Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating Selection Intensity on Synonymous Codon Usage in a Nonequilibrium Population

Codon usage bias is the nonrandom use of synonymous codons for the same amino acid. Most population genetic models of codon usage evolution assume that the population is at mutation–selection–drift equilibrium. Natural populations, however, frequently deviate from equilibrium, often because of recent demographic changes. Here, we construct a matrix model that includes the effects of a recent change in population size on estimates of selection on preferred vs. unpreferred codons. Our results suggest that patterns of synonymous polymorphisms affecting codon usage can be quite erratic after such a change; statistical methods that fail to take demographic effects into account can then give incorrect estimates of important parameters. We propose a new method that can accurately estimate both demographic and codon usage parameters. The method also provides a simple way of testing for the effects of covariates such as gene length and level of gene expression on the intensity of selection, which we apply to a large Drosophila melanogaster polymorphism data set. Our analyses of twofold degenerate codons reveal that (i) selection acts in favor of preferred codons, (ii) there is mutational bias in favor of unpreferred codons, (iii) shorter genes and genes with higher expression levels are under stronger selection, and (iv) there is little evidence for a recent change in population size in the Zimbabwe population of D. melanogaster.
Creativity in MS/OR: Choosing the Appropriate Technique

There is a great need for creativity within the MS/OR environment. Managers must be capable of defining problems, developing novel solutions, and implementing them effectively. A lot of research has focused on creativity. Researchers, for example, discussed methods of improving creative thinking in people, presented techniques that can encourage participants to develop more novel ideas, described the creative problem-solving process.I focus on creative problem-solving (CPS) techniques and how best to choose the most appropriate for a given situation. To this end, therefore, I have categorized the techniques and placed them in a continuum ranging from paradigm-preserving techniques to paradigm-breaking techniques.
Mean platelet volume is an independent risk factor for myocardial infarction but not for coronary artery disease

Summary. After rupture of an arteriosclerotic plaque in a coronary artery, platelets play a crucial role in the subsequent thrombus formation, leading to myocardial infarction. An increased mean platelet volume (MPV), as an indicator of larger, more reactive platelets, may represent a risk factor for myocardial infarction. However, this hypothesis is still controversial and most studies addressing the role of MPV were performed comparing patients suffering from myocardial infarction with healthy controls. We intended to identify patients at high risk of suffering myocardial infarction in a group of patients with known coronary artery disease. One hundred and eighty‐five consecutive patients with stable coronary artery disease were compared with 188 individuals who had suffered myocardial infarction. Patients within the highest quintile of MPV (≥ 11·6 fl) had a significantly higher risk of experiencing a myocardial infarction compared with patients within the lowest quintile (OR = 2·6, 95% CI 1·3–5·1) in a multivariate analysis that included sex, age, body mass index, hyperlipidaemia, hypertension, smoking and diabetes mellitus. Our results indicate that patients with pre‐existing coronary artery disease and an increased MPV (≥ 11·6 fl) are at higher risk of myocardial infarction. These patients can be easily identified during routine haematological analysis and could possibly benefit from preventive treatment.
Abort-Oriented Concurrency Control for Real-Time Databases

There has been growing interest in the performance of transaction systems that have significant response time requirements. These requirements are usually specified as hard or soft deadlines on individual transactions and a concurrency control algorithm must attempt to meet the deadlines as well as preserve data consistency. This paper proposes a class of simple and efficient abort-oriented concurrency control algorithms in which the schedulability of a transaction system is improved by aborting transactions that introduce excessive blockings. We consider different levels of the aborting relationship among transactions and evaluate the impacts of the aborting relationship when the relationship is built in an online or offline fashion. We measure aborting overheads on a system running the LynxOS real time operating system. The strengths of the work are demonstrated by improving the worst-case schedulability of an avionics example, a satellite control system, and randomly generated transaction sets.
Characteristic modes analysis for pattern reconfigurable antenna design

A novel pattern reconfigurable antenna operating at 2.45 GHz is designed by exploiting the characteristic modes analysis (CMA). More in detail, this compact antenna is capable to steer the pattern null within a beam of 64° centered at broadside direction (θ = 0°), with a depth nulls greater than 18 dB. The pattern reconfigurability is obtained by changing the phase of two capacitive exciters hosted above the considered conductive plane. The study of the involved characteristic mode is presented and the proposed phase shifter microstrip network is introduced.
A Study of Causes and Consequences of Client-Side JavaScript Bugs

Client-side JavaScript is widely used in web applications to improve user-interactivity and minimize client-server communications. Unfortunately, JavaScript is known to be error-prone. While prior studies have demonstrated the prevalence of JavaScript faults, no attempts have been made to determine their causes and consequences. The goal of our study is to understand the root causes and impact of JavaScript faults and how the results can impact JavaScript programmers, testers and tool developers. We perform an empirical study of 502 bug reports from 19 bug repositories. The bug reports are thoroughly examined to classify and extract information about each bug' cause (the error) and consequence (the failure and impact). Our results show that the majority (68 percent) of JavaScript faults are DOM-related, meaning they are caused by faulty interactions of the JavaScript code with the Document Object Model (DOM). Further, 80 percent of the highest impact JavaScript faults are DOM-related. Finally, most JavaScript faults originate from programmer mistakes committed in the JavaScript code itself, as opposed to other web application components. These results indicate that JavaScript programmers and testers need tools that can help them reason about the DOM. Additionally, developers can use the error patterns we found to design more powerful static analysis tools for JavaScript.
MatrixConverter: Facilitating construction of phenomic character matrices1

Premise of the study: While numerous software packages enable scientists to evaluate molecular data and transform them for phylogenetic analyses, few such tools exist for phenomic data. We introduce MatrixConverter, a program that helps expedite and facilitate the transformation of raw phenomic character data into discrete character matrices that can be used in most evolutionary inference programs. Methods and Results: MatrixConverter is an open source program written in Java; a platform-independent binary executable, as well as sample data sets and a user's manual, are available at https://github.com/gburleigh/MatrixConverter/tree/master/distribution. MatrixConverter has a simple, intuitive user interface that enables the user to immediately begin scoring phenomic characters. We demonstrate the performance of MatrixConverter on a phenomic data set from cycads. Conclusions: New technologies and software make it possible to obtain phenomic data from species across the tree of life, and MatrixConverter helps to transform these new data for evolutionary or ecological inference.
Routines and Other Recurring Action Patterns of Organizations: Contemporary Research Issues

This paper reports and extends discussions carried out during a workshop held at the Santa Fe Institute in August 1995 by the authors. It treats eight major topics: (i) the importance of carefully examining research on routine, (ii) the concept of 'action patterns' in general and in terms of routine, (iii) the useful categorization of routines and other recurring patterns, (iv) the research implications of recent cognitive results, (v) the relation of evolution to action patterns, (vi) the contributions of simulation modeling for theory in this area, (vii) examples of various approaches to empirical research that reveal key problems, and (viii) a possible definition of 'routine'. An extended appendix by Massimo Egidi provides a lexicon of synonyms and opposites covering use of the word 'routine' in such areas as economics, organization theory and artificial intelligence. Coauthors are Roger Burkhart, Giovanni Dosi, Massimo Egidi, Suigi Marengo, Massimo Warglien, and Sidney Winter. Copyright 1996 by Oxford University Press.
Activity in descending dopaminergic neurons represents but is not required for leg movements in the fruit fly Drosophila

Modulatory descending neurons (DNs) that link the brain to body motor circuits, including dopaminergic DNs (DA‐DNs), are thought to contribute to the flexible control of behavior. Dopamine elicits locomotor‐like outputs and influences neuronal excitability in isolated body motor circuits over tens of seconds to minutes, but it remains unknown how and over what time scale DA‐DN activity relates to movement in behaving animals. To address this question, we identified DA‐DNs in the Drosophila brain and developed an electrophysiological preparation to record and manipulate the activity of these cells during behavior. We find that DA‐DN spike rates are rapidly modulated during a subset of leg movements and scale with the total speed of ongoing leg movements, whether occurring spontaneously or in response to stimuli. However, activating DA‐DNs does not elicit leg movements in intact flies, nor do acute bidirectional manipulations of DA‐DN activity affect the probability or speed of leg movements over a time scale of seconds to minutes. Our findings indicate that in the context of intact descending control, changes in DA‐DN activity are not sufficient to influence ongoing leg movements and open the door to studies investigating how these cells interact with other descending and local neuromodulatory inputs to influence body motor output.
Global Governance and the New Wars: The Merging of Development and Security

ing examples include the interpretation of indigent policy. She notes that indigent does not translate well into Zulu, but it is associated with giving to those in need and restoring dignity (134). This positive interpretation of indigence explains why some poor people will continue to expect free services. She also notes that some South Africans interpret policy instruments such as water meters as another round of dispossession (107). These interpretations highlight that there is a need for us to examine how citizens interpret government’s policy instruments. For example, what do porter toilets or a lack of service delivery mean to the citizens who experience it? Hart offers interesting insights into the state of the South African nation. She links interpretations of past and present economic and political developments. She draws our attention to these linkages to highlight why we continue to experience inequality in South Africa. She directs attention to how government responds to citizens (policy) and how citizens interpret these responses. The value of her work also lies in the fact that she gives developments in post-apartheid prominence when explaining the current state of affairs in South Africa. To conclude, apart from the other listed reasons, Hart’s book requires our attention because it tells the story of how those South Africans who have remained disadvantaged are continuing their struggle, but only this time, it is against their democratically elected government.
Propagation Strategies for Building Temporal Ontologies

In this paper, we propose to build temporal ontologies from WordNet. The underlying idea is that each synset is augmented with its temporal connotation. For that purpose, temporal classifiers are iteratively learned from an initial set of time-sensitive synsets and different propagation strategies to give rise to different TempoWordNets.
Handbook of instructional communication : rhetorical and relational perspectives

It's not surprisingly when entering this site to get the book. One of the popular books now is the handbook of instructional communication rhetorical and relational perspectives. You may be confused because you can't find the book in the book store around your city. Commonly, the popular book will be sold quickly. And when you have found the store to buy the book, it will be so hurt when you run out of it. This is why, searching for this popular book in this website will give you benefit. You will not run out of this book.
Partial view modeling and validation in 3D laser scans for grasping

Humanoid robots performing every day tasks in human environments need a strong perception system in order to operate successfully. As 3D data acquisition devices like laser scanners and time of flight cameras get better and cheaper, we expect three-dimensional perception to become more important. We describe a new method for detecting surfaces of revolution in point clouds within our Sample Consensus Framework. Cylinders, cones and arbitrary rotational surfaces can be reliably and efficiently detected. Symmetry assumptions can be hypothesized and verified in order to complete the model from a single view, i.e. to generate data on the occluded parts of the object. These complete models can be used for grasp analysis. Additionally, we propose a new method for scoring models within the Sample Consensus Framework in order to get better shapes.
Single Subcortical Infarction and Atherosclerotic Plaques in the Middle Cerebral Artery: High-Resolution Magnetic Resonance Imaging Findings

Background and Purpose— Single subcortical infarction (SSI) may be classified as proximal SSI (pSSI) or distal SSI (dSSI) according to its extension to the middle cerebral artery (MCA). We investigated the differences between pSSI and dSSI in terms of their clinical features, lesion size, and the frequency of MCA plaques detected by high-resolution MRI. Methods— Thirty-nine patients with SSI (20 pSSI and 19 dSSI) were prospectively enrolled who did not show relevant MCA disease on MR angiography. Lesion size, neurological status (initial National Institutes of Health Stroke Scale score and modified Rankin Scale at 3 months), and the presence and location (superior versus inferior) of high-resolution MRI–identified plaques were evaluated. Results— The frequencies of MCA plaques did not differ between patients with pSSI and those with dSSI (8 [40%] versus 12 [63.2%]; P=0.205); however, superiorly located plaques were significantly more common in patients with pSSI than in those with dSSI (6 [75%] versus 2 [16.7%]; P=0.019). Initial lesion volumes were larger (1.96±1.18 versus 1.11±1.11 mm3; P=0.025), National Institutes of Health Stroke Scale scores were higher (5 [3–6.75] versus 3 [1–3] points; P=0.017), and microbleeds were fewer (1 [5%] versus 10 [52.6%]; P=0.001) in patients with pSSI than in those with dSSI. Three-month modified Rankin Scale scores were higher in patients with superior plaques than in those with inferior plaques. Conclusions— Compared with dSSI, pSSI is closely associated with large lesions, severe clinical symptoms, and superiorly located MCA plaques, suggesting that the location, rather than simple presence of plaques, determines the SSI location.
Visualização tridimensional de grandes volumes de informação

Na actual era da informacao o dificil nao e produzir ou mesmo aceder a informacao; encontrar e recuperar informacao relevante entre a imensidade de informacao disponivel e a parte mais ardua. Grandes esforcos estao a ser efectuados para atacar este problema. Motores de busca mais poderosos e inteligentes estao a ser desenvolvidos numa tentativa de simplificar o problema de data mining. Mas esta nao e a unica dificuldade e conduz directamente a seguinte questao: uma vez conseguido o acesso a informacao, como poderemos tirar partido dela? A visualizacao da informacao e uma das melhores solucoes. Este artigo descreve como utilizar a visualizacao tridimensional de informacao para apresentar e interagir com grandes volumes de dados.
Using REDItools to Detect RNA Editing Events in NGS Datasets

RNA editing is a post‐transcriptional/co‐transcriptional molecular phenomenon whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions, and/or deletions. It occurs in a variety of organisms and different cellular locations through evolutionally and biochemically unrelated proteins. RNA editing has a plethora of biological effects including the modulation of alternative splicing and fine‐tuning of gene expression. RNA editing events by base substitutions can be detected on a genomic scale by NGS technologies through the REDItools package, an ad hoc suite of Python scripts to study RNA editing using RNA‐Seq and DNA‐Seq data or RNA‐Seq data alone. REDItools implement effective filters to minimize biases due to sequencing errors, mapping errors, and SNPs. The package is freely available at Google Code repository (http://code.google.com/p/reditools/) and released under the MIT license. In the present unit we show three basic protocols corresponding to three main REDItools scripts. © 2015 by John Wiley & Sons, Inc.
Region-based memory management in cyclone

Cyclone is a type-safe programming language derived from C. The primary design goal of Cyclone is to let programmers control data representation and memory management without sacrificing type-safety. In this paper, we focus on the region-based memory management of Cyclone and its static typing discipline. The design incorporates several advancements, including support for region subtyping and a coherent integration with stack allocation and a garbage collector. To support separate compilation, Cyclone requires programmers to write some explicit region annotations, but a combination of default annotations, local type inference, and a novel treatment of region effects reduces this burden. As a result, we integrate C idioms in a region-based framework. In our experience, porting legacy C to Cyclone has required altering about 8% of the code; of the changes, only 6% (of the 8%) were region annotations.
From overcoming limitations to securing safety: Defining the new mission of human-machine systems

Abstract Beginning with the launch of human factors engineering in 1945, but actually with intellectual roots that go back to at least the school of Scientific Management, the design of human-machine systems (HMS) has been focused on overcoming human limitations and constraining human performance variability. This approach is, however, only warranted if the work environment is simple enough to be tractable. While this may have been the case 50 years ago, it is no longer so. Most work systems today are intractable, due to tight couplings and non-linear interactions. Under these conditions human performance variability becomes an asset rather than a liability, and the goal of HMS design should therefore be to enhance the capabilities of humans rather than to constrain them.
OMNI and Borg scales for the prescription of cycle ergometer exercise

The Borg and OMNI scales of perceived exertion have been widely validated for the identification of exercise intensity. The objective of this study was to test the agreement between the categories of the Borg (6-20) and OMNI-Cycle scales for the prescription of cycle ergometer exercise and to propose a new conversion table. Twenty-six male indoor cyclists (17-41 years) pedalled for 3 min at six self-selected increasing loads. These loads corresponded to categories 9, 11, 13, 15, 17, and 19 of the Borg scale in one session, and to categories 2, 4, 5, 7, 8, and 10 of the OMNI scale in the other session. At the end of each stage, heart rate (HR) and power (W) were recorded. Pearson’s correlation coefficient between scales was calculated. Agreement between the categories of the scales was tested by ANOVA for repeated measures, followed by the Tukey test (p < 0.05). The correlation between the two scales was high (r = 0.87, p < 0.05). Significant difference between the two scales was observed for HR in the first three categories. W differed significantly only in the first two categories. The conversion tested showed a significant correlation. However, there were significant differences in HR in the first three categories and in W in the first two. The following agreement is proposed: Borg 11, 13, 15, 17, and 19 corresponding to OMNI 2, 4, 7, 8, and 10.
A thin monitoring layer for top-k aggregation queries over a database

We consider the problem of maintaining a large set of top-k rankings over the update stream of a database. The rankings stem from top-k aggregation queries that are given a-priori based on the application scenario, for instance created along dimensions of a traditional data warehouse, for efficient automated reporting/detection of changes. The focus on only the top part of a ranking enables efficient buffering techniques to limit expensive interactions with the underlying database, while still guaranteeing correct top-k rankings at all times. This is achieved by employing conservative rank (score) estimates of previously unseen items that are not in the top-k result so far. The proposed family of maintenance algorithms further exploits the relations between the monitored rankings known from multi-query optimisation. We present results of a preliminary experimental evaluation using TPC-H data to study the performance of our algorithms.
How does academic preparation influence how engineering students solve problems?

In first year engineering courses, students possess a wide range of academic preparation such as their exposure to various mathematics courses and pre-engineering programs. Additionally, students bring perceptions about their abilities, and have already begun practicing preferred methods of analysis and documentation. Understanding how students with different backgrounds develop problem solving skills in first year engineering programs is of critical importance in order to close achievement gaps between diverse populations. This study examines how students solve engineering problems and identifies variations based on student factors of gender, ethnicity, mathematics preparation and achievement, and prior engineering experience. Solutions for three problems from 27 students were analyzed (n = 68 solutions). Students worked out problems using custom-designed software that digitally records ink strokes and allows researchers to associate codes to the problem solution at any point, even in portions of the problem solution that would not have been available without the use of this technology, such as in erased work. Differences in how students solve problems were assessed based on the prevalence (or absence) of elements and errors in the problem solving process, which were evaluated using task analysis. Results indicated that pre-engineering experience did not have a significant impact on successfully solving problems; however, having completed a calculus course was significantly related to successful problem solving. Future research will expand the study population to a larger sample of first year engineering students across multiple semesters, identifying key strategies that are absent for students with low mathematics preparation, and to investigate relationships between prior academic preparation and indicators of metacognition.