Miracle-dz/UniFAR-FTUs huggingface dataset:
Designing synthetic superagonists of C3a anaphylatoxin.

An extensive structure-activity study of synthetic analogues of the C3a anaphylatoxin was conducted. Our goal was to map C3a-C3a receptor interactions by designing synthetic analogue molecules having maximal biologic potency. Nonspecific binding of the polycationic C3a to polyanionic molecules on cellular surfaces often obscures specific binding to the receptor. Less cationic synthetic C3a analogues would be useful tools in identifying and characterizing the various cell types having C3a receptors. These factors should also be useful as pharmacologic probes for mechanism studies, as high-affinity ligands for target cell identification, and for receptor isolation. Attachment of amino-terminal hydrophobic groups such as Fmoc to C3a analogues [as orginally introduced by Gerardy-Schahn et al. (1988) Biochem. J. 255, 209] markedly enhanced the potency of synthetic C3a peptides. The enhancement effect on potency from introducing hydrophobic groups to C3a analogues was interpreted as possibly being nonspecific. Our systematic search for an optimal peptide length, composition, and N-terminal hydrophobic unit resulted in several superpotent C3a analogues having 200-1500% the potency of natural C3a. One particularly potent C3a peptide was designed by incorporating two tryptophanyl residues at the N-terminal end of a 15-residue C3a analogue. The superpotent peptide W-W-G-K-K-Y-R-A-S-K-L-G-L-A-R has several residues differing (underlined) from the sequence corresponding to positions 63-77 in human C3a, a region that contains the essential functional site of the molecule. This 15-residue model peptide exhibited the greatest biological potency of all peptides tested, being 12-15 times more active than natural C3a. Since an optimal distance was found to exist between the N-terminal hydrophobic unit (W-W) and the C-terminal primary binding site (LGLAR), we concluded that the hydrophobic unit interacts specifically with a secondary binding site on the C3a receptor. The presence of both a primary (effector) and secondary (hydrophobic) binding site on these linear synthetic ligands, which can interact cooperatively with the C3a receptor, presumably accounts for the high relative potency of the analogues. Our design of superpotent analogues of C3a demonstrates the feasibility for constructing small synthetic peptides to mimic natural biologic factors that depend on secondary or tertiary structure for their activity. These synthetic peptide studies demonstrate that a linear array of amino acids (e.g., W-W) can successfully substitute for a conformation-dependent binding site on a bioactive factor.
Loss of Heterozygosity at the Ink4a/ArfLocus Facilitates Abelson Virus Transformation of Pre-B Cells

ABSTRACT In many tumor systems, analysis of cells for loss of heterozygosity (LOH) has helped to clarify the role of tumor suppressor genes in oncogenesis. Two important tumor suppressor genes, p53 and the Ink4a/Arf locus, play central roles in the multistep process of Abelson murine leukemia virus (Ab-MLV) transformation. p53 and the p53 regulatory protein, p19Arf, are required for the apoptotic crisis that characterizes the progression of primary transformed pre-B cells to fully malignant cell lines. To search for other tumor suppressor genes which may be involved in the Ab-MLV transformation process, we used endogenous proviral markers and simple-sequence length polymorphism analysis to screen Abelson virus-transformed pre-B cells for evidence of LOH. Our survey reinforces the role of the p53-p19 regulatory pathway in transformation; 6 of 58 cell lines tested had lost sequences on mouse chromosome 4, including theInk4a/Arf locus. Consistent with this pattern, a high frequency of primary pre-B-cell transformants derived fromInk4a/Arf +/− mice became established cell lines. In addition, half of them retained the single copy of the locus when the transformation process was complete. These data demonstrate that a single copy of the Ink4a/Arf locus is not sufficient to fully mediate the effects of these genes on transformation.
A comparison of bronchoscopic vs blind protected specimen brush sampling in patients with suspected ventilator-associated pneumonia.

BACKGROUND Pneumonia is a common complication in patients undergoing mechanical ventilation and increases ICU mortality. The clinical diagnosis of ventilator-associated, however, pneumonia is unreliable, and many consider bronchoscopic-directed protected specimen brush sampling and quantitative culture the diagnostic method of choice. Bronchoscopy, however, is expensive and not readily available in many ICUs. OBJECTIVE To test the hypothesis that "blind" protected specimen brush (PSB) sampling may produce results similar to that of bronchoscopic-directed sampling. SETTING The medical ICU of a university-affiliated teaching hospital. INTERVENTION Patients with suspected ventilator-associated pneumonia (VAP) who had not received antibiotics for at least 48 h underwent "blind" and bronchoscopic-directed PSB sampling with quantitative culture. RESULTS Fifty-five paired PSB specimens were obtained from 53 patients. There was an 85% quantitative agreement between the blind and bronchoscopic-directed specimens. The agreement was independent of the bronchopulmonary segment from which the bronchoscopic sampling was directed. CONCLUSION The results of this study are consistent with the notion that blind PSB sampling and quantitative culture may prove to be a useful, cost-effective, and minimally invasive method of diagnosing VAP.
Expression and characterization of nonmammalian selenoprotein P in the zebrafish, Danio rerio

Selenoprotein P is a protein of considerable intrigue, due to its unusual composition and requirements for its biosynthesis. Whereas most selenoproteins contain a single selenocysteine residue, the human, bovine and rodent selenoprotein P genes encode proteins containing 10–12 selenocysteines. Selenoprotein P genes have, to date, only been reported in mammals, and the function of the protein remains elusive.
Essays in Public Economics and Health Economics

“Essays in Public Economics and Health Economics” Tomasz Andrzej Zawisza In Chapter 1 of this thesis we examine two key empirical questions in public economics by exploiting the 2009 Polish tax reforms. First, we estimate the degree of substitution between employment and self-employment tax bases – on the extensive margin. In particular, we quantify the impact of changes in the differential in rates of taxation between the two tax bases on the propensity of taxpayers to declare any positive level of employment or self-employment income. Second, we contribute to the literature on elasticities of taxable income on the intensive margin – the responsiveness of taxable income to changes in marginal tax rates – by providing estimates which are more likely to be robust to changes in year-to-year income dynamics than previous estimates. To identify these effects, we exploit variation in marginal and total tax rates around the 2009 reforms which occurs independently of an individual’s position in the income distribution as a result of joint reporting with a spouse. At the same time, to obtain the extensive-margin responses, we exploit the uniqueness of the 2009 Polish tax reforms, which left the tax schedule unchanged for some types of self-employment while changing the tax schedule for the employed. The baseline estimates of the intensive-margin elasticities are around 0.2-0.3 for the employed and around 0.5-0.7 for the self-employed.
A method for optimizing coasting phases in railway speed profiles: An application to an Italian route

This paper focuses on railway speed profiles and energy efficiency. It examines the train motion equations and proposes a novel procedure to determine a feasible eco-driving technique. The approach proposes to optimize the energy consumption in a railway route by maximizing the coasting phases. The method is applied by a series of successive steps. It finds the sections where coasting driving is applicable and classifies them in terms of energy efficiency, verifying if the coasting is applicable in the respect of the assigned regulation margin time. The procedure is tested on a real railway route. The aim of the paper is double: i) to focus on the feasibility of the proposal in terms of reduction of energy consumption; ii) to give evidence to numerical results obtained for a real railway route.
Effects of three parameters on graphene synthesis by chemical vapor deposition

A high quality graphene film on a copper foil was successfully grown by a CVD process using ethanol as a carbon source. The effect of growth temperatures (650-850°C), reaction times (5-50 min) and post-CVD cooling process rates (slow-cooling, fast-cooling and fast-cooling under ethanol exposure) on the formation of graphenes was investigated by Raman spectroscopy and scanning electron microscopy (SEM). The graphene film deposited under the optimal conditions showed features of a high quality such as a high I2D/IG ratio of ~8, a low ID/IG ratio of 0.28 and a narrow full width half maximum (FWHM) of Lorentzian-shaped 2D peak of ~35 cm-1. It was found that the quality of graphene film could be enhanced by optimizing the growth temperature and time, while the number of graphene layer was less sensitive to the cooling rate. However, the fast cooling process under ethanol exposure was found to be a key process for obtaining graphenes with a large domain size. These findings may help to fabricate high-quality graphenes on a copper foil for electronic applications.
Production of a Heterozygous Mutant Cell Line by Homologous Recombination (Single Knockout)

Gene targeting by homologous recombination is a powerful and widely used technique for introduction of specific gene mutations (frequently a gene inactivation) in transgenic animals. The basic method detailed in this unit uses sequences homologous to the endogenous gene flanking the mutation. While methods using bacterial artificial chromosomes (BACs) and recombineering may be used, in most cases simpler bacterial plasmid clones with several kb of homology are sufficient. This protocol details the strategic factors in designing the constructs for selection and screening for homologous recombination. Curr. Protoc. Neurosci. 55:4.30. 1‐4.30. 12. © 2011 by John Wiley & Sons, Inc.
Cbfβ deletion in mice recapitulates cleidocranial dysplasia and reveals multiple functions of Cbfβ required for skeletal development

Significance Cleidocranial dysplasia (CCD) is a hereditary human skeletal disease. Mutations in Runt-related transcription factor 2, which functions as a heterodimer with core binding factor β (Cbfβ), are found in most individuals with CCD. It has been suspected that Cbfβ may be responsible for other CCD cases. The pathogenesis of CCD and the role of Cbfβ in postnatal skeletogenesis remain unclear. There has been no animal model to study this disease. We demonstrate that ablation of Cbfβ in various skeletal cells results in severe craniofacial and skeletal dysplasia with the phenotype recapitulating clinical features of CCD. The findings from this study of Cbfβ in the skeleton provide insight into the role of Cbfβ in postnatal skeletogenesis and pathogenesis of CCD, which may assist in developing new therapies for CCD and osteoporosis. The pathogenesis of cleidocranial dysplasia (CCD) as well as the specific role of core binding factor β (Cbfβ) and the Runt-related transcription factor (RUNX)/Cbfβ complex in postnatal skeletogenesis remain unclear. We demonstrate that Cbfβ ablation in osteoblast precursors, differentiating chondrocytes, osteoblasts, and odontoblasts via Osterix-Cre, results in severe craniofacial dysplasia, skeletal dysplasia, abnormal teeth, and a phenotype recapitulating the clinical features of CCD. Cbfβf/fOsterix-Cre mice have fewer proliferative and hypertrophic chondrocytes, fewer osteoblasts, and almost absent trabecular bone, indicating that Cbfβ may maintain trabecular bone formation through its function in hypertrophic chondrocytes and osteoblasts. Cbfβf/fCollagen, type 1, alpha 1 (Col1α1)–Cre mice show decreased bone mineralization and skeletal deformities, but no radical deformities in teeth, mandibles, or cartilage, indicating that osteoblast lineage-specific ablation of Cbfβ results in milder bone defects and less resemblance to CCD. Activating transcription factor 4 (Atf4) and Osterix protein levels in both mutant mice are dramatically reduced. ChIP assays show that Cbfβ directly associates with the promoter regions of Atf4 and Osterix. Our data further demonstrate that Cbfβ highly up-regulates the expression of Atf4 at the transcriptional regulation level. Overall, our genetic dissection approach revealed that Cbfβ plays an indispensable role in postnatal skeletal development and homeostasis in various skeletal cell types, at least partially by up-regulating the expression of Atf4 and Osterix. It also revealed that CCD may result from functional defects of the Runx2/Cbfβ heterodimeric complex in various skeletal cells. These insights into the role of Cbfβ in postnatal skeletogenesis and CCD pathogenesis may assist in the development of new therapies for CCD and osteoporosis.
Negative Self-Imagery Among Adolescents with Social Phobia: A Test of an Adult Model of the Disorder

Based on findings from the adult literature, this study examined the role of negative self-images (NSI) in social phobia during adolescence. NSI was manipulated among 21 nonphobic (IMAG) adolescents (M age = 14.05 years, SD = 1.56) during two social tasks. Self and observer-rated anxiety and performance as well as co-occurring cognition were compared to 21 adolescents with social phobia (SOC) and 21 control adolescents not instructed to use self-imagery. Few differences in observer-rated anxiety or performance were found between the IMAG and control groups, whereas SOC adolescents were consistently rated as more anxious and poorer social performers. Nonsignificantly higher rates of anxiety were reported by the IMAG group compared to controls, but anxiety was not associated with decrements in performance or social skill. A significantly fewer number of on-task thoughts reported by IMAG adolescents suggests that inability to attend to the interaction itself, rather the presence of NSI, served to increase anxiety.
Amygdala reactivity to masked negative faces is associated with automatic judgmental bias in major depression: a 3 T fMRI study.

OBJECTIVE In a previous study, we demonstrated that amygdala reactivity to masked negative facial emotions predicts negative judgmental bias in healthy subjects. In the present study, we extended the paradigm to a sample of 35 inpatients suffering from depression to investigate the effect of amygdala reactivity on automatic negative judgmental bias and clinical characteristics in depression. METHODS Amygdala activity was recorded in response to masked displays of angry, sad and happy facial expressions by means of functional magnetic resonance imaging at 3 T. In a subsequent experiment, the patients performed an affective priming task that characterizes automatic emotion processing by investigating the biasing effect of subliminally presented emotional faces on evaluative ratings to subsequently presented neutral stimuli. RESULTS Significant associations between (right) amygdala reactivity and automatic negative judgmental bias were replicated in our patient sample (r=-0.59, p<0.001). Further, negatively biased evaluative processing was associated with severity and longer course of illness (r=-0.57, p=0.001). CONCLUSION Amygdala hyperactivity is a neural substrate of negatively biased automatic emotion processing that could be a determinant for a more severe disease course.
Hydrogen-bonding and pi-pi stacking interactions in aquachloridobis(1,10-phenanthroline)cobalt(II) chloride dichloridobis(1,10-phenanthroline)cobalt(II) hexahydrate.

The title compound, [CoCl(C(12)H(8)N(2))(2)(H(2)O)]Cl. [CoCl(2)(C(12)H(8)N(2))(2)]. 6H(2)O, is the first example of a new 1:1 cocrystal of the octahedral [CoCl(2)(phen)(2)] and [CoCl(phen)(2)(H(2)O)](+). Cl(-) complexes (phen is 1,10-phenanthroline). The latter form heterochiral dimers held by strong pi-pi stacking interactions via their phenathroline ligands, which confirms that pi stacking is an important and reliable synthon in supramolecular design. In addition, the crystal structure is networked by H(2)O.H(2)O, H(2)O.Cl(-) and H(2)O.Cl hydrogen bonds, which interconnect the different units of the cobalt complexes.
The Effect of the Post-Socialist Transition on Inequality of Educational Opportunity: Evidence from German Unification

In 1990, German unification led to an abrupt and extensive restructuring of the educational system and economy of the German Democratic Republic (GDR) as the latter was reintegrated into the Federal Republic of Germany (FRG). However, the consequences of this large- scale institutional change for the educational inequality between children from different social class backgrounds in East Germany continue to be poorly understood. This article seeks to shed new light on this question by using a quasi-experimental approach to examine the difference in educational inequality between East and West Germany before and after German unification. We compare changes in the class gradient in educational attainment in East and West Germany across six birth cohorts, including three cohorts of individuals who completed their schooling after unification. Contrasting with past findings, our results show that before unification, educational inequality at the mid-secondary, upper-secondary and tertiary level was substantially lower in East Germany than in West Germany and that unification led to a substantial and sustained convergence of the level of educational inequality in East Germany towards that of West Germany.
Modelling the &Vdot;O2 kinetic response to heavy intensity exercise in children

The purpose of this study was to apply a series of mathematical models in order to investigate the nature of the kinetic response to heavy intensity exercise with children and identify a suitable model with which to estimate parameters of the response. Sixty two children (35 male, 27 female aged 10 – 15 years) completed four transitions from baseline pedalling to 40% of the difference between their previously determined anaerobic threshold and peak [Vdot]O2 on an electronically braked cycle ergometer. Initially three models were fitted to the averaged response profiles following the end of phase 1, and their residuals compared; 1, a single exponential with a delay term; 2, an exponential and linear term with independent delays; and 3, a double exponential with independent delays. Up to 95% of the response profiles were better fitted by either model 2 or 3 (p < 0.05), and model 3 was a statistically better fit (p < 0.05) than model 2 in 77% of cases. Residual inspection confirmed the superior fit by model 3. A fourth model which consisted of a single exponential with a delay term was fitted within the phase 2 fitting window. Estimated parameters (A1 and τ1), using model 4 were not significantly different from model 3, and model 4 was identified as the model of choice due to the wide confidence intervals in τ2 and A2 using model 3. It was concluded that the nature of the response to heavy intensity exercise in children is similar to that previously reported with adults and that the response should be modelled accordingly.
In Vitro and In Vivo Activities of HPi1, a Selective Antimicrobial against Helicobacter pylori

ABSTRACT A high-throughput screen (HTS) was performed to identify molecules specifically active against Helicobacter pylori, the causative agent of peptic ulcer and gastric carcinoma. Currently, treatment of H. pylori infection is suboptimal, with failure rates approaching 25%, despite triple therapy with two broad-spectrum antibiotics and a proton pump inhibitor or quadruple therapy with added bismuth. The HTS was performed in 384-well plates, and reduction of the metabolic indicator resazurin was used as a reporter for cell growth. Diverse molecules from commercial sources were identified as hits, and in vitro validations included measurements of MIC and time-dependent killing as well as anaerobic susceptibility testing against a panel of gut microbes. In vivo validation included testing in the mouse model of H. pylori infection. The small molecule HPi1 (3-hydrazinoquinoxaline-2-thiol) had excellent potency, with an MIC of 0.08 to 0.16 μg/ml and good selectivity for H. pylori compared to a panel of commensal bacteria. HPi1 was also effective in a mouse model of H. pylori infection, reducing colony counts to below the limit of detection after oral dosing of 25 mg/kg/day for 3 days. HPi1 is a promising lead in the search for more effective and specific H. pylori therapeutics.
The HECT Ubiquitin Ligase Rsp5p Is Required for Proper Nuclear Export of mRNA in Saccharomyces cerevisiae

The nuclear transport of both proteins and RNAs has attracted considerable interest in recent years. However, regulation pathways of the nuclear transport machineries are still not well characterized. Previous studies indicated that ubiquitination is involved in poly(A)+ RNA nuclear export. For this reason, we systematically investigated ubiquitin‐protein ligasess from the homologous to E6‐AP carboxy terminus (HECT) family for potential individual roles in nuclear transport in Saccharomyces cerevisiae. Here we report that Rsp5, an essential yeast ubiquitin ligase involved in many cellular functions, when deleted or mutated in ligase activity, blocks the nuclear export of mRNAs. Affected messenger RNAs include both total poly(A)+ mRNA and heat‐shock mRNAs. Mutation of Rsp5 does not affect nuclear protein import or export. Deletion of RSP5 blocks mRNA export, even under conditions where its essential role in unsaturated fatty acids biosynthesis is bypassed. Using domain mapping, we find that the ligase activity is required for proper mRNA export, indicating that ubiquitination by Rsp5 acts directly or indirectly to affect RNA export. The finding that Rsp5p ligase mutations cause a more pronounced defect at high temperatures suggests that ubiquitination of transport factors by Rsp5p may also be essential during stress conditions.
Design method and control optimization of an Extended Range Electric Vehicle

Extended Range Electric Vehicle (EREV) is a promising choice to overcome the limitation on the driving range of Electric Vehicle. However, its potential advantages extremely depend on the system design, especially the battery. This paper focuses on the component sizing of the energy and power of battery system, power design of R-Ext and the traction motor. The control strategy is discussed in this paper, and control parameters optimization of the EREV based on global optimization is implemented, aiming to minimizing the loss of power-train in view of prolonging battery life. A comparative analysis is given to assess the optimization results.