Visualising ribosome profiling and using it for reading frame detection and exploration of eukaryotic translation initiation

Ribosome profiling (ribo-seq) is a recently developed technique that provides genomewide information on protein synthesis (GWIPS) in vivo. The high resolution of ribo-seq is one of the exciting properties of this technique. In Chapter 2, I present a computational method that utilises the sub-codon precision and triplet periodicity of ribosome profiling data to detect transitions in the translated reading frame. Application of this method to ribosome profiling data generated for human HeLa cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame. Since the initial publication of the ribosome profiling technique in 2009, there has been a proliferation of studies that have used the technique to explore various questions with respect to translation. A review of the many uses and adaptations of the technique is provided in Chapter 1. Indeed, owing to the increasing popularity of the technique and the growing number of published ribosome profiling datasets, we have developed GWIPS-viz (http://gwips.ucc.ie), a ribo-seq dedicated genome browser. Details on the development of the browser and its usage are provided in Chapter 3. One of the surprising findings of ribosome profiling of initiating ribosomes carried out in 3 independent studies, was the widespread use of non-AUG codons as translation initiation start sites in mammals. Although initiation at non-AUG codons in mammals has been documented for some time, the extent of non-AUG initiation reported by these ribo-seq studies was unexpected. In Chapter 4, I present an approach for estimating the strength of initiating codons based on the leaky scanning model of translation initiation. Application of this approach to ribo-seq data illustrates that initiation at non-AUG codons is inefficient compared to initiation at AUG codons. In addition, our approach provides a probability of initiation score for each start site that allows its strength of initiation to be evaluated.

Elicitation techniques for the evaluation of speech under stress: Towards a framework for use in a controlled environment

Existing work in Computer Science and Electronic Engineering demonstrates that Digital Signal Processing techniques can effectively identify the presence of stress in the speech signal. These techniques use datasets containing real or actual stress samples i.e. real-life stress such as 911 calls and so on. Studies that use simulated or laboratory-induced stress have been less successful and inconsistent. Pervasive, ubiquitous computing is increasingly moving towards voice-activated and voice-controlled systems and devices. Speech recognition and speaker identification algorithms will have to improve and take emotional speech into account. Modelling the influence of stress on speech and voice is of interest to researchers from many different disciplines including security, telecommunications, psychology, speech science, forensics and Human Computer Interaction (HCI). The aim of this work is to assess the impact of moderate stress on the speech signal. In order to do this, a dataset of laboratory-induced stress is required. While attempting to build this dataset it became apparent that reliably inducing measurable stress in a controlled environment, when speech is a requirement, is a challenging task. This work focuses on the use of a variety of stressors to elicit a stress response during tasks that involve speech content. Biosignal analysis (commercial Brain Computer Interfaces, eye tracking and skin resistance) is used to verify and quantify the stress response, if any. This thesis explains the basis of the author’s hypotheses on the elicitation of affectively-toned speech and presents the results of several studies carried out throughout the PhD research period. These results show that the elicitation of stress, particularly the induction of affectively-toned speech, is not a simple matter and that many modulating factors influence the stress response process. A model is proposed to reflect the author’s hypothesis on the emotional response pathways relating to the elicitation of stress with a required speech content. Finally the author provides guidelines and recommendations for future research on speech under stress. Further research paths are identified and a roadmap for future research in this area is defined.

It Takes Two to Tango: Entrepreneurship and Creativity in Troubled Times – Vietnam 2012

Strikingly, most literature suggests that market competition will push firms to take creativity/innovation seriously as matter of death or survival. Using the data, we examined creativity methods (Napier and Nilsson, 2008; Napier, 2010) in conjunction with three influential cultural values – namely risk tolerance, relationship, and dependence on resources – to assess how they influence decisions of entrepreneurs.The primary objective of this study focuses on perceived values of entrepreneurship and creativity in business conducted within a turbulent environment. Our initial hypothesis is that a typical entrepreneurial process carries with it “creativity-enabling elements.” In a normal situation, when businesses focus more on optimizing their resources for commercial gains, perceptions about values of entrepreneurial creativity are usually vague. However, in difficult times and harsh competition, the difference between survival and failure may be creativity. This paper also examines many previous findings on both entrepreneurship and creativity and suggests a highly possible “organic growth” of creativity in an entrepreneurial environment and reinforcing value of entrepreneurship when creativity power is present. In other words, we see each idea reinforcing the other. We use data from a survey of sample Vietnamese firms during the chaotic economic year 2012 to learn about the ‘entrepreneurshipcreativity nexus.’ A data set of 137 responses qualified for a statistical examination was obtained from an online survey, which started on February 16 and ended May 24, 2012, sent to local entrepreneurs and corporate managers using social networks. The authors employed categorical data analysis (Agresti, 2002; Azen & Walker, 2011). Statistical analyses confirm that for business operation, the creativity and entrepreneurial spirit could hardly be separate; and, this is not only correct with entrepreneurial firm, but also well established companies. The single most important factor before business startup and during early implementation in Vietnam is what we call “connection/relationship.” However, businesspeople are increasingly aware of the need of creativity/innovation. In fact, we suggest that creativity and entrepreneurial spirit cannot be separated in entrepreneurial firms as well as established companies.

TCR V alpha- and V beta-gene segment use in T-cell subcultures derived from a type-III bare lymphocyte syndrome patient deficient in MHC class-II expression.

Previously, we and others have shown that MHC class-II deficient humans have greatly reduced numbers of CD4+CD8- peripheral T cells. These type-III Bare Lymphocyte Syndrome patients lack MHC class-II and have an impaired MHC class-I antigen expression. In this study, we analyzed the impact of the MHC class-II deficient environment on the TCR V-gene segment usage in this reduced CD4+CD8- T-cell subset. For these studies, we employed TcR V-region-specific monoclonal antibodies (mAbs) and a semiquantitative PCR technique with V alpha and V beta amplimers, specific for each of the most known V alpha- and V beta-gene region families. The results of our studies demonstrate that some of the V alpha-gene segments are used less frequent in the CD4+CD8- T-cell subset of the patient, whereas the majority of the TCR V alpha- and V beta-gene segments investigated were used with similar frequencies in both subsets in the type-III Bare Lymphocyte Syndrome patient compared to healthy control family members. Interestingly, the frequency of TcR V alpha 12 transcripts was greatly diminished in the patient, both in the CD4+CD8- as well as in the CD4-CD8+ compartment, whereas this gene segment could easily be detected in the healthy family controls. On the basis of the results obtained in this study, it is concluded that within the reduced CD4+CD8- T-cell subset of this patient, most of the TCR V-gene segments tested for are employed. However, a skewing in the usage frequency of some of the V alpha-gene segments toward the CD4-CD8+ T-cell subset was noticeable in the MHC class-II deficient patient that differed from those observed in the healthy family controls.

Analysis of educational materials and destruction/opt-out initiatives for storage and use of residual newborn screening samples.

In recent years, the storage and use of residual newborn screening (NBS) samples has gained attention. To inform ongoing policy discussions, this article provides an update of previous work on new policies, educational materials, and parental options regarding the storage and use of residual NBS samples. A review of state NBS Web sites was conducted for information related to the storage and use of residual NBS samples in January 2010. In addition, a review of current statutes and bills introduced between 2005 and 2009 regarding storage and/or use of residual NBS samples was conducted. Fourteen states currently provide information about the storage and/or use of residual NBS samples. Nine states provide parents the option to request destruction of the residual NBS sample after the required storage period or the option to exclude the sample for research uses. In the coming years, it is anticipated that more states will consider policies to address parental concerns about the storage and use of residual NBS samples. Development of new policies regarding storage and use of residual NBS samples will require careful consideration of impact on NBS programs, parent and provider educational materials, and respect for parents among other issues.

Effect of primary care physicians' use of estimated glomerular filtration rate on the timing of their subspecialty referral decisions.

BACKGROUND: Primary care providers' suboptimal recognition of the severity of chronic kidney disease (CKD) may contribute to untimely referrals of patients with CKD to subspecialty care. It is unknown whether U.S. primary care physicians' use of estimated glomerular filtration rate (eGFR) rather than serum creatinine to estimate CKD severity could improve the timeliness of their subspecialty referral decisions. METHODS: We conducted a cross-sectional study of 154 United States primary care physicians to assess the effect of use of eGFR (versus creatinine) on the timing of their subspecialty referrals. Primary care physicians completed a questionnaire featuring questions regarding a hypothetical White or African American patient with progressing CKD. We asked primary care physicians to identify the serum creatinine and eGFR levels at which they would recommend patients like the hypothetical patient be referred for subspecialty evaluation. We assessed significant improvement in the timing [from eGFR < 30 to ≥ 30 mL/min/1.73m(2)) of their recommended referrals based on their use of creatinine versus eGFR. RESULTS: Primary care physicians recommended subspecialty referrals later (CKD more advanced) when using creatinine versus eGFR to assess kidney function [median eGFR 32 versus 55 mL/min/1.73m(2), p < 0.001]. Forty percent of primary care physicians significantly improved the timing of their referrals when basing their recommendations on eGFR. Improved timing occurred more frequently among primary care physicians practicing in academic (versus non-academic) practices or presented with White (versus African American) hypothetical patients [adjusted percentage(95% CI): 70% (45-87) versus 37% (reference) and 57% (39-73) versus 25% (reference), respectively, both p ≤ 0.01). CONCLUSIONS: Primary care physicians recommended subspecialty referrals earlier when using eGFR (versus creatinine) to assess kidney function. Enhanced use of eGFR by primary care physicians' could lead to more timely subspecialty care and improved clinical outcomes for patients with CKD.

"It is Quietly Chaotic. It Confuses Time"*: Final Report of Excavations at the Bordley-Randall Site in Annapolis, Maryland, 1993-1995 (18AP50)

*This extract is from Gay P. Crowther's description of the Randall Court pathway (Cowther 1985).

Explanatory Model for the Use of Traditional Medicines in Kilimanjaro, Tanzania

Introduction: Traditional medicines are one of the most important means of achieving total health care coverage globally, and their importance in Tanzania extends beyond the impoverished rural areas. Their use remains high even in urban settings among the educated middle and upper classes. They are a critical component healthcare in Tanzania, but they also can have harmful side effects. Therefore we sought to understand the decision-making and reasoning processes by building an explanatory model for the use of traditional medicines in Tanzania.

Methods: We conducted a mixed-methods study between December 2013 and June 2014 in the Kilimanjaro Region of Tanzania. Using purposive sampling methods, we conducted focus group discussions (FGDs) and in-depth interviews of key informants, and the qualitative data were analyzed using an inductive Framework Method. A structured survey was created, piloted, and then administered it to a random sample of adults. We reported upon the reliability and validity of the structured survey, and we used triangulation from multiple sources to synthesize the qualitative and quantitative data.

Results: A total of five FGDs composed of 59 participants and 27 in-depth interviews were conducted in total. 16 of the in-depth interviews were with self-described traditional practitioners or herbal vendors. We identified five major thematic categories that relate to the decision to use traditional medicines in Kilimanjaro: healthcare delivery, disease understanding, credibility of the traditional practices, health status, and strong cultural beliefs.

A total of 473 participants (24.1% male) completed the structured survey. The most common reasons for taking traditional medicines were that they are more affordable (14%, 12.0-16.0), failure of hospital medicines (13%, 11.1-15.0), they work better (12%, 10.7-14.4), they are easier

to obtain (11%, 9.48-13.1), they are found naturally or free (8%, 6.56-9.68), hospital medicines have too many chemical (8%, 6.33-9.40), and they have fewer side effects (8%, 6.25-9.30). The most common uses of traditional medicines were for symptomatic conditions (42%), chronic diseases (14%), reproductive problems (11%), and malaria and febrile illnesses (10%). Participants currently taking hospital medicines for chronic conditions were nearly twice as likely to report traditional medicines usage in the past year (RR 1.97, p=0.05).

Conclusions: We built broad explanatory model for the use of traditional medicines in Kilimanjaro. The use of traditional medicines is not limited to rural or low socioeconomic populations and concurrent use of traditional medicines and biomedicine is high with frequent ethnomedical doctor shopping. Our model provides a working framework for understanding the complex interactions between biomedicine and traditional medicine. Future disease management and treatment programs will benefit from this understanding, and it can lead to synergistic policies with more effective implementation.

ANALYSIS AND SIMULATION OF ENERGY USE AND COST AT A MUNICIPAL WASTEWATER TREATMENT PLANT

The cost of electricity, a major operating cost of municipal wastewater treatment plants, is related to influent flow rate, power price, and power load. With knowledge of inflow and price patterns, plant operators can manage processes to reduce electricity costs. Records of influent flow, power price, and load are evaluated for Blue Plains Advanced Wastewater Treatment Plant. Diurnal and seasonal trends are analyzed. Power usage is broken down among treatment processes. A simulation model of influent pumping, a large power user, is developed. It predicts pump discharge and power usage based on wet-well level. Individual pump characteristics are tested in the plant. The model accurately simulates plant inflow and power use for two pumping stations [R2 = 0.68, 0.93 (inflow), R2 =0.94, 0.91(power)]. Wet-well stage-storage relationship is estimated from data. Time-varying wet-well level is added to the model. A synthetic example demonstrates application in managing pumps to reduce electricity cost.

USE OF VARIATION AND FUGUE IN PIANO MUSIC FOLLOWING THE CLASSICAL PERIOD

The variation and fugue originated from the 15th and 16th centuries and blossomed during the Baroque and Classical Periods. In a variation, a theme with a particular structure precedes a series of pieces that usually have the same or very similar structure. A fugue is a work written in imitative counterpoint in which the theme is stated successively in all voices of polyphonic texture. Beethoven’s use of variation and fugue in large scale works greatly influenced his contemporaries. After the Classical Period, variations continued to be popular, and numerous composers employed the technique in various musical genres. Fugues had pedagogical associations, and by the middle of 19th century became a requirement in conservatory instruction, modeled after Bach’s Well-Tempered Clavier. In the 20th century, the fugue was revived in the spirit of neoclassicism; it was incorporated in sonatas, and sets of preludes and fugues were composed. Schubert's Wanderer Fantasy presents his song Der Wanderer through thematic transformations, including a fugue and a set of variations. Liszt was highly influenced by this, as shown in his thematic transformations and the fugue as one of the transformations in his Sonata in b. In Schumann’s Symphonic Études, Rachmaninoff's Rhapsody on a Theme of Paganini and Copland’s Piano Variations, the variation serves as the basis for the entire work. Prokofiev and Schubert take a different approach in Piano Concerto No. 3 and Wanderer Fantasy, employing the variation in a single movement. Unlike Schubert and Liszt's use of the fugue as a part of the piece or movement, Franck’s Prelude Chorale et Fugue and Shchedrin’s Polyphonic Notebook use it in its independent form. Since the Classical Period, the variation and fugue have evolved from stylistic and technical influences of earlier composers. It is interesting and remarkable to observe the unique effects each had on a particular work. As true and dependable classic forms, they remain popular by offering the composer an organizational framework for musical imagination.

The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling.

Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer.

We want to touch IT. Are hybrid laptops just new fancy gadgets or a new revolution?

While the number of traditional laptops and computers sold has dipped slightly year over year, manufacturers have developed new hybrid laptops with touch screens to build on the tactile trend. This market is moving quickly to make touch the rule rather than the exception and the sales of these devices have tripled since the launch of Windows 8 in 2012, to reach more than sixty million units sold in 2015. Unlike tablets, that benefit from easy-to-use applications specially designed for tactile interactions, hybrid laptops are intended to be used with regular user-interfaces. Hence, one could ask whether tactile interactions are suited for every task and activity performed with such interfaces. Since hybrid laptops are increasingly used in educational situations, this study focuses on information search tasks which are commonly performed for learning purposes. It is hypothesized that tasks that require complex and/or less common gestures will increase user's cognitive load and impair task performance in terms of efficacy and efficiency. A study was carried out in a usability laboratory with 30 participants for whom prior experience with tactile devices has been controlled. They were asked to perform information search tasks on an online encyclopaedia by using only the touch screen of and hybrid laptop. Tasks were selected with respect to their level of cognitive demand (amount of information that had to be maintained in working memory) and the complexity of gestures needed (left and/or right clicks, zoom, text selection and/or input.), and grouped into 4 sets accordingly. Task performance was measured by the number of tasks succeeded (efficacy) and time spent on each task (efficiency). Perceived cognitive load was assessed thanks to a questionnaire given after each set of tasks. An eye tracking device was used to monitor users' attention allocation and to provide objective cognitive load measures based on pupil dilation and the Index of Cognitive Activity. Each experimental run took approximately one hour. The results of this within-subjects design indicate that tasks involving complex gestures led to a lower efficacy, especially when the tasks were cognitively demanding. Regarding efficacy, there is no significant differences between sets of tasks excepted for tasks with low cognitive demand and complex gestures that required more time to be achieved. Surprisingly, users that declared the biggest experience with tactile devices spent more time than less frequent users. Cognitive load measures indicate that participants reported having devoted more mental effort in the interaction when they had to use complex gestures.

Chemically tagging the Hyades stream: does it partly originate from the Hyades cluster?

The Hyades stream has long been thought to be a dispersed vestige of the Hyades cluster. However, recent analyses of the parallax distribution, of the mass function, and of the action-space distribution of stream stars have shown it to be rather composed of orbits trapped at a resonance of a density disturbance. This resonant scenario should leave a clearly different signature in the element abundances of stream stars than the dispersed cluster scenario, since the Hyades cluster is chemically homogeneous. Here, we study the metallicity as well as the element abundances of Li, Na, Mg, Fe, Zr, Ba, La, Ce, Nd and Eu for a random sample of stars belonging to the Hyades stream, and compare them with those of stars from the Hyades cluster. From this analysis: (i) we independently confirm that the Hyades stream cannot be solely composed of stars originating in the Hyades cluster; (ii) we show thatsomestars (namely 2/21) from the Hyades stream nevertheless have abundances compatible with an origin in the cluster; (iii) we emphasize that the use of Li as a chemical tag of the cluster origin of main-sequence stars is very efficient in the range 5500K ≤Teff≤ 6200K, since the Li sequence in the Hyades cluster is very tight, while at the same time spanning a large abundance range; (iv) we show that, while this evaporated population has a metallicity excess of ~0.2 dex with respect to the local thin-disc population, identical to that of the Hyades cluster, the remainder of the Hyades stream population has still a metallicity excess of ~0.06-0.15 dex, consistent with an origin in the inner Galaxy and (v) we show that the Hyades stream can be interpreted as an inner 4:1 resonance of the spiral pattern: this then also reproduces an orbital family compatible with the Sirius stream, and places the origin of the Hyades stream up to 1kpc inwards from the solar radius, which might explain the observed metallicity excess of the stream population. © 2011 The Authors Monthly Notices of the Royal Astronomical Society © 2011 RAS.

Computational model for prediction of particle degradation during dilute phase pneumatic conveying: the use of a laboratory scale degradation tester for the determination of degradation propensity

The overall objective of this work is to develop a computational model of particle degradation during dilute-phasepneumatic conveying. A key feature of such a model is the prediction of particle breakage due to particle–wall collisions in pipeline bends. This paper presents a method for calculating particle impact degradation propensity under a range of particle velocities and particle sizes. It is based on interpolation on impact data obtained in a new laboratory-scale degradation tester. The method is tested and validated against experimental results for degradation at 90± impact angle of a full-size distribution sample of granulated sugar. In a subsequent work, the calculation of degradation propensity is coupled with a ow model of the solids and gas phases in the pipeline.

An information system to exploit the use of metadata within film and television production

The article focuses on an information system to exploit the use of metadata within film and television production. It is noted that the television and film industries are used to working on big projects. This involves the use of actual film, video tape, and P.E.R.T charts for project planning. Scripts are in most instances revised. It is essential to attach information on these in order to manage, track and retrieve them. The use of metadata eases the operations involved in these industries.