Online Model Server for the Jefferson Lab accelerator

A beam physics model server (Art++) has been developed for the Jefferson Lab accelerator. This online model server is a redesign of the ARTEMIS model server. The need arose from an impedance mismatch between the current requirements and ARTEMIS capabilities. The purpose of the model server is to grant access to both static (machine lattice parameters) and dynamic (actual machine settings) data using a single programming interface. A set of useful optics calculations (R-matrix, orbit fit, etc.) has also been implemented and can be invoked by clients via the model interface. Clients may also register their own dynamic models in the server. The server interacts with clients using the CDEV protocol and data integrity is guaranteed by a relational database (Oracle8i) accessed through a persistence layer. By providing a centralized repository for both data and optics calculations, the following benefits were achieved: optimal use of network consumption, software reuse, and ease of maintenance

Fish evacuate smoothly respecting a social bubble

Crowd movements are observed among different species and on different scales, from insects to mammals, as well as in non-cognitive systems, such as motile cells. When forced to escape through a narrow opening, most terrestrial animals behave like granular materials and clogging events decrease the efficiency of the evacuation. Here, we explore the evacuation behavior of macroscopic, aquatic agents, neon fish, and challenge their gregarious behavior by forcing the school through a constricted passage. Using a statistical analysis method developed for granular matter and applied to crowd evacuation, our results clearly show that, unlike crowds of people or herds of sheep, no clogging occurs at the bottleneck. The fish do not collide and wait for a minimum waiting time between two successive exits, while respecting a social distance. When the constriction becomes similar to or smaller than their social distance, the individual domains defined by this cognitive distance are deformed and fish density increases. We show that the current of escaping fish behaves like a set of deformable 2D-bubbles, their 2D domain, passing through a constriction. Schools of fish show that, by respecting social rules, a crowd of individuals can evacuate without clogging, even in an emergency situation.Comment: 7 pages, 4 figure

A feasibility randomised controlled trial of the New Orleans intervention of infant mental health: a study protocol

Child maltreatment is associated with life-long social, physical, and mental health problems. Intervening early to provide maltreated children with safe, nurturing care can improve outcomes. The need for prompt decisions about permanent placement (i.e., regarding adoption or return home) is internationally recognised. However, a recent Glasgow audit showed that many maltreated children “revolve” between birth families and foster carers. This paper describes the protocol of the first exploratory randomised controlled trial of a mental health intervention aimed at improving placement permanency decisions for maltreated children. This trial compares an infant's mental health intervention with the new enhanced service as usual for maltreated children entering care in Glasgow. As both are new services, the trial is being conducted from a position of equipoise. The outcome assessment covers various fields of a child’s neurodevelopment to identify problems in any ESSENCE domain. The feasibility, reliability, and developmental appropriateness of all outcome measures are examined. Additionally, the potential for linkage with routinely collected data on health and social care and, in the future, education is explored. The results will inform a definitive randomised controlled trial that could potentially lead to long lasting benefits for the Scottish population and which may be applicable to other areas of the world

Modelling the probability of microhabitat formation on trees using cross-sectional data

The rate of TreM formation per unit diameter growth was modelled as a function of tree diameter at breast height (DBH), and the model was calibrated considering cross-sectional observations TreMs on trees of different sizes. The model predicted realistic TreM formation rates at the tree and stand levels in forests dominated by Abies alba and Fagus sylvatica. This approach opens new perspectives to the analysis of forest biodiversity conservation strategies

Correlation study between the access mark and the performance in project-based and standard courses

The access mark to engineering studies is often used as an a priori success estimator. In our institution, we have observed that the correlation of the access mark with the grades obtained in project-based courses (R=0.52) is slightly lower than the one obtained with the average of the other non-project-based courses (R=0.58), and is especially low in capstone projects (R=0.31). Project-based and Challenge-based courses are one of the most acknowledged ways of promoting the learning of transversal skills, specifically innovation and entrepreneurship skills. In our institution, ICT engineering bachelor students perform a project-courses path, with three subjects of growing complexity in the 2nd, 3d and 4th year. While the first two are partially guided and with challenges proposed by the faculty members, the 3d one is a 12 ECTS capstone project with challenges proposed by industry or external institutions. In this study, we have analyzed the performance of the students along 10 academic years (2011-2012 to 2020-2021). Not only the correlation with the access mark in these courses is lower but the prediction interval is also different. While it is almost impossible that a student with a low access mark gets an outstanding average mark in the bachelor and vice-versa, there are students with a low access mark which have an outstanding performance in the capstone project and students with a very high access mark and with high results in analytical courses but with a poor performance in capstone projects. Therefore, a different kind of skills are promoted in these courses

Challenges in dengue research: A computational perspective

This is the final version of the article. Available from Wiley via the DOI in this record.The dengue virus is now the most widespread arbovirus affecting human populations, causing significant economic and social impact in South America and South-East Asia. Increasing urbanization and globalization, coupled with insufficient resources for control, misguided policies or lack of political will, and expansion of its mosquito vectors are some of the reasons why interventions have so far failed to curb this major public health problem. Computational approaches have elucidated on dengue's population dynamics with the aim to provide not only a better understanding of the evolution and epidemiology of the virus but also robust intervention strategies. It is clear, however, that these have been insufficient to address key aspects of dengue's biology, many of which will play a crucial role for the success of future control programmes, including vaccination. Within a multiscale perspective on this biological system, with the aim of linking evolutionary, ecological and epidemiological thinking, as well as to expand on classic modelling assumptions, we here propose, discuss and exemplify a few major computational avenues—real-time computational analysis of genetic data, phylodynamic modelling frameworks, within-host model frameworks and GPU-accelerated computing. We argue that these emerging approaches should offer valuable research opportunities over the coming years, as previously applied and demonstrated in the context of other pathogens.JL, AW and SG received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement no. 268904 - DIVERSITY. MR was supported by a Royal Society University Research Fellowship. NRF by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant number 204311/Z/16/Z). WT has received funding from a doctoral scholarship from the Engineering and Physical Sciences Research Council (EPSRC) Doctoral Training Partnership

Nuclear rupture at sites of high curvature compromises retention of DNA repair factors.

The nucleus is physically linked to the cytoskeleton, adhesions, and extracellular matrix-all of which sustain forces, but their relationships to DNA damage are obscure. We show that nuclear rupture with cytoplasmic mislocalization of multiple DNA repair factors correlates with high nuclear curvature imposed by an external probe or by cell attachment to either aligned collagen fibers or stiff matrix. Mislocalization is greatly enhanced by lamin A depletion, requires hours for nuclear reentry, and correlates with an increase in pan-nucleoplasmic foci of the DNA damage marker γH2AX. Excess DNA damage is rescued in ruptured nuclei by cooverexpression of multiple DNA repair factors as well as by soft matrix or inhibition of actomyosin tension. Increased contractility has the opposite effect, and stiff tumors with low lamin A indeed exhibit increased nuclear curvature, more frequent nuclear rupture, and excess DNA damage. Additional stresses likely play a role, but the data suggest high curvature promotes nuclear rupture, which compromises retention of DNA repair factors and favors sustained damage

Evaluation of serological tests for Trichinella infections in pigs

The Dutch slaughter pig population is practically free of Trichinella spiralis. However, at slaughter every pig is tested for presence of larvae using the digestion method for export certification . A new 2006 EU directive concerning meat inspection for Trichinella spp. offers new opportunities to monitor Trichinella at herd level instead. Also serological methods are allowed when approved by the Commumty Reference Laboratory (CRL). To evaluate the usefulness of serological tests for momtoring a virtually free population for Trichinella, Bayesian methodology was used to estimate the diagnostic test parameters sensitivity and specificity, in the absence of a Gold Standard test

Microtubules Deform the Nuclear Membrane and Disrupt Nucleocytoplasmic Transport in Tau-Mediated Frontotemporal Dementia

The neuronal microtubule-associated protein tau, MAPT, is central to the pathogenesis of many dementias. Autosomal-dominant mutations in MAPT cause inherited frontotemporal dementia (FTD), but the underlying pathogenic mechanisms are unclear. Using human stem cell models of FTD due to MAPT mutations, we find that tau becomes hyperphosphorylated and mislocalizes to cell bodies and dendrites in cortical neurons, recapitulating a key early event in FTD. Mislocalized tau in the cell body leads to abnormal microtubule movements in FTD-MAPT neurons that grossly deform the nuclear membrane. This results in defective nucleocytoplasmic transport, which is corrected by microtubule depolymerization. Neurons in the post-mortem human FTD-MAPT cortex have a high incidence of nuclear invaginations, indicating that tau-mediated nuclear membrane dysfunction is an important pathogenic process in FTD. Defects in nucleocytoplasmic transport in FTD point to important commonalities in the pathogenic mechanisms of tau-mediated dementias and ALS-FTD due to TDP-43 and C9orf72 mutations