Miracle-dz/UniFAR-FTUs huggingface dataset:
Explorer Splicing-Dependent RNA Polymerase Pausing in Yeast

General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact openaccess@ed.ac. uk providing details, and we will remove access to the work immediately and investigate your claim. SUMMARY In eukaryotic cells, there is evidence for functional coupling between transcription and processing of pre-mRNAs. To better understand this coupling, we performed a high-resolution kinetic analysis of transcription and splicing in budding yeast. This revealed that shortly after induction of transcription, RNA poly-merase accumulates transiently around the 3 0 end of the intron on two reporter genes. This apparent tran-scriptional pause coincides with splicing factor recruitment and with the first detection of spliced mRNA and is repeated periodically thereafter. Pausing requires productive splicing, as it is lost upon mutation of the intron and restored by suppressing the splicing defect. The carboxy-terminal domain of the paused polymerase large subunit is hyperphosphorylated on serine 5, and phosphorylation of serine 2 is first detected here. Phosphorylated polymerase also accumulates around the 3 0 splice sites of constitutively expressed , endogenous yeast genes. We propose that transcriptional pausing is imposed by a checkpoint associated with cotranscriptional splicing.
Spin-Valve Behavior in Aligned Arrays of Carbon Nanotubes

iii Acknowledgments. v Vita . vii List of Tables . x List of Figures . xi Chapter 1: Introduction . 1 Chapter 2: Background on Carbon Nanotubes: Structure and Charge Transport . 4 2.1 Structure of Carbon Nanotubes . 4 2.2 Charge Transport in Carbon Nanotubes . 10 2.2.1 Classical Transport . 10 2.2.2 Ballistic Transport in SWNT . 11 2.2. 3 Diffusive Transport in SWNT . 13 2.2. 4 Transport in MWNT . 14 Chapter 3: Background on Spin Transport . 17 3.1 Spin Transport in Nonmagnetic Material . 19 3.2 LSMO . 21 ix Chapter 4: Experimental Techniques . 23 4.1 Sample preparation . 23 4.1. 1 Growth of Vertically Aligned Carbon Nanotube Arrays . 23 4.1. 2 Spin-Valves Prepared with Conventional Ferromagnets . 26 4.1. 3 Spin-Valves Prepared with LSMO . 30 4.1. 4 Spin-Valves Prepared from Aligned Arrays Grown in an Alumina Matrix . 32 4.2 Measurement Methods and Equipment . 34 Chapter 5: Study 1: Spin-Valves Incorporating Aligned Arrays of Carbon Nanotubes, Metallic Nanoparticles, and Conventional Ferromagnetic Films . 37 5.1 Spin Valves from Freestanding Aligned Arrays . 37 5.2 Spin Valves from Aligned Arrays Grown in an Alumina Matrix . 42 Chapter 6: Study 2: Spin-Valves Incorporating Aligned Arrays of Carbon Nanotubes, Metallic Nanoparticles, and the Manganite Half-Metal, LaSrMnO . 46 Chapter 7: Conclusions and Further Work . 54 7.1 Summary and Conclusions . 54 7.2 Further Research . 55 References . 56
Efficacy of Tamsulosin, Oxybutynin, and their combination in the control of double-j stent-related lower urinary tract symptoms

ABSTRACT Introduction and objective Indwelling double J ureteral stents are used routinely in the resolution of ureteral obstruction caused by different etiologies. Evaluation of urinary symptoms related to double-J stent, indicate that these affect 73-90% of patients. We conducted a prospective, randomized study, to evaluate the efficacy of tamsulosin, oxybutinin and combination therapy in improving the urinary symptoms. Methods Patients who underwent ureteral stent placement after ureterolithotripsy (total 51), were randomized into three groups: Group I: Tamsulosin 0.4 mg. once per day(17 patients), Group II: Oxybutinin 5 mg. once per day (17 patients), Group III: Tamsulosin+ oxybutynin once per day (17 patients). All the groups received the drugs for three weeks and completed a Spanish validated Ureteral Stent Symptom Questionnaire (USSQ) at day 7 and 21. Results Repeated measures ANOVA showed mean urinary symptom index score was 22.3 vs. 15.5 in group three (p<0.001) at day 7 and 21 respectively. The mean work performance index was 6.6 vs 8.1 (p=0.049) favoring tamsulosin group, the mean sexual score was 0.5 vs 1.5 (p=0.03). Among additional problems the mean was 7.2 vs 6.2 (p=0.03). No significant difference was noted among pain and general health index. No side effects were reported. Conclusions Combination therapy with tamsulosin and oxybutynin improved irritative symptoms and work performance as well as sexual matters. Combination therapy should be considered for patients who complained of stent related symptoms.
Code optimization and analysis for multiple-input and multiple-output communication systems

Code Optimization and Analysis for Multiple-input and Multiple-output Communication Systems. (August 2004) Guosen Yue, B.S., Nanjing University, P.R. China; M.S., Nanjing University, P.R. China Co–Chairs of Advisory Committee: Dr. Xiaodong Wang Dr. Krishna R. Narayanan Design and analysis of random-like codes for various multiple-input and multipleoutput communication systems are addressed in this work. Random-like codes have drawn significant interest because they offer capacity-achieving performance. We first consider the analysis and design of low-density parity-check (LDPC) codes for turbo multiuser detection in multipath CDMA channels. We develop techniques for computing the probability density function (pdf) of the extrinsic messages at the output of the soft-input soft-output (SISO) multiuser detectors as a function of the pdf of input extrinsic messages, user spreading codes, channel impulse responses, and signal-to-noise ratios. Using these techniques, we are able to accurately compute the thresholds for LDPC codes and design good irregular LDPC codes. We then apply the tools of density evolution with mixture Gaussian approximations to optimize irregular LDPC codes and to compute minimum operational signal-to-noise ratios for ergodic MIMO OFDM channels. In particular, the optimization is done for various MIMO OFDM system configurations which include different number of antennas, different channel models and different demodulation schemes. We also study the coding-spreading tradeoff in LDPC coded CDMA systems employing multiuser joint decoding. We solve the coding-spreading optimization based on the extrinsic information SNR evolution curves for the SISO multiuser detectors and the SISO LDPC decoders. Both single-cell and multi-cell scenarios will be considered. For
Learning in the Multi-agent Setting

The study of multi-agent systems investigates the interaction between agents in the setting where multiple agents exist and their behaviour affects each other’s. Because in most environments agents are not likely to know ahead of time what other agents will do, what the world will be after the agents’ joint behaviour, or sometimes even the existence of other agents, it is reasonable that they will try to learn from history so as to act in a way that is most beneficial to them. Multi-agent learning (MAL) has emerged as a field at the intersection of multiagent systems and machine learning. It concerns the application of learning techniques to the multi-agent setting. Over recent years, MAL has drawn significant attention from the research communities of game theory and artificial intelligence (AI). This paper presents a survey of recent work in the literature and integrates some comment and remarks from different papers in an organized structure. Beyond this, we also discuss and compare the different remarks, and offer our own thoughts about the work we survey and where the literature might head in the future.
Intra Marriage Bargaining Power and Fertility Decisions for Women in Developing Countries

Two types of theoretical bargaining models can be employed to study issues on intra marriage bargaining - a competitive and a cooperative bargaining model. While many seem to support the idea that couples make their decisions together in trying to maximize household level welfare, there is no general consensus on which type of model is more appropriate. One particular result that seems to suggest that couples do actually bargain competitively is the result that links fertility decisions to bargaining power. The argument is that women prefer less children than men, and that bargaining power influences fertility. However, we argue, these studies are suffering from endogeneity issues that are not properly instrumented for. We propose instruments for bargaining power based on individual risk and time preferences which affect the threat point and bargaining power of spouses, but not the fertility decisions directly. Using this identification strategy, we show that fertility decisions do not depend on bargaining power, which supports the unitary bargaining model. We argue that the previous results were either not addressing the endogeneity issues at all, or based on invalid instruments that were not fully exogenous.
Control versus Effort in Privacy Warnings for Webforms

Webforms are the primary way of collecting information online. However, some users may wish to limit the amount of personal information they provide and only fill out the minimum required for the transaction. With less than one third of websites marking fields as mandatory or optional, limiting disclosure can be a daunting task. This paper reports on a large behavioural online experiment on user reactions to warnings alerting them that they are about to submit non-mandatory information. Eight warning dialogues were tested between 4,620 participants. We found that warnings mentioning security or privacy threats both significantly reduced the disclosure of personal information in the webforms used (e.g., -27 percentage points for date of birth). The most actionable warning was not the one that minimised user effort but the one that left participants most in control. We consider our study useful to establish what kind of warning messages could help users manage their privacy. In order not to contribute to the ever increasing warning fatigue, a good real-world implementation of over-disclosure indicators would be for the browser to provide users with real-time information on mandatoriness/optionality when the webform loads, for example by highlighting optional fields.
2 M ar 2 00 5 Neutrinospheres , resonant neutrino oscillations , and pulsar kicks

Pulsars are rapidly rotating neutron stars and are the outcome of the collapse of the core of a massive star with a mass of the order of or larger than eight solar masses. This process releases a huge gravitational energy of about 10 erg, mainly in the form of neutrinos. During the collapse the density increases, and so does the magnetic field due to the trapping of the flux lines of the progenitor star by the high conductivity plasma. When the density reaches a value of around 10 g cm neutrinos become trapped within the protoneutron star and a neutrinosphere, characterized inside by a diffusive transport of neutrinos and outside by a free streaming of neutrinos, is formed and lasts for a few seconds. Here we focus on the structure of the neutrinosphere, the resonant flavor conversion that can happen in its interior, and the neutrino flux anisotropies induced by this phenomena in the presence of a strong magnetic field. We present a detailed discussion in the context of the spherical Eddington model, which provides a simple but reasonable description of a static neutrino atmosphere, locally homogenous and isotropic. Energy and momentum are transported by neutrinos and antineutrinos flowing through an ideal gas of nonrelativistic, nondegenerate nucleons and relativistic, degenerate electrons and positrons. We examine the details of the asymmetric neutrino emission driven by active-sterile neutrino oscillations in the magnetized protoneutron star, and the possibility for this mechanism to explain the intrinsic large velocities of pulsars respect to nearby stars and associated supernova remnants.
The Genome of the Obligately Intracellular Bacterium Ehrlichia canis Reveals Themes of Complex Membrane Structure and Immune Evasion Strategies

ABSTRACT Ehrlichia canis, a small obligately intracellular, tick-transmitted, gram-negative, α-proteobacterium, is the primary etiologic agent of globally distributed canine monocytic ehrlichiosis. Complete genome sequencing revealed that the E. canis genome consists of a single circular chromosome of 1,315,030 bp predicted to encode 925 proteins, 40 stable RNA species, 17 putative pseudogenes, and a substantial proportion of noncoding sequence (27%). Interesting genome features include a large set of proteins with transmembrane helices and/or signal sequences and a unique serine-threonine bias associated with the potential for O glycosylation that was prominent in proteins associated with pathogen-host interactions. Furthermore, two paralogous protein families associated with immune evasion were identified, one of which contains poly(G-C) tracts, suggesting that they may play a role in phase variation and facilitation of persistent infections. Genes associated with pathogen-host interactions were identified, including a small group encoding proteins (n = 12) with tandem repeats and another group encoding proteins with eukaryote-like ankyrin domains (n = 7).
The Arabidopsis CSN5A and CSN5B Subunits Are Present in Distinct COP9 Signalosome Complexes, and Mutations in Their JAMM Domains Exhibit Differential Dominant Negative Effects on Development

The COP9 signalosome (CSN) is an evolutionarily conserved multisubunit protein complex involved in a variety of signaling and developmental processes through the regulation of protein ubiquitination and degradation. A known biochemical role attributed to CSN is a metalloprotease activity responsible for the derubylation of cullins, core components for several types of ubiquitin E3 ligases. The CSN's derubylation catalytic center resides in its subunit 5, which in Arabidopsis thaliana is encoded by two homologous genes, CSN5A and CSN5B. Here, we show that CSN5A and CSN5B subunits are assembled into distinct CSN complexes in vivo, which are present in drastically different abundances, with CSNCSN5A appearing to be the dominant one. Transgenic CSN5A and CSN5B proteins carrying a collection of single mutations in or surrounding the metalloprotease catalytic center are properly assembled into CSN complexes, but only mutations in CSN5A result in a pleiotropic dominant negative phenotype. The extent of phenotypic effects caused by mutations in CSN5A is reflected at the molecular level by impairment in Cullin1 derubylation. These results reveal that three key metal binding residues as well as two other amino acids outside the catalytic center play important roles in CSN derubylation activity. Taken together, our data provide physiological evidence on a positive role of CSN in the regulation of Arabidopsis SCF (for Skp1-Cullin-F-box) E3 ligases through RUB (for Related to Ubiquitin) deconjugation and highlight the unequal role that CSNCSN5A and CSNCSN5B play in controlling the cellular derubylation of cullins. The initial characterization of CSN5A and CSN5B insertion mutants further supports these findings and provides genetic evidence on their unequal role in plant development.
RELATIONSHIPS BETWEEN SUCCESS ORIENTATION, SELF EFFICACY ON SCIENTIFIC RESEARCH AND METACOGNITIVE THINKING SKILLS

In this study, relations between metacognition, achievement orientation and scientific research self-efficacy were investigated. Research findings attested that metacognitive thinking skills play a mediator effect between success orientations and self-efficacy on scientific research. Further to that, success orientation rendered a positive impact on the perception of scientific research self-efficacy and success orientations positively affected meta-cognitive thinking. On the other hand, self-efficacy on scientific research had a negatively insignificant effect on meta-cognitive thinking skills. At the end of this research, it can be suggested to instructors that in tracking and learning processes in their class if they employ activities that stimulate metacognitive thinking skills after completing success-orientated activities, positive feedbacks could be obtained on students' perception of scientific research self-efficacy level. Aside from that since the paths between divergent and success orientations; problem solving, decision making, alternative evaluation and metacognitive thinking and conclusion and discussion, method and literature review and perception of scientific research self-efficacy show; it can be argued that these correlational results would be safely employed in academic processes. Article visualizations:
Lameness Detection in Dairy Cows: Part 1. How to Distinguish between Non-Lame and Lame Cows Based on Differences in Locomotion or Behavior

Simple Summary Scoring cattle for lameness based on changes in locomotion or behavior is essential for farmers to find and treat their lame animals. This review discusses the normal locomotion of cows in order to define abnormal locomotion due to lameness. It furthermore provides an overview of various relevant visual locomotion scoring systems that are currently being used as well as practical considerations when assessing lameness on a commercial farm. Abstract Due to its detrimental effect on cow welfare, health and production, lameness in dairy cows has received quite a lot of attention in the last few decades—not only in terms of prevention and treatment of lameness but also in terms of detection, as early treatment might decrease the number of severely lame cows in the herds as well as decrease the direct and indirect costs associated with lameness cases. Generally, lame cows are detected by the herdsman, hoof trimmer or veterinarian based on abnormal locomotion, abnormal behavior or the presence of hoof lesions during routine trimming. In the scientific literature, several guidelines are proposed to detect lame cows based on visual interpretation of the locomotion of individual cows (i.e., locomotion scoring systems). Researchers and the industry have focused on automating such observations to support the farmer in finding the lame cows in their herds, but until now, such automated systems have rarely been used in commercial herds. This review starts with the description of normal locomotion of cows in order to define ‘abnormal’ locomotion caused by lameness. Cow locomotion (gait and posture) and behavioral features that change when a cow becomes lame are described and linked to the existing visual scoring systems. In addition, the lack of information of normal cow gait and a clear description of ‘abnormal’ gait are discussed. Finally, the different set-ups used during locomotion scoring and their influence on the resulting locomotion scores are evaluated.
Magnetic patterns based global localization for a mobile robot using hall sensors

In this paper, we present a global localization and position error compensation method in a known indoor environment using magnet hall sensors. In previous our researches, it was possible to compensate the pose errors of xe, ye, θe correctly on the surface of indoor environment with magnets sets by regularly arrange the magnets sets of identical pattern. To improve the proposed method, new strategy that can realize the global localization by changing arrangement of magnet pole is presented in this paper. Total six patterns of the magnets set form the unique landmarks. Therefore, the virtual map can be built by using the six landmarks randomly. The robots search a pattern of magnets set by rotating, and obtain the current global pose information by comparing the measured neighboring patterns with the map information that is saved in advance. We provide experimental results to show the effectiveness of the proposed method for a differential drive wheeled mobile robot.
CORDIC architecture based 2-D DCT and IDCT for image compression

Generally, 2-D DCT/IDCT (Two dimensional discrete cosine transform and its inverse) are widely used in many image processing systems. In this paper, efficient architectures are proposed. These architectures have parallel and pipelined structures which are used to implement 8×8 DCT/IDCT processors. These processors involve two 8-point DCT/IDCT processors along with a dual-bank of SRAM (128 words) and a coefficient ROM (6 words), a control unit and two multiplexers. Here, CORDIC arithmetic is used to design the kernel arithmetic unit (AU). The proposed architectures for 2-D DCT/IDCT not only reduce the power consumption but also simplify the hardware with a very high performance.
Adopting a combination of Scrum and Waterfall methodologies in developing Tailor-made SaaS products for Thai Service and manufacturing SMEs

Software as a Service (SaaS) is a concept for delivering software applications, the service runs on cloud and provides benefits to small and medium enterprise (SMEs), offering the advantage of 7 day 24 hour access ability and is truly ubiquitous. This case study examines the implementation of combining Scrum and Waterfall approaches to develop a set of Tailor-made Software as a Service to assist SMEs in the east of Thailand and to manage their business processes. The Waterfall model emphasizes early stage planning and identifies design flaws before they develop. The Scrum process encourages business stakeholders and developers to work together to align the product with customer needs and company goals. The implementation of these models has significant benefits which include: increased user and customer satisfaction IT services; financial savings and less time consuming and better alignment, based on the business focus.
A Capsid-Encoded PPxY-Motif Facilitates Adenovirus Entry

Viruses use cellular machinery to enter and infect cells. In this study we address the cell entry mechanisms of nonenveloped adenoviruses (Ads). We show that protein VI, an internal capsid protein, is rapidly exposed after cell surface attachment and internalization and remains partially associated with the capsid during intracellular transport. We found that a PPxY motif within protein VI recruits Nedd4 E3 ubiquitin ligases to bind and ubiquitylate protein VI. We further show that this PPxY motif is involved in rapid, microtubule-dependent intracellular movement of protein VI. Ads with a mutated PPxY motif can efficiently escape endosomes but are defective in microtubule-dependent trafficking toward the nucleus. Likewise, depletion of Nedd4 ligases attenuates nuclear accumulation of incoming Ad particles and infection. Our data provide the first evidence that virus-encoded PPxY motifs are required during virus entry, which may be of significance for several other pathogens.