Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality

Significance Genomics has revealed that even well-studied bacteria maintain many more biosynthetic gene clusters (BGCs) predicted to encode specialized metabolites than expected based on product discovery. These orphan BGCs are often assumed to be transcriptionally silent. Here, we show that a majority of the 46 BGCs observed in four strains of the marine actinomycete Salinispora are transcribed at levels that should facilitate product detection. In five cases, similar BGCs were differentially expressed among strains, suggesting that simple presence or absence analyses are not good predictors of metabolic output. Highly expressed BGCs were bioinformatically linked to their products, including a series of salinipostins not previously reported from Salinispora pacifica. Subsequent genetic experiments established a formal link between salinipostins and their cognate BGC. Bacterial natural products remain an important source of new medicines. DNA sequencing has revealed that a majority of natural product biosynthetic gene clusters (BGCs) maintained in bacterial genomes have yet to be linked to the small molecules whose biosynthesis they encode. Efforts to discover the products of these orphan BGCs are driving the development of genome mining techniques based on the premise that many are transcriptionally silent during normal laboratory cultivation. Here, we employ comparative transcriptomics to assess BGC expression among four closely related strains of marine bacteria belonging to the genus Salinispora. The results reveal that slightly more than half of the BGCs are expressed at levels that should facilitate product detection. By comparing the expression profiles of similar gene clusters in different strains, we identified regulatory genes whose inactivation appears linked to cluster silencing. The significance of these subtle differences between expressed and silent BGCs could not have been predicted a priori and was only revealed by comparative transcriptomics. Evidence for the conservation of silent clusters among a larger number of strains for which genome sequences are available suggests they may be under different regulatory control from the expressed forms or that silencing may represent an underappreciated mechanism of gene cluster evolution. Coupling gene expression and metabolomics data established a bioinformatic link between the salinipostins and their associated BGC, while genetic manipulation established the genetic basis for this series of compounds, which were previously unknown from Salinispora pacifica.
Secrecy Outage Analysis of Buffer-Aided Cooperative MIMO Relaying Systems

This paper investigates the secrecy outage performance of buffer-aided multirelay multiple-input multiple-output cooperative systems in the presence of a passive eavesdropper. Due to the unavailability of the channel state information of eavesdropper's channel, a buffer-aided joint transmit antenna and relay selection scheme based on the main channel is proposed to enhance the secrecy performance. Specifically, we model the evolution of the relay buffers as a Markov chain and derive new exact and asymptotic closed-form expressions for the secrecy outage probability, which provides an efficient way to assess the effect of system parameters on the secrecy outage probability. Moreover, simple asymptotic results are further exploited under two special scenarios, i.e., <inline-formula><tex-math notation="LaTeX">$L \rightarrow \infty$</tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$L \not\rightarrow \infty$</tex-math></inline-formula> (where <inline-formula> <tex-math notation="LaTeX">$L$</tex-math></inline-formula> denotes the size of the relay buffers), for characterizing the achievable secrecy diversity gain, the secrecy coding gain, and the secrecy diversity-multiplexing tradeoff. Our results reveal that: 1) a secrecy diversity gain of <inline-formula><tex-math notation="LaTeX">$N_RM{\rm min}(N_S,N_D)$</tex-math></inline-formula> is achieved when <inline-formula><tex-math notation="LaTeX">$L \not\rightarrow \infty$</tex-math></inline-formula>, however, when <inline-formula><tex-math notation="LaTeX">$L \rightarrow \infty$</tex-math></inline-formula>, the secrecy diversity gain increases to <inline-formula> <tex-math notation="LaTeX">$N_RM(N_S+N_D)$</tex-math></inline-formula>, where <inline-formula> <tex-math notation="LaTeX">$N_S$</tex-math></inline-formula>, <inline-formula><tex-math notation="LaTeX">$N_R$ </tex-math></inline-formula>, and <inline-formula><tex-math notation="LaTeX">$N_D$</tex-math></inline-formula> represent the number of antennas at the source, each of <inline-formula><tex-math notation="LaTeX">$M$</tex-math> </inline-formula> relays and the destination, respectively. 2) The eavesdropper's channel does not affect the secrecy diversity gain but only the secrecy coding gain in both the two scenarios.
Improving Latent Factor Models via Personalized Feature Projection for One Class Recommendation

Latent Factor models, which transform both users and items into the same latent feature space, are one of the most successful and ubiquitous models in recommender systems. Most existing models in this paradigm define both users' and items' latent factors to be of the same size and use an inner product to represent a user's "compatibility" with an item. Intuitively, users' factors encode "preferences" while item factors encode "properties", so that the inner product encodes how well an item matches a user's preferences. However, a user's opinion of an item may be more complex, for example each dimension of each user's opinion may depend on a combination of multiple item factors simultaneously. Thus it may be better to view each dimension of a user's preference as a personalized projection of an item's properties so that the preference model can capture complex relationships between items' properties and users' preferences. Therefore, in this paper we propose a novel personalized feature projection method to model users' preferences over items. Specifically, for each user, we define a personalized projection matrix, which takes the place of user-specific factors from existing models. This matrix describes a mapping between items' factors and users' preferences in order to build personalized preference models for each user and item. The proposed personalized feature projection method is quite general and existing latent factor models, for example, can be cast as a special case. We present three objective functions to optimize predictions in the form of ranked lists of users' preferences over items, and demonstrate how each can be used to improve one-class recommendation performance. Experiments are conducted on four real-world datasets and our results show that our personalized feature projection method outperforms several state-of-the-art methods on various evaluation metrics.
A game-theoretic strategy for pareto-optimal cooperation in resource constrained vehicular ad-hoc networks

Vehicular Ad-hoc Networks may be used for multitude of services including those related to human safety, traffic management and providing comfort to the users as applicable to Intelligent Transportation Systems, Smart Communication Systems, Internet-of-Things etc. In most scenarios, vehicles are owned by different entities and therefore it may not be in the best of interest of VANETs nodes to forward data belonging to different entities indiscriminately. This is so because it involves absorbing the incurred cost in terms of available resources. Such strategy may lead to packet drops and consequent delays leading to overall performance of the VANET-in-question. On the other hand if vehicles are readily agrees to forward any data that they receives, it would lead to a complete cooperation scenario, but might prove costly in terms of resources for the involved nodes. Both of these described conditions represents extreme scenarios and are thus undesirable. This opens up an opportunity for devising a new solution that could be built upon a balanced cooperation enforcement scheme involving all the participating nodes in a resource constrained VANET. In this paper, we present an approach for mathematical modeling of VANETs in form of non-cooperative game. Using this model probability by which a particular vehicular node would accept the relay request of other vehicular nodes has been calculated by involving a combination of an available degree of resource and a resilient reciprocating strategy that we call V-TFT i.e. Vehicular-Tit-for-Tat. The presented simulation result demonstrates that the V-TFT converges to pareto-optimal solution. In addition, it is capable to perform so in presence of non-cooperative nodes and variable sized network.
Approaches to Early Childhood Education

I. INTRODUCTION 1. Historical Perspectives on Early Childhood Education. 2. Child Care. 3. The Head Start Program. II. BROAD APPROACHES. 4. Classes for Parents and Young Children: The Family Center Model. 5. The Eriksonian Approach. 6. Behavior Analysis and Principles in Early Childhood Education. 7. The Constructivist Perspective on Early Education: Applications to Children's Museums. 8. The Project Approach: An Overview. 9. Montessori Education Today. 10. Mixed-Age Classrooms for Young Children. III. SPECIFIC PROGRAMS. 11. The Portage Project: An International Home Approach to Early Intervention for Young Children and Their Families. 12. The Developmental-Interaction Approach at Bank Street College of Education. 13. The High/Scope Curriculum for Early Childhood Care and Education. 14. The Ausubelian Preschool Classroom. 15. Educating the Young Thinker Model from Research to Practice: A Case Study of Program Development, or the Place of Theory and Research in the Development of Educational Programs. 16. Reggio Emilia: An Approach or an Attitude? IV. INTEGRAL DIMENSIONS. 17. Including Everyone: A Model Preschool Program for Typical and Special-Needs Children. 18. A Framework for Culturally Relevant, Multicultural, and Anti-Bias Education in the 21st Century. Epilogue. Index.
WLCp2-07: Cyclically Shifted Multiple Interleavers

We propose a simple strategy to generate multiple interleavers. As suggested in literature, using user-distinct interleavers is an effective means to separate multiple users, if applied in addition to user-specific spreading codes in code division multiple access (CDMA). In this paper we particularly focus on interleave division multiple access (IDMA), which has a close relation to CDMA, but users are separated only by user- distinct interleavers. Hence, multiple interleavers are essential system components for IDMA. Despite its importance, usually interleavers for such systems are randomly chosen and there are only few papers on the generation of multiple interleavers. We show that the conventional multiple interleavers proposed for CDMA are not sufficient for the user separation in IDMA. Moreover, in order to minimize memory requirements and signaling overheads to store and exchange interleavers, a simple interleaver construction rule is desirable in practical systems. Therefore, we propose to derive multiple interleavers from a single interleaver, common for all users, with only a few user- distinct cyclic shifts. Although this simple design is empirical and no optimality is claimed, simulation results show sufficiently good performance. We also proposed a simple procedure to exchange the information of interleavers.
Family unification, exotic states and light magnetic monopoles

Models with fermions in bifundamental representations can lead naturally to family unification as opposed to family replication. Such models typically predict (exotic) color singlet states with fractional electric charge, and magnetic monopoles with multiple Dirac charge. The exotics may be at the TeV scale, and relatively light magnetic monopoles (107? GeV) can be present in the galaxy with abundance near the Parker bound. We focus on three family SU(4) ? SU(3) ? SU(3) models.
Infection of the Central Nervous System, Sepsis and Amyotrophic Lateral Sclerosis

Background Severe infections may lead to chronic inflammation in the central nervous system (CNS) which may in turn play a role in the etiopathogenesis of amyotrophic lateral sclerosis (ALS). The relentless progression and invasive supportive treatments of ALS may on the other hand induce severe infections among ALS patients. Methodology and Principal Findings The present study included 4,004 ALS patients identified from the Swedish Patient Register during 1991–2007 and 20,020 age and sex matched general population controls. Conditional logistic regression was used to estimate the odds ratios (ORs) of ALS given a previous hospitalization for CNS infection or sepsis. Cox models were used to estimate the hazard ratios (HRs) of hospitalization for CNS infection or sepsis after ALS diagnosis. Overall, previous CNS infection (OR: 1.3, 95% confidence interval [CI]: 0.8, 2.4) or sepsis (OR: 1.2, 95% CI: 0.9, 1.6) was not associated with ALS risk. However, compared to ALS free individuals, ALS cases were more likely to be hospitalized for sepsis after diagnosis (HR: 2.6, 95% CI: 1.9, 3.5). We did not observe a higher risk of CNS infection after ALS diagnosis. Conclusions/Significance Our results suggest that acute and severe infections unlikely contribute to the development of ALS; however, ALS patients are at a higher risk of sepsis after diagnosis, compared to ALS free individuals.
Privatisation and commercialization: two globalizing practices affecting Australian universities

The fundamental force underpinning neoliberal globalisation is the privatisation of the economy. It is commonly understood that this movement to shift substantial resources from the public sector to the private sector began simultaneously in the United States with the Reagan government and in the United Kingdom with the Thatcher government. From these two countries, privatisation, sometimes referred to as economic rationalism or applying market forces to public sector agencies, spread to other Anglo-derived countries, such as Canada, New Zealand and Australia, and then to many other countries around the world. However, it is noteworthy that many European countries have resisted this trend towards privatisation, especially in regard to universities. An important distinction can be made between the privatisation and the commercialisation of higher education; nevertheless, the fact that there is an interaction between privatisation and commercialisation makes it difficult to untangle the impetus for these practices in universities. Both of these globalising forces are affecting Australia's higher education sector as public universities become more like private institutions and the locus of funding shifts from the taxpayer to students and their families. This privatisation process has been accompanied by commercial behaviour that may put Australia's research base at risk. This article addresses the impact of these two globalising forces on the quality of education and academic freedom in Australian universities. It argues that there is a greater chance that research will be curiosity-driven and critical education will thrive if profit is not the major determinant of university research and teaching agendas. To protect the independence of research and the enviable reputation that Australian universities currently have in providing high quality education, the Commonwealth government may need to reduce its drive to privatise universities and commercialise research.
Interactive cutting of finite elements based deformable objects in virtual environments

There is a wide range of virtual reality (VR) applications that benefit from physically based modeling, such as assembly simulation, robotics, training and teaching (e.g., medical, military, sports) and entertainment. The dynamics of rigid bodies is well understood and several open source as well as commercial physics engines supporting articulated rigid bodies and particle systems are available. On the other hand, the simulation of deformable bodies is an objective of current research. The main application areas of deformable objects simulation in computer graphics and VR are the simulation of cloth and medical simulation. The challenge of VR applications is the real time simulation requirement. The raising computational power of the last decades allowed for adapting selected methods known from engineering sciences for interactive simulation. The simulation of cutting is especially challenging though, as most methods suffer from both performance and stability issues. Although a number of approaches have been presented over the last decade, the problem has not been solved satisfyingly, yet. This thesis presents methods for an interactive simulation of finite elements based deformable objects as used, e.g., in VR surgical simulators. The main objectives of such simulators are stability and performance of the employed methods allowing for an interactive object manipulation including topological changes in real time. A novel method for interactive cutting of deformable objects in virtual environments is presented. The key to this method is the usage of the extended finite elements method (XFEM). The XFEM can effectively model discontinuities within an FEM mesh without creating new mesh elements and thus minimizing the impact on the performance of the simulation. The XFEM can be applied to advanced constitutive models used for the interactive simulation of large deformations. Moreover, an analysis of mass lumping techniques, showing that the stability of the simulation is guaranteed even when small portions of the material are cut is presented. The XFEM based cutting surpasses the currently most widely used remeshing methods in both, performance and stability and is suitable for interactive VR simulation. Further, a software architecture for physical simulation of deformable objects in VR applications is proposed. The framework is suitable for the creation of complex VR applications as, e.g., a virtual surgical trainer. It uses thread level task parallelization for the concurrent execution of visualization, collision detection, haptics and deformation. Moreover, a parallelization approach for the deformation algorithm, which is the most computationally intensive part is proposed. The presented solution based on OpenMP requires only minimal changes to the source code while achieving a speedup comparable to the results of more sophisticated approaches. The presented framework benefits from the current developments in the computing industry and allows an optimal utilization of multicore CPUs.
The Accountant's Ethical Code of Conduct and Moral Reasoning from an Islamic Environment: Case in Yemen

An ethical code of conduct is developed to guide behaviors of members in or of organizations. Accountants, in this context, are not an exception. The availability of such ethical code of conduct is extremely important for both accountants and users of accounting information. However, currently in Yemen, there is no ethical code of conduct for Yemeni professional accountants. It is also equally important to know how Yemeni professional accountants perceive prescriptively and deliberatively on issues related to the ethical code of conduct. Hence, two phases of study were carried out to tap the issues. The first phase was sought to address the question of what constitutes the ethical code of conduct among Yemeni professional accountants. Data were collected from 386 users of accounting information in Yemen. The study employed interdependency analysis to reveal and confirm the domain of the accountants' ethical code of conduct. Results show that the ethical code of conduct consists of several ethical constructs. The second phase of the study was to know to what extent Yemeni professional accountants behave ethically at work. This is important because Islam emphasizes consistency between thought and action. Data were collected from 138 professional accountants in four main cities of Yemen i.e. Sana'a, Hadhramout, Taiz, and Aden. Results showed that Yemeni professional accountants exhibit higher level of moral reasoning beyond the conventional level. The findings of this study contribute to the body of knowledge by providing an Islamic perspective to the ethical issues which has similarities and differences vis-a-vis the Western perspective.
Capacity theorems for the relay channel

A relay channel consists of an input x_{l} , a relay output y_{1} , a channel output y , and a relay sender x_{2} (whose transmission is allowed to depend on the past symbols y_{1} . The dependence of the received symbols upon the inputs is given by p(y,y_{1}|x_{1},x_{2}) . The channel is assumed to be memoryless. In this paper the following capacity theorems are proved. 1)If y is a degraded form of y_{1} , then C \: = \: \max \! _{p(x_{1},x_{2})} \min \,{I(X_{1},X_{2};Y), I(X_{1}; Y_{1}|X_{2})} . 2)If y_{1} is a degraded form of y , then C \: = \: \max \! _{p(x_{1})} \max_{x_{2}} I(X_{1};Y|x_{2}) . 3)If p(y,y_{1}|x_{1},x_{2}) is an arbitrary relay channel with feedback from (y,y_{1}) to both x_{1} \and x_{2} , then C\: = \: \max_{p(x_{1},x_{2})} \min \,{I(X_{1},X_{2};Y),I \,(X_{1};Y,Y_{1}|X_{2})} . 4)For a general relay channel, C \: \leq \: \max_{p(x_{1},x_{2})} \min \,{I \,(X_{1}, X_{2};Y),I(X_{1};Y,Y_{1}|X_{2}) . Superposition block Markov encoding is used to show achievability of C , and converses are established. The capacities of the Gaussian relay channel and certain discrete relay channels are evaluated. Finally, an achievable lower bound to the capacity of the general relay channel is established.
The Ecological Rift: Capitalism’s War on the Earth

Humanity in the twenty-first century is facing what might be described as its ultimate environmental catastrophe: the destruction of the climate that has nurtured human civilization and with it the basis of life on earth as we know it. All ecosystems on the planet are now in decline. Enormous rifts have been driven through the delicate fabric of the biosphere. The economy and the earth are headed for a fateful collision if we don t alter course.In The Ecological Rift: Capitalism s War on the Earth environmental sociologists John Bellamy Foster, Brett Clark, and Richard York offer a radical assessment of both the problem and the solution. They argue that the source of our ecological crisis lies in the paradox of wealth in capitalist society, which expands individual riches at the expense of public wealth, including the wealth of nature. In the process, a huge ecological rift is driven between human beings and nature, undermining the conditions of sustainable existence: a rift in the metabolic relation between humanity and nature that is irreparable within capitalist society, since integral to its very laws of motion.Critically examining the sanguine arguments of mainstream economists and technologists, Foster, Clark, and York insist instead that fundamental changes in social relations must occur if the ecological (and social) problems presently facing us are to be transcended. Their analysis relies on the development of a deep dialectical naturalism concerned with issues of ecology and evolution and their interaction with the economy. Importantly, they offer reasons for revolutionary hope in moving beyond the regime of capital and toward a society of sustainable human development. "