Miracle-dz/UniFAR-FTUs huggingface dataset:
GC-Content of Synonymous Codons Profoundly Influences Amino Acid Usage

Amino acids typically are encoded by multiple synonymous codons that are not used with the same frequency. Codon usage bias has drawn considerable attention, and several explanations have been offered, including variation in GC-content between species. Focusing on a simple parameter—combined GC proportion of all the synonymous codons for a particular amino acid, termed GCsyn—we try to deepen our understanding of the relationship between GC-content and amino acid/codon usage in more details. We analyzed 65 widely distributed representative species and found a close association between GCsyn, GC-content, and amino acids usage. The overall usages of the four amino acids with the greatest GCsyn and the five amino acids with the lowest GCsyn both vary with the regional GC-content, whereas the usage of the remaining 11 amino acids with intermediate GCsyn is less variable. More interesting, we discovered that codon usage frequencies are nearly constant in regions with similar GC-content. We further quantified the effects of regional GC-content variation (low to high) on amino acid usage and found that GC-content determines the usage variation of amino acids, especially those with extremely high GCsyn, which accounts for 76.7% of the changed GC-content for those regions. Our results suggest that GCsyn correlates with GC-content and has impact on codon/amino acid usage. These findings suggest a novel approach to understanding the role of codon and amino acid usage in shaping genomic architecture and evolutionary patterns of organisms.
A Biomechanical Model for Dictyostelium Motility

The crawling motion of Dictyostelium discoideum on substrata involves a number of coordinated events including cell contractions and cell protrusions. The mechanical forces exerted on the substratum during these contractions have recently been quantified using traction force experiments. Based on the results from these experiments, we present a biomechanical model of Dictyostelium discoideum motility with an emphasis on the adhesive properties of the cell-substratum contact. Our model assumes that the cell contracts at a constant rate and is bound to the substratum by adhesive bridges which are modeled as elastic springs. These bridges are established at a spatially uniform rate while detachment occurs at a spatially varying, load-dependent rate. Using Monte-Carlo simulations and assuming a rigid substratum, we find that the cell speed depends only weakly on the adhesive properties of the cell-substratum, in agreement with experimental data. Varying the parameters that control the adhesive and contractile properties of the cell we are able to make testable predictions. We also extend our model to include a flexible substrate and show that our model is able to produce substratum deformations and force patterns that are quantitatively and qualitatively in agreement with experimental data.
An Adaptive Robust Nonlinear Motion Controller Combined With Disturbance Observer

Parameter adaptation and disturbance observer (DOB) have been considered as two contrastively different approaches to handle uncertainties in motion control problems. The purpose of this brief is to merge both techniques into one control design with theoretically guaranteed performance. It is shown that the DOB compensates low-passed components of the lumped uncertainties without the necessity of parameterization, whereas the adaptive mechanism is only automatically activated in the cases where the fast-changing components of the uncertainties beyond the pass-band of the DOB can be parameterized by unknown parameters. It is thus shown theoretically how the DOB and adaptive mechanism play in a cooperative way so that the controller is more effective than the individual ones. Simulation results are provided to support the theoretical results.
A Distributed Theatre Experiment with Shakespeare

This paper reports on an experimental production of The Tempest that was developed in collaboration with Miracle Theatre Company realised as a distributed performance from two separate stages through a dynamically configured telepresence system. The production allowed an exploration of the way a range of technologies, including consumer grade broadband, cameras and projection technologies could affect the development and delivery of live theatre by regional touring company. The architecture of the communication platform used to deliver the performance is introduced as are two novel software tools that are used to describe and control the way the play should be captured and represented. The experimental production was thoroughly evaluated and the feedback from audience and theatre professionals is presented in some detail. A considered observation of the process and the way it differs from film, TV and theatre suggest that distributed theatre can be treated as a new genre of storytelling.
Botulinum Neurotoxin for Pain Management: Insights from Animal Models

The action of botulinum neurotoxins (BoNTs) at the neuromuscular junction has been extensively investigated and knowledge gained in this field laid the foundation for the use of BoNTs in human pathologies characterized by excessive muscle contractions. Although much more is known about the action of BoNTs on the peripheral system, growing evidence has demonstrated several effects also at the central level. Pain conditions, with special regard to neuropathic and intractable pain, are some of the pathological states that have been recently treated with BoNTs with beneficial effects. The knowledge of the action and potentiality of BoNTs utilization against pain, with emphasis for its possible use in modulation and alleviation of chronic pain, still represents an outstanding challenge for experimental research. This review highlights recent findings on the effects of BoNTs in animal pain models.
Motivational differences in problem video game play

Self-determination theory states that motivation plays an important role in initiating, developing and maintaining involvement within an activity. The present study applied this theory to video game playing and surveyed 399 video game players, 82 percent of which were male with a mean age of 20.3 years old, on measures of video game playing involvement, motivation to play video games and problem video game play. Participants were obtained from various video game retail outlets, Internet cafes, and LAN gaming businesses. The results showed that extrinsic motivations to play video games, such as tension release, social approval and external regulation by in-game rewards, and amotivation, or playing without a sense of purpose about the activity, were significant predictors of problem video game playing. The results were discussed in terms of their application to identifying and assisting young people with potentially problematic levels of video game playing.
Euro-Dollar Real Exchange Rate Dynamics in an Estimated Two-Country Model: What is Important and What is Not

Central puzzles in international macroeconomics are why fluctuations of the real exchange rate are so volatile with respect to other macroeconomic variables, and the contradiction of efficient risk-sharing. Several theoretical contributions have evaluated alternative forms of pricing under nominal rigidities along with different asset markets structures to explain real exchange dynamics. In this paper, we use a Bayesian approach to estimate a standard two-country New Open Economy Macroeconomics (NOEM) using data for the United States and the Euro Area, and perform model comparisons to study the importance of departing from the law of one price and complete markets assumptions. Our results can be summarized as follows. First, we find that the baseline model does a good job in explaining real exchange rate volatility, but at the cost of implying too high volatility in output and consumption. Second, the introduction of incomplete markets allows the model to better match the volatilities of all real variables. Third, introducing sticky prices in local currency pricing (LCP) improves the fit of the baseline model, but not by as much as by introducing incomplete markets. Finally, we show that monetary shocks have played a minor role in explaining the behavior of the real exchange rate, while both demand and technology shocks have been important
Evolutionary dynamics of highly pathogenic avian influenza A/H5N1 HA clades and vaccine implementation in Vietnam

Based on hemagglutinin (HA) and neuraminidase (NA), influenza A virus is divided into 18 different HA (H1 to H18) and 11 NA types (N1 to N11), opening the possibility for reassortment between the HA and NA genes to generate new HxNy subtypes (where x could be any HA and y is any NA, possibly). In recent four years, since 2010, highly pathogenic avian influenza (HPAI) viruses of H5N1 subtype (HPAI A/H5N1) have become highly enzootic and dynamically evolved to form multiple H5 HA clades, particularly in China, Vietnam, Indonesia, Egypt, Cambodia, and Bangladesh. So far, after more than 10 years emerged in Vietnam (since late 2003), HPAI A/H5N1 is still posing a potential risk of causing outbreaks in poultry, with high frequency of annual endemics. Intragenic variation (referred to as antigenic drift) in HA (e.g., H5) has given rise to form numerous clades, typically marking the major timelines of the evolutionary status and vaccine application in each period. The dominance of genetically and antigenically diversified clade 2.3. 2.1 (of subgroups a, b, c), clade 1.1 (1.1.1/1.1.2) and re-emergence of clade 7.1/7.2 at present, has urged Vietnam to the need for dynamically applied antigenicity-matching vaccines, i.e., the plan of importing Re-6 vaccine for use in 2014, in parallel use of Re-1/Re-5 since 2006. In this review, we summarize evolutionary features of HPAI A/H5N1 viruses and clade formation during recent 10 years (2004-2014). Dynamic of vaccine implementation in Vienam is also remarked.
Understanding the role of social situations on continuance participation intention in online communities: an empirical perspective

In recent years, the mushrooming development of Online Communities (OCs) has ushered a new paradigm of research for organizational sustainability in IS. In essence, the growth and survival of an online community relies predominantly on the continuous participation of its members. Given that the emergence of OCs may decay or even diminish due to the lack of consistent involvement of members, it is of paramount importance to fathom how to retain and entice members of OCs in terms of their continuous participation in the online platform. Extant studies have focused mostly on personal belief constructs and subjective norm constructs to study users' continuous behavior. However, the important role of social situations has not been sufficiently explored and investigated in IS, particularly in the emerging context of OCs. Drawing on the Triandis model, this study proposes a research model incorporating social situations as the moderator on the continuance participation intention in OCs. We collected data from two large OCs to examine whether congruence exists between situation perceptions and situation reactions. The empirical results show that social situations play an important role in determining the strength of the relationships between affect, social factors, and perceived consequences and the continuance intention in OCs.
Genomic RNA profiling and the programme controlling preimplantation mammalian development

Preimplantation development shifts from a maternal to embryonic programme rapidly after fertilization. Although the majority of oogenetic products are lost during the maternal to embryonic transition (MET), several do survive this interval to contribute directly to supporting preimplantation development. Embryonic genome activation (EGA) is characterized by the transient expression of several genes that are necessary for MET, and while EGA represents the first major wave of gene expression, a second mid-preimplantation wave of transcription that supports development to the blastocyst stage has been discovered. The application of genomic approaches has greatly assisted in the discovery of stage specific gene expression patterns and the challenge now is to largely define gene function and regulation during preimplantation development. The basic mechanisms controlling compaction, lineage specification and blastocyst formation are defined. The requirement for embryo culture has revealed plasticity in the developmental programme that may exceed the adaptive capacity of the embryo and has fostered important research directions aimed at alleviating culture-induced changes in embryonic programming. New levels of regulation are emerging and greater insight into the roles played by RNA-binding proteins and miRNAs is required. All of this research is relevant due to the necessity to produce healthy preimplantation embryos for embryo transfer, to ensure that assisted reproductive technologies are applied in the most efficient and safest way possible.
MicroRNA-32 promotes calcification in vascular smooth muscle cells: Implications as a novel marker for coronary artery calcification

Cardiovascular calcification is one of the most severe outcomes associated with cardiovascular disease and often results in significant morbidity and mortality. Previous reports indicated that epigenomic regulation of microRNAs (miRNAs) might play important roles in vascular smooth muscle cell (VSMC) calcification. Here, we identified potential key miRNAs involved in vascular calcification in vivo and investigated the role of miR-32-5p (miR-32). According to microarray analysis, we observed increased expression of miR-125b, miR-30a, and miR-32 and decreased expression of miR-29a, miR-210, and miR-320 during the progression of vascularcalcification. Additionally, gain- and loss-of-function studies of miR-32 confirmed promotion of VSMC calcification in mice through the enhanced expression of bonemorphogenetic protein-2, runt-related transcription factor-2(RUNX2), osteopontin, and the bone-specific phosphoprotein matrix GLA protein in vitro. Moreover, miR-32 modulated vascularcalcification progression by activating phosphoinositide 3-kinase (PI3K)signaling and increasing RUNX2 expression and phosphorylation by targeting the 3′-untranslated region of phosphatase and tensin homolog Mrna (PTEN) in mouse VSMCs. Furthermore, we detected higher miR-32 levels in plasmafrom patients with coronary artery disease with coronary artery calcification (CAC) as compared with levels observed in non-CAC patients (P = 0.016), further confirming miR-32 as a critical modulator and potential diagnostic marker for CAC.
A Mutual Self- and Informant-Report of Cognitive Complaint Correlates with Neuropathological Outcomes in Mild Cognitive Impairment

Background This study examines whether different sources of cognitive complaint (i.e., self and informant) predict Alzheimer’s disease (AD) neuropathology in elders with mild cognitive impairment (MCI). Methods Data were drawn from the National Alzheimer’s Coordinating Center Uniform and Neuropathology Datasets (observational studies) for participants with a clinical diagnosis of MCI and postmortem examination (n = 1843, 74±8 years, 52% female). Cognitive complaint (0.9±0.5 years prior to autopsy) was classified into four mutually exclusive groups: no complaint, self-only, informant-only, or mutual (both self and informant) complaint. Postmortem neuropathological outcomes included amyloid plaques and neurofibrillary tangles. Proportional odds regression related complaint to neuropathology, adjusting for age, sex, race, education, depressed mood, cognition, APOE4 status, and last clinical visit to death interval. Results Mutual complaint related to increased likelihood of meeting NIA/Reagan Institute (OR = 6.58, p = 0.004) and Consortium to Establish a Registry for Alzheimer’s Disease criteria (OR = 5.82, p = 0.03), and increased neurofibrillary tangles (OR = 3.70, p = 0.03), neuritic plaques (OR = 3.52, p = 0.03), and diffuse plaques (OR = 4.35, p = 0.02). Informant-only and self-only complaint was not associated with any neuropathological outcome (all p-values>0.12). Conclusions In MCI, mutual cognitive complaint relates to AD pathology whereas self-only or informant-only complaint shows no relation to pathology. Findings support cognitive complaint as a marker of unhealthy brain aging and highlight the importance of obtaining informant corroboration to increase confidence of underlying pathological processes.
A Hybrid User Model in Text Categorization

A user model that specifies user preferences on message handling is an essential component of an e-mail message categorizer. We present an approach that combines two learning algorithms, i.e. the Naïve Bayesian Classifier (NBC) and Progol, to model implicitly and explicitly reflected user preferences that may not be modeled by using either the algorithms alone. An experiment demonstrates the improvement of categorization performance compared to that of using the two algorithms independently
Psychological and demographic predictors of undergraduate non-attendance at university lectures and seminars

Abstract Absenteeism from university teaching sessions is increasingly becoming a common phenomenon and remains a major concern to universities. Poor attendance has significant and detrimental effects on students themselves, their peers and teaching staff. There is, however, a lack of previous research investigating demographic and psychological predictors of non-attendance alongside salient reasons students offer for their absence; it is this ‘gap’ that the present study attempts to fill. We approached 618 undergraduate university students from a single UK university studying various courses to complete a bespoke questionnaire assessing their estimated percentage attendance at lectures and seminars over the academic year. Students answered demographic questions, completed psychometric tests of perceived confidence (Perceived Confidence for Learning) and university belongingness (Psychological Sense of School Membership), and rated the degree to which possible reasons for non-attendance applied to themselves. Multiple regression analyses were carried out separately for estimated attendance at lectures and seminars. Results demonstrated that significant predictors of poorer attendance for both scenarios were experiencing a lower sense of belongingness to university; working more hours in paid employment; having more social life commitments; facing coursework deadlines; and experiencing mental health issues. Improving a sense of belonging to university and targeting interventions at students working in paid employment may be effective means of increasing attendance. Providing support for students with mental health issues, structuring courses around coursework deadlines and helping students to organise their attendance around social activities could also be advantageous.
Marx and Veblen on Human Nature, History, and Capitalism: Vive la Différence!

There has been a long-standing controversy over the relationship between Marx's and Veblen's social theories. At the turn of the century, within the covers of one journal one commentator claimed that major differences existed between Marx and Veblen, whereas another emphasized the Marxian character of Veblen's economic thought [Walling 1905; LaMont 1905]. A similar range of interpretations has persisted,' but the majority have concluded that "Veblen was not an 'American Marxist'. "2 However, this orthodoxy has come under increasing attack, first by Arthur K Davis, whose position on the Veblen-Marx affinity debate seems to have hardened over the years, notwithstanding his detailing of
Applying Social Psychology in the Classroom

Introduction The classroom is the core unit of our educational system, and it illustrates many common social-psychological concepts and phenomena. Whenever people come together for the purpose of learning, social-psychological principles may be applied to further educational goals. Applying these principles to the classroom may help increase students’ commitment to learning, make their attitudes towards school more positive, reduce their feeling of failure and related negative effects or emotions, and improve their level of aspiration as well as their grades. Clearly, education is – at least in part – applied social psychology. Indeed, in the past three decades, a new scientific area has emerged, the so-called ‘social psychology of education’, ‘educational social psychology’, or sometimes even ‘social educational psychology’. According to Feldman (1986), this area represents an amalgamation of social psychology and education, and has produced a broad range of theories, research, and data that speak to the interests of both educators and psychologists. Our purpose here is not to describe all the current themes of interest that characterize this interface, but rather to focus on a limited set of social-psychological concepts and phenomena in relation to major processes in the classroom. First, we focus on the role of comparisons that students are constantly making with each other. Today, there is ample evidence that social comparisons contribute to students’ academic achievements, and we examine here the meaning and consequences of such comparisons in the classroom. Second, we focus on students’ ‘theories’ of intelligence. Over time, students come to believe that their performance in a wide range of tasks is or is not narrowly constrained by innate attributes, and that they can or cannot change their level of intelligence. We describe how such beliefs may affect students’ academic achievement. Third, we focus on students’ academic self-concept. Over time, students develop positive or negative views about their abilities in such-and-such an academic domain (e.g., math), which become an integral part of their ‘academic self-concept’. Does this self-concept also make a difference, and how? Fourth, we focus on social stereotypes. Students belong to social groups and may sometimes suffer from the negative stereotypes associated with these groups. Are these negative stereotypes a real problem for students, and why? Finally, we focus on the ‘classroom climate’.
Variations of mean cold season temperature, precipitation and snow depths during the last 100 years in the former Soviet Union (FSU)

Abstract Variations of temperature, precipitation and snow depths during the last 50–100 years, up to 1984, are investigated for mean cold season values (November to April) for 110 locations in the Former Soviet Union (FSU). Following quality checking, statistical analyses are performed on the data. There is cold season warming after 1953 or after 1966 over almost all the FSU apart from eastern Siberia, but temperature variations significantly affect the mean snow depths only in some sensitive areas of the Caucasus, central Asia, and the western European territory. Mean snow depth time series reveal contrasting local trends. Higher precipitation and snow depths are measured in eastern European Russia from 50° to 65 °N and in some areas of western Siberia at the beginning of the twentieth century. Otherwise, precipitation variations have little influence on the mean cold season snow depths over much of the FSU after 1930. Some predominant periodicities are detected for mean cold season temperature, but not.