Ruliology: Linking Computation, Observers and Physical Law

Stephen Wolfram has recently outlined an unorthodox, multicomputational approach to fundamental theory, encompassing not only physics but also mathematics in a structure he calls The Ruliad, understood to be the entangled limit of all possible computations. In this framework, physical laws arise from the the sampling of the Ruliad by observers (including us). This naturally leads to several conceptual issues, such as what kind of object is the Ruliad? What is the nature of the observers carrying out the sampling, and how do they relate to the Ruliad itself? What is the precise nature of the sampling? This paper provides a philosophical examination of these questions, and other related foundational issues, including the identification of a limitation that must face any attempt to describe or model reality in such a way that the modeller-observers are include

Performance analysis of a parallel, multi-node pipeline for DNA sequencing

Post-sequencing DNA analysis typically consists of read mapping followed by variant calling and is very time-consuming, even on a multi-core machine. Recently, we proposed Halvade, a parallel, multi-node implementation of a DNA sequencing pipeline according to the GATK Best Practices recommendations. The MapReduce programming model is used to distribute the workload among different workers. In this paper, we study the impact of different hardware configurations on the performance of Halvade. Benchmarks indicate that especially the lack of good multithreading capabilities in the existing tools (BWA, SAMtools, Picard, GATK) cause suboptimal scaling behavior. We demonstrate that it is possible to circumvent this bottleneck by using multiprocessing on high-memory machines rather than using multithreading. Using a 15-node cluster with 360 CPU cores in total, this results in a runtime of 1 h 31 min. Compared to a single-threaded runtime of similar to 12 days, this corresponds to an overall parallel efficiency of 53%

Bubble formation in ϕ6\phi^6 potential

Scalar field theory with an asymmetric potential is studied at zero temperature and high-temperature for $\phi^6$ potential. The equations of motion are solved numerically to obtain O(4) spherical symmetric and O(3) cylindrical symmetric bounce solutions. These solutions control the rates for tunneling from the false vacuum to the true vacuum by bubble formation. The range of validity of the thin-wall approximation (TWA) is investigated. An analytical solution for the bounce is presented, which reproduces the action in the thin-wall as well as the thick-wall limits.Comment: 22 pag

A woman living with osteoarthritis: A case report

Osteoarthritis is a common condition that is typically associated with older adults. Other causes of osteoarthritis, such as those cases resulting from childhood Perthes disease, can affect younger people and frequently have a major impact on the lives of those affected. This case report describes the experiences of one patient with osteoarthritis, using examples of her poetry to illustrate her social, psychological and emotional transformation

CD146, a novel target of CD44-signaling, suppresses breast tumor cell invasion.

We have previously validated three novel CD44-downstream positively regulated transcriptional targets, including Cortactin, Survivin and TGF-β2, and further characterized the players underlying their separate signaling pathways. In the present study, we identified CD146 as a potential novel target, negatively regulated by CD44. While the exact function of CD146 in breast cancer (BC) is not completely understood, substantial evidence from our work and others support the hypothesis that CD146 is a suppressor of breast tumor progression. Therefore, using molecular and pharmacological approaches both in vitro and in breast tissues of human samples, the present study validated CD146 as a novel target of CD44-signaling suppressed during BC progression. Our results revealed that CD44 activation could cause a substantial decrease of CD146 expression with an equally notable converse effect upon CD44-siRNA inhibition. More interestingly, activation of CD44 decreased cellular CD146 and increased soluble CD146 through CD44-dependent activation of MMP. Here, we provide a possible mechanism by which CD146 suppresses BC progression as a target of CD44-downstream signaling, regulating neovascularization and cancer cell motility

An extensive computational approach to analyze and characterize the functional mutations in the galactose-1-phosphate uridyl transferase (GALT) protein responsible for classical galactosemia

Type I galactosemia is a very rare autosomal recessive genetic metabolic disorder that occurs because of the mutations present in the galactose-1-phosphate uridyl transferase (GALT) gene, resulting in a deficiency of the GALT enzyme. The action of the GALT enzyme is to convert galactose-1-phosphate and uridine diphosphate glucose into glucose-1-phosphate (G1P) and uridine diphosphate-galactose, a crucial second step of the Leloir pathway. A missense mutation in the GALT enzyme leads to variable galactosemia's clinical presentations, ranging from mild to severe. Our study aimed to employ a comprehensive computational pipeline to analyze the most prevalent missense mutations (p.S135L, p.K285 N, p.Q188R, and p.N314D) responsible for galactosemia; these genes could serve as potential targets for chaperone therapy. We analyzed the four mutations through different computational analyses, including amino acid conservation, in silico pathogenicity and stability predictions, and macromolecular simulations (MMS) at 50 ns The stability and pathogenicity predictors showed that the p.Q188R and p.S135L mutants are the most pathogenic and destabilizing. In agreement with these results, MMS analysis demonstrated that the p.Q188R and p.S135L mutants possess higher deviation patterns, reduced compactness, and intramolecular H-bonds of the protein. This could be due to the physicochemical modifications that occurred in the mutants p.S135L and p.Q188R compared to the native. Evolutionary conservation analysis revealed that the most prevalent mutations positions were conserved among different species except N314. The proposed research study is intended to provide a basis for the therapeutic development of drugs and future treatment of classical galactosemia and possibly other genetic diseases using chaperone therapy

The European Network for Translational Research in Atrial Fibrillation (EUTRAF): objectives and initial results.

Atrial fibrillation (AF) is the most common sustained arrhythmia in the general population. As an age-related arrhythmia AF is becoming a huge socio-economic burden for European healthcare systems. Despite significant progress in our understanding of the pathophysiology of AF, therapeutic strategies for AF have not changed substantially and the major challenges in the management of AF are still unmet. This lack of progress may be related to the multifactorial pathogenesis of atrial remodelling and AF that hampers the identification of causative pathophysiological alterations in individual patients. Also, again new mechanisms have been identified and the relative contribution of these mechanisms still has to be established. In November 2010, the European Union launched the large collaborative project EUTRAF (European Network of Translational Research in Atrial Fibrillation) to address these challenges. The main aims of EUTRAF are to study the main mechanisms of initiation and perpetuation of AF, to identify the molecular alterations underlying atrial remodelling, to develop markers allowing to monitor this processes, and suggest strategies to treat AF based on insights in newly defined disease mechanisms. This article reports on the objectives, the structure, and initial results of this network

A national survey of medical education fellowships

Purpose: The purpose of our study was to determine the prevalence, focus, time commitment, graduation requirements and programme evaluation methods of medical education fellowships throughout the United States. Medical education fellowships are defined as a single cohort of medical teaching faculty who participate in an extended faculty development programme. Methods: A 26-item online questionnaire was distributed to all US medical schools (n=127) in 2005 and 2006. The questionnaire asked each school if it had a medical education fellowship and the characteristics of the fellowship programme. Results: Almost half (n=55) of the participating schools (n=120, response rate 94.5 %) reported having fellowships. Duration (10–584 hours) and length (<1 month–48 months) varied; most focused on teaching skills, scholarly dissemination and curriculum design, and required the completion of a scholarly project. A majority collected participant satisfaction; few used other programme evaluation strategies. Conclusions: The number of medical education fellowships increased rapidly during the 1990s and 2000s. Across the US, programmes are similar in participant characteristics and curricular focus but unique in completion requirements. Fellowships collect limited programme evaluation data, indicating a need for better outcome data. These results provide benchmark data for those implementing or revising existing medical education fellowships

Spin driven emergent antiferromagnetism and metal insulator transition in nanoscale p-Si

The entanglement of the charge, spin and orbital degrees of freedom can give rise to emergent behavior especially in thin films, surfaces and interfaces. Often, materials that exhibit those properties require large spin orbit coupling. We hypothesize that the emergent behavior can also occur due to spin, electron and phonon interactions in widely studied simple materials such as Si. That is, large intrinsic spin-orbit coupling is not an essential requirement for emergent behavior. The central hypothesis is that when one of the specimen dimensions is of the same order (or smaller) as the spin diffusion length, then non-equilibrium spin accumulation due to spin injection or spin-Hall effect (SHE) will lead to emergent phase transformations in the non-ferromagnetic semiconductors. In this experimental work, we report spin mediated emergent antiferromagnetism and metal insulator transition in a Pd (1 nm)/Ni81Fe19 (25 nm)/MgO (1 nm)/p-Si (~400 nm) thin film specimen. The spin-Hall effect in p-Si, observed through Rashba spin-orbit coupling mediated spin-Hall magnetoresistance behavior, is proposed to cause the spin accumulation and resulting emergent behavior. The phase transition is discovered from the diverging behavior in longitudinal third harmonic voltage, which is related to the thermal conductivity and heat capacity.Comment: 34 pages, Physica Status Solidi B- Physics, 201