Miracle-dz/UniFAR-FTUs huggingface dataset:
Yersinia pestis with Regulated Delayed Attenuation as a Vaccine Candidate To Induce Protective Immunity against Plague

ABSTRACT Two mutant strains of Yersinia pestis KIM5+, a Δcrp mutant and a mutant with arabinose-dependent regulated delayed-shutoff crp expression (araC PBADcrp), were constructed, characterized in vitro, and evaluated for virulence, immunogenicity, and protective efficacy in mice. Both strains were highly attenuated by the subcutaneous (s.c.) route. The 50% lethal doses (LD50s) of the Δcrp and araC PBADcrp mutants were approximately 1,000,000-fold and 10,000-fold higher than those of Y. pestis KIM5+, respectively, indicating that both strains were highly attenuated. Mice vaccinated s.c. with 3.8 × 107 CFU of the Δcrp mutant developed high anti-Y. pestis and anti-LcrV serum IgG titers, both with a strong Th2 bias, and induced protective immunity against subcutaneous challenge with virulent Y. pestis (80% survival) but no protection against pulmonary challenge. Mice vaccinated with 3.0 × 104 CFU of the araC PBADcrp mutant also developed high anti-Y. pestis and anti-LcrV serum IgG titers but with a more balanced Th1/Th2 response. This strain induced complete protection against s.c. challenge and partial protection (70% survival) against pulmonary challenge. Our results demonstrate that arabinose-dependent regulated crp expression is an effective strategy to attenuate Y. pestis while retaining strong immunogenicity, leading to protection against the pneumonic and bubonic forms of plague.
Analysis of Earnings, Stock Prices and Bond Yields: The Fed Model Approach

Author: Antti Helkala Title: Analysis of Earnings, Stock Prices and Bond Yields: The Fed Model Approach Faculty: School of Business Major: Finance Year: 2008 Master’s Thesis: Lappeenranta University of Technology 71 Pages, 8 Tables, 7 Figures Examiners: Professor Mika Vaihekoski Professor Minna Martikainen
An Event-B Interpretation for SPARDL Model

Real time systems consisting of periodic behaviors together with the mode transition mechanism are largely applied in the development of control systems for spacecrafts and automobiles in industry. We have proposed a requirement modeling language called SPARDL for modeling and analyzing such periodic control systems in [11]. In this paper, we specify an Event-B interpretation for the SPARDL model. The semantics of SPARDL is presented by Event-B and a refinement framework is introduced to develop the Event-B models based on the features of the SPARDL model. Furthermore, a case study is analyzed to show the effectiveness of our proposed approach to modeling and validation of the SPARDL model by Event-B.
Yaratıcı Drama ve Diğer Etkileşimli Öğretim Yöntemleri ile Geleceğin Vatandaşlık, Demokrasi ve İnsan Hakları Eğitimi

In this study, by using Citizenship and Democracy Education Curricula (CDEC) with creative drama and other interactive teaching methods, it was aimed to determine the academic achievement of students, their commitment to democratic values, the reasons of successful student’s being successful, and suggest a program for the future education. The study, utulized experimental embedded design, which is one of the mixed method designs, It was conducted with 80 students (Experiment: 30; Control 1: 28, Control 2: 22) in secondary school, which is under the aegis of Cankaya District National Education Directorate. Data was gathered with “Primary School Citizenship and Democracy Education Course Achievement Test”, “The Scale of Commitment to Democratic Values”, and “Semi-Structured Interview Form”; data was analyzed by using “Content Analysis” with “Two Factor Anova for Mixed Measures”, “Wilcoxon Signed Ranks” and “Mann Withney U” tests. As a result of the study, it is determined that CDEC, which is richened with creative drama and other interactive teaching methods, increases the achievement of students meaningfully, and creates a commitment to democratic values among students. The program is suggested to be used in future citizenship, democracy, and human rights education.
Cardiovascular effects of social support in the work place: twenty‐four‐hour ECG monitoring of men and women.

&NA; Psychosocial work characteristics, such as work demand, work control, and social support at work, have been shown to be related to the development of coronary heart disease in epidemiological studies. However, the mechanisms which mediate the social and psychological effects on the cardiovascular system are not known. We have studied the direct cardiovascular effects of psychosocial work environment characteristics in 148 working men and women, representing seven different occupational groups (physicians, teachers, musicians, policemen, train engineers, prison personnel, and saw mill workers). Besides standardized measures of work demand, work control, and social support, ambulatory 24‐hour monitoring of electrocardiograms in the customary work and home environment was performed. Systolic and diastolic blood pressure were measured as well as other standard physiologic risk factors for coronary heart disease. Mean heart rates were found to be significantly higher in persons reporting low social support at work. This effect was maintained during working hours as well as during leisure time and rest. Of the other related physiologic risk factors, systolic, but not diastolic blood pressure was found to be higher in persons reporting low social support. Smoking, alcohol consumption and relative body mass index were not related to social support at work. Controlling for age, sex and physical strain at work, strengthened the association of low social support with elevated heart rates.
Association between sonographically measured mesenteric fat thickness and brachial artery flow-mediated dilation in Chinese young male adults

Objective To investigate the potential correlation between sonographically measured mesenteric fat thickness (MFT) and brachial artery flow-mediated dilation (FMD) in a sample of healthy Chinese male young adults. Methods Healthy male participants were recruited from Hong Kong Polytechnic University for this prospective observational study. The physical activity readiness questionnaire and ultrasound measurements of carotid intima media thickness were used to screen for clinically healthy subjects. MFT and brachial artery FMD were measured by ultrasound, and body mass index (BMI) was recorded. Results A total of 34 healthy male subjects, aged 19–26 years (mean ± SD BMI, 21.7 ± 3.2 kg/m2) were included. Pearson's correlation coefficient test showed that brachial artery FMD had a statistically significant inverse relationship with BMI and with Log (MFT). Further stepwise multiple linear regression analysis showed that Log (MFT), and not BMI, was an independent predictor of impaired brachial artery FMD. Conclusions Sonographic measurements of MFT were an independent predictor of brachial artery FMD in Chinese male young adults.
SBML Level 3 package: Qualitative Models, Version 1, Release 1

Summary Quantitative methods for modelling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modelling methods using information such as, for example, gene expression data coming from functional genomic experiments. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding qualitative models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Qualitative Models package for SBML Level 3 adds features so that qualitative models can be directly and explicitly encoded. The approach taken in this package is essentially based on the definition of regulatory or influence graphs. The SBML Qualitative Models package defines the structure and syntax necessary to describe qualitative models that associate discrete levels of activities with entity pools and the transitions between states that describe the processes involved. This is particularly suited to logical models (Boolean or multi-valued) and some classes of Petri net models can be encoded with the approach.
Thermal Gradient Gel Electrophoresis Analysis of Bioprotection from Pollutant Shocks in the Activated Sludge Microbial Community

ABSTRACT We used a culture-independent approach, namely, thermal gradient gel electrophoresis (TGGE) analysis of ribosomal sequences amplified directly from community DNA, to determine changes in the structure of the microbial community following phenol shocks in the highly complex activated sludge ecosystem. Parallel experimental model sewage plants were given shock loads of chlorinated and methylated phenols and simultaneously were inoculated (i) with a genetically engineered microorganism (GEM) able to degrade the added substituted phenols or (ii) with the nonengineered parental strain. The sludge community DNA was extracted, and 16S rDNA was amplified and analyzed by TGGE. To allow quantitative analysis of TGGE banding patterns, they were normalized to an external standard. The samples were then compared with each other for similarity by using the coefficient of Dice. The Shannon index of diversity, H, was calculated for each sludge sample, which made it possible to determine changes in community diversity. We observed a breakdown in community structure following shock loads of phenols by a decrease in the Shannon index of diversity from 1.13 to 0.22 in the noninoculated system. Inoculation with the GEM (Pseudomonas sp. strain B13 SN45RE) effectively protected the microbial community, as indicated by the maintenance of a high diversity throughout the shock load experiment (Hdecreased from 1.03 to only 0.82). Inoculation with the nonengineered parental strain, Pseudomonas sp. strain B13, did not protect the microbial community from being severely disturbed;H decreased from 1.22 to 0.46 for a 3-chlorophenol–4-methylphenol shock and from 1.03 to 0.70 for a 4-chlorophenol–4-methylphenol shock. The catabolic trait present in the GEM allowed for bioprotection of the activated sludge community from breakdown caused by toxic shock loading. In-depth TGGE analysis with similarity and diversity algorithms proved to be a very sensitive tool to monitor changes in the structure of the activated sludge microbial community, ranging from subtle shifts during adaptation to laboratory conditions to complete collapse following pollutant shocks.
The role of cognitive schemata in the development of posttraumatic stress disorder: results of cross-sectional and longitudinal studies

ObjectiveThere are two theories (by Horowitz and by Foa) which attempt at explaining the process of posttraumatic stress disorder (PTSD) development by information dissonance. The purpose of the present study was to verify these theories via cross-sectional and longitudinal studies.Materials and MethodsThe study based on a cross-sectional design was performed on a representative group of Polish firefighters. The study using a longitudinal protocol was conducted among police officers. The level of PTSD was assessed using the Questionnaire for PTSD Measurement (K-PTSD). The sense of coherence (SOC) was measured with the Polish adaptation of the Orientation to Life Questionnaire by A. Antonovsky.ResultsIn the cross-sectional study, the correlation coefficients between K-PTSD and SOC were −0.35 (p < 0.001) in the group of firefighters and −0.47 (p < 0.001) in that of police officers. In the longitudinal study, the relationship between SOC and PTSD symptoms appeared to be curvilinear and had the U-letter shape. Therefore, we used ANOVA for statistical analysis. Unfortunately, the F(2.31) = 1.900 and p > 0.05 indicated that the tendency we observed was not statistically significant.ConclusionsWe would like to propose two possible explanations for the difference in the relationships between SOC and PTSD symptoms obtained in the studies employing the cross-sectional and the longitudinal protocols.
The Dynamics of Elite Endorsements in Professional Sports Facility Referendums

Over the past 20 years, nearly every major city in the United States has faced making the decision of whether to build a new stadium or other professional sports facility. In this period, 41 referendums have been held to authorize the public financing of such a facility. Previous studies have demonstrated that elite endorsements affect referendum voters, but these studies have not differentiated the effects of different kinds of elites on public support. We examine the differing effects of the support and opposition of elected officials, business groups, minority leaders, and community groups when modeling referendum outcomes. Our analysis reveals that among these elites' cues, opposition by elected officials (either Republican or Democratic) has the greatest effect on the final referendum vote and that the size of the public subsidy has a significant influence on public support. We also find evidence that opposition by elected officials is exogenous to public opinion.
A Comparative Electrophysiologic Study of Diazepam and Tetrazepam in Patients with Spasticity

In 14 patients with spasticity, efficacy and tolerance of 10 mg diazepam and 50 mg tetrazepam have been compared in a double-blind double-dummy cross-over study. To assess efficacy, the changes in four electrophysiologic tests have been used: Hmax/Mmax ratio, Tmax/Mmax ratio, vibratory inhibition of H reflex, and conditioned amplitudes of Sol H reflex at 70 and 200 ms after stimulation of the tibial nerve at the ankle. Tolerance was evaluated by the induced somnolence (intensity x duration). Electrophysiologic test results were moderately modified in the same direction after both drugs. For the Hmax/Mmax, Tmax/Mmax ratio, and conditioned values, the differences between diazepam and tetrazepam were not significant. For vibratory inhibition, changes induced by tetrazepam were more intense and of longer duration than after diazepam (p = 0.07), indicating that tetrazepam is more potent for reinforcing presynaptic inhibition. Tolerance, as assessed by intensity and duration of somnolence, was significantly better for tetrazepam. The efficacy and tolerance of tetrazepam suggest that it is a more useful agent for the treatment of spasticity than diazepam.
Maximizing the Contribution of Irrigated Agriculture to Poverty Alleviation

This paper investigates the water use and marketing behaviour of smallholder cabbage producers from the Zanyokwe Irrigation Scheme in South Africa to identify the behaviour associated with the highest financial returns to water allocated to smallholder farmers to decrease rural poverty. The blue water footprint for cabbages was estimated; the value of the water was then calculated as the gross margin and value added per cubic metre of water at the respective stages along the value chain. The analyses show that the attributes of the products have a major influence on the degree of access to the highest value market alternatives, and hence on the ability of smallholder farmers to generate the highest possible return from the water they receive for agricultural purposes.
How to measure interest group influence: Italy’s professional orders and liberalization policy

The question of who wins or loses in the policy process lies at the heart of recent research into both interest groups and public policy. However, one of the most difficult challenges when empirically analysing interest groups consists in knowing exactly how to measure their influence: despite the fact that this question has been addressed by political scientists for decades, significant problems remain regarding both the conceptual definition and empirical measurement of influence. In order to develop a better understanding of interest group influence, I recommend as follows: (a) that such influence be conceptualized as a degree of preference attainment; (b) that the degree of generality of the concept be downgraded, by breaking it up on the basis of two fundamental dimensions: the lobbying direction (pro-status quo or anti-status quo) and the policy-making stage (agenda setting; decision making; implementation); (c) to proceed with a manual hand-coding in order to obtain a list of the policy issues around which interest groups lobby; (d) to resort to an expert survey in order to evaluate these issues. This methodological approach is used to empirically measure the influence that Italy’s professional orders had on the liberalization process championed by the second Prodi government in 2006.
Phenome-Wide Interaction Study (PheWIS) in Aids Clinical Trials Group Data (ACTG)

Association studies have shown and continue to show a substantial amount of success in identifying links between multiple single nucleotide polymorphisms (SNPs) and phenotypes. These studies are also believed to provide insights toward identification of new drug targets and therapies. Albeit of all the success, challenges still remain for applying and prioritizing these associations based on available biological knowledge. Along with single variant association analysis, genetic interactions also play an important role in uncovering the etiology and progression of complex traits. For gene-gene interaction analysis, selection of the variants to test for associations still poses a challenge in identifying epistatic interactions among the large list of variants available in high-throughput, genome-wide datasets. Therefore in this study, we propose a pipeline to identify interactions among genetic variants that are associated with multiple phenotypes by prioritizing previously published results from main effect association analysis (genome-wide and phenome-wide association analysis) based on a-priori biological knowledge in AIDS Clinical Trials Group (ACTG) data. We approached the prioritization and filtration of variants by using the results of a previously published single variant PheWAS and then utilizing biological information from the Roadmap Epigenome project. We removed variants in low functional activity regions based on chromatin states annotation and then conducted an exhaustive pairwise interaction search using linear regression analysis. We performed this analysis in two independent pre-treatment clinical trial datasets from ACTG to allow for both discovery and replication. Using a regression framework, we observed 50,798 associations that replicate at p-value 0.01 for 26 phenotypes, among which 2,176 associations for 212 unique SNPs for fasting blood glucose phenotype reach Bonferroni significance and an additional 9,970 interactions for high-density lipoprotein (HDL) phenotype and fasting blood glucose (total of 12,146 associations) reach FDR significance. We conclude that this method of prioritizing variants to look for epistatic interactions can be used extensively for generating hypotheses for genomewide and phenome-wide interaction analyses. This original Phenome-wide Interaction study (PheWIS) can be applied further to patients enrolled in randomized clinical trials to establish the relationship between patient's response to a particular drug therapy and non-linear combination of variants that might be affecting the outcome.
Dimerization Is Not a Determining Factor for Functional High Affinity Human Plasminogen Binding by the Group A Streptococcal Virulence Factor PAM and Is Mediated by Specific Residues within the PAM a1a2 Domain*

Background: High affinity human plasminogen (hPg) binding to Group A Streptococcus (GAS) is mediated by the coiled-coil M-like protein, PAM. Results: Amino acid residues in the a1a2 domain of PAM direct high affinity PAM/hPg binding regardless of oligomerization status of PAM. Conclusion: The a1a2 domain defines its hPg binding site, regardless of PAM dimerization. Significance: The virulence of GAS is altered by mutations in PAM(a1a2). A emm53 subclass of Group A Streptococcus pyogenes (GAS) interacts tightly with human plasma plasminogen (hPg) and plasmin (hPm) via the kringle 2 (K2hPg) domain of hPg/hPm and the N-terminal a1a2 regions of a GAS coiled-coil M-like protein (PAM). Previous studies have shown that a monomeric PAM fragment, VEK30 (residues 97–125 + Tyr), interacted specifically with isolated K2hPg. However, the binding strength of VEK30 (KD = 56 nm) was ∼60-fold weaker than that of full-length dimeric PAM (KD = 1 nm). To assess whether this attenuated binding was due to the inability of VEK30 to dimerize, we defined the minimal length of PAM required to dimerize using a series of peptides with additional PAM residues placed at the NH2 and COOH termini of VEK30. VEK64 (PAM residues 83–145 + Tyr) was found to be the smallest peptide that adopted an α-helical dimer, and was bound to K2hPg with nearly the same affinity as PAM (KD = 1–2 nm). However, addition of two PAM residues (Arg126-His127) to the COOH terminus of VEK30 (VEK32) maintained a monomeric peptidic structure, but exhibited similar K2hPg binding affinity as full-length dimeric PAM. We identified five residues in a1a2 (Arg113, His114, Glu116, Arg126, His127), mutation of which reduced PAM binding affinity for K2hPg by ∼1000-fold. Replacement of these critical residues by Ala in the GAS genome resulted in reduced virulence, similar to the effects of inactivating the PAM gene entirely. We conclude that rather than dimerization of PAM, the five key residues in the binding domain of PAM are essential to mediate the high affinity interaction with hPg, leading to increased GAS virulence.
The barriers to a community contracts approach in post-disaster reconstruction.

The need to involve communities in post disaster reconstruction is seen as an imperative for sustainable if not ‘sensible’ post disaster reconstruction. One contractual approach is the use of community contracts. Such approaches seek to facilitate an integrated process whereby communities identify and prioritise their ‘problems’, set out agreements and then action plans to be realised through the guidance and technical assistance of the implementing agencies (e.g. NGOs, UN agencies, government authorities). The obvious advantage of a community contract approach is realised through community empowerment ensuring both social and economic accountability. This approach is different from the conventional empowerment practices of say employing affected beneficiaries to provide labour. In that situation, the community only benefits from the ‘output’ rather than the ‘process’ of disaster reconstruction. On the other hand, the community and beneficiaries in community contracts are at the centre of the decision-making process, which should foster a deeper sense of ownership and consequent long-term maintenance and sustainability. Nonetheless, in practice such an approach seemingly runs counter to the reality within implementing teams. Why are there such barriers? This paper reviews the origin and theoretical background of the community contracts approach and researches these barriers based on a pattern and clustering analysis of structured interviews of members of a significant implementing team in Port au Prince Haiti in 2012 to examine the apparent gap between an ‘attractive’ theoretical approach and its perhaps not so ‘attractive’ implementation.
Rates of Return and Early Retirement Disincentives: Evidence from a German Pension Reform

Abstract To counteract the financial pressure emerging in aging societies, statutory pension schemes are undergoing fundamental reforms in many Western countries. Starting with cohort 1937, Germany introduced permanent pension deductions for early retirement. This study examines the profitability of pension contributions against the background of this reform for cohorts 1935-1945. Internal rates of return (IRR) are used to measure the profitability. For men, the IRR declines from 2.4% to 1.2% and for women from 5.2% to 3.7%. The results suggest that the majority of the trend, about 75-80%, is caused by increased pension contributions and not by the reform.