Fourth Order Algorithms for Solving the Multivariable Langevin Equation and the Kramers Equation

We develop a fourth order simulation algorithm for solving the stochastic Langevin equation. The method consists of identifying solvable operators in the Fokker-Planck equation, factorizing the evolution operator for small time steps to fourth order and implementing the factorization process numerically. A key contribution of this work is to show how certain double commutators in the factorization process can be simulated in practice. The method is general, applicable to the multivariable case, and systematic, with known procedures for doing fourth order factorizations. The fourth order convergence of the resulting algorithm allowed very large time steps to be used. In simulating the Brownian dynamics of 121 Yukawa particles in two dimensions, the converged result of a first order algorithm can be obtained by using time steps 50 times as large. To further demostrate the versatility of our method, we derive two new classes of fourth order algorithms for solving the simpler Kramers equation without requiring the derivative of the force. The convergence of many fourth order algorithms for solving this equation are compared.Comment: 19 pages, 2 figure

Superdomain dynamics in ferroelectric-ferroelastic films: Switching, jamming, and relaxation

Recent experimental work shows that ferroelectric switching can occur in large jumps in which ferroelastic superdomains switch together, rather than having the numerous smaller ferroelectric domains switch within them. In this sense, the superdomains play a role analogous to that of Abrikosov vortices in thin superconducting films under the Kosterlitz-Thouless framework, which control the dynamics more than individual Cooper pairs within them do. Here, we examine the dynamics of ferroelastic superdomains in ferroelastic ferroelectrics and their role in switching devices such as memories. Jamming of ferroelectric domains in thin films has revealed an unexpected time dependence of t-1/4 at long times (hours), but it is difficult to discriminate between power-law and exponential relaxation. Other aspects of this work, including spatial period doubling of domains, led to a description of ferroelastic domains as nonlinear processes in a viscoelastic medium, which produce folding and metastable kinetically limited states. This 1/4 exponent is a surprising agreement with the well-known value of 1/4 for coarsening dynamics in viscoelastic media. We try to establish a link between these two processes, hitherto considered unrelated, and with superdomains and domain bundles. We note also that high-Tc superconductors share many of the ferroelastic domain properties discussed here and that several new solar cell materials and metalinsulator transition systems are ferroelastic

Superdomain dynamics in ferroelectric-ferroelastic films: Switching, jamming, and relaxation

Recent experimental work shows that ferroelectric switching can occur in large jumps in which ferroelastic superdomains switch together, rather than having the numerous smaller ferroelectric domains switch within them. In this sense, the superdomains play a role analogous to that of Abrikosov vortices in thin superconducting films under the Kosterlitz-Thouless framework, which control the dynamics more than individual Cooper pairs within them do. Here, we examine the dynamics of ferroelastic superdomains in ferroelastic ferroelectrics and their role in switching devices such as memories. Jamming of ferroelectric domains in thin films has revealed an unexpected time dependence of t-1/4 at long times (hours), but it is difficult to discriminate between power-law and exponential relaxation. Other aspects of this work, including spatial period doubling of domains, led to a description of ferroelastic domains as nonlinear processes in a viscoelastic medium, which produce folding and metastable kinetically limited states. This 1/4 exponent is a surprising agreement with the well-known value of 1/4 for coarsening dynamics in viscoelastic media. We try to establish a link between these two processes, hitherto considered unrelated, and with superdomains and domain bundles. We note also that high-Tc superconductors share many of the ferroelastic domain properties discussed here and that several new solar cell materials and metalinsulator transition systems are ferroelastic

Towards a Convergent Development of Learning Analytics

In the last 7 years, since the first LAK conference, Learning Analytics has grown rapidly as a field from a small group of interested scholars and practitioners to one of the most scientifically successful and institutionally accepted areas of Learning and Educational Technologies. Learning Analytics is often referred as a "Middle-Space" where experts from diverse fields (from the Learning Sciences, Computer Science, Human-Computer Interaction, Psychology and Behavioural Sciences, just to name a few) share their perspectives on how to better understand and optimize learning processes and environments using this new instrument called Data Science

Learning Analytics: Looking to the Future

This second issue of the Journal of Learning Analytics in 2017 is the first edited by the full new journal editorial team. As the baton is passed on, we would like to thank the founding editors for their work initiating the journal and nurturing its development over the past several years. We look forward to continuing that tradition of excellence. This issue includes four research paper contributions, and a special section on the ‘Shape of Educational Data’. This editorial is also an opportunity for us to reflect on the development of the journal so far, and describe some changes we are making to continue the expansion and maturation of a growing community of learning analytics researchers and practitioners.</jats:p

Thaptomys Thomas 1915 (Rodentia, Sigmodontinae, Akodontini) with karyotypes 2n = 50, FN = 48, and 2n = 52, FN = 52: Two monophyletic lineages recovered by molecular phylogeny

A novel karyotype with 2n = 50, FN = 48, was described for specimens of Thaptomys collected at Una, State of Bahia, Brazil, which are morphologically indistinguishable from Thaptomys nigrita, 2n = 52, FN = 52, found in other localities. It was hence proposed that the 2n = 50 karyotype could belong to a distinct species, cryptic of Thaptomys nigrita, once chromosomal rearrangements observed, along with the geographic distance, might represent a reproductive barrier between both forms. Phylogenetic analyses using maximum parsimony and maximum likelihood based on partial cytochrome b sequences with 1077 bp were performed, attempting to establish the relationships among the individuals with distinct karyotypes along the geographic distribution of the genus; the sample comprised 18 karyotyped specimens of Thaptomys, encompassing 15 haplotypes, from eight different localities of the Atlantic Rainforest. The intra-generic relationships corroborated the distinct diploid numbers, once both phylogenetic reconstructions recovered two monophyletic lineages, a northeastern clade grouping the 2n = 50 and a southeastern clade with three subclades, grouping the 2n = 52 karyotype. The sequence divergence observed between their individuals ranged from 1.9% to 3.5%

The MentDis_ICF65+ study protocol: prevalence, 1-year incidence and symptom severity of mental disorders in the elderly and their relationship to impairment, functioning (ICF) and service utilisation.

Background: The EU currently lacks reliable data on the prevalence and incidence of mental disorders in older people. Despite the availability of several national and international epidemiological studies, the size and burden of mental disorders in the elderly remain unclear due to various reasons. Therefore, the aims of the MentDis_ICF65+ study are (1) to adapt existing assessment instruments, and (2) to collect data on the prevalence, the incidence, and the natural course and prognosis of mental disorders in the elderly. Method/design: Using a cross-sectional and prospective longitudinal design, this multi-centre study from six European countries and associated states (Germany, Great Britain, Israel, Italy, Spain, and Switzerland) is based on age-stratified, random samples of elderly people living in the community. The study program consists of three phases: (1) a methodological phase devoted primarily to the adaptation of age- and gender-specific assessment tools for older people (e.g., the Composite International Diagnostic Interview, CIDI) as well as psychometric evaluations including translation, back translation; (2) a baseline community study in all participating countries to assess the lifetime, 12 month and 1 month prevalence and comorbidity of mental disorders, including prior course, quality of life, health care utilization and helpseeking, impairments and participation and, (3) a 12 month follow-up of all baseline participants to monitor course and outcome as well as examine predictors. Discussion: The study is an essential step forward towards the further development and improvement of harmonised instruments for the assessment of mental disorders as well as the evaluation of activity impairment and participation in older adults. This study will also facilitate the comparison of cross-cultural results. These results will have bearing on mental health care in the EU and will offer a starting point for necessary structural changes to be initiated for mental health care policy at the level of mental health care politics

Finding 3D motifs in ribosomal RNA structures

The identification of small structural motifs and their organization into larger subassemblies is of fundamental interest in the analysis, prediction and design of 3D structures of large RNAs. This problem has been studied only sparsely, as most of the existing work is limited to the characterization and discovery of motifs in RNA secondary structures. We present a novel geometric method for the characterization and identification of structural motifs in 3D rRNA molecules. This method enables the efficient recognition of known 3D motifs, such as tetraloops, E-loops, kink-turns and others. Furthermore, it provides a new way of characterizing complex 3D motifs, notably junctions, that have been defined and identified in the secondary structure but have not been analyzed and classified in three dimensions. We demonstrate the relevance and utility of our approach by applying it to the Haloarcula marismortui large ribosomal unit. Pending the implementation of a dedicated web server, the code accompanying this article, written in JAVA, is available upon request from the contact author

Neonate Human Remains: A Window of Opportunity to the Molecular Study of Ancient Syphilis

Ancient DNA (aDNA) analysis can be a useful tool in bacterial disease diagnosis in human remains. However, while the recovery of Mycobacterium spp. has been widely successful, several authors report unsuccessful results regarding ancient treponemal DNA, casting doubts on the usefulness of this technique for the diagnosis of ancient syphilis. Here, we present results from an analysis of four newborn specimens recovered from the crypt of “La Ermita de la Soledad” (XVI–XVII centuries), located in the province of Huelva in the southwest of Spain. We extracted and analyzed aDNA in three independent laboratories, following specific procedures generally practiced in the aDNA field, including cloning of the amplified DNA fragments and sequencing of several clones. This is the most ancient case, reported to date, from which detection of DNA from T. pallidum subspecies pallidum has been successful in more than one individual, and we put forward a hypothesis to explain this result, taking into account the course of the disease in neonate individuals

Detection and Molecular Characterization of 9000-Year-Old Mycobacterium tuberculosis from a Neolithic Settlement in the Eastern Mediterranean

Background: Mycobacterium tuberculosis is the principal etiologic agent of human tuberculosis. It has no environmental reservoir and is believed to have co-evolved with its host over millennia. This is supported by skeletal evidence of the disease in early humans, and inferred from M. tuberculosis genomic analysis. Direct examination of ancient human remains for M. tuberculosis biomarkers should aid our understanding of the nature of prehistoric tuberculosis and the host/pathogen relationship.Methodology/Principal Findings: We used conventional PCR to examine bone samples with typical tuberculosis lesions from a woman and infant, who were buried together in the now submerged site of Atlit-Yam in the Eastern Mediterranean, dating from 9250-8160 years ago. Rigorous precautions were taken to prevent contamination, and independent centers were used to confirm authenticity of findings. DNA from five M. tuberculosis genetic loci was detected and had characteristics consistent with extant genetic lineages. High performance liquid chromatography was used as an independent method of verification and it directly detected mycolic acid lipid biomarkers, specific for the M. tuberculosis complex.Conclusions/Significance: Human tuberculosis was confirmed by morphological and molecular methods in a population living in one of the first villages with evidence of agriculture and animal domestication. The widespread use of animals was not a source of infection but may have supported a denser human population that facilitated transmission of the tubercle bacillus. The similarity of the M. tuberculosis genetic signature with those of today gives support to the theory of a long-term co-existence of host and pathogen