Miracle-dz/UniFAR-FTUs huggingface dataset:
Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators

Significance Perturbation of transcription register by RNA polymerase, transcription slippage, is used to yield additional protein products. Known functionally important cases involve a small number of short sequences without secondary structure. The discovery reported here of the dependence of a newly identified motif on nascent RNA forming a stem loop structure within the RNA exit channel of the polymerase greatly extends the potential for a broad variety of putative slippage sequences, especially as the phenomenon has been observed with both bacterial and eukaryotic RNA polymerases. Characterization of the mechanism involved shows similarities with, and differences from, intrinsic transcription termination, which also depends on formation of RNA stem loop structures. Our findings reveal novel insights to RNA polymerase versatility and functioning. Escherichia coli and yeast DNA-dependent RNA polymerases are shown to mediate efficient nascent transcript stem loop formation-dependent RNA-DNA hybrid realignment. The realignment was discovered on the heteropolymeric sequence T5C5 and yields transcripts lacking a C residue within a corresponding U5C4. The sequence studied is derived from a Roseiflexus insertion sequence (IS) element where the resulting transcriptional slippage is required for transposase synthesis. The stability of the RNA structure, the proximity of the stem loop to the slippage site, the length and composition of the slippage site motif, and the identity of its 3′ adjacent nucleotides (nt) are crucial for transcripts lacking a single C. In many respects, the RNA structure requirements for this slippage resemble those for hairpin-dependent transcription termination. In a purified in vitro system, the slippage efficiency ranges from 5% to 75% depending on the concentration ratios of the nucleotides specified by the slippage sequence and the 3′ nt context. The only previous proposal of stem loop mediated slippage, which was in Ebola virus expression, was based on incorrect data interpretation. We propose a mechanical slippage model involving the RNAP translocation state as the main motor in slippage directionality and efficiency. It is distinct from previously described models, including the one proposed for paramyxovirus, where following random movement efficiency is mainly dependent on the stability of the new realigned hybrid. In broadening the scope for utilization of transcription slippage for gene expression, the stimulatory structure provides parallels with programmed ribosomal frameshifting at the translation level.
Trust, honesty and corruption: reflection on the state-building process

Honesty and trust affect the functioning of the state and the market, and, conversely, the quality of formal rules and institutions has an impact on interpersonal trust. This paper organizes and critiques research on the relationship between trust and government; it stresses the mutual interaction between trust and democracy and the impact of corruption. Given this context, the concluding section discusses the transition process in post-socialist countries, highlighting the tensions between interpersonal trust and trust in public institutions. L'honnêteté et la confiance ont des incidences sur le fonctionnement de l'État et du marché. Inversement, la nature des règles juridiques et des institutions influent sur la confiance interpersonnelle. L'article propose une critique organisée des recherches sur la relation entre confiance et gouvernement; il souligne l'interaction mutuelle entre confiance et démocratie ainsi que l'impact de la corruption. La conclusion porte particulièrement sur le processus de transition dans les pays ex-communistes qui engendre des tensions fortes entre confiance interpersonnelle et confiance dans les institutions publiques. Aufrichtigkeit und Vertrauen beeinflussen die Staatsgeschäfte und die Wirtschaft. Umgekehrt bestimmt die Qualität des Rechtsstaats das persönliche Vertrauen. Es folgt eine Diskussion der Forschungsarbeiten über das Verhältnis von Vertrauen und Regierung; sie unterstreicht die Beziehung von Vertrauen und Demokratie sowie die Bedeutung der Korruption. Die Studie schließt mit der Wende in den ehemaligen kommunistischen Staaten, die zu starken Spannungen zwischen persönlichem Vertrauen und Vertrauen in die öffentlichen Behörden führt.
Use of Management Accounting Practices in Carbon Emission Management: Evidence from Australian Companies

This study examines the use of management accounting practices by companies in managing carbon emission issues. The sample consists of 69 Australian companies that participated in the Carbon Disclosure Project (CDP) 2009 survey. Both qualitative and quantitative analyses of survey responses are conducted. In this investigation, relative absence of the use of accounting practices was uncovered. Given that the companies examined were large companies and the majority of them operated in carbon intensive or climate change exposed sectors, it is likely that this under-utilisation of accounting practices translates into a corresponding under-performance in carbon emission management. Acknowledgement: This paper is drawn from Kumarasiri's (2015) unpublished PhD thesis.
Sperm DNA Methylation Analysis in Swine Reveals Conserved and Species-Specific Methylation Patterns and Highlights an Altered Methylation at the GNAS Locus in Infertile Boars1

ABSTRACT Male infertility is an increasing health issue in today's society for both human and livestock populations. In livestock, male infertility slows the improvement of animal selection programs and agricultural productivity. There is increasing evidence that epigenetic marks play an important role in the production of good-quality sperm. We therefore screened for specific or common epigenetic signatures of livestock infertility. To do so, we compared DNA methylation level in sperm DNA from fertile and infertile boars. We evaluated first the global level of sperm DNA methylation and found no difference between the two groups of boars. We then selected 42 loci of interest, most of them known to be imprinted in human or mice, and assessed the imprinting status of five of them not previously described in swine tissues: WT1, CNTN3, IMPACT, QPCT, and GRB10. DNA methylation level was then quantified in fertile and infertile boars at these 42 loci. Results from fertile boars indicated that the methylation level of the selected loci is highly conserved between pig, human, and mice, with a few exceptions, including the POU5F1 (OCT4) promoter and RTL1. Comparison between fertile and infertile boars revealed that one imprinted region, the GNAS locus, shows an increase in sperm DNA methylation in three out of eight infertile boars with low semen quality. This increase in DNA methylation is associated with an altered expression of the genes belonging to the GNAS locus, suggesting a new role for GNAS in the proper formation of functional gametes.
Evolution of Communicative Flexibility - Complexity, Creativity, and Adaptability in Human and Animal Communication.

The evolutionary roots of human communication are difficult to trace, but recent comparative research suggests that the first key step in that evolutionary history may have been the establishment of basic communicative flexibility--the ability to vocalize freely combined with the capability to coordinate vocalization with communicative intent. The contributors to this volume investigate how some species (particularly ancient hominids) broke free of the constraints of "fixed signals," actions that were evolved to communicate but lack the flexibility of language--a newborn infant's cry, for example, always signals distress and has a stereotypical form not modifiable by the crying baby. Fundamentally, the contributors ask what communicative flexibility is and what evolutionary conditions can produce it. The accounts offered in these chapters are notable for taking the question of language origins farther back in evolutionary time than in much previous work. Many contributors address the very earliest communicative break of the hominid line from the primate background; others examine the evolutionary origins of flexibility in, for example, birds and marine mammals. The volume's interdisciplinary theoretical perspectives illuminate issues that are on the cutting edge of recent research on this topic.Stephanie Barbu, Curt Burgess, Josep Call, Laurance Doyle, Julia Fischer, Michael Goldstein, Ulrike Griebel, Kurt Hammerschmidt, Sean Hanser, Martine Hausberger, Laurence Henry, Allison Kaufman, Stan Kuczaj, Robert F. Lachlan, Brian MacWhinney, Radhika Makecha, Brenda McCowan, D. Kimbrough Oller, Michael Owren, Ron Schusterman, Charles T. Snowdon, Kim Sterelny, Benoit Teste, Gert Westermann
The glycolytic enzymes of guinea-pig lung in experimental bagassosis.

Note added in proof. Since submitting this paper, we have observed that both caeruloplasmin and a globulin-haem complex (see Nyman, 1960) react with the dianisidine reagent used to detect the haptoglobin-haemoglobin complex after paper electrophoresis. Although caeruloplasmin migrates clearly ahead ofthe haptoglobin-haemoglobin complex on paper electrophoresis at pH 6-5, the globulinhaem complex and the haptoglobin-haemoglobin complex do not separate under these conditions. Accordingly the finding of a dianisidine reactive area in the ac2-globulin zone (pH 6.5) does not necessarily indicate the presence of the haptoglobin-haemoglobin complex. Since some ofthe 800 normal Caucasian sera examined by paper electrophoresis were found to contain methaemalbumin, it is possible that they also contained the globulinhaem complex. Consequently our findings do not necessarily exclude a haptoglobinaemia in these sera.
Line segment-based fast 3D plane extraction using nodding 2D laser rangefinder

SUMMARY Three-dimensional (3D) data processing has applications in solving complex tasks such as object recognition, environment modeling, and robotic mapping and localization. Because using raw 3D data without preprocessing is very time-consuming, extraction of geometric features that describe the environment concisely is essential. In this sense, a plane can be a suitable geometric feature due to its simplicity of extraction and the abundance in indoor environments. This paper presents an online incremental plane extraction method using line segments for indoor environments. Our data collection system is based on a “nodding” laser scanner, so we exploit the incremental nature of its data acquisition in which physical rotation and 3D data processing are conducted in parallel. Line segments defined by two end points become supporting elements that comprise a plane, so a large proportion of scan points can be ignored once the line segments are extracted from each scan slice. This elimination of points reduces the algorithm complexity and computation time. Experiments with the tens of complete scan data sets which were acquired from a typical indoor environment demonstrated that our method was at least three times faster than the state-of-the-art methods.
SRDL: A Simple Role-Based Delegation Logic

With the appearance and growing application of open systems such as Internet, delegation is a primary mechanism to enforce access control in such systems. This paper distinguishes two kinds of delegation: authority delegation (AUD) and access delegation (ACD), and proposes a first-order logic system SRDL to capture the features of the two kinds of delegation models. SRDL properly describes AUD and ACD respectively by using domain-roles and delegating-roles. SRDL provides a flexible approach to control the depth and width of delegation, which is absent in many delegation models such as SRC logic and RT.
On the Spectrum-Efficient Overlay Multicast in Elastic Optical Networks Built with Multicast-Incapable Switches

We study overlay multicast (OL-M) in multicast-incapable elastic optical networks (EONs), and propose a spectrum-efficient OL-M scheme that relies on the spectrum-flexible member-only relay, i.e., OL-M-SFMOR. Our simulation results indicate that OL-M-SFMOR achieves significant improvements on the spectrum-efficiency of multicast in EONs, when compared with other multicast schemes, even including the all-optical multicast schemes in multicast-capable EONs.
Activation of the Bur1-Bur2 Cyclin-Dependent Kinase Complex by Cak1

ABSTRACT Cyclin-dependent kinases (Cdks) were originally identified as regulators of eukaryotic cell cycle progression, but several Cdks were subsequently shown to perform important roles as transcriptional regulators. While the mechanisms regulating the Cdks involved in cell cycle progression are well documented, much less is known regarding how the Cdks that are involved in transcription are regulated. In Saccharomyces cerevisiae, Bur1 and Bur2 comprise a Cdk complex that is involved in transcriptional regulation, presumably mediated by its phosphorylation of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II. To investigate the regulation of Bur1 in vivo, we searched for high-copy-number suppressors of a bur1 temperature-sensitive mutation, identifying a single gene, CAK1. Cak1 is known to activate two other Cdks in yeast by phosphorylating a threonine within their conserved T-loop domains. Bur1 also has the conserved threonine within its T loop and is therefore a potential direct target of Cak1. Additional tests establish a direct functional interaction between Cak1 and the Bur1-Bur2 Cdk complex: Bur1 is phosphorylated in vivo, both the conserved Bur1 T-loop threonine and Cak1 are required for phosphorylation and Bur1 function in vivo, and recombinant Cak1 stimulates CTD kinase activity of the purified Bur1-Bur2 complex in vitro. Thus, both genetic and biochemical evidence demonstrate that Cak1 is a physiological regulator of the Bur1 kinase.
Single-cell protein as an alternative food for zebrafish, Danio rerio: a toxicological assessment

Single-cell protein (SCP) refers to the dried cells of microorganisms. The aim of this research was to evaluate the nutrional characteristics and possible toxic effects of the SCP of Trichoderma harzianum. First, T. harzianum was grown on whey filtrate agar medium and the obtained SCP was analysed. It was rich in both total protein (34.21%) and ash (4.78%). Furthermore, the biomass contained all the essential amino acids, and the amino acid concentrations were very close to the FAO reference protein levels. Second, we exposed zebrafish (Danio rerio) embryos to diluted SCP at various concentrations for 96 hours postfertilization (hpf). Compared with the control group, we did not observe any developmental abnormalities, delayed hatching, and lethal effects on zebrafish embryos (96 hpf) found in the SCP group. To test diet effects on spawning success and growth of embryos, adult zebrafish were fed on SCP and flake feed diets for 10 weeks. The number of laid eggs, wet weight and diameter of eggs, and the percentages of hatched eggs from fish fed the flake diet and SCP diet were not significantly different from each other. Also, larval length and weight were not significantly affected by diets. Finally, SCP did not cause any toxic effect on zebrafish adults and their offsprings and could be useful as fish food or food additive.
Family of complex Hadamard transforms: relationship with other transforms and complex composite spectra

Relationship of the recently introduced family of unified complex Hadamard transforms with other transforms used in binary and multiple-valued logic design are investigated in this paper. All the complex Hadamard matrices can be generated by a common unifying formula presented here. Only half of all possible 64 unified complex Hadamard transforms have half-spectrum property. The existence of such a property for 32 transformation matrices is proven for the first time in this paper. Half-spectrum property is important as h reduces the required computer storage by half when compared to other transforms operating on complex numbers. The method is also presented to evaluate complex Hadamard spectra of AND, OR, and XOR of Boolean functions directly from the spectra of the separate Boolean functions. The results are given using a general coding scheme, and different possible codings of Boolean functions are discussed. Moreover, new definition of the convolution operation called complex convolution is derived. Different properties of such a convolution are presented. Theorem giving final formulae for composite complex Hadamard spectra of Boolean functions is stated in terms of complex convolution. By using presented methods, many of the Boolean operations in original domain can be represented much simpler in terms of their composite complex spectra.
Community-based Management: Developing the Fan Base of Professional Baseball Teams

The purpose of this study is to examine the concept of community-based management (CBM) and to elucidate the in‰uential factors formulating the strategies for developing the fan base of professional baseball teams. Semi-structured interviews were conducted among staŠ members of four Paciˆc League teams on having regional team names and adopting ``community-based management'' or ``regional outreach activities'' in their team philosophy. In‰uenced by the reorganization of the Nippon Professional Baseball organization, the Paciˆc League teams have focused on a speciˆc community or region, rather than the entire nation, for better management. Teams are concentrating on garnering customer loyalty from avid fan club members and repeat customers, and then trying to retain and attract customers while expanding the customer target area in their community. The community-based approach implies developing a bond between local residents and teams. Through this study, CBM is deˆned as ``developing consumers' attachment to and building their bond with a team through various local promotional or outreach activities within their speciˆc area. '' There are two signiˆcant factors emerged that in‰uence formulating the strategies for developing the fan base: (1) agreements between teams and stadium proprietors, and (2) relationships with local promotional vehicles such as local media companies and a railway company.
Posterior-Predictive Evidence on US Inflation Using Phillips Curve Models with Non-Filtered Time Series

Changing time series properties of US inflation and economic activity are analyzed within a class of extended Phillips Curve (PC) models. First, the misspecification effects of mechanical removal of low frequency movements of these series on posterior inference of a basic PC model are analyzed using a Bayesian simulation based approach. Next, structural time series models that describe changing patterns in low and high frequencies and backward as well as forward inflation expectation mechanisms are incorporated in the class of extended PC models. Empirical results indicate that the proposed models compare favorably with existing Bayesian Vector Autoregressive and Stochastic Volatility models in terms of fit and predictive performance. Weak identification and dynamic persistence appear less important when time varying dynamics of high and low frequencies are carefully modeled. Modeling inflation expectations using survey data and adding level shifts and stochastic volatility improves substantially in sample fit and out of sample predictions. No evidence is found of a long run stable cointegration relation between US inflation and marginal costs. Tails of the complete predictive distributions indicate an increase in the probability of disinflation in recent years.
Birdshot-like chorioretinopathy in common variable immunodeficiency.

PURPOSE To describe a patient with ocular manifestations secondary to common variable immunodeficiency. METHODS A 17-year-old adolescent girl presented with asymptomatic bilateral optic disk edema and chorioretinal infiltrates. These findings were noted during routine follow-up visits for hydroxychloroquine use for lymphoid interstitial pneumonia. She underwent a full ophthalmologic and systemic work-up. RESULTS At the age of 13, the patient was diagnosed with common variable immunodeficiency with splenomegaly, lymphadenopathy, and lymphoid interstitial pneumonia. Progressive generalized lymphadenopathy developed thereafter. Since the diagnosis of common variable immunodeficiency, she received monthly intravenous immunoglobulin, systemic corticosteroids and later on, oral hydroxychloroquine. Annual routine screening visits to exclude retinal hydroxychloroquine toxicity were unremarkable until age 17. Unaided visual acuity was 6/5 in both eyes. Slit-lamp examination was normal, whereas fundoscopy revealed bilateral optic disk edema and birdshot-like chorioretinal infiltrates, without signs of vitritis. A bilateral hot disk was seen on fluorescein angiography, but there were no signs of vasculitis. Indocyanine green angiography showed macular and midperipheral choroidal granulomas. A brain magnetic resonance imaging scan revealed no signs of raised intracranial pressure. Human leukocyte antigen-typing was negative for HLA-A29, making birdshot chorioretinopathy highly unlikely. The results of a work-up for sarcoidosis were not typical of that disease. During the past months, a remarkable episode of lacrimal gland swelling with spontaneous recovery was noted. CONCLUSION We describe a case of ocular manifestations of common variable immunodeficiency, including asymptomatic bilateral chorioretinal granulomas mimicking birdshot chorioretinopathy, combined with optic nerve sheath infiltration, and lacrimal gland involvement.
Targeting Young Adults: The Effectiveness Of Social Media Use For Local Businesses

Social media has been constantly evolving and growing in popularity since its development. Approximately 65% of adults are using some form of social media (Pew Research Center, 2015). Social media is also growing as a powerful marketing tool for many reasons, including its ability to reach a wide audience, provide immediate information, and build relationships. Research show that a majority of social media users think that companies should have a presence on social media and use it to interact with their consumers. Over half of current social media users feel a greater connection with companies they interact with via social media (Cone Communications, 2008). Social media is allowing companies to solve customer service issues immediately, gain feedback directly from consumers on their products or marketing campaigns, provide information on new products, and interact with consumers quickly and on a seemingly more personal level (Marginy Research Group, Inc., 2008). Companies can increase their engagement with consumers on social media through the use of polls, reviews, feedback, and contests (Mangold & Faulds, 2009).
An Aboriginal Perspective of the Influences of Food Intake

2 ACKNOWLEDGEMENTS . 4 LIST OF FIGURES . 7 LIST OF TABLES . 7 INTRODUCTION . 8 Purpose of this research project . 8 LITERATURE REVIEW . 9 The Problem of Obesity . 9 Quality of Life in Aboriginal Peoples . 10 Aboriginal Peoples and Healthy Eating . 11 Determinants of Healthy Eating in Aboriginal Peoples . 13 METHODOLOGY RESEARCH TRADITION: QUALITATIVE PHENOMENOLOGY.17 Theory of Planned Behaviour . 19 Research Questions and Objectives . 19 Data Collection Overview of the Process . 20 Participant Recruitment . 21 Eating Well with Canada’s Food Guide – First Nations, Inuit and Métis . 23 Semi-Structured Interviews . 24 Phenomenological Data Analysis (PDA) . 25 Participant Findings . 25 Horizonalization . 37 Discussion Themes . 38 Potential Limitations . 42 Conclusion . 43 Future Implications . 44