Miracle-dz/UniFAR-FTUs huggingface dataset:
Induction of a Novel Class of Diacylglycerol Acyltransferases and Triacylglycerol Accumulation in Mycobacterium tuberculosis as It Goes into a Dormancy-Like State in Culture

ABSTRACT Mycobacterium tuberculosis enters the host by inhalation of an infectious aerosol and replicates in the alveolar macrophages until the host's immune defense causes bacteriostasis, which leads the pathogen to go into nonreplicative drug-resistant dormancy. The dormant pathogen can survive for decades till the host's immune system is weakened and active tuberculosis develops. Even though fatty acids are thought to be the major energy source required for the persistence phase, the source of fatty acids used is not known. We postulate that the pathogen uses triacylglycerol (TG) as a storage form of fatty acids. Little is known about the biosynthesis of TG in M. tuberculosis. We show that 15 mycobacterial genes that we identified as putative triacylglycerol synthase (tgs) when expressed in Escherichia coli showed TGS activity, and we report some basic catalytic characteristics of the most active enzymes. We show that several tgs genes are induced when the pathogen goes into the nonreplicative drug-resistant state caused by slow withdrawal of O2 and also by NO treatment, which is known to induce dormancy-associated genes. The gene (Rv3130c) that shows the highest TGS activity when expressed in E. coli shows the highest induction by hypoxia and NO treatment. Biochemical evidence shows that TG synthesis and accumulation occur under both conditions. We conclude that TG may be a form of energy storage for use during long-term dormancy. Therefore, TG synthesis may be an appropriate target for novel antilatency drugs that can prevent the organism from surviving dormancy and thus assist in the control of tuberculosis.
Intergovernmental Alignment, Program Effectiveness, and U.S. Homelessness Policy

In the U.S. intergovernmental system, state governments can voluntarily and strategically align with federal government strategies and objectives. This study examines the effect of intergovernmental alignment on federal homelessness program outcomes. In 2010, the U.S. Interagency Council on Homelessness started the first national-level comprehensive strategic plan on homelessness: Opening Doors. The Opening Doors plan highlights intergovernmental partnerships as effective tools to implement federal homeless programs to different levels of governments in order to achieve federal outcomes. Using a difference-in-differences methodology, we find that county governments that align their homelessness program with the federal and state government have better program outcomes than those that do not align intergovernmentally. Our findings help to expand our understanding of intergovernmental mechanisms as effective policy tools to achieve federal program outcomes at the local level in the absence of financial inducements or legal mandates.
Circularly Polarized Arrowhead-Shape Slotted Microstrip Antenna

A novel single-feed arrowhead-shape slotted microstrip antenna for circular polarization (CP) is proposed. To achieve CP radiation and antenna size reduction, an arrowhead-shaped slot is embedded in the first quadrant along the diagonal axes of a square patch. Thus, the structure is asymmetric, and good-quality CP performance can be achieved by adjusting the size of the slot. The antenna is simulated and practically fabricated. Measured results confirm the validity of this design and show a good agreement with simulated results. The antenna generates CP radiation at 911 MHz with an overall size of 87 × 87 × 4.572 mm 3. The fabricated antenna shows an impedance bandwidth of 35.0 MHz (888.0-923.0 MHz) with 8.0 MHz (908.0-916.0 MHz) 3-dB axial-ratio bandwidth (ARBW).
Identification of RTF1, a novel gene important for TATA site selection by TATA box-binding protein in Saccharomyces cerevisiae

Interaction of the TATA box-binding protein (TBP) with promoters of RNA polymerase II-transcribed genes is an early and essential step in mRNA synthesis. Previous studies have demonstrated that the rate-limiting binding of TBP to a TATA element can be influenced by transcriptional regulatory proteins. To identify additional factors that may regulate DNA binding by TBP in vivo, we performed a genetic selection for extragenic suppressors of a yeast TBP mutant that exhibits altered and relaxed DNA binding specificity. This analysis has led to the discovery of a previously unidentified gene, RTF1. The original rtf1 suppressor mutation, which encodes a single amino acid change in Rtf1, and an rtf1 null allele suppress the effects of the TBP specificity mutant by altering transcription initiation. Differences in the patterns of transcription initiation in these strains strongly suggest that the rtf1 missense mutation is distinct from a simple loss-of-function allele. The results of genetic crosses indicate that suppression of TBP mutants by mutations in RTF1 occurs in an allele-specific fashion. In a strain containing wild-type TBP, the rtf1 null mutation suppresses the transcriptional effects of a Ty delta insertion mutation in the promoter of the HIS4 gene, a phenotype also conferred by the TBP altered-specificity mutant. Finally, as shown by indirect immunofluorescence experiments, Rtf1 is a nuclear protein. Taken together, our findings suggest that Rtf1 either directly or indirectly regulates the DNA binding properties of TBP and, consequently, the relative activities of different TATA elements in vivo.
Designing Neural Networks using Genetic Algorithms

RoboCup has come a long way since it’s creation in ’97 [1] and is a respected place for machine learning researchers to try out new algorithms in a competitive fashion. RoboCup is now an international competition that draws many teams and respected researchers looking for a chance to create the best team. Originally we set out to create a team to compete in RoboCup. This was an ambitious project, and we had hopes to finish within the next year. For this semester, we chose to scale down the RoboCup team towards a smaller research area to try our learning algorithm on. The scaled down version of the RoboCup soccer environment is known as the ”Keepaway Testbed” and was started by Peter Stone, University of Texas [2]. Here the task is simple, you have two teams on the field each with the same number of players. Instead of trying to score a goal on the opponent the teams are given tasks, and one team is labeled the keepers and the other is labeled the takers. It is the task of the keepers to maintain possesion of the ball and it is the task of the takers to take the ball. The longer the keepers are able to maintain possesion of the ball the better the team. There are several advantages to this environment. First, it provides some of the essential characteristics of a real soccer game. Typically it is believed that if a team is able to maintain possesion of the ball for long periods of time they will win the match. Secondly, it provides realistic behavior much the same as the original RoboCup server. This is accomplished by introducing noise into the system similar to the original RoboCup, and similar to what would be received by real robots. Finally, when you want to go through the learning process this environment is capable of stopping play once the takers have touched the ball, and the environment is capable of starting a new trial based on that occurrence. Although the RoboCup Keepaway Machine Learning testbed provided an excellent environment to train our agents, we still needed to scale down the problem in order to do a feasibility study. Based on the Keepaway testbed, we created a simulation world with one simple task. One agent is placed into the world and has to locate the position of the goal. This can be thought of as an agent in a soccer environment needing to locate either the ball or another teammate. It was in this environment where we tested our methods for learning autonomous agents.
A Discrete Time Approach to Option Pricing

The goal of the PhD thesis is to propose a very general and fully analytical option pricing framework encompassing a wide class of discrete time models. The framework features multiple components structure in both volatility and leverage, and a flexible pricing kernel with multiple risk premia. The proposed approach is general enough to include either GARCH-type volatility, Realized Volatility or a combination of the two.Exploiting the general framework we propose three new option pricing models with original dynamics under physical measure. We start with an extension of HARG-RV model with heterogenous and analytically tractable leverage structure called LHARG-RV. Then we propose a model being mixture of LHARG-RV and GARCH approach acronymed GARCH-LHARG-RV and finally we consider an extension of LHARG-RV with jumps called JLHARG-RV. We also reconsider the CGARCH model of Christoffersen et al. (2008) by applying two-dimensional pricing kernel. Since our framework guarantees existence of semi-closed form formulas for option prices, the option pricing methodology is fast and efficient in implementation. In addition, by applying family of our fully analytically models with multi-component structure in volatility on a large sample of S&P 500 options, we show the superior ability of our models in pricing out-of-the-money (OTM) options compared to the existing benchmarks. Moreover, we derive an analytic relation between equity risk premium and the term structure of variance risk premium (VRP). Motivated by this result, we estimate the VRP term structure implied by CGARCH model and we show its ability to reproduce a realistic family of term structures of variance risk premium including the empirically observed hump-shaped curves. We finally uncover the strong predictive power of the shape of the VRP term structure, summarized by its slope, on future stock-index returns. Our findings reveal that stock investors should not only follow the popular Wall Street’s wisdom which suggests to look at the level of VIX Index but they also should look at the level of the term spread of variance risk premium, defined as the difference between monthly and annual VRP.A novel contribution of the thesis is an introduction of the new model, GARCH-LHARG-RV, (Section 3.3 and empirical results in Chapter 4). The new model, being combination of realized and latent volatility approaches, highlights the strength of the proposed general option pricing framework by delivering a superior option pricing performance. Moreover, thesis provides generalisation of result in Buhlmann et al. (1998) to multi-dimensional case (Theorem 10 in the thesis is showing that multi-dimensional Esscher transform satisfies Pareto equilibrium).
Change in teacher professionalism in further education : a case study.

This study explores the effect of policy and funding changes in the further education (FE) sector on the nature of teacher professionalism and the general vocational curriculum. In the last decade there has been tremendous change in the FE sector. It has been argued that this has been the result of fundamental alterations in the organization and distribution of work. The consequence has been that much governmental attention has been paid to the post-school sector. The recent White Paper Learning to Succeed (DfEE, 1999b) has been one of a number of attempts to redress the perceived failure of the sector to provide a skilled workforce for the needs of industry. My thesis seeks to reflect upon the effects of policy and funding changes in one further education college. It concentrates on changes in general vocational education and training. It reflects on the impact of those changes upon teacher professionalism in further education. The research took place in a college of further education using case study methods. The data for my findings are derived from participant observation techniques and semi-structured interviews with teaching staff. It utilized a qualitative critical ethnographic methodology with the aim of giving a voice to those most affected by the changes. Lecturers believe that significant changes to the sector were initiated by the Incorporation of colleges (April, 1993) and have accelerated since. The fieldwork took place in the academic year 1998-99. The literature review part of my research found that, in order to advance the government's vision for a 'learning society', it opined that alterations in the general vocational curriculum were necessary. I believe that changes to the professional lives of college lecturers were required in order to implement that end. It is my conviction that the changes are instrumental. They are about preparing young people for the needs of industry alone. The lecturers in my study believe such changes have had a negative effect on their definitions of the concept of professionalism. Further to this, they feel that the new qualifications and the way they had to be taught, to the backdrop of, for example, cuts in class contact hours, have had a detrimental effect on the education and training of students. These developments, they maintain, will militate against any evolution of a true 'learning society', if such a society would have the aim of producing a future citizenry (not just workers) in a 'reflective participatory democracy'.
Early‐Stage of Innovations: Selection System Criteria for Funding U.S. Biotech SMEs

The focus of this paper is small and medium‐sized enterprises (SMEs) operating in the U.S. biotechnology industry and how they compete for financial resources during the early stages of innovation development. We utilize selection system theory, which describes how selectors use reputation‐based information about selectees as decision factors when making investments. Our findings suggest that there are different predictive variables for SME categories and the types of investors attracted to these categories, which is consistent with selection system theory. We extend prior studies by providing context to early‐stage innovation investment funding within an environment characterized as having a long development cycle and representing high uncertainty.
High-risk enteric pathogens associated with HIV infection and HIV exposure in Kenyan children with acute diarrhoea

Objective:HIV infection is an established risk for diarrhoeal severity, less is known about specific enteric pathogens associated with HIV status. We determined associations of selected enteric pathogens with HIV infection and HIV exposure among Kenyan children. Design:A cross-sectional study among 6 months to 15 year olds presenting to two Western Kenya District hospitals with acute diarrhoea between 2011 and 2013. Methods:Stool was tested using standard bacterial culture and microscopy for ova and parasites. HIV status was obtained from children and mothers. Enteric pathogen prevalence was compared between HIV-infected and HIV-uninfected children and between HIV-exposed uninfected (HEU) and HIV-unexposed. Unadjusted and adjusted prevalence ratios for selected pathogens by HIV status were estimated using relative risk (RR) regression. Age, site, income, household crowding, water source/treatment, anthropometrics, cotrimoxazole use and breastfeeding history were accounted for in multivariable models. Results:Among 1076 children, median age was 22 months (interquartile range: 11–42 months), 56 (5.2%) were HIV-infected and 105 (11.3%) of 926 HIV-uninfected children in whom maternal HIV status was obtained were HIV-exposed. The following organisms were most frequently isolated from stool: enteroaggregative Escherichia coli (13.3%), Giardia species (spp.) (11.1%), Campylobacter spp. (6.3%), enteropathogenic E. coli (EPEC) (6.1%) and Cryptosporidium spp. (3.7%). Accounting for age, HIV-infection was associated with typical EPEC infection (prevalence ratio 3.70, P = 0.002) while HIV-exposure was associated with Cryptosporidium among HIV-uninfected children (prevalence ratio 2.81, P = 0.005). Conclusion:EPEC and Cryptosporidium infections were more common in HIV-infected and HIV-exposed children, respectively. This could explain the increased mortality attributed to these pathogens in other studies. Interventions targeting EPEC and Cryptosporidium may reduce morbidity and mortality in high HIV-prevalence settings.
Blood glucose, plasma insulin and sensory responses to guar-containing wheat breads: effects of molecular weight and particle size of guar gum

The effectiveness of guar gum in reducing post-prandial blood glucose and plasma insulin levels in human subjects seems to depend mainly on its ability to increase the viscosity of digesta in the small intestine. However, the precise relationship between the rheological properties of guar gum (either in vitro or in vivo) and the changes in blood metabolites and hormones is unknown. The aim of the present study, therefore, was to investigate the effects of wheat breads containing guar gum samples varying in molecular weight (Mw) and particle size (characteristics that strongly influence the rheological properties of guar gum) on post-prandial blood glucose and plasma insulin levels in healthy subjects. The sensory qualities of breads containing guar-gum flours of different Mw were also evaluated using a hedonic scoring technique. No significant differences in the post-prandial blood glucose responses were found between the control and guar breads. However, all the guar breads elicited significant (P < 0.05) decreases in the post-prandial rise in plasma insulin, an effect that did not appear to be influenced by large variations in Mw or particle size of guar gum. Moreover, the sensory qualities of guar bread were markedly improved by using low Mw grades of guar gum.
The Distribution of Top Incomes in Australia

Using taxation statistics, we estimate the income share held by top income groups in Australia over the period 1921–2003. We find that the income share of the richest fell from the 1920s until the mid-1940s, rose briefly in the postwar decade, and then declined until the early 1980s. During the 1980s and 1990s, top income shares rose rapidly. At the start of the twenty-first century, the income share of the richest was higher than it had been at any point in the previous 50 years. Among top income groups, recent decades have also seen a rise in the share of top income accruing to the super-rich. Trends in top income shares are similar to those observed among other elite groups, such as judges, politicians, top bureaucrats and chief executive officers.
ON THE STRENGTH AND WEAKNESS OF BINOMIAL MODEL FOR PRICING VANILLA OPTIONS

This paper presents binomial model for pricing vanilla options. Binomial model can be used to accurately price American style options than the Black-Scholes model as it takes into consideration the possibilities of early exercise and other factors like dividends. The strength and weakness of this model were considered. This model is both computationally efficient and accurate but not adequate to deal with path dependent options.
Delivering Equality Of Opportunity In Schools - An Action Plan for Educational Inclusion

This action plan focuses on addressing the educational needs of children and young people from disadvantaged communities, from pre-school through second-level education (3 to18 years). Its frame of reference is based on the definition of “educational disadvantage” in the Education Act (1998) as: “. the impediments to education arising from social or economic disadvantage which prevent students from deriving appropriate benefit from education in schools. ” The action plan is, therefore, one element of a continuum of interventions to address disadvantage, which include second-chance education and training and access measures for adults to support increased participation by under-represented groups in further and higher education. A further element of this continuum is the ongoing development of provision for pupils with special educational needs in light of the enactment of the Education for Persons with Special Needs Act (2004) and the establishment of the National Council for Special Education.
DNA in situ hybridization as a diagnostic tool in the discrimination of melanoma and spitz naevus

As the clinical and histological differential diagnosis between Spitz naevus and cutaneous melanoma may be very difficult, we have investigated whether DNA in situ hybridization may be helpful in resolving this problem. To this end, routinely‐processed paraffin sections of 15 typical Spitz naevi, 15 typical nodular melanomas, and five cases originally misdiagnosed as Spitz naevi but which later metastasized and were reclassified as melanoma were analysed using a method previously described (De Wit et al., J Invest Dermatol 1992; 98: 450–458). Microscopical semi‐quantitative evaluation revealed that the number of nuclei with supernumerary aberrations of the centromere region of chromosome 1, suggestive of aneuploidy, was significantly different in Spitz naevi and nodular melanoma. The mean number of aberrant nuclei per high power field was 0.41 and 4.01, respectively (P=0.0001). On applying the results of the typical lesions to the equivocal, originally misdiagnosed lesions, three out of five could be identified as melanoma. These results suggest that the application of DNA in situ hybridization may contribute to the positive identification of histologically equivocal pigmented lesions. The advantages of this technique are that it is cheap, requires little tissue, and can be applied on routinely‐processed paraffin sections.
Stereoselective glucuronidation of carvedilol by Chinese liver microsomes

ObjectiveTo study the stereoselective glucuronidation of carvedilol (CARV) by three Chinese liver microsomes.MethodsThe metabolites of CARV were identified by a hydrolysis reaction with β-glucuronidase and HPLC-MS/MS. The enzyme kinetics for CARV enantiomers glucuronidation was determined by a reversed phase-high pressure liquid chromatography (RP-HPLC) assay using (S)-propafenone as internal standard after precolumn derivatization with 2,3,4,6-tetra-O-acetyl-β-D-glucopyranosylisothiocyanate.ResultsTwo CARV glucuronides were found in three Chinese liver microsomes incubated with CARV. The non-linear regression analysis showed that the values of Km and Vmax for (S)-CARV and (R)-CARV enantiomers were (118±44) μmol/L, (2500±833) pmol/(min·mg protein) and (24±7) μmol/L, (953±399) pmol/(min·mg protein), respectively.ConclusionThese results suggested that there was a significant (P<0.05) stereoselective glucuronidation of CARV enantiomers in three Chinese liver microsomes, which might partly explain the enantioselective pharmacokinetics of CARV.
Structural and functional analysis of long terminal repeats of Suncus murinus mammary tumor virus

A 2.7-kilobase (kb) cDNA sequence complementary to Suncus murinus mammary tumor virus (Sm-MTV) genomic RNA [corrected] was prepared using purified virions produced by the Sm-MT cell line, which had been established from a spontaneous mammary tumor of S. murinus. It was found, by using this cDNA in Southern hybridization experiments, that Sm-MTV was endogenous to this animal and that some 50 copies of endogenous provirus were present per haploid cellular genome. In addition, a proviral Sm-MTV DNA sequence, 9.4 kb long (Sm-P-MTV10), was cloned from a Sm-MT cell genomic library, and its long terminal repeat was found to be 720 base pairs (bp) long, with the U3.R and U5 regions 574 and 146 bp long, respectively. The boundary between U3 and R was not determined with certainty, though in the cDNA, the U3 and R regions were 462 and 105 bp long, respectively. The overall homology between the U3.R regions in the cDNA and Sm-P-MTV was 75%. These two DNAs differed in such transcription regulatory signals as CCAAT and TATAA, the first being missing from the cDNA. Nevertheless, chloramphenicol acetyltransferase assays showed that the long terminal repeats of the cDNA and the Sm-P-MTV were transcriptionally active but not steroid hormone responsive. Like Mason-Pfizer monkey virus, Sm-MTV used tRNA(1,2Lys) as a primer for reverse transcription. In addition, the immunosuppressive peptide sequence common to many retroviruses was found in the env region of Sm-MTV. In these two points, Sm-MTV differed from mouse MTV.