Miracle-dz/UniFAR-FTUs huggingface dataset:
The CHH motif in sugar beet satellite DNA: a modulator for cytosine methylation.

Methylation of DNA is important for the epigenetic silencing of repetitive DNA in plant genomes. Knowledge about the cytosine methylation status of satellite DNAs, a major class of repetitive DNA, is scarce. One reason for this is that arrays of tandemly arranged sequences are usually collapsed in next-generation sequencing assemblies. We applied strategies to overcome this limitation and quantified the level of cytosine methylation and its pattern in three satellite families of sugar beet (Beta vulgaris) which differ in their abundance, chromosomal localization and monomer size. We visualized methylation levels along pachytene chromosomes with respect to small satellite loci at maximum resolution using chromosome-wide fluorescent in situ hybridization complemented with immunostaining and super-resolution microscopy. Only reduced methylation of many satellite arrays was obtained. To investigate methylation at the nucleotide level we performed bisulfite sequencing of 1569 satellite sequences. We found that the level of methylation of cytosine strongly depends on the sequence context: cytosines in the CHH motif show lower methylation (44-52%), while CG and CHG motifs are more strongly methylated. This affects the overall methylation of satellite sequences because CHH occurs frequently while CG and CHG are rare or even absent in the satellite arrays investigated. Evidently, CHH is the major target for modulation of the cytosine methylation level of adjacent monomers within individual arrays and contributes to their epigenetic function. This strongly indicates that asymmetric cytosine methylation plays a role in the epigenetic modification of satellite repeats in plant genomes.
The making and remaking of organization context

Institutional theory is becoming one of the dominant theoretical perspectives in organization theory and is increasingly being applied in accounting research to study the practice of accounting in organizations. However, most institutional theory research has adequately theorized neither the institutionalization process through which change takes place nor the socio‐political context of the institutional formations. We propose a social theory based framework for grounding and expanding institutional theory to more fully articulate institutionalization processes. Specifically, we incorporate institutional theory and structuration theory and draw on the work of Max Weber in developing a framework of the context and the processes associated with creating, adopting and discarding institutional practices. We propose that the expanded framework depicts the socio‐economic and political context better and more directly addresses the dynamics of enacting, embedding and changing organizational features and processes. Expanding the focus of the institutional theory based accounting research can facilitate a more comprehensive representation of accounting as the object of institutional practices as well as provide a better articulation of the role of accounting in the institutionalization process.
Comparison of Oral Hygiene Levels and Behaviors Between First and Final Year Dental Students in Jordan

Background: Achieving and maintaining good oral hygiene is essential for gingival health. However, oral hygiene attitudes and behaviors may vary according to knowledge, beliefs, and education. Objective: To compare and quantify discrepancies in oral health attitudes and self-care levels between first and final year dental students. Methodology: Two hundred and seventy seven dental students at the University of Jordan were recruited in this study. The sample involved 162 first year and 115 final year students with age ranges of 18-19 and 21-22 years, respectively. Subjects were asked to fill a structured questionnaire about their oral hygiene habits. Clinical examinations were performed at the Periodontal Department of Jordan University Hospital. Oral hygiene levels were clinically assessed by the plaque index (PI) and gingival index (GI). Results: Analysis showed that final year students brushed their teeth, flossed, and maintained regular dental visits. They also brushed their teeth twice more frequently and changed the brush more often per year. However, both first and final year students used mouthwash almost equally. Final year students also have less bacterial plaque and suffered less gingival inflammation in prevalence and severity. Conclusion: It was concluded that final year dental students have a significantly better gingival status than first year students.
Vitamin D Hormone Confers Neuroprotection in Parallel with Downregulation of L-Type Calcium Channel Expression in Hippocampal Neurons

Although vitamin D hormone (VDH; 1,25-dihydroxyvitamin D3), the active metabolite of vitamin D, is the major Ca2+-regulatory steroid hormone in the periphery, it is not known whether it also modulates Ca2+ homeostasis in brain neurons. Recently, chronic treatment with VDH was reported to protect brain neurons in both aging and animal models of stroke. However, it is unclear whether those actions were attributable to direct effects on brain cells or indirect effects mediated via peripheral pathways. VDH modulates L-type voltage-sensitive Ca2+ channels (L-VSCCs) in peripheral tissues, and an increase in L-VSCCs appears linked to both brain aging and neuronal vulnerability. Therefore, we tested the hypothesis that VDH has direct neuroprotective actions and, in parallel, targets L-VSCCs in hippocampal neurons. Primary rat hippocampal cultures, treated for several days with VDH, exhibited a U-shaped concentration–response curve for neuroprotection against excitotoxic insults: lower concentrations of VDH (1–100 nm) were protective, but higher, nonphysiological concentrations (500–1000 nm) were not. Parallel studies using patch-clamp techniques found a similar U-shaped curve in which L-VSCC current was reduced at lower VDH concentrations and increased at higher (500 nm) concentrations. Real-time PCR studies demonstrated that VDH monotonically downregulated mRNA expression for the α1C and α1D pore-forming subunits of L-VSCCs. However, 500 nm VDH also nonspecifically reduced a range of other mRNA species. Thus, these studies provide the first evidence of (1) direct neuroprotective actions of VDH at relatively low concentrations, and (2) selective downregulation of L-VSCC expression in brain neurons at the same, lower concentrations.
Primordial black holes in braneworld cosmologies: Accretion after formation

We recently studied the formation and evaporation of primordial black holes in a simple braneworld cosmology, namely the Randall-Sundrum type II cosmology. Here we study the effect of accretion from the cosmological background onto the black holes after formation. While it is generally believed that in the standard cosmology such accretion is of negligible importance, we find that during the high-energy regime of braneworld cosmology accretion can be the dominant effect and lead to a mass increase of potentially orders of magnitude. However, unfortunately the growth is exponentially sensitive to the accretion efficiency, which cannot be determined accurately. Since accretion becomes unimportant once the high-energy regime is over, it does not affect any constraints expressed at the time of black hole evaporation, but it can change the interpretation of those constraints in terms of early Universe formation rates.
Evaluation of sunflower collection by genetic variability based on germination and plantlet development parameters using Artificial Neural Networks

The aim of the research work was to study the genetic variability of sunflower (Heliantus annuus L.) seeds collection. From 1500 available genotypes a set of 120 recombinant inbred lines coming from different countries were selected to perform the study. The genetic variability consisted in two types of experiments: in vivo and in vitro cultures. The recombinant inbred lines were classified using Artificial Neuronal Networks (ANNs). A first ANN was designed according to genotype origin and variety. Results confirm the ability of the ANN to predict the genotype origin and variety of the sunflower lines of seeds, based on the germination and plantlet development parameters. A second ANN was successfully designed and tested to classify the category of germination plantlet. Classification was performed, for the test set of data, and the results show a very good accuracy.
Extracting the cliques from a neighbourhood system

A method is proposed for obtaining the local clique set from a neighbourhood system. The Markov random field model, which is used extensively in image processing, is defined with respect to a neighbourhood system. The mathematical interpretation of the model is defined with respect to the corresponding clique set. A systematic method is presented for extracting the complete local clique set from any neighbourhood system on which a Markov random field may be defined.
Slotted Scheduled Tag Access in Multi-Reader RFID Systems

Radio frequency identification (RFID) is a technology where a reader device can "sense" the presence of a close-by object by reading a tag device attached to the object. To improve coverage, multiple RFID readers can be deployed in the given region. In this paper, we consider the problem of slotted scheduled access of RFID tags in a multiple reader environment. In particular, we develop centralized algorithms in a slotted time model to read all the tags using near-optimal number of time slots. We consider two scenarios -one wherein the tag distribution in the physical space is unknown, and the other where tag distribution is known or can be estimated a priori. For each of these scenarios, we consider two cases depending on whether a single channel or multiple channels are available. All the above version of the problem are NP-hard. We design approximation algorithms for the single channel and heuristic algorithms for the multiple channel cases. Through extensive simulations, we show that for the single channel case, our heuristics perform close to the approximation algorithms. In general, our simulations show that our algorithms significantly outperform colorwave, an existing algorithm for similar problems.
QMOOD metric sets to assess quality of Java program

This paper describes the model to evaluate and grade the Java programs, based on QMOOD (Quality Model for Object Oriented Design). QMOOD is the hierarchical model that defines relation between qualities attributes(like reusability, functionality, effectiveness, understand ability, extendibility, flexibility) and design properties with the help of equations. In this research we have developed the system based on QMOOD which is use to evaluate the quality of JAVA programs. In this we would try evaluate all quality attributes by finding the design metrics that is based on design property of object oriented design. Though QMOOD metrics are subjective in nature but still with the help of relationship between quality attributes and design property defined, we have calculated and aggregated these qualities attributes and evaluate the quality of program input We have tested the system with number of different programs that vary in their complexities and functionalities.
3D-Radiation Hydro Simulations of Disk-Planet Interaction

We study the evolution of an embedded protoplanet in a circumstellar disk using the 3D-Radiation Hydro code TRAMP, and treat the thermodynamics of the gas properly in three dimensions. The primary interest of this work lies in the demonstration and testing of the numerical method. We show how far numerical parameters can influence the simulalions of gap opening. We study a standard reference model under various numerical approximations. Then we compare the commonly used locally isothermal approximation to the radialion hydro simulation using an equation for the internal energy. Models with different treatments of the mass accretion process are compared. Often mass accumulates in the Roche lobe of the planet creating a hydrostatic atmosphere around the planet. The gravitational torques induced by the spiral pattern of the disk onto the planet are not strongly affected in the average magnitude, but the short time scale fluctuations are stronger in the radiation hydro models. An interesting result of this work lies in the analysis of the temperature structure around the planet. The most striking effect of treating the thermodynamics properly is the formation of a hot pressure-supported bubble around the planet with a pressure scale height of H/R 0.5 rather than a thin Keplerian circumplanetary accretion disk.
Mechanisms of right heart failure—A work in progress and a plea for failure prevention

The right ventricle (RV) of the heart, which pumps blood through a low pressure, low resistance “lesser” circulation, is now receiving more attention by researchers and clinicians, after many years of benign neglect. [1-7] Some of the many reasons for neglecting the RV assumed that (1) In the context of global cardiac performance, the RV was not very important;[2] and (2) The cellular and molecular mechanisms of RV failure (RVF) were not different from those responsible for LV failure. Perhaps the biggest knowledge gap originated from the lack of experimental studies modeling the development of RVF, and from attempts to extrapolate mechanisms of chronic RVF from studies originally designed to study acute RVF. These likely explain why “pressure overload” is the most frequent—and sometimes exclusively—quoted mechanism of RVF. Indeed, patients with chronic, progressive pulmonary vascular disease most frequently die of RV failure. [8,9] However, as we enlarge our knowledge of in the pathobiology of RVF, we should also begin to consider RVF as a “progressive,” but not necessarily “chronic,” phenomenon.
Towards an Efficient and Secure Online Digital Rights Management Scheme in Cloud Computing

Streaming media is widely adopted by thousands of applications in cloud computing, how to effectively protect streaming media contents is a new challenge. In this paper, we propose an efficient online digital rights management (DRM) scheme supporting dynamic license in cloud computing. The content provider encrypts media content and outsources the encrypted content to cloud storage, while the user acquires dynamic license from the license server and consumes the streaming media content from the cloud storage. Further, we present a secure key distribution protocol based on proxy re-encryption, which protects the confidentiality of content encryption key, and reduces the work of key management in the cloud, and also supports domain key to realize user domain management. In addition, we develop a prototype system with Google cloud storage APIs based on the proposed scheme, and the implementation and comparison results show that the proposed scheme satisfies the requirements of online media content protection in cloud computing.
Towards an executive without a homunculus: computational models of the prefrontal cortex/basal ganglia system

The prefrontal cortex (PFC) has long been thought to serve as an ‘executive’ that controls the selection of actions and cognitive functions more generally. However, the mechanistic basis of this executive function has not been clearly specified often amounting to a homunculus. This paper reviews recent attempts to deconstruct this homunculus by elucidating the precise computational and neural mechanisms underlying the executive functions of the PFC. The overall approach builds upon existing mechanistic models of the basal ganglia (BG) and frontal systems known to play a critical role in motor control and action selection, where the BG provide a ‘Go’ versus ‘NoGo’ modulation of frontal action representations. In our model, the BG modulate working memory representations in prefrontal areas to support more abstract executive functions. We have developed a computational model of this system that is capable of developing human-like performance on working memory and executive control tasks through trial-and-error learning. This learning is based on reinforcement learning mechanisms associated with the midbrain dopaminergic system and its activation via the BG and amygdala. Finally, we briefly describe various empirical tests of this framework.
Lower Bounds for the Parameterized Complexity of Minimum Fill-in and Other Completion Problems

In this work, we focus on several completion problems for subclasses of chordal graphs: MINIMUM FILL-IN, INTERVAL COMPLETION, PROPER INTERVAL COMPLETION, TRIVIALLY PERFECT COMPLETION, and THRESHOLD COMPLETION. In these problems, the task is to add at most k edges to a given graph to obtain a chordal, interval, proper interval, threshold, or trivially perfect graph, respectively. We prove the following lower bounds for all these problems, as well as for the related CHAIN COMPLETION problem: • Assuming the Exponential Time Hypothesis, none of these problems can be solved in time 2O(n1/2/logc n) or 2O(k1/4/logc k)· nO(1), for some integer c. • Assuming the non-existence of a subexponential-time approximation scheme for MIN BISECTION on d-regular graphs, for some constant d, none of these problems can be solved in time 2o(n) or 2o√k)}· nO(1). For all the aforementioned completion problems, apart from PROPER INTERVAL COMPLETION, FPT algorithms with running time of the form 2O(√k log k)· nO(1) are known. Thus, the second result proves that a significant improvement of any of these algorithms would lead to a surprising breakthrough in the design of approximation algorithms for MIN BISECTION. To prove our results, we use a reduction methodology based on combining the classic approach of starting with a sparse instance of 3-SAT, prepared using the Sparsification Lemma, with the existence of almost linear-size Probabilistically Checkable Proofs. Apart from our main results, we also obtain lower bounds excluding the existence of subexponential algorithms for the OPTIMUM LINEAR ARRANGEMENT problem, as well as improved, yet still not tight, lower bounds for FEEDBACK ARC SET IN TOURNAMENTS.
‘One Woman's Prejudice’: Did Margaret Thatcher Cause Britain's Anti‐Europeanism?

type="short"> This article is part of the January 2015 Special Issue titled ‘Interpreting British European Policy’, which also includes Interpreting British European Policy by Mark Bevir, Oliver Daddow and Pauline Schnapper (DOI: 10.1 111/jcms.12201 ), Safeguarding British Identity or Betraying It? The Role of British ‘Tradition’ in the Parliamentary Great Debate on EC Membership, October 1971 by N. Piers Ludlow (DOI: 10.1 111/jcms.12202 ), The Return of ‘Englishness’ in British Political Culture – The End of the Unions? by Michael Kenny (DOI: 10.1 111/jcms.12203 ), Interpreting the Outsider Tradition in British European Policy Speeches from Thatcher to Cameron by Oliver Daddow (DOI: 10.1 111/jcms.12204 ), Between One-Nation Toryism and Neoliberalism: The Dilemmas of British Conservatism and Britain's Evolving Place in Europe by Mark I. Vail (DOI: 10.1 111/jcms.12206 ), Euroscepticism and the Anglosphere: Traditions and Dilemmas in Contemporary English Nationalism by Ben Wellings and Helen Baxendale (DOI: 10.1 111/jcms.12207 ), Reworking the Eurosceptic and Conservative Traditions into a Populist Narrative: UKIP's Winning Formula? by Karine Tournier-Sol (DOI: 10.1 111/jcms.12208 ), The Labour Party and Europe from Brown to Miliband: Back to the Future? by Pauline Schnapper (DOI: 10.1 111/jcms.12209 ), Educating Britain? Political Literacy and the Construction of National History by Helen Brocklehurst (DOI: 10.1 111/jcms.12211 )
Academic Analytics: A New Tool for a New Era.

The importance of student success (commonly measured as degree completion) continues to rise, as does the demand for institutional accountability. Academic analytics can help institutions address student success and accountability while better fulfilling their academic missions. Academic systems generate a wide array of data that can predict retention and graduation. Academic analytics marries that data with statistical techniques and predictive modeling to help faculty and advisors determine which students may face academic difficulty, allowing interventions to help them succeed. This paper highlights what IT and institutional leaders need to understand about academic analytics, including changes it may require in data standards, systems, processes, policies, and institutional culture.
Simpson's Paradox in a Synthetic Microbial System

The maintenance of “public” or “common good” producers is a major question in the evolution of cooperation. Because nonproducers benefit from the shared resource without bearing its cost of production, they may proliferate faster than producers. We established a synthetic microbial system consisting of two Escherichia coli strains of common-good producers and nonproducers. Depending on the population structure, which was varied by forming groups with different initial compositions, an apparently paradoxical situation could be attained in which nonproducers grew faster within each group, yet producers increased overall. We show that a simple way to generate the variance required for this effect is through stochastic fluctuations via population bottlenecks. The synthetic approach described here thus provides a way to study generic mechanisms of natural selection.
Feasibility Study of Using Mobile Laser Scanning Point Cloud Data for GNSS Line of Sight Analysis

The positioning accuracy with good GNSS observation can easily reach centimetre level, supported by advanced GNSS technologies. However, it is still a challenge to offer a robust GNSS based positioning solution in a GNSS degraded area. The concept of GNSS shadow matching has been proposed to enhance the GNSS based position accuracy in city canyons, where the nearby high buildings block parts of the GNSS radio frequency (RF) signals. However, the results rely on the accuracy of the utilized ready-made 3D city model. In this paper, we investigate a solution to generate a GNSS shadow mask with mobile laser scanning (MLS) cloud data. The solution includes removal of noise points, determining the object which only attenuated the RF signal and extraction of the highest obstruction point, and eventually angle calculation for the GNSS shadow mask generation. By analysing the data with the proposed methodology, it is concluded that the MLS point cloud data can be used to extract the GNSS shadow mask after several steps of processing to filter out the hanging objects and the plantings without generating the accurate 3D model, which depicts the boundary of GNSS signal coverage more precisely in city canyon environments compared to traditional 3D models.
RETINOCHOROIDAL MORPHOLOGY DESCRIBED BY WIDE-FIELD MONTAGE IMAGING OF SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY

Purpose: To present baseline images of the vitreous, retina, and choroid from the macula to the periphery in normal patients using a novel montaging technique of spectral domain optical coherence tomography. Methods: Twenty-six normal eyes of 22 healthy volunteers were enrolled in this study. Montaged images of four radial optical coherence tomography scans through the fovea were obtained from each subject. Results: In the macula, there were six identifiable retinal layers as well as four bands in the outer retina. In the periphery, the ganglion cell layer was not identifiable. The external limiting membrane, the second band, and the retinal pigment epithelium were continuously delineated from the macula to the periphery. The third band was not visible in the periphery. Conclusion: Spectral domain optical coherence tomography montaged images provide wide-angle images of the vitreous, retina, and choroid, allowing for evaluation of peripheral findings and examination of relationships between peripheral and posterior disease. The maximum scan length achieved here was 36 mm. The scan length is approximately three times than that provided by conventional posterior scanning and is consistent with known dimensions of the eye. This method is achievable with current commercially available devices and may contribute to decision making in clinical practice.