Miracle-dz/UniFAR-FTUs huggingface dataset:
Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics

Physicochemical properties of DNA, such as shape, affect protein-DNA recognition. However, the properties of DNA that are most relevant for predicting the binding sites of particular transcription factors (TFs) or classes of TFs have yet to be fully understood. Here, using a model that accurately captures the melting behavior and breathing dynamics (spontaneous local openings of the double helix) of double-stranded DNA, we simulated the dynamics of known binding sites of the TF and nucleoid-associated protein Fis in Escherichia coli. Our study involves simulations of breathing dynamics, analysis of large published in vitro and genomic datasets, and targeted experimental tests of our predictions. Our simulation results and available in vitro binding data indicate a strong correlation between DNA breathing dynamics and Fis binding. Indeed, we can define an average DNA breathing profile that is characteristic of Fis binding sites. This profile is significantly enriched among the identified in vivo E. coli Fis binding sites. To test our understanding of how Fis binding is influenced by DNA breathing dynamics, we designed base-pair substitutions, mismatch, and methylation modifications of DNA regions that are known to interact (or not interact) with Fis. The goal in each case was to make the local DNA breathing dynamics either closer to or farther from the breathing profile characteristic of a strong Fis binding site. For the modified DNA segments, we found that Fis-DNA binding, as assessed by gel-shift assay, changed in accordance with our expectations. We conclude that Fis binding is associated with DNA breathing dynamics, which in turn may be regulated by various nucleotide modifications.
Comparative Genomic Analysis of Buffalo (Bubalus bubalis) NOD1 and NOD2 Receptors and Their Functional Role in In-Vitro Cellular Immune Response

Nucleotide binding and oligomerization domain (NOD)-like receptors (NLRs) are innate immune receptors that recognize bacterial cell wall components and initiate host immune response. Structure and function of NLRs have been well studied in human and mice, but little information exists on genetic composition and role of these receptors in innate immune system of water buffalo—a species known for its exceptional disease resistance. Here, a comparative study on the functional domains of NOD1 and NOD2 was performed across different species. The NOD mediated in-vitro cellular responses were studied in buffalo peripheral blood mononuclear cells, resident macrophages, mammary epithelial, and fibroblast cells. Buffalo NOD1 (buNOD1) and buNOD2 showed conserved domain architectures as found in other mammals. The domains of buNOD1 and buNOD2 showed analogy in secondary and tertiary conformations. Constitutive expressions of NODs were ubiquitous in different tissues. Following treatment with NOD agonists, peripheral lymphocytes showed an IFN-γ response along-with production of pro-inflammatory cytokines. Alveolar macrophages and mammary epithelial cells showed NOD mediated in-vitro immune response through NF-κB dependent pathway. Fibroblasts showed pro-inflammatory cytokine response following agonist treatment. Our study demonstrates that both immune and non-immune cells could generate NOD-mediated responses to pathogens though the type and magnitude of response depend on the cell types. The structural basis of ligand recognition by buffalo NODs and knowledge of immune response by different cell types could be useful for development of non-infective innate immune modulators and next generation anti-inflammatory compounds.
Ocean acidification alters the otoliths of a pantropical fish species with implications for sensory function

Ocean acidification affects a wide diversity of marine organisms and is of particular concern for vulnerable larval stages critical to population replenishment and connectivity. Whereas it is well known that ocean acidification will negatively affect a range of calcareous taxa, the study of fishes is more limited in both depth of understanding and diversity of study species. We used new 3D microcomputed tomography to conduct in situ analysis of the impact of ocean acidification on otolith (ear stone) size and density of larval cobia (Rachycentron canadum), a large, economically important, pantropical fish species that shares many life history traits with a diversity of high-value, tropical pelagic fishes. We show that 2,100 μatm partial pressure of carbon dioxide (pCO2) significantly increased not only otolith size (up to 49% greater volume and 58% greater relative mass) but also otolith density (6% higher). Estimated relative mass in 800 μatm pCO2 treatments was 14% greater, and there was a similar but nonsignificant trend for otolith size. Using a modeling approach, we demonstrate that these changes could affect auditory sensitivity including a ∼50% increase in hearing range at 2,100 μatm pCO2, which may alter the perception of auditory information by larval cobia in a high-CO2 ocean. Our results indicate that ocean acidification has a graded effect on cobia otoliths, with the potential to substantially influence the dispersal, survival, and recruitment of a pelagic fish species. These results have important implications for population maintenance/replenishment, connectivity, and conservation efforts for other valuable fish stocks that are already being deleteriously impacted by overfishing.
Oral and Gastric Helicobacter Pylori: Effects and Associations

Introduction This study consisted in the comparison of the prevalence of Helicobacter pylori (H. pylori) present in the stomach and in saliva of a sample of Portuguese adolescents and the assessment of the association between H. pylori infection with socio-demographic variables and prevalence of dental caries. Materials and Methods A cross-sectional study was designed including a sample of 447 adolescents aged 12 to 19 years old, attending a public school in Sátão, Portugal. A questionnaire about socio-demographic variables and oral health behaviors was applied. Gastric H. pylori infection was determined using the urease breath test (UBT). Saliva collection was obtained and DNA was extracted by Polymerase Chain Reaction (PCR) in order to detect the presence of oral H. pylori. Results The prevalence of gastric H. pylori detected by UBT was 35.9%. Within the adolescents with a gastric UBT positive, only 1.9% were positive for oral H. pylori. The presence of gastric H. pylori was found to be associated with age (>15years, Odds ratio (OR)=1.64,95%CI=1.08-2.52), residence area (urban,OR=1.48,95%CI=1.03-2.29) and parents´ professional situation (unemployed,OR=1.22,95%CI=1.02-1.23). Among those with detected dental caries during the intra-oral observation, 37.4% were positive for gastric H. pylori and 40.2% negative for the same bacterial strain (p=0.3). Conclusions The oral cavity cannot be considered a reservoir for infection of H. pylori. Gastric H. pylori infection was found to be associated with socio-demographic variables such as age, residence area and socioeconomic status.
Libraries, literacy and poverty reduction: a key to African development

The role that libraries in Africa could play in reducing poverty has not been sufficiently recognised and hence the necessary policy developments and investment in the library network have not yet been made. Policy makers and donors, recognising the link between poverty reduction and literacy, have given centre stage to textbooks in policies to increase literacy and student achievement levels. Yet textbooks are the beginning of the solution, not the complete answer. Libraries sustain literacy and do so on a reuse basis providing a costeffective means of support for a whole community of readers who seek information for tackling their own problems. This paper, written by a respected and experienced African educator and librarian, points the way ahead for Africa with affordable and achievable library strategies to enable the poorest communities to participate in their own development. [report archived with permission of both authors]
Interleukin-1 Receptor Antagonist Protects against Lipopolysaccharide Induced Diaphragm Weakness in Preterm Lambs

Chorioamnionitis (inflammation of the fetal membranes) is strongly associated with preterm birth and in utero exposure to inflammation significantly impairs contractile function in the preterm lamb diaphragm. The fetal inflammatory response to intra-amniotic (IA) lipopolysaccharide (LPS) is orchestrated via interleukin 1 (IL-1). We aimed to determine if LPS induced contractile dysfunction in the preterm diaphragm is mediated via the IL-1 pathway. Pregnant ewes received IA injections of recombinant human IL-1 receptor antagonist (rhIL-1ra) (Anakinra; 100 mg) or saline (Sal) 3 h prior to second IA injections of LPS (4 mg) or Sal at 119d gestational age (GA). Preterm lambs were killed after delivery at 121d GA (term = 150 d). Muscle fibres dissected from the right hemi-diaphragm were mounted in an in vitro muscle test system for assessment of contractile function. The left hemi-diaphragm was snap frozen for molecular and biochemical analyses. Maximum specific force in lambs exposed to IA LPS (Sal/LPS group) was 25% lower than in control lambs (Sal/Sal group; p=0.025). LPS-induced diaphragm weakness was associated with higher plasma IL-6 protein, diaphragm IL-1β mRNA and oxidised glutathione levels. Pre-treatment with rhIL-1ra (rhIL-1ra/LPS) ameliorated the LPS-induced diaphragm weakness and blocked systemic and local inflammatory responses, but did not prevent the rise in oxidised glutathione. These findings indicate that LPS induced diaphragm dysfunction is mediated via IL-1 and occurs independently of oxidative stress. Therefore, the IL-1 pathway represents a potential therapeutic target in the management of impaired diaphragm function in preterm infants.
Understanding User Revisions When Using Information Systems Features: Adaptive System Use and Triggers

Post-adoptive system use is often characterized by cycles of adaptation, in which people actively revise how they use information systems. This paper investigates how and why individual users revise their system use at the feature level. A new concept, adaptive system use (ASU), is conceptualized as a user's revisions of which and how system features are used. This research identifies four specific ASU behaviors that collectively describe how people revise their use of system features. A model of ASU is developed based on Louis and Sutton's (1991) research on how people switch to active thinking from automatic thinking. The model specifies three antecedents of ASU (novel situations, discrepancies, and deliberate initiatives) and two moderators (personal innovativeness in IT and facilitating conditions). An empirical study of 253 Microsoft Office users largely supported the research model. The findings suggest that triggers--including novel situations, discrepancies, and deliberate initiatives--are a significant impetus to ASU. This research also confirms moderating effects of personal innovativeness in IT. The findings also show the relationships among triggers: in addition to their direct impact on ASU, novel situations and deliberate initiatives exert their influence on ASU indirectly by giving rise to discrepancies in system use. Moreover, a cluster analysis identifies three heterogeneous triggering conditions and reveals that people engage in different ASU behaviors under different triggering conditions.
Levels of Environmental Uncertainty of a Site-Based Management School within a Minority/Majority Context

The focus of this study was the perceived environmental uncertainty (PEU) of teachers in two selected elementary schools in a minority/majority context. It attempted to determine the sources of uncertainty that are perceived by teachers in a site-based management (SBM) elementary school and a non-site-based management elementary school. Specific items were examined to determine which indistrict and out-district matters were related to uncertainty and to explore whether or not the two groups of teachers in the selected schools were different regarding their perceived environmental uncertainty. A basic causal-comparative design was employed and the Perceived Environmental Uncertainty Index (PEUI) developed by Singh (1991) was used to collect data. Means, standard deviations and t-tests were calculated to quantify and summarize the data. Findings indicate that the PEU levels for the SBM school were lower than that of the non-SBM school; specific in-district and out-district items rated as most unclear and significant are different for both schools. However, both schools were concerned with the impact of state legislature on job. There is a significant difference in in-district PEU, out-of-district PEU and total PEU between the two schools. These results seem to suggest that site-based management is a viable alternative for reducing and coping with environmental uncertainty. However, further research needs to focus on other levels of school following a SBM approach. Additional studies should address correlations between perceived environmental uncertainty and student success.
When Do You Get Economists as Policy-Makers?

We analyze when economists become top-level “economic policy-makers,” focusing on financial crises and the partisanship of a country’s leader. We present a new dataset of the educational and occupational background of 1200 political leaders, finance ministers, and central bank governors from 40 developed democracies from 1973 to 2010. We find that left leaders appoint economic policy-makers who are more highly trained in economics and finance ministers who are less likely to have private finance backgrounds but more likely to be former central bankers. Finance ministers appointed during financial crises are less likely to have a financial services background. A leader’s exposure to economics training is also related to appointments. This suggests one crucial mechanism for affecting economic policy is through the selection of certain types of economic policy-makers.
Relativistic blue- and red-shifted absorption lines in AGNs

Current, accumulating evidence for (mildly) relativistic blue- and red-shifted absorption lines in AGNs is reviewed. XMM-Newton and Chandra sensitive X-ray observations are starting to probe not only the kinematics (velocity) but also the dynamics (accelerations) of highly ionized gas flowing in-and-out from, likely, a few gravitational radii from the black hole. It is thus emphasized that X-ray absorption-line spectroscopy provides new potential to map the accretion flows near black holes, to probe the launching regions of relativistic jets/outflows, and to quantify the cosmological feedback of AGNs. Prospects to tackle these issues with future high energy missions are briefly addressed. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
A Broadband and Miniaturized Common-Mode Filter for Gigahertz Differential Signals Based on Negative-Permittivity Metamaterials

A novel wideband and miniaturized common-mode noise suppression filter is proposed based on the concept of an effective negative-permittivity metamaterial (MM) transmission line (TL). The propagation properties for the odd and even modes in the proposed structure are derived from the TL theory and Bloch theorem. Two- and four-port equivalent-circuit models are developed to explain the common-mode suppression characteristics. The dispersion relation has a good agreement with the full-wave simulation and measurement result. Based on the low-temperature co-fired ceramic fabrication technology, miniaturized common-mode filters with four and eight cells are realized using the concept of the effective negative-permittivity MM. For the four-cell structure, the filter size is 0.16 ¿g × 0.26 ¿g with the corresponding real size of 3.2 mm × 5.12 mm. It is found that the common-mode noise can be reduced over 10 dB from 3.8 to 7.1 GHz with the fractional bandwidth of 60% in the frequency domain, and is reduced over 50% for voltage amplitude in the time domain. More importantly, the differential signal integrity, in terms of insertion loss and group delay in the frequency domain and eye diagrams in the time domain, is not degraded within the wide stopband. To our best knowledge, it is the first broadband common-mode filter designed for gigahertz differential signals based on the concept of MM TL with most compact size.
Is movement better?: comparing sedentary and motion-based game controls for older adults

Providing cognitive and physical stimulation for older adults is critical for their well-being. Video games offer the opportunity of engaging seniors, and research has shown a variety of positive effects of motion-based video games for older adults. However, little is known about the suitability of motion-based game controls for older adults and how their use is affected by age-related changes. In this paper, we present a study evaluating sedentary and motion-based game controls with a focus on differences between younger and older adults. Our results show that older adults can apply motion-based game controls efficiently, and that they enjoy motion-based interaction. We present design implications based on our study, and demonstrate how our findings can be applied both to motion-based game design and to general interaction design for older adults.
Network delay tomography using flexicast experiments

Summary. Estimating and monitoring the quality of service of computer and communications networks is a problem of considerable interest. The paper focuses on estimating link level delay distributions from end‐to‐end path level data collected by using active probing experiments. This is an interesting large scale statistical inverse (deconvolution) problem. We describe a flexible class of probing experiments (‘flexicast’) for data collection and develop conditions under which the link level delay distributions are identifiable. Maximum likelihood estimation using the EM algorithm is studied. It does not scale well for large trees, so a faster algorithm based on solving for local maximum likehood estimators and combining their information is proposed. The usefulness of the methods is illustrated on real voice over Internet protocol data that were collected from the University of North Carolina campus network.
A Novel Approach for Computing Dynamic Slices of Aspect-Oriented Programs

We propose a dynamic slicing algorithm to compute the slices of aspect-oriented programs. We use a dependence based intermediate program representation called Aspect System Dependence Graph (AOSG) to represent aspect-oriented programs. Then, we propose the dynamic slicing algorithm for AOPs, which is an extended version of EMDS algorithm for object-oriented programs. Our algorithm is based on marking and unmarking of the edges of AOSG appropriately during runtime.
Ecological Influences on Weight Status in Urban African-American Adolescent Females: A Structural Equation Analysis

The present study employed a quantitative, non-experimental, multivariate correlational research design to test a hypothesized model examining associative paths of influence between ecological factors and weight status of urban, African-American adolescent females. Anthropometric and self-report survey data of 182 urban, AfricanAmerican adolescent females were collected during after-school programs, health and physical education classes, and community events in an urban area in northeast Florida. Descriptive analyses were conducted to characterize the study participants based upon their age, study setting, and weight status. A scale reliability analysis was conducted to assess the internal consistency reliability of the sample data using selected measures within the context of the study’s specific population and subsequently guided the structural equation model (SEM) analyses. The SEM path analysis was used to develop two measurement models to control for observed error variance for variables demonstrating poor internal consistency reliability (diet behaviors and nutrition selfefficacy) and a final structural model to test the associative paths of influence between latent (diet behaviors and nutrition self-efficacy) and manifest variables (teacher social support and friend social support) on weight status. The results of the path analysis indicated that both teacher social support and friend social support demonstrated a positive, indirect influence on child weight status through nutrition self-efficacy and diet behaviors following two different and specific paths of influence. Diet behaviors, in turn, demonstrated a positive, direct effect on child weight status. These findings provide clear implications for educational leaders that call for the integration of health behavior change theory into traditional education and
Role-Based Security in a Distributed Resource Environment

There are many technologies for distributed processing/interoperation, including CORBA, DCE, DCOM, Enterprise Java Beans, Java IDL, JDBC, etc. Most promising, is the emergence of the distributed resource environment, which allows all of the components that comprise a distributed application (i.e., software components like servers, legacy systems, databases, COTs, etc., and hardware components like printers, scanners, etc.) to be treated akin to operating system resources, where each component (resource) can publish services (an API). Once published, these services are available for use by clients and resources alike. However, distributed resource environments have lagged in support of security, providing minimal functionality to control the availability of a resource’s services to clients. To address this deficiency, this paper concentrates on proposing a technique for seamlessly integrating a role-based security model, authorization, authentication, and enforcement into a distributed resource environment. In addition, we consider the specific challenges and problems in supporting role-based security and authorization in an actual distributed resource environment, namely Sun’s Java-based JINI. JINI promotes the construction and deployment of robust and scalable distributed applications via leasing of services by resources and two-phase commit transactions.
‘One Size Does Not Fit All’

Abstract The article presents a comparative analysis of mandatory networks used as an integrated part of local governance of the primary medical service in Norway, and their management. Both the networks and their management showed considerable variation in their basic characteristics, and three different management roles are described: ‘the diplomat’, ‘the adversary’ and ‘the equal partner’. The article argues that the managerial role of a network is a result of, as well as inflicting on, the distribution of power between the participants in the network.
Endocrine Symptoms as the Initial Manifestation of Wilson’s Disease

Wilson’s disease is a rare genetic disorder of copper metabolism. The difference in copper tissue accumulation is responsible for the various clinical manifestations of this disorder. If left untreated, Wilson’s disease progresses to hepatic failure, severe neurological disability, and even death. Due to the complex clinical picture of Wilson’s disease, its diagnosis relies on a high index of suspicion. In our paper, we present endocrine symptoms suggesting the presence of insulinoma and hyperprolactinemia as the initial clinical manifestation of Wilson’s disease in a young female. Zinc acetate treatment resulted in the disappearance of hypoglycemia, galactorrhea, and menstrual abnormalities.