Miracle-dz/UniFAR-FTUs huggingface dataset:
Timely binding of IHF and Fis to DARS2 regulates ATP–DnaA production and replication initiation

In Escherichia coli, the ATP-bound form of DnaA (ATP–DnaA) promotes replication initiation. During replication, the bound ATP is hydrolyzed to ADP to yield the ADP-bound form (ADP–DnaA), which is inactive for initiation. The chromosomal site DARS2 facilitates the regeneration of ATP–DnaA by catalyzing nucleotide exchange between free ATP and ADP bound to DnaA. However, the regulatory mechanisms governing this exchange reaction are unclear. Here, using in vitro reconstituted experiments, we show that two nucleoid-associated proteins, IHF and Fis, bind site-specifically to DARS2 to activate coordinately the exchange reaction. The regenerated ATP–DnaA was fully active in replication initiation and underwent DnaA–ATP hydrolysis. ADP–DnaA formed heteromultimeric complexes with IHF and Fis on DARS2, and underwent nucleotide dissociation more efficiently than ATP–DnaA. Consistently, mutant analyses demonstrated that specific binding of IHF and Fis to DARS2 stimulates the formation of ATP–DnaA production, thereby promoting timely initiation. Moreover, we show that IHF–DARS2 binding is temporally regulated during the cell cycle, whereas Fis only binds to DARS2 in exponentially growing cells. These results elucidate the regulation of ATP–DnaA and replication initiation in coordination with the cell cycle and growth phase.
Measuring the barriers to investment in emerging economies : the case of some African countries

This dissertation is made up of stand-alone essays on the determinants of the investment climate in emerging market economies. Chapter One presents the purpose of this study, the significance of the research to policy makers, researchers and investors and the limitations of the research. Chapter Two investigates empirically whether business regulations, as measured by the „Doing Business‟ indicators, have an impact on investment in 29 emerging market economies in Africa, Asia, Latin America and emerging Europe. The results show that secure property rights and the level of business entry regulation influence the investment climate in these economies. In addition, efficiency of the judicial system, investor protection and the flexibility of employment regulation were found to be insignificant determinants of investment. Chapter Three explores the effect of business regulation on stock market liquidity, using data from a selection of 15 stock markets in Africa. The results from the panel data analysis show that the degree of business regulation does not influence stock liquidity. However, the results confirm that greater protection of minority share-holders' rights, as well as lender and better collateral and bankruptcy laws enhance stock market liquidity. There was anecdotal evidence to suggest that improved judicial efficiency enhances stock market liquidity. The legal origin was found to be significant in explaining the differences in the legal systems of these countries. Countries that have adopted French legal traditions were found to have less active stock markets and less investor and property rights protection compared to countries that have adopted English legal traditions. Chapter Four investigates the effect of the level of business regulation, infrastructure and political environment on investment in 29 African countries. The results provide evidence to show that lower levels of business regulation, less corruption and a stable political environment are important in enhancing investment. The final essay examines the effect of business regulation and geography on investment in a sample of 37 countries in Africa. The results show that more secure property rights and fewer import and export regulations have a significantly positive effect on private investment. In addition, being landlocked and distant from the sea has a negative effect on investment. Furthermore, the findings revealed that property rights protection in landlocked economies is not significantly different from that in coastal economies. iv In all the studies, the legal origin was found to be significant in explaining cross-country differences in the legal systems of the selected countries. These findings have important implications for policy makers, multi-lateral organisations and investors.
Nano-BaSO4: a novel antimicrobial additive to pellethane

Hospital-acquired infections remain a costly clinical problem. Barium sulfate (BaSO4, in micron particulate form) is a common radiopacifying agent that is added to catheters and endotracheal tubes. Due to the recently observed ability of nanostructured surface features to decrease functions of bacteria without the aid of antibiotics, the objective of this in vitro study was to incorporate nano-barium sulfate into pellethane and determine the antimicrobial properties of the resulting composites. The results demonstrated for the first time that the incorporation of nano-barium sulfate into pellethane enhanced antimicrobial properties (using Staphylococcus aureus and Pseudomonas aeruginosa) compared to currently used pellethane; properties that warrant further investigation for a wide range of clinical applications.
On the Dynamics of the Spontaneous Activity in Neuronal Networks

Most neuronal networks, even in the absence of external stimuli, produce spontaneous bursts of spikes separated by periods of reduced activity. The origin and functional role of these neuronal events are still unclear. The present work shows that the spontaneous activity of two very different networks, intact leech ganglia and dissociated cultures of rat hippocampal neurons, share several features. Indeed, in both networks: i) the inter-spike intervals distribution of the spontaneous firing of single neurons is either regular or periodic or bursting, with the fraction of bursting neurons depending on the network activity; ii) bursts of spontaneous spikes have the same broad distributions of size and duration; iii) the degree of correlated activity increases with the bin width, and the power spectrum of the network firing rate has a 1/f behavior at low frequencies, indicating the existence of long-range temporal correlations; iv) the activity of excitatory synaptic pathways mediated by NMDA receptors is necessary for the onset of the long-range correlations and for the presence of large bursts; v) blockage of inhibitory synaptic pathways mediated by GABAA receptors causes instead an increase in the correlation among neurons and leads to a burst distribution composed only of very small and very large bursts. These results suggest that the spontaneous electrical activity in neuronal networks with different architectures and functions can have very similar properties and common dynamics.
Volume seedlings

Recent advances in software and hardware technology have made direct ray-traced volume rendering of 3-d scalar data a feasible and effective method for imaging of the data’s contents. The time costs of these rendering techniques still do not permit full interaction with the data, and all of the parameters effecting the resulting images. This paper presents a set of real-time interaction techniques which have been developed to permit exploration of a volume data set. Within the limitation of a static viewpoint, the user is able to interactively alter the position and shape of an area of interest, and modify local viewing parameters. A run length encoded cache of volume rendering samples provides the means to rerender the volume at interactive rates. The user locates and plants “seeds” in areas of interest through the use of data slicing and isosurface techniques. Image processing techniques applied to volumes ( i.e. volume processing), can then automatically form regions of interest which in turn modify the rendering parameters. This “region growing” of “seedlings” incrementally alters the image in real-time providing further visual cues concerning the contents of the data. These tools allow interactive exploration of internal structures in the data which may be obscured by other imaging algorithms. Magnetic Resonance Angiography (MRA) provides a driving application for this technology. Results from preliminary studies of MRA data are included.
On Comparisons of Random, Partition, and Proportional Partition Testing

Early studies of random versus partition testing used the probability of detecting at least one failure as a measure of test effectiveness and indicated that partition testing is not significantly more effective than random testing. More recent studies have focused on proportional partition testing because a proportional allocation of the test cases (according to the probabilities of the subdomains) can guarantee that partition testing will perform at least as well as random testing. We show that this goal for partition testing is not a worthwhile one. Guaranteeing that partition testing has at least as high a probability of detecting a failure comes at the expense of decreasing its relative advantage over random testing. We then discuss other problems with previous studies and show that failure to include important factors (cost, relative effectiveness) can lead to misleading results.
Educational Experiences of Children in Foster Care

The educational achievements of children in foster care have been determined to be below average in individual studies. In the present investigation, 31 studies were examined via four meta-analyses to answer questions regarding the educational status of children in out-of-home placements in multiple countries. Data analysis encompassed the following variables: special education eligibility rates, grade retention rates and disciplinary rates. Exploratory meta-analyses uncovered conclusive results in this project, illuminating common educational challenges faced by children living in foster care across countries. Students living in out-of-home care are disproportionately represented in special education. They are prevented from moving to advanced grade levels at alarming rates. In addition, these students are disciplined frequently in the school setting. Implications for serving fostered youth include promoting pre-referral interventions and positive behavioural supports.
MAGE‐D4B is a novel marker of poor prognosis and potential therapeutic target involved in breast cancer tumorigenesis

Melanoma‐associated antigen (MAGE) family members are generally described as tumor‐specific antigens. An association between MAGE‐D4B and breast cancer has yet to be reported and the functional role of the encoded protein has never been established. We performed microarray analysis of 104 invasive breast tumors and matched non‐cancerous breast biopsies. qPCR was used for validation in an independent biobank. To investigate the biological relevance of MAGE‐D4B in breast tumorigenesis, its phenotypic effects were assessed in vitro. Overall, MAGE‐D4B was detected in 43% of tumors while undetected in normal breast tissue. MAGE‐D4B was found to correlate with tumor progression and to be an independent prognostic marker for poor outcome in term of relapse‐free and overall survival, with potential predictive relevance in relation to response to chemotherapy. RNA interference‐mediated knockdown of MAGE‐D4B significantly hampered the invasive properties of Hs578T cells by affecting anchorage‐independent growth, adhesion, migration and invasion affecting anchorage‐independent growth, adhesion, migration and invasion and by modulating expression of invasion‐suppressor gene E‐cadherin.
Square patterns and quasipatterns in weakly damped Faraday waves.

Pattern formation in parametric surface waves is studied in the limit of weak viscous dissipation. A set of quasipotential equations (QPEs) is introduced that admits a closed representation in terms of surface variables alone. A multiscale expansion of the QPEs reveals the importance of triad resonant interactions, and the saturating effect of the driving force leading to a gradient amplitude equation. Minimization of the associated Lyapunov function yields standing wave patterns of square symmetry for capillary waves, and hexagonal patterns and a sequence of quasipatterns for mixed capillary-gravity waves. Numerical integration of the QPEs reveals a quasipattern of eightfold symmetry in the range of parameters predicted by the multiscale expansion. {copyright} {ital 1996 The American Physical Society. }
Transfer of antimicrobial resistance plasmids from Klebsiella pneumoniae to Escherichia coli in the mouse intestine

Objectives and methods Klebsiella pneumoniae is a nosocomial pathogen and is considered the most common Gram-negative bacterium that exhibits multiple antimicrobial resistances. In this study, the transfer of antimicrobial resistance genes from the clinical multiresistant K. pneumoniae MGH75875 isolate was assessed in vitro and in vivo in an intestinal colonization animal model. The ability to colonize and transfer was tested under different antimicrobial treatments. The frequency of the horizontal gene transfer was also examined in vitro. Results The clinical isolate of K. pneumoniae colonized the intestine of mice at levels up to 109 cfu/g faeces in antimicrobial-treated mice. In mice without antimicrobial treatment, the strain quickly decreased to below the detection limit due to competitive exclusion by the indigenous mouse flora. Onset of antimicrobial treatment gave immediate rise to detectable levels of the strain in the faeces of up to 109 cfu/g faeces. The experiment clearly shows that the treatment selects resistant strains and gives advantages to colonize the gastrointestinal tract. Furthermore, high transfer frequency of different plasmids was observed during colonization of the mouse intestine. The blaSHV and blaTEM genotypes were transferred to both an indigenous recipient in the in vivo setting and to an MG1655 Escherichia coli recipient strain in vitro. Conclusions K. pneumoniae is an excellent colonizer of the intestine and is extremely promiscuous with respect to the transferability of its numerous plasmids. Antimicrobial treatment enhances the selection of resistant strains and results in an increase in the resistance gene pool, which ultimately raises the risk of spreading resistance genes.
Discriminant analysis and eigenspace partition tree for face and object recognition from views

The method we have been using is based on our Self-Organizing Hierarchical Optimal Subspace Learning and Inference Framework (SHOSLIF). It uses the theories of linear discriminant projection for automatic optimal feature selection in each of the internal nodes of a Space-Tessellation Tree. In this paper, we present our recent study on the applicability of the approach to variability in position, size, and 3D orientation. In the work presented here, we require "well-framed" images os input for recognition. By well-framed images we mean that only a relatively small variation in the size, position, and orientation of the objects in the input images is allowed. We report the experimental results that show the performance difference between the subspaces of linear discriminant analysis and the principle component analysis and the effect of using a tree as opposed to a flat eigenspace.
The Untranslated Regions of Eukaryotic MRNAs: Structure, Function, Evolution and Bioinformatic Tools for Their Analysis

The crucial role of the non-coding portion of genomes is now widely acknowledged. In particular, mRNA untranslated regions are involved in many post-transcriptional regulatory pathways that control mRNA localisation, stability and translation efficiency. A review is given of the most recent research works on the functional characterisation of eukaryotic mRNA untranslated regions. In order to make possible a systematic and detailed sequence analysis of mRNA untranslated regions (UTRs), a non-redundant database of metazoan mRNA untranslated sequences annotated for the occurrence of specific functional elements, UTRdb, was devised. These elements, whose consensus structure has been devised on the basis of experimental assays and of comparative analyses, have been collected in the UTRsite database. A suitable pattern-matching software has been devised to search UTRsite patterns in user-submitted sequences, also assessing their statistical significance. Structural, compositional and evolutionary features of untranslated sequences of metazoan mRNAs have been investigated showing peculiar intra- and interspecific patterns.
Prognostic Value and Implication for Chemotherapy Treatment of ABCB1 in Epithelial Ovarian Cancer: A Meta-Analysis

Background Chemotherapy resistance is reported to correlate with up-regulation of anti-tumor agent transporter ABCB1 (p-gp) in epithelial ovarian cancer (EOC), but the results remain controversial. To reconcile the results, a systematic review followed by meta-analysis was performed to assess the association between high ABCB1 status or ABCB1 gene variants and overall survival (OS), progression free survival (PFS), and total response rate (TR) in patients with EOC. Materials and Methods Electronic searches were performed using Pubmed, EMBASE, Web of Science and Chinese Wanfang databases from January 1990 to February 2016. Summary hazard ratio (HR), risk ratio (RR) and 95% confidence intervals (CIs) were combined using fixed or random-effects models as appropriate. Results Thirty-eight retrospective studies of 8607 cases qualified for meta-analysis were identified. Our results suggested that ABCB1 over-expression was significantly associated with unfavorable OS (HR = 1.54; 95% CI, 1.25–1.90), PFS (HR = 1.49; 95% CI, 1.22–1.82) and TR (RR = 0.63; 95% CI, 0.54–0.75). After adjustment for age, clinical stage, residual disease, histological type and tumor grade, high ABCB1 status remained to be a significant risk factor for adverse OS and PFS. Patients with recurrent ABCB1 positivity suffered from poorer OS than those with primary ABCB1 positivity. However, stratified by chemotherapy regimen, inverse correlation between high ABCB1 status and poor OS, PFS and TR were only found in patients underwent platinum-based chemotherapy but not in patients received standard platinum/paclitaxel-based chemotherapy. No evidence was found for any association between ABCB1 gene polymorphisms and OS, PFS or TR. Conclusion High ABCB1 status is significantly associated with chemo-resistance and poor prognosis in patients with EOC. Large-scale, prospective studies are needed to assess the clinical value of ABCB1 expression in EOC more accurately.
Liking low-status? Contextual and individual differences in attributional biases of low-status outgroup members

Previous studies on biased intergroup perceptions of outgroups’ irrationality mostly treated the target groups as opponents and rivals. In three studies, we extended this line of research and tested the hypothesis that individuals who challenge the existing social hierarchy exhibit more positive biases toward low-status outgroup members. We also hypothesized that when irrational thinking is framed as an important human trait, this bias is reduced among low social dominance orientation (SDO) individuals. In three studies (N = 169, N = 450, and N = 161), conducted in countries that vary in power distance levels (Poland, Spain, Sweden and Turkey), we examined under which conditions low-status outgroups are perceived as more rational than ingroup members. The results show that in a condition without irrationality framed as a human trait, psychology students (Study 1 and Study 2) and nonstudents low in group-based dominance orientation (Study 3) perceive outgroup members as less irrational than ingroup members. However, when participants were reminded that irrationality is a human trait, the perceived differences between in- and outgroup members were reduced. This effect was observed in all four countries (Study 1 and Study 2) and held when variables related to the tendency to behave in a socially desirable way were controlled for (Study 3).
Critical thinking, cognitive presence, and computer conferencing in distance education

Abstract This article describes a practical approach to judging the nature and quality of critical discourse in a computer conference. A model of a critical community of inquiry frames the research. A core concept in defining a community of inquiry is cognitive presence. In turn, the practical inquiry model operationalizes cognitive presence for the purpose of developing a tool to assess critical discourse and reflection. The authors present encouraging empirical findings related to an attempt to create an efficient and reliable instrument to assess the nature and quality of critical discourse and thinking in a text‐based educational context. Finally, the authors suggest that cognitive presence (i.e., critical, practical inquiry) can be created and supported in a computer‐conference environment with appropriate teaching and social presence.
An Exploratory Look at Early Online Auction Decisions: Extending Signal Theory

Extant literature in decision theory suggests that online auction buyers depend on signals for mitigating uncertainty that influence bidder behavior at multiple points. However, the depth and breadth of the use of signals has only been partially explored. Using data from 242 online auction users, we show that eight emergent factors influence decisions of auction selection and initial bid in different ways. We further find that two ethical perspectives impact the evaluation of seller uncertainty in unique ways, although neither perspective predominates within our sample. These results enable sellers and online auction marketplaces to better design and implement auction systems that provide signals that buyers most desire.
Ustilago maydis populations tracked maize through domestication and cultivation in the Americas

The domestication of crops and the development of agricultural societies not only brought about major changes in human interactions with the environment but also in plants' interactions with the diseases that challenge them. We evaluated the impact of the domestication of maize from teosinte and the widespread cultivation of maize on the historical demography of Ustilago maydis, a fungal pathogen of maize. To determine the evolutionary response of the pathogen's populations, we obtained multilocus genotypes for 1088 U. maydis diploid individuals from two teosinte subspecies in Mexico and from maize in Mexico and throughout the Americas. Results identified five major U. maydis populations: two in Mexico; two in South America; and one in the United States. The two populations in Mexico diverged from the other populations at times comparable to those for the domestication of maize at 6000–10 000 years before present. Maize domestication and agriculture enforced sweeping changes in U. maydis populations such that the standing variation in extant pathogen populations reflects evolution only since the time of the crop's domestication.