by restricting the data to the period stated. Based on the theoretical issues discussed and the literature surveyed the model is built around the augmented Solow growth model whose operational framework is the Lobb-Douglas production function. Econometric evidence reveals stationarity of the variables at their first differences while the Johansen co-integration approach also confirms the presences of one co-integrating relationship at one percent and five percent levels of significance. The study further shows that bank liquidity rate reforms have proven to have very high explanatory influence on Nigerian economy, which indicates that bank liquidity reform is a veritable tool for repositioning and reorienting Nigerian economy. Based on the findings and conclusions, the study recommend that the central bank of Nigeria and other relevant regulators must insist that banks maintain sound and stable liquidity ratios in order to promote sound financial system and enhance potentials of economic growth of Nigeria.
Mucosal gene signatures to predict response to infliximab in patients with ulcerative colitis

Background and aims: Infliximab is an effective treatment for ulcerative colitis with over 60% of patients responding to treatment and up to 30% reaching remission. The mechanism of resistance to anti-tumour necrosis factor α (anti-TNFα) is unknown. This study used colonic mucosal gene expression to provide a predictive response signature for infliximab treatment in ulcerative colitis. Methods: Two cohorts of patients who received their first treatment with infliximab for refractory ulcerative colitis were studied. Response to infliximab was defined as endoscopic and histological healing. Total RNA from pre-treatment colonic mucosal biopsies was analysed with Affymetrix Human Genome U133 Plus 2.0 Arrays. Quantitative RT-PCR was used to confirm microarray data. Results: For predicting response to infliximab treatment, pre-treatment colonic mucosal expression profiles were compared for responders and non-responders. Comparative analysis identified 179 differentially expressed probe sets in cohort A and 361 in cohort B with an overlap of 74 probe sets, representing 53 known genes, between both analyses. Comparative analysis of both cohorts combined, yielded 212 differentially expressed probe sets. The top five differentially expressed genes in a combined analysis of both cohorts were osteoprotegerin, stanniocalcin-1, prostaglandin-endoperoxide synthase 2, interleukin 13 receptor alpha 2 and interleukin 11. All proteins encoded by these genes are involved in the adaptive immune response. These markers separated responders from non-responders with 95% sensitivity and 85% specificity. Conclusion: Gene array studies of ulcerative colitis mucosal biopsies identified predictive panels of genes for (non-)response to infliximab. Further study of the pathways involved should allow a better understanding of the mechanisms of resistance to infliximab therapy in ulcerative colitis. ClinicalTrials.gov number, NCT00639821.
The Boom and Bust Phenomenon and U. S. Bank Failure Experience, 1914-1934

This paper is a theoretical and empirical investigation of the causes for the widespread bank failures of the 1920s. The purpose is to formalize and compare some of the extant arguments for failure, and to re-examine the particular historical period 1914-34 with the benefit of new evidence. A model is developed that is sufficiently general to capture the effects of extreme competition, heterogeneity among bankers, and macroeconomic surprises on bank solvency. Both entry into the banking industry and macroeconomic surprises have the potential to increase the failure rate. The model motivates an empirical study of annual statewide aggregate data on bank balance sheets, income statements, and failure rates. The empirics suggest that the high rates of bank failure observed in the 1920s are part of a boom- and-bust phenomenon. Specifically, we find that high statewide failure rates were preceded by large growth rates in the number of banks.
Survival after Major Cardiac Surgery: Performance and Comparison of Predictive Ability of EuroSCORE II and Logistic EuroSCORE in a Sample of Mediterranean Population

Abstract Background The European System for Cardiac Operative Risk Evaluation (EuroSCORE) II has been recently introduced to improve mortality prediction in cardiac surgery. We compare the predictive ability of the new EuroSCORE II with that of the original logistic EuroSCORE and we made an evaluation of a sample of our population submitted to major cardiac surgery in the context of a Mediterranean country. Materials and Methods Predicted and observed mortality were recorded in 1,200 consecutive patients undergoing major cardiac surgery at our institution with both logistic EuroSCORE and EuroSCORE II. Patients were grouped according to type of surgery: isolated valvular (n = 538), isolated coronary (n = 322), combined (n = 192), and miscellaneous (n = 148). Predictive capacity of both scales was compared for overall population and for each group in terms of calibration and discrimination using the observed by expected mortality rate, Hosmer–Lemeshow test, and C-statistic. Results Overall mortality was 6.8%, whereas that predicted by logistic EuroSCORE and EuroSCORE II was 9.7 and 3.7%, respectively. Mortality in our population was higher than mortality expected according to the original EuroSCORE II database. For all groups included in our population, logistic EuroSCORE overestimated mortality and EuroSCORE II underestimated the outcome even more. However, EuroSCORE II showed better calibration than logistic EuroSCORE for overall, valvular, and combined surgery. In contrast, logistic EuroSCORE demonstrated better calibration for coronary surgery. Discrimination capacity was good for both risk scores, but it was superior for logistic EuroSCORE than for EuroSCORE II in all considered subgroups unless combined surgery. Conclusion Mortality in our population was higher than the mortality that would have been expected by the new EuroSCORE II analysis. Although EuroSCORE II has good calibration and discrimination capacity, both are worse than those demonstrated by logistic EuroSCORE. Forthcoming evaluations are necessary when the new model will be widely used.
Offer patterns of nationally placed livers by donation service area

We previously reported that national liver distribution is highly concentrated in 6 US centers, and this raises the possibility of expedited placement. Therefore, we evaluated all national offers of nationally placed livers (n=1625) to adult wait‐list candidates from February 2005 to January 2010. We developed a model to predict national utilization pathways; pathways exceeding the best‐fit linear unbiased predictions by ≥3 standard errors were defined as preferred. All 51 donation service areas (DSAs) placed 1 or more livers nationally, but the percentage per DSA ranged from 1% to 36%. Of 2830 possible national DSA‐center pathways, 87% were used. Five hundred eighty livers (36%) were accepted on the first national offer. Four DSAs accounted for 47% of first‐national‐offer livers, and 44% of these were accepted by a single center. In comparison with first‐offer livers using nonpreferred pathways, first offers along a preferred pathway were offered to fewer status 1 candidates (19% versus 61%) and had lower median Model for End‐Stage Liver Disease (MELD) scores (22 versus 36, P<0.001). In conclusion, DSA placement patterns of national livers vary widely, with 4 DSAs exporting a high proportion of national livers on the first national offer to non–status 1 candidates with MELD scores less than their local transplant MELD scores. Although this practice may facilitate liver placement, it raises the possibility of expedience trumping patient need. Here we propose changes to the national liver distribution system that will help to balance equity, efficiency, and transparency. Liver Transpl 19:404–410, 2013. © 2013 AASLD.
The whole-process reliability evaluation of power system including generation, transmission, transformation and distribution

Aiming at the problem that using current reliability evaluation indices, which can reflect only one segment of power system, for power system planning leads to partial planning results and is hard to achieve the goal of global programming, this paper proposes an approach to evaluate the reliability of the entire power system, considering the effect of generation, transmission, transformation and distribution system. The power supply reliability not only depends on the structure of the distribution system, but also on the main grid. In the proposed evaluation procedure electrical connection of substation is firstly equated to some equivalent branches based on minimal cut-set method. Then Monte Carlo Simulation (MCS) is used to assess the reliability of generation and transmission composite system and substation system simultaneously by sampling and to obtain hierarchical available capacities and probabilities. Finally, the hierarchical reliability indices of the main grid are used as multi-state equivalent sources to assess the distribution system reliability. The proposed method is tested using a system constituted by the IEEE RTS 79 and feeder of IEEE RBTS-bus6. The results show that the main grid has obvious influence on the reliability of distribution system, and the proposed method can provide more details for system planning and operation.
Structural and Biochemical Characterization of the Salicylyl-acyltranferase SsfX3 from a Tetracycline Biosynthetic Pathway*♦

Background: SsfX3 is an acyltransferase that can acylate tetracycline-like molecules at C-4. Results: Crystal structure showed SsfX3 contains a structural N-terminal β-sandwich domain and a catalytic C-terminal hydrolase domain. Mutagenesis revealed both are essential for activity. Conclusion: The N-terminal domain is recruited to bind the large “small molecule” substrate. Significance: New structural knowledge enables engineering of the acyltransferase toward synthesis of tetracycline analogs. SsfX3 is a GDSL family acyltransferase that transfers salicylate to the C-4 hydroxyl of a tetracycline intermediate in the penultimate step during biosynthesis of the anticancer natural product SF2575. The C-4 salicylate takes the place of the more common C-4 dimethylamine functionality, making SsfX3 the first acyltransferase identified to act on a tetracycline substrate. The crystal structure of SsfX3 was determined at 2.5 Å, revealing two distinct domains as follows: an N-terminal β-sandwich domain that resembles a carbohydrate-binding module, and a C-terminal catalytic domain that contains the atypical α/β-hydrolase fold found in the GDSL hydrolase family of enzymes. The active site lies at one end of a large open binding pocket, which is spatially defined by structural elements from both the N- and C-terminal domains. Mutational analysis in the putative substrate binding pocket identified residues from both domains that are important for binding the acyl donor and acceptor. Furthermore, removal of the N-terminal carbohydrate-binding module-like domain rendered the stand-alone α/β-hydrolase domain inactive. The additional noncatalytic module is therefore proposed to be required to define the binding pocket and provide sufficient interactions with the spatially extended tetracyclic substrate. SsfX3 was also demonstrated to accept a variety of non-native acyl groups. This relaxed substrate specificity toward the acyl donor allowed the chemoenzymatic biosynthesis of C-4-modified analogs of the immediate precursor to the bioactive SF2575; these were used to assay the structure activity relationships at the C-4 position.
Function of a Bovine Papillomavirus Type 1 Exonic Splicing Suppressor Requires a Suboptimal Upstream 3′ Splice Site

ABSTRACT Alternative splicing is an important mechanism for the regulation of bovine papillomavirus type 1 (BPV-1) gene expression during the virus life cycle. Previous studies in our laboratory have identified two purine-rich exonic splicing enhancers (ESEs), SE1 and SE2, located between two alternative 3′ splice sites at nucleotide (nt) 3225 and nt 3605. Further analysis of BPV-1 late-pre-mRNA splicing in vitro revealed a 48-nt pyrimidine-rich region immediately downstream of SE1 that inhibits utilization of the nt 3225 3′ splice site. This inhibitory element, which we named an exonic splicing suppressor (ESS), has a U-rich 5′ end, a C-rich central part, and an AG-rich 3′ end (Z. M. Zheng, P. He, and C. C. Baker, J. Virol. 70:4691–4699, 1996). The present study utilized in vitro splicing of both homologous and heterologous pre-mRNAs to further characterize the ESS. The BPV-1 ESS was inserted downstream of the 3′ splice site in the BPV-1 late pre-mRNA, Rous sarcoma virussrc pre-mRNA, human immunodeficiency virustat-rev pre-mRNA, and Drosophila dsx pre-mRNA, all containing a suboptimal 3′ splice site, and in the human β-globin pre-mRNA, which contains a constitutive 3′ splice site. These studies demonstrated that suppression of splicing by the BPV-1 ESS requires an upstream suboptimal 3′ splice site but not an upstream ESE. Furthermore, the ESS functions when located either upstream or downstream of BPV-1 SE1. Mutational analyses demonstrated that the function of the ESS is sequence dependent and that only the C-rich region of the ESS is essential for suppression of splicing in all the pre-mRNAs tested.
The Comet Assay of Nasal Epithelia: Measurement of DNA Damage for the Assessment of Genotoxic Air Pollution

Objectives: The alkaline single cell gel electrophoresis or “comet” assay allows measurement of DNA damage in single cells with a high degree of sensitivity, e.g., for investigations of the effect of environmental agents with DNA‐damaging potential. This study aimed to adapt this test to respiratory cells of the human nasal mucosa to examine the genotoxic effect of air pollution (cigarette smoke).
Thiazole Synthase from Escherichia coli

Thiamine is biosynthesized by combining two heterocyclic precursors. In Escherichia coli and other anaerobes, one of the heterocycles, 4-methyl-5-(β-hydroxyethyl) thiazole phosphate, is biosynthesized from 1-deoxyxylulose-5-phosphate, tyrosine, and cysteine. Genetic evidence has identified thiH, thiG, thiS, and thiF as essential for thiazole biosynthesis in E. coli. In this paper, we describe the measurement of the thiazole phosphate-forming reaction using purified protein components. The activity is shown to require four proteins isolated as heterodimers: ThiGH and ThiFS. Reconstitution of the [4Fe-4S] cluster in ThiH was essential for activity, as was the use of ThiS in the thiocarboxylate form. Spectroscopic studies with ThiGH strongly suggested that S-adenosylmethionine (AdoMet) bound to the [4Fe-4S] cluster, which became more susceptible to reduction to the +1 state. Assays of thiazole phosphate formation showed that, in addition to the proteins, Dxp, tyrosine, AdoMet, and a reductant were required. The analysis showed that no more than 1 mol eq of thiazole phosphate was formed per ThiGH. Furthermore, for each mole of thiazole-P formed, 1 eq of AdoMet and 1 eq of tyrosine were utilized, and 1 eq of 5′-deoxyadenosine was produced. These results demonstrate that ThiH is a member of the “radical-AdoMet” family and support a mechanistic hypothesis in which AdoMet is reductively cleaved to yield a highly reactive 5′-deoxyadenosyl radical. This radical is proposed to abstract the phenolic hydrogen atom from tyrosine, and the resultant substrate radical cleaves to yield dehydroglycine, which is required by ThiG for the thiazole cyclization reaction.