Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes1[OPEN]

Reannotation of the maize genome using MAKER-P results in many revised and new gene models. The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-P to update and revise the maize (Zea mays) B73 RefGen_v3 annotation build (5b+) in less than 3 h using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, well-supported protein-coding genes not present in the 5b+ annotation build, added additional untranslated regions to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of large and diverse evidence data sets), identified 104,215 pseudogene fragments, and created an additional 2,522 noncoding gene annotations. We also describe a method for de novo training of MAKER-P for the annotation of newly sequenced grass genomes. Collectively, these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes.
Streptolysin S Promotes Programmed Cell Death and Enhances Inflammatory Signaling in Epithelial Keratinocytes during Group A Streptococcus Infection

ABSTRACT Streptococcus pyogenes, or group A Streptococcus (GAS), is a pathogen that causes a multitude of human diseases from pharyngitis to severe infections such as toxic shock syndrome and necrotizing fasciitis. One of the primary virulence factors produced by GAS is the peptide toxin streptolysin S (SLS). In addition to its well-recognized role as a cytolysin, recent evidence has indicated that SLS may influence host cell signaling pathways at sublytic concentrations during infection. We employed an antibody array-based approach to comprehensively identify global host cell changes in human epithelial keratinocytes in response to the SLS toxin. We identified key SLS-dependent host responses, including the initiation of specific programmed cell death and inflammatory cascades with concomitant downregulation of Akt-mediated cytoprotection. Significant signaling responses identified by our array analysis were confirmed using biochemical and protein identification methods. To further demonstrate that the observed SLS-dependent host signaling changes were mediated primarily by the secreted toxin, we designed a Transwell infection system in which direct bacterial attachment to host cells was prevented, while secreted factors were allowed access to host cells. The results using this approach were consistent with our direct infection studies and reveal that SLS is a bacterial toxin that does not require bacterial attachment to host cells for activity. In light of these findings, we propose that the production of SLS by GAS during skin infection promotes invasive outcomes by triggering programmed cell death and inflammatory cascades in host cells to breach the keratinocyte barrier for dissemination into deeper tissues.
Antibacterial Efficacy of Temperate Phage-Mediated Inhibition of Bacterial Group Motilities

ABSTRACT Phage therapy against bacterial pathogens has been resurrected as an alternative and supplementary anti-infective modality. Here, we observed that bacterial group motilities were impaired in Pseudomonas aeruginosa strain PA14 lysogens for some temperate siphophages; the PA14 lysogens for DMS3 and MP22 were impaired in swarming motility, whereas the PA14 lysogen for D3112 was impaired in twitching motility. The swarming and twitching motilities of PA14 were also affected in the presence of MP22 and D3112, respectively. The in vitro killing activities of D3112 and MP22 toward PA14 did not differ, and neither did their in vivo persistence in the absence of bacterial infections in mice as well as in flies. Nevertheless, administration of D3112, not MP22, significantly reduced the mortality and the bacterial burdens in murine peritonitis-sepsis and Drosophila systemic infection caused by PA14. Taken together, we suggest that a temperate phage-mediated twitching motility inhibition might be comparably effective to control the acute infections caused by P. aeruginosa.
Brain mercury in neurodegenerative disorders.

BACKGROUND Trace element neurotoxicity has long been invoked as an etiologic factor for Alzheimer's disease. This study was conducted to determine the concentrations of mercury in seven different brain regions from deceased patients histologically confirmed with Alzheimer's disease or multiple sclerosis as compared to control subjects without known central nervous system and renal disorders. Brain mercury concentrations in all deceased subjects can arise from amalgam restorations, diet, and the working environment. METHODS Autopsy frozen specimens (control, Alzheimer's disease and multiple sclerosis) from seven brain regions, which included frontal cortex, temporal cortex, occipital cortex, putamen, hippocampus, corona radiata and corpus callosum were assayed for the concentrations of selenium using instrumental neutron activation analysis and mercury using radiochemical neutron activation analysis. RESULTS We found that the concentrations of mercury and the mercury/selenium molar ratios were significantly lower in the hippocampi of multiple sclerosis patients as compared to aged-matched controls. However, no statistically significant differences were detected for the concentrations of mercury and the mercury/ selenium molar ratios for the remaining six brain regions among these groups. CONCLUSIONS Since brain mercury concentrations from deceased subjects with either Alzheimer's disease or multiple sclerosis are not significantly higher than controls, the present study provides no scientific support that mercury plays a significant role in the pathogenesis of these neurologic disorders.
Connectivity Transitions in Networks with Super-Linear Preferential Attachment

We analyze an evolving network model of Krapivsky and Redner in which new nodes arrive sequentially, each connecting to a previously existing node b with probability proportional to the pth power of the in-degree of b. We restrict to the super-linear case p > 1. When , the structure of the final countable tree is determined. There is a finite tree T with distinguished v (which has a limiting distribution) on which is "glued" a specific infinite tree; v has an infinite number of children, an infinite number of which have k - 1 children, and there are only a finite number of nodes (possibly only v) with k or more children. Our basic technique is to embed the discrete process in a continuous time process using exponential random variables, a technique that has previously been employed in the study of balls-in-bins processes with feedback.
Picture-word interference is semantically based.

RosINSKI, RICHARD R. Picture-Word Interference Is Semantically Based. CHILD DEVELOPMENT, 1977, 48, 643-647. To explore semantic effects in word processing, a set of picture-word interference tasks were administered to second-, fourth-, sixth-grade, and college-level subjects. Results indicated that distractor words belonging to the same semantic category as the pictures produced more interference than either unrelated words or nonsense trigrams; the latter two conditions produced equivalent interference. The effect of semantic category relation was consistent over grade indicating that children and adults experience an equivalent amount of semantic interference. The results are interpreted as indicating the interference between pictures and words takes place in a single semantic store accessed by both pictorial and verbal material.
Positive Psychology and Positive Education: Old Wine in New Bottles?

The recently fashionable theories of positive psychology have educational ramifications at virtually every level of engagement, culminating in the model of positive education. In this critical review, I scrutinize positive education as a potential theory in educational psychology. Special attention is given to conceptual controversies and suggested educational interventions. Positive psychologists have yet to explore in detail the school as a positive institution. They have written at length, however, about such positive personal traits as moral virtue and resiliency, and about positive emotions both as embodied in experiences of classroom “flow” and as facilitators of students’ personal resources. Because the empirical evidence concerning these positive factors remains partly mixed or tentative, and because most of them had a home in other theoretical frameworks before the advent of positive psychology, searching questions remain about the effectiveness and originality of positive education. This article addresses some of those questions.
Predicting Friendship Stability During Early Adolescence

This study examined the stability of early adolescent best friendships across a school year. Grade 7 students (N = 174) participated in group-testing sessions in the fall and spring of their school year. Participants completed peer-nomination measures, described the quality of their best friendships, their knowledge of their best friend, and their typical conflict-resolution strategies in response to peer conflicts. Approximately 50% of the reciprocated best friendships remained stable across the school year. Friendship quality and knowledge were unrelated to friendship stability. However, stability of boys’ friendships was positively correlated with minimization strategies, whereas stability of girls’ best friendships was negatively correlated with minimization strategies but positively related to greater use of negative (i.e., confrontational) strategies in response to peer conflict. Results are discussed with reference to the rules of friendship and to the conflicting demands for compliance and autonomy within a close relationship.
“With recruitment I always feel I need to listen to my gut”: the role of intuition in employee selection

Purpose – This qualitative study of managers’ use of intuition in the selection process aimed to understand if and how managers use intuition in employee hiring decisions and suggest ways in which the use of intuition might be improved. The paper aims to discuss these issues. Design/methodology/approach – Semi-structured, in-depth interviews were conducted with managers from a range of backgrounds, and with varying experience of recruitment and selection. Findings – Findings revealed that reasons for the use of intuition included personal preferences, resource constraints and recognition of the limitations of more structured approaches. Intuition was used an indicator for performance, personality and person-environment fit. Intuition tended to be used with requisite caution; participants were aware of its limits, the potential for bias and the difficulties in justifying its use; several participants used their intuitions in concert with more structured, non-intuition based approaches. Research limitations.
The Fibonacci Dimension of a Graph

The Fibonacci dimension ${\rm fdim}(G)$ of a graph $G$ is introduced as the smallest integer $f$ such that $G$ admits an isometric embedding into $\Gamma_f$, the $f$-dimensional Fibonacci cube. We give bounds on the Fibonacci dimension of a graph in terms of the isometric and lattice dimension, provide a combinatorial characterization of the Fibonacci dimension using properties of an associated graph, and establish the Fibonacci dimension for certain families of graphs. From the algorithmic point of view, we prove that it is NP-complete to decide whether ${\rm fdim}(G)$ equals the isometric dimension of $G$, and show that no algorithm to approximate ${\rm fdim}(G)$ has approximation ratio below $741/740$, unless P$=$NP. We also give a $(3/2)$-approximation algorithm for ${\rm fdim}(G)$ in the general case and a $(1+\varepsilon)$-approximation algorithm for simplex graphs.
L2 lexis in L1: Reluctance to translate out of concern for referential meaning

Abstract Using evidence from the Hong Kong Chinese press, this paper shows that intra-sentential code-alternation may be due to linguistic, especially semantic, factors at work, which explain why the bilingual is reluctant to translate the English expressions into Chinese, resulting in code-alternation. This observation amounts to a challenge to a tacit assumption behind social or discourse-related explanations of code-alternation, that referential meaning may be kept constant and that code-alternated expressions in the guest language could always be ‘replaced’, paradigmatically or otherwise, by a semantically ‘equivalent’ expression in the host language. The basic premise of ‘translation equivalent’ is illusory. Given the strong social norms disapproving the use of English-only discourse for intra-ethnic communication in Hong Kong, it is argued that intra-sentential code-alternation typical of bilingual Chinese Hongkongers is more adequately explained by the bilingual's reluctance to translate the original English expressions into Cantonese or modern standard Chinese. In this light, Cantonese-English code-alternation in Hong Kong is most appropriately seen as the result of the Chinese bilingual's attempt to guard against unwanted semantic loss or gain.
Learning together, living apart: the experiences of university students in Northern Ireland

Elementary (primary) and high (secondary) school education in Northern Ireland (NI) is essentially segregated along religious lines. The vast majority of young people from the Protestant/Unionist/British community attend state “Controlled” schools while Catholics/ Nationalists/Irish attend schools in the Catholic Church‐based “Maintained” sector. Going to university represents for many the first opportunity to share a significant educational experience with someone from a different politico‐religious group and cultural background. This paper presents the results of a focus‐group based study designed to illuminate students' experiences of intergroup relations at a NI university. Through focus‐group discussions information was generated on cross‐community contact, the influence of group difference, prevalence, and identity, on attitudes and intergroup communication. The university environment as a factor in potential relational development, the role which student bodies and academic staff may play, and policies and practices on accepting diversity are discussed. Recommendations and considerations are highlighted for other pedagogical institutes where complex and difficult intergroup dynamics exist.
Stochastic Averaging of Dynamical Systems with Multiple Time Scales Forced with α-Stable Noise

Stochastic averaging allows for the reduction of the dimension and complexity of stochastic dynamical systems with multiple time scales, replacing fast variables with statistically equivalent stochastic processes in order to analyze variables evolving on the slow time scale. These procedures have been studied extensively for systems driven by Gaussian noise, but very little attention has been given to the case of $\alpha$-stable noise forcing which arises naturally from heavy-tailed stochastic perturbations. In this paper, we study nonlinear fast-slow stochastic dynamical systems in which the fast variables are driven by additive $\alpha$-stable noise perturbations and the slow variables depend linearly on the fast variables. Using a combination of perturbation methods and Fourier analysis, we derive stochastic averaging approximations for the statistical contributions of the fast variables to the slow variables. In the case that the diffusion term of the reduced model depends on the state of the slow variable, we show that this term is interpreted in terms of the Marcus calculus. For the case $\alpha = 2$, which corresponds to Gaussian noise, the results are consistent with previous results for stochastic averaging in the Gaussian case. Although the main results are derived analytically for $1 < \alpha < 2$, we provide evidence of their validity for $\alpha < 1$ with numerical examples. We numerically simulate both linear and nonlinear systems and the corresponding reduced models, demonstrating good agreement for their stationary distributions and temporal dependence properties.
Limiting flooding expenses in on-demand source-initiated protocols for mobile wireless networks

Summary form only given. We study on-demand source initiated protocols for mobile wireless networks. In particular, we study the flooding procedure commonly used by these protocols to set up temporary communication paths. The benefit of the flooding technique is its generosity regarding changes in network structure. On the other hand, each time a message is sent, the entire network will be involved to set up the communication path from the source node, to the target node. We propose a new approach, which we call limited broadcasting. It is aimed to reduce the overhead by localizing the search for the target node both in terms of the time the process needs to globally stop after the target has been reached and/or in terms of the region which is affected by the search. It works in unknown networks and does not need any kind of additional information.
Predicting memory completeness and accuracy: emotion and exposure in repeated autobiographical recall

Using a repeated testing procedure modified for an autobiographical event, individuals provided narrative accounts of their memory for the announcement of the verdict in a widely publicized murder trial. The goal of the study was to determine whether different factors would predict initial versus final recall performance. Ratings of negative emotional reaction during the event predicted initial amount recalled, and frequency of exposure to the event predicted final amount recalled. Judged completeness of recall and phenomenological ratings of the vividness of the memory were also related to final amount recalled. The measured variables were unrelated to recall accuracy. Examining memory over repeated recall attempts offers a fruitful way to examine processes in autobiographical memory. Copyright © 2001 John Wiley & Sons, Ltd.
Implications of Using Male and Female Voices in Commercials: An Exploratory Study

Abstract Male and female voices were evaluated in terms of their communication effectiveness in delivering advertising messages. It was hypothesized that the sex of presenters in ads has a significant effect on evaluations of commercials for gender-imaged products but not for products with no gender image (neutral products). As hypothesized, men and women were judged equally effective as presenters for neutral products. For a female-gender-imaged product, the sex of the spokesperson and the announcer significantly affected advertising evaluations. However, results showed that, for a male-gender-imaged product, the sex of the presenters had no impact on evaluations of the commercials. There is only one advertising scenario in which a male voice is preferred as a presenter. Implications of these findings for advertising practice are discussed.
Outcomes in CKD: What We Know and What We Need to Know

Chronic kidney disease (CKD) is a major public health concern. The high prevalence of reduced estimated glomerular filtration (eGFR) in the elderly has led to speculation as to whether it should really be regarded as a disease in all. Patients with CKD exhibit considerable cardiovascular morbidity and mortality but until recently data regarding the natural history of CKD, particularly in the elderly, has been somewhat lacking. As such the clinical significance of K/DOQI’s CKD definition in terms of additional morbidity, mortality and progression to end-stage renal disease (ESRD) remains uncertain. Data have shown that death from cardiovascular disease is far more common than progression to renal replacement therapy in the elderly. Factors which increase the risks of progression to ESRD include younger age, proteinuria and diabetes. Although the elderly have high rates of cardiovascular death, comparatively younger patients with CKD have substantially increased relative risks of death. Specialist renal review should be targeted towards these high-risk patients while the majority of elderly patients can be safely monitored in primary care. It remains doubtful whether labelling all elderly CKD patients with a ‘disease’ confers any additional benefit.
The influence of color on student emotion, heart rate, and performance in learning environments

In this study, six colors (vivid red, vivid blue, vivid yellow, pale red, pale blue, and pale yellow†) were manipulated in a simulated study environment to determine their effects on university students' learning performance, emotions, and heart rate. It was hypothesized that learning, physiological and emotional states would be affected by different colors in private study spaces. A total of 24 undergraduate and postgraduate students participated in this study. The dependent variables were reading task performance, emotional responses, and changes in heart rate. The results showed that, although participants assessed the situation as relaxed, calm, and pleasant in the pale color conditions, reading scores were significantly higher in the vivid color conditions. Heart rates were significantly affected by hue; they increased in the red and yellow conditions. In addition, the results suggested that, regardless of the degree of whiteness, the hue had a significant impact on participants' emotions; blue increased relaxation and calmness feelings of participants compared to the other colors. Implications of these findings and suggestions for further research are discussed. © 2015 Wiley Periodicals, Inc. Col Res Appl, 41, 196–205, 2016
Dealer Inventory and the Cross-Section of Corporate Bond Returns

Inventory models of dealership markets imply that intermediaries reduce their exposure to inventory risk by offering prices different from fundamental values. Therefore, inventory levels should affect asset prices and thus returns. We explore the cross-sectional relation between US corporate bond inventories and returns. Our findings provide strong support for the asset pricing implication of inventory models, that is, the risk-adjusted return of a high-minus-low inventory-sorted portfolio is 21 basis points per week. Furthermore, we examine several drivers of the inventory risk premium; for example, we emphasize the importance of inventory risk sharing in pricing bonds.