Miracle-dz/UniFAR-FTUs huggingface dataset:
JOBIM 2002 G + C 3 structuring along the genome : A universal feature in Bacteria

As small and containing few non-coding sequences, bacterial genomes are considered to be very optimized. Moreover, it has been shown that codon usage is very biased in most species, and often correlated with transfer RNA (tRNA) abundance, suggesting adaptation for a better translation accuracy and/or a higher level of expression. However, codon usage is also influenced by mutation pressure. Hence, the codon composition of a gene is the result of concurrent evolutionary forces that are differently balanced from one gene to another, depending on its function, expression rate, and position in the genome. For example, it has been shown in enterobacteria that genes close to the replication origin are more conserved between species. Moreover, in a species like Escherichia coli, it seems that the genome is structured for the G+C3 of its genes, this possibly in relation with a mutational process correlated to replication. These views suggest that genes undergo different mutation and selection pressures depending on their position in the genome. In this paper, we analyzed the structuration of different codon usage measures (such as G+C3 and CAI) along the bacterial genomes available from the EMGLib database. We show that most bacterial genomes are highly structured with some notable exceptions. A peculiar pattern of genome structure, with a tendency toward an A+T-enrichment near the replication terminus, seems to be common to every bacterial phylum. Several species have lost this pattern because of genome rearrangement or integration of foreign DNA. We discuss evolutionary implications of these results and the fact that this natural structuring of bacterial genomes may be a cause of overestimation of lateral gene transfer predictions.
Toxin production and haemagglutination in strains of Escherichia coli from diarrhoea in Brescia, Italy

SUMMARY Two hundred and ninety-nine different strains of Escherichia coli, isolated from 172 patients with diarrhoea and 113 healthy subjects, were examined for enterotoxin, cytotoxin and haemolysin (Hly) production and for mannose-resistant haemagglutination (MRHA) and invasive properties. Three strains proved enterotoxigenic, none enteroinvasive; cytotoxin and Hly production was shown in 25 strains from patients and in 3 from controls. Ten strains produced the cytotoxic necrotizing factor (CNF), 6 released other factors which kill cell cultures. Hly production was shown in 21 strains, 9 of which were also positive for CNF. MRHA was detected in 26% of strains from diarrhoca compared with 14% of strains from healthy people. A strong association between toxin production and MRHA was demonstrated. Serotyping results showed that the strains exhibiting virulence traits mostly belonged to serogroups commonly involved in extra-intestinal infections. The possible role of strains of E. coli showing one or more virulence factors as opportunistic pathogens in diarrhoeal diseases is discussed.
Is the number of antral follicles an interesting selection criterium for fertility in cattle

Recent studies indicate that the antral follicle population may be of paramount importance to improve reproductive performance in cows. There is already an agreement that the antral follicle count (AFC; follicles ≥3 mm in diameter) is a highly variable trait among animals, but with high repeatability in the same individual. Thus, females can be classified into low, intermediate or high AFC. Several studies in Bos taurus show a positive correlation between AFC and fertility parameters, such as increased quantity and quality of embryos, better pregnancy rates, higher progesterone levels, among others. However, there is still no consensus on AFC in Bos indicus females and indicustaurus. This article aims to discuss the main aspects related to the population of antral follicles and its relation to the reproductive performance associated with the most common techniques in assisted reproduction (timed artificial insemination, in vitro embryo production, embryo transfer and superovulation).
The endothelium: Dysfunction and beyond

Since its anatomic discovery in the 19th century, the endothelium was considered to fulfill no other purpose than that of a physical barrier between blood and tissue, until Furchgott and colleagues defined endothelium-dependent vasoreactivity in the late 1970s. Henceforth, a functional paradigm defined the balance between endothelium-derived relaxing factors and endothelium-derived contracting factors as the hallmark of endothelial cell integrity. As a consequence, any reflection of a deviation from this state was defined as endothelial dysfunction, most notably the impairment of vasorelaxation in response to pharmacologic stimuli such as acetylcholine or nonpharmacologic stimuli such as shear stress and cold pressor. Within the coronary artery tree these alterations have been recognized before the development of obstructive coronary artery disease, affecting the microcirculation before the epicardial conduit vessel. Furthermore, recent clinical trials outlined the prognostic significance of these changes, whereby impairment of increase in coronary blood flow in response to endothelium-dependent stimuli seemed to be of utmost importance. Thus it is intriguing to speculate on the evolving role of myocardial perfusion imaging in combination with pharmacologic and nonpharmacologic stimuli for the noninvasive assessment of coronary endothelial dysfunction in patients at risk for future adverse events. At a minimum, this review aims to put endothelial dysfunction into an imaging perspective beyond the scope of the conventional approach.
Osteoporosis and related factors in older females with skeletal pain or numbness: A retrospective study in East China

Objective To analyse relationships between incidence of osteoporosis, age and clinical symptoms in older female patients in East China. Methods Data from females aged ≥30 years, admitted to QiLu Hospital between January 1999 and December 2011 were retrospectively assessed for osteoporosis. Correlations between osteoporosis diagnosis, age and clinical symptoms were analysed. Factors associated with osteoporosis were assessed using logistic regression. Results Out of 4212 patients enrolled, 1673 were assigned to the osteoporosis group and 2539 to the nonosteoporosis group. Neck, shoulder and arm pain negatively correlated with osteoporosis diagnosis. Lumbar and back pain had no correlation with osteoporosis diagnosis. In patients with osteoporosis there was no relationship between bone density and site of clinical symptoms. Bone density decreased, as age increased, in patients aged >50 years in the osteoporosis group. Conclusion The present study revealed a relationship between epidemiological distribution of osteoporosis and associated factors in adult females suffering from pain or numbness, in East China.
An Active Steganalysis Method of Block-DCT Image Information Hiding

An active steganalysis method is proposed based on HMT (hiding Morkov tree) model and independence component analysis (ICA) methods, aimed at the block-DCT coefficients steganography in this paper (here we assume only one copy of stego message image is supplied). The simulation experiments in Matlab7.0 show that the active steganalysis method can not only improve the steganalysis the efficiency and the accuracy, but also improve the reliability of estimated message length.
Bayesian Analysis of Hierarchical Effects

The idea of hierarchical, sequential, or intermediate effects has long been posited in textbooks and academic literature. Hierarchical effects occur when relationships among variables are mediated through other variables. Challenges in studying hierarchical effects in marketing include the large number of items present in most commercial studies and the presence of heterogeneous relationships among the variables. Existing approaches have dealt with the large number of variables by employing a factor structure representation of the data and have used standard mixture distributions for representing different response segments. In this paper, we propose a Bayesian model for the analysis of hierarchical data using the actual response items and incorporating heterogeneity that better reflects consumer stages in a decision process. Cross-sectional data from a national brand-tracking study are used to illustrate our model, where we find empirical support for a hierarchical relationship among media recall, brand beliefs, and intended actions. We find these effects to be insignificant when measured with standard models and aggregate analyses. The proposed model is useful for understanding the influence of variables that lead to intermediate as opposed to direct effects on brand choice.
Interacting sources of information in word naming: a study of individual differences

Hypothetically, words can be named by spelling-soun d translation rules or by looking up a phonological code in a lexicon. Following J. Baron and C. Strawson (1976), naming performance was measured as a function of skill with each route, using sets of stimuli varying in reliance on either route. "Phoenicians" were defined to be better with rules than with look-up; "Chinese" were better at look-up than with rules. As predicted by J. Baron and C. Strawson, Phoenicians named low-frequency regular words and nonwords faster than Chinese. Contrary to predictions, Phoenicians were also faster at naming irregular words of various frequencies. Implications of these results for various dual-route models versus single-route models are discussed. The dual-route model of word naming (Coltheart, 1978) is still accepted in some form by most theorists, although there have been challenges (Glushko, 1979; Humphreys & Evett, 1985; Seidenberg & McClelland, 1989; Van Orden, Pennington, & Stone, 1990). According to the standard version of the model, words can be named in either of two ways. One, referred to as the assembly route, is based on the idea that readers use knowledge of common spelling-tosound relationships to derive a likely set of sounds that are then assembled into a complete phonological code. The second, referred to as the lexical route, is based on use of word-specific association mechanisms. Readers identify the word as a pattern that allows them to access the appropriate location in lexical memory and then retrieve the corresponding phonological code. There has been considerable debate about the nature of the assembly route (Brown & Besner, 1987; Carr & Pollatsek, 1985; Paap & Noel, 1991; Patterson & Coltheart, 1987; Seidenberg & McClelland, 1989; Van Orden, Johnston, & Hale, 1988). The general assumption is that this route allows the naming of nonwords and contributes to the naming of words that follow common spelling-to-sound rules. The
Design and implementation of low sidelobe slot array antennas with full and half mode substrate integrated waveguide technology

In this paper, the investigations on low sideloble slot array antennas based on the full and half mode substrate integrated waveguide technology are presented. The design procedures are described. For verification purpose, several linear and planar arrays are simulated and fabricated with a normal low cost printed circuit board (PCB) process. Both measured and simulated results are in good agreement which demonstrated the capability of sidelobe suppression.
Diverse roles for the ror‐family receptor tyrosine kinases in neurons and glial cells during development and repair of the nervous system

The Ror‐family of receptor tyrosine kinases (RTKs) are involved critically in tissue genesis and organogenesis during development. In mammals, Ror1 and Ror2, members of the Ror‐family RTKs, have been shown to mediate cell polarity, migration, proliferation, and differentiation through the activation of noncanonical Wnt signaling by acting as receptors or co‐receptors for Wnt5a. Nematodes bearing mutations within the cam‐1 gene, encoding a Ror2 ortholog, exhibit defects in various developmental processes of the nervous system, including neuronal cell migration, polarization, axonal extension, and synaptic transmission. In mice, Ror2 and/or Ror1 are also shown to play roles in regulating neurite extension, synapse formation, and synaptic transmission of hippocampal neurons, indicating that the Ror‐family RTKs have evolutionarily conserved functions at least in part in neurons during development. Furthermore, Ror2 and/or Ror1 are expressed in neural stem/progenitor cells of the developing brain and in astrocytes of the adult brain after injury, and they play important roles in regulating cell proliferation under these different contexts. In this article, we overview recent advances in our understanding of the roles of the Ror‐family RTKs in the development and repair of the nervous system and discuss their potential for therapeutic targets to neurodegenerative diseases. Developmental Dynamics 247:24–32, 2018. © 2017 Wiley Periodicals, Inc.
Social Network Sites: Indispensable or Optional Social Tools?

Much research has enumerated potential benefits of online social network sites. Given the pervasiveness of these sites and the numbers of people that use them daily, both research and media tend to make the assumption that social network sites have become indispensible to their users. Based on the analysis of qualitative data from users of social network sites in Russia and Kazakhstan, this paper considers under what conditions social network sites can become indispensable to their users and when these technologies remain on the periphery of life despite fulfilling useful functions. For some respondents, these sites had become indispensable tools as they were integrated into everyday routines of communicating with emotionally important and proximal contacts and were often used for coordination of offline activities. For others social network sites remained spaces where they occasionally visited with people who may have been important at some point in the past but who had little connection to the daily business of living. In these cases social network sites were seen as convenient spaces of lightweight connectivity, but by no means indispensable.
The evolution of nodular goiter.

SIMPLE goiter occurs sporadically all over the world and in the form of endemic goiter affects millions of people in every continent, as a recent World Health Organization conference1 so clearly showed. Simple goiter almost inevitably progresses to the nodular form, and thus a clear knowledge of how these nodules arise and what changes they may undergo is of importance to the doctor, whether he is working in office, hospital, laboratory or public health department. Nodular goiter may become the seat of hyperthyroidism. When this occurs, Plummer (1, 2) and others have stressed that the clinical picture is different from that seen in the younger patient with the non-nodular gland of Graves' disease. Finally, the quickening of interest in thyroid cancer and its possible association with nodular goiter makes a study of the latter mandatory. This particular investigation started with an attempt to calculate more accurately the amount of irradiation received by the thyroid when radioactive iodine is administere.
Thermosensing ability of Trg and Tap chemoreceptors in Escherichia coli

The thermosensing ability of the Trg and Tap chemoreceptors in Escherichia coli was investigated after amplifying these receptors in a host strain lacking all four known chemoreceptors (Tar, Tsr, Trg, and Tap). Cells with an increased amount of either Trg or Tap showed mostly smooth swimming and no response to thermal stimuli. However, when the smooth-swimming bias of the cells was reduced by adding Trg- or Tap-mediated repellents, the cells showed clear changes in the swimming pattern upon temperature changes; Trg-containing cells showed tumbling at 23 degrees C but mostly smooth swimming at 32 degrees C, while Tap-containing cells showed smooth swimming at 20 degrees C but tumbling at 32 degrees C. These results indicate that although both Trg and Tap have the ability to sense thermal stimuli, Trg functions as a warm receptor, as reported previously for Tar and Tsr, while Tap functions as a cold receptor.
Structure of solid-state systems from embedded-cluster calculations: A divide-and-conquer approach.

The first-principles divide-and-conquer density-functional approach has been extended to solid-state systems. The method has the following features. (1) It divides a periodic solid-state system into equivalent primitive cells and further divides each cell into subsystems. The electron density of each subsystem is determined through the local representation of the one-electron Hamiltonian and used to form the total density per primitive cell. The method calculates the electronic structure of solids without involving the reciprocal space and its associated band structure. (2) It uses numerical atomic orbitals as basis functions with great variational flexibility. The Hamiltonian and other matrix elements are evaluated by numerical integration without any shape approximation to the effective one-electron potential. (3) This method, based on real space partition, can be applied to extended solid-state systems without translational symmetry, such as defects and surface chemisorption. As the first step, we have applied and tested the method to the electronic structure calculations of various crystalline solids: metallic lithium and copper, ionic sodium chloride, and covalent diamond and silicon. The self-consistently computed cohesive energies, structural properties, and density of states are in good agreement with those from the local-density approximation band-structure calculations and experimental results.
Ultrafast dynamics in DNA-mediated electron transfer: base gating and the role of temperature.

The ultrafast dynamics of electron transfer (ET) between bases in DNA have been determined to elucidate the critical role of base-pair gating on the timescale of the electron transport and the temperature dependence of the rates. ET occurs only through DNA duplexes that adopt a specific, well-coupled alignment of bases (ET-active; see picture). Descriptions of ET dynamics must include fluctuations of DNA bases.
A Comparison of the Fagerström Test for Cigarette Dependence and Cigarette Dependence Scale in a Treatment-Seeking Sample of Pregnant Smokers.

INTRODUCTION Valid and reliable brief measures of cigarette dependence are essential for research purposes and effective clinical care. Two widely-used brief measures of cigarette dependence are the six-item Fagerström Test for Cigarette Dependence (FTCD) and five-item Cigarette Dependence Scale (CDS-5). Their respective metric characteristics among pregnant smokers have not yet been studied. METHODS This was a secondary analysis of data of pregnant smokers (N = 476) enrolled in a smoking cessation study. We assessed internal consistency, reliability, and examined correlations between the instruments and smoking-related behaviors for construct validity. We evaluated predictive validity by testing how well the measures predict abstinence 2 weeks after quit date. RESULTS Cronbach's alpha coefficient for the CDS-5 was 0.62 and for the FTCD 0.55. Measures were strongly correlated with each other, although FTCD, but not CDS-5, was associated with saliva cotinine concentration. The FTCD, CDS-5, craving to smoke, and withdrawal symptoms failed to predict smoking status 2 weeks following the quit date. CONCLUSIONS Suboptimal reliability estimates and failure to predict short-term smoking call into question the value of including either of the brief measures in studies that aim to explain the obstacles to smoking cessation during pregnancy.
Economic development, climate and values: making policy

The two defining challenges of this century are overcoming poverty and managing the risks of climate change. Over the past 10 years, we have learned much about how to tackle them together from ideas on economic development and public policy. My own work in these areas over four decades as an academic and as a policy adviser in universities and international financial institutions has focused on how the investment environment and the empowerment of people can change lives and livelihoods. The application of insights from economic development and public policy to climate change requires rigorous analysis of issues such as discounting, modelling the risks of unmanaged climate change, climate policy targets and estimates of the costs of mitigation. The latest research and results show that the case for avoiding the risks of dangerous climate change through the transition to low-carbon economic development and growth is still stronger than when the Stern Review was published. This is partly because of evidence that some of the impacts of climate change are happening more quickly than originally expected, and because of remarkable advances in technologies, such as solar power. Nevertheless, significant hurdles remain in securing the international cooperation required to avoid dangerous climate change, not least because of disagreements and misunderstandings about key issues, such as ethics and equity.
Transient Neutralization of Tumor Necrosis Factor Alpha Can Produce a Chronic Fungal Infection in an Immunocompetent Host: Potential Role of Immature Dendritic Cells

ABSTRACT The mechanisms underlying induction of immune dysregulation and chronic fungal infection by a transient tumor necrosis factor alpha (TNF-α) deficiency remain to be defined. The objective of our studies was to determine the potential contribution of neutropenia and immature dendritic cells to the immune deviation. Administration of an anti-TNF-α monoclonal antibody at day 0 neutralized TNF-α only during the first week of a pulmonary Cryptococcus neoformans infection. Transient neutralization of TNF-α resulted in transient depression of interleukin-12 (IL-12), monocyte chemotactic protein 1 (MCP-1), and gamma interferon (IFN-γ) production but permanently impaired long-term clearance of the infection from the lungs even after the levels of these cytokines increased and a vigorous inflammatory response developed. Early neutrophil recruitment was defective in the absence of TNF-α. However, as demonstrated by neutrophil depletion studies, this did not account for the decrease in IL-12 and IFN-γ levels and did not play a role in establishing chronic pulmonary cryptococcal infection. Transient TNF-α neutralization also produced a deficiency in CD11c+ MHC II+ cells and IL-12 in the lymph nodes, potentially implicating a defect in mature dendritic cell trafficking. Transfer of cryptococcal antigen-pulsed immature dendritic cells into naïve mice prior to intratracheal challenge resulted in the development of a nonprotective immune response to C. neoformans that was similar to that observed in anti-TNF-α-treated mice (increased IL-4, IL-5, and IL-10 levels, pulmonary eosinophilia, and decreased clearance). Thus, stimulation of an antifungal response by immature dendritic cells can result in an immune deviation similar to that produced by transient TNF-α deficiency, identifying a new mechanism by which a chronic fungal infection can occur in an immunocompetent host.