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The production of simulated datasets for use by physics analyses consumes a large fraction of ATLAS computing resources, a problem that will only get worse as increases in the instantaneous luminosity provided by the LHC lead to more collisions per bunch crossing (pile-up). One of the more resource-intensive steps in the Monte Carlo production is reconstructing the tracks in the ATLAS Inner Detector, which takes up about 60% of the total detector reconstruction time. This talk discusses a novel technique called track overlay, which substantially speeds up the Inner Detector reconstruction. In track overlay the pile-up Inner Detector tracks are reconstructed ahead of time and overlaid onto the Inner Detector tracks from the simulated hard-scatter event. We present our implementation of this track overlay approach as part of the ATLAS Fast Chain simulation, as well as a method for deciding in which cases it is possible to use track overlay in the reconstruction of simulated data without performance degradation, and in which it is preferable to use the current approach.

The ATLAS physics program relies on very large samples of Geant4 simulated events, which provide a highly detailed and accurate simulation of the ATLAS detector. However, this accuracy comes with a high price in CPU, and the sensitivity of many physics analyses is already limited by the available Monte Carlo statistics and will be even more so in the future. Therefore, sophisticated fast simulation tools have been developed. In Run 3 we aim to replace the calorimeter shower simulation for most samples with a new parametrised description of longitudinal and lateral energy deposits, including machine learning approaches, to achieve a fast and accurate description. Looking further ahead, prototypes are being developed using cutting edge machine learning approaches to learn the appropriate calorimeter response, which are expected to improve modeling of correlations within showers. Two different approaches, using Variational Auto-Encoders (VAEs) or Generative Adversarial Networks (GANs), are trained to model the shower simulation. Additional fast simulation tools will replace the inner detector simulation, as well as digitization and reconstruction algorithms, achieving up to two orders of magnitude improvement in speed. In this talk, we will describe the new tools for fast production of simulated events and an exploratory analysis of the deep learning methods.

Estimations of the CPU resources that will be needed to produce simulated data for the future runs of the ATLAS experiment at the LHC, indicate a compelling need to speed-up the process to reduce the computational time required. While different fast simulation projects are ongoing, full Geant4 based simulation will still be heavily used and is expected to consume the biggest portion of the total estimated processing time. In order to run effectively on modern architectures and profit from multi-core designs a migration of the Athena framework to a multi-threading processing model was performed. A multi-threaded simulation based on AthenaMT and Geant4MT, enables substantial decreases in the memory footprint of jobs, largely from shared geometry and cross-section tables. This approach scales better with respect to the multi-processing approach (AthenaMP) especially on the architectures that are foreseen to be used in the next LHC runs. In these proceedings we report about the status of the multi-threaded simulation in ATLAS, focusing on the different challenges of its validation process. We demonstrate the different tools and strategies that have been used for debugging multi-threaded runs versus the corresponding sequential ones, in order to have a fully reproducible and consistent simulation result.

Software improvements in the ATLAS Geant4-based simulation are critical to keep up with evolving hardware and increasing luminosity. Geant4 simulation currently accounts for about 50% of CPU consumption in ATLAS and it is expected to remain the leading CPU load during Run 4 (HL-LHC upgrade) with an approximately 25% share in the most optimistic computing model. The ATLAS experiment recently developed two algorithms for optimizing Geant4 performance: Neutron Russian Roulette (NRR) and range cuts for electromagnetic processes. The NRR randomly terminates a fraction of low energy neutrons in the simulation and weights energy deposits of the remaining neutrons to maintain physics performance. Low energy neutrons typically undergo many interactions with the detector material and their path becomes uncorrelated with the point of origin. Therefore, the response of neutrons can be efficiently estimated only with a subset of neutrons. Range cuts for electromagnetic processes exploit a built-in feature of Geant4 and terminate low energy electrons that originate from physics processes including conversions, the photoelectric effect, and Compton scattering. Both algorithms were tuned to maintain physics performance in ATLAS and together they bring about a 20% speed-up of the ATLAS Geant4 simulation. Additional ideas for improvements, currently under investigation, will also be discussed in this paper. Lastly, this paper presents how the ATLAS experiment utilizes software packages such as Intel’s VTune to identify and resolve hot-spots in simulation.

In this article, we seek to discuss the tension between relational personhood, characterised by ‘dividuals’, and the individualisation of persons whose driving force was the creation of new embodied skills learnt to perform the wide range of new tasks which defined the farming way of life. This is, in effect, an exploration of the consequences of a vivid new world itself created by the interactions of a wider variety of individuals with different skills than had ever been seen before, including those required for domesticating animals, potting, building rectangular houses, growing cereals and pulses and polishing stone tools and ornaments.

Abstract Background Parkinson's disease (PD) is a slowly progressive neurodegenerative disorder which affects widespread areas of the brainstem, basal ganglia and cerebral cortex. A number of proteins are known to accumulate in parkinsonian brains including ubiquitin and α-synuclein. Prion diseases are sporadic, genetic or infectious disorders with various clinical and histopathological features caused by prion proteins as infectious proteinaceous particles transmitting a misfolded protein configuration through brain tissue. The most important form is Creutzfeldt-Jakob disease which is associated with a self-propagating pathological precursor form of the prion protein that is physiologically widely distributed in the central nervous system. Discussion It has recently been found that α-synuclein may behave similarly to the prion precursor and propagate between cells. The post-mortem proof of α-synuclein containing Lewy bodies in embryonic dopamine cells transplants in PD patient suggests that the misfolded protein might be transmitted from the diseased host to donor neurons reminiscent of prion behavior. The involvement of the basal ganglia and brainstem in the degenerative process are other congruencies between Parkinson's and Creutzfeldt-Jakob disease. However, a number of issues advise caution before categorizing Parkinson's disease as a prion disorder, because clinical appearance, brain imaging, cerebrospinal fluid and neuropathological findings exhibit fundamental differences between both disease entities. Most of all, infectiousness, a crucial hallmark of prion diseases, has never been observed in PD so far. Moreover, the cellular propagation of the prion protein has not been clearly defined and it is, therefore, difficult to assess the molecular similarities between the two disease entities. Summary At the current state of knowledge, the molecular pathways of transmissible pathogenic proteins are not yet fully understood. Their exact involvement in the pathophysiology of prion disorders and neurodegenerative diseases has to be further investigated in order to elucidate a possible overlap between both disease categories that are currently regarded as distinct entities.

Abstract Background Female mice and rats injected with estrogen perinatally become anovulatory and develop follicular cysts. The current consensus is that this adverse response to estrogen involves the hypothalamus and occurs because of an estrogen-induced alteration in the GnRH delivery system. Whether or not this is true has yet to be firmly established. The present study examined an alternate possibility in which anovulation and cyst development occurs through an estrogen-induced disruption in the immune system, achieved through the intermediation of the thymus gland. Methods, Results and Conclusion A putative role for the thymus in estrogen-induced anovulation and follicular cyst formation (a model of PCOS) was examined in female mice by removing the gland prior to estrogen injection. Whereas all intact, female mice injected with 20 ug estrogen at 5–7 days of age had ovaries with follicular cysts, no cysts were observed in animals in which thymectomy at 3 days of age preceded estrogen injection. In fact, after restoring immune function by thymocyte replacement, the majority of thymectomized, estrogen-injected mice had ovaries with corpora lutea. Thus, when estrogen is unable to act on the thymus, ovulation occurs and follicular cysts do not develop. This implicates the thymus in the cysts' genesis and discounts the role of the hypothalamus. Subsequent research established that the disease is transferable by lymphocyte infusion. Transfer took place between 100-day-old estrogen-injected and 15-day-old naïve mice only when recipients were thymectomized at 3 days of age. Thus, a prerequisite for cyst formation is the absence of regulatory T cells. Their absence in donor mice was judged to be the result of an estrogen-induced increase in the thymus' vascular permeability, causing de facto circumvention of the final stages of regulatory T cell development. The human thymus has a similar vulnerability to steroid action during the fetal stage. We propose that in utero exposure to excessive levels of steroids such as estrogen has a long-term effect on the ability of the thymus to produce regulatory T cells. In female offspring this can lead to PCOS.

Abstract Background At diagnosis, 16% of rheumatoid arthritis (RA) patients may have foot joint involvement, increasing to 90% as disease duration increases. This can lead to joint instability, difficulties in walking and limitation in functional ability that restricts activities of daily living. The podiatrist plays an important role in the multidisciplinary team approach to the management of foot problems. The aim of this study was to undertake a clinical audit of foot problems in patients with RA treated at Counties Manukau District Health Board. Methods Patients with RA were identified through rheumatological clinics run within CMDHB. 100 patients were eligible for inclusion. Specific foot outcome tools were used to evaluate pain, disability and function. Observation on foot lesions were noted and previous history of foot assessment, footwear/insoles and foot surgery were evaluated. Results The median age of the cohort was 60 (IQR: 51–64) years old with median disease duration of 15 (IQR: 7.3–25) years. Over 85% presented with foot lesions that included corns and callus over the forefoot region and lesser toe deformities. Moderate to high disability was noted. High levels of forefoot structural damage were observed. 76% had not seen a podiatrist and 77% reported no previous formal foot assessment. 40% had been seen at the orthotic centre for specialised footwear and insoles. 27% of RA patients reported previous foot surgery. A large proportion of patients wore inappropriate footwear. Conclusion This clinical audit suggests that the majority of RA patients suffer from foot problems. Future recommendations include the provision of a podiatrist within the current CMDHB multidisciplinary rheumatology team to ensure better services for RA patients with foot problems.

Abstract Background CD4+CD25high regulatory T (TReg) cells modulate antigen-specific T cell responses, and can suppress anti-viral immunity. In HTLV-1 infection, a selective decrease in the function of TReg cell mediated HTLV-1-tax inhibition of FOXP3 expression has been described. The purpose of this study was to assess the frequency and phenotype of TReg cells in HTLV-1 asymptomatic carriers and in HTLV-1-associated neurological disease (HAM/TSP) patients, and to correlate with measures of T cell activation. Results We were able to confirm that HTLV-I drives activation, spontaneous IFNγ production, and proliferation of CD4+ T cells. We also observed a significantly lower proportion of CTLA-4+ TReg cells (CD4+CD25high T cells) in subjects with HAM/TSP patients compared to healthy controls. Ki-67 expression was negatively correlated to the frequency of CTLA-4+ TReg cells in HAM/TSP only, although Ki-67 expression was inversely correlated with the percentage of CD127low TReg cells in healthy control subjects. Finally, the proportion of CD127low TReg cells correlated inversely with HTLV-1 proviral load. Conclusion Taken together, the results suggest that TReg cells may be subverted in HAM/TSP patients, which could explain the marked cellular activation, spontaneous cytokine production, and proliferation of CD4+ T cells, in particular those expressing the CD25highCD127low phenotype. TReg cells represent a potential target for therapeutic intervention for patients with HTLV-1-related neurological diseases.

Abstract In mouse ovaries, the enzyme 3 beta-hydroxysteroid dehydrogenase (HSD) is distributed between microsomes and mitochondria. Throughout the follicular phase of the estrous cycle, the HSD activity in microsomes is predominant; whereas, after LH stimulation, HSD activity during the luteal phase is highest in the mitochondria. The current study examined whether or not LH stimulation always results in an increase in mitochondrial HSD activity. This was accomplished by measuring the HSD activity in microsomal and mitochondrial fractions from ovaries of pregnant mice. These animals have two peaks of LH during gestation, and one peak of LH after parturition. It was found that mitochondrial HSD activity was highest after each peak of LH. It is proposed that mitochondrial HSD is essential for the synthesis of high levels of progesterone. The increase in HSD activity in mitochondria after LH stimulation occurs because: 1) LH initiates the simultaneous synthesis of HSD and the cholesterol side-chain cleavage enzyme (P450scc); and, 2) HSD and P450scc bind together to form a complex, which becomes inserted into the inner membrane of the mitochondria. High levels of progesterone are synthesized by mitochondrial HSD because: 1) the requisite NAD+ cofactor for progesterone synthesis is provided directly by the mitochondria, rather than indirectly via the rate limiting malate-aspartate shuttle; and, 2) the end-product inhibition of P450scc by pregnenolone is eliminated because pregnenolone is converted to progesterone.

Abstract Condensation of sperm chromatin occurs after spermatozoa have left the caput epididymis and are in transit to the cauda epididymis, during which time large numbers of disulfide bonds are formed. The formation of these disulfide bonds requires the repeated oxidation of the cofactor, NAD(P)H. To date, the means by which this oxidation is achieved has yet to be elucidated. Spermatozoa lose the bulk of their cytoplasm prior to leaving the testis; and, as a result, any shuttle systems for removing and transferring reducing equivalents into the mitochondria are unlikely to be operational. In an apparent preparation for the loss of cytoplasm, however, the following events occur during spermatogenesis. First, androgen-binding protein (ABP) is produced by the Sertoli cells of the testis; second, high affinity binding sites for ABP are inserted into the membrane surrounding the nucleus; and third, a nuclear location is acquired for the enzyme, 3α-hydroxysteroid dehydrogenase (3α-HSD). We propose that after the loss of cytoplasm, the nuclear region of spermatozoa is directly accessible to constituents contained in the lumen of the caput epididymis. As a consequence, luminal ABP attaches itself to the nuclear membrane via its binding sites, and is internalized. After internalization, ABP exerts its principle function, which is to bind to luminal 5α-dihydrotestosterone (5α-DHT), thereby ensuring its availability to the enzyme, 3α-HSD. In the conversion of 5α-DHT to 3α-androstanediol (3α-Diol), NAD(P)H is oxidized. Spermatozoa that reach the cauda epididymis have fully condensed chromatin. In addition, the nuclear region retains appreciable amounts of 5α-DHT and 3α-Diol, both bound to ABP. During fertilization, the bound 3α-Diol is converted back to 5α-DHT, reducing equivalents are transferred to NAD(P)+, and disulfide bonds are broken. IVF clinics report that spermatozoa with incompletely condensed chromatin have a low percentage of fertilization. If our proposed mechanism for chromatin condensation/decondensation is borne out by further research, IVF clinics might consider preincubating spermatozoa with 5α-DHT in order to increase the efficiency of fertilization.

Stimuli-responsive materials are exploited in biological, materials, and sensing applications. We introduce a new endogenous stimulus, biomacromolecule crowding, which we achieve by leveraging changes in thermoresponsive properties of polymers upon high concentrations of crowding agents. We prepare poly(2-oxazoline) amphiphiles that exhibit lower critical solution temperatures (LCST) in serum above physiological temperature. These amphiphiles stabilize oil-in-water nanoemulsions at temperatures below the LCST but are ineffective surfactants above the LCST, resulting in emulsion fusion. We find that the transformations observed upon heating nanoemulsions above their surfactant's LCST can instead be induced at physiological temperatures through the addition of polymers and protein, rendering thermoresponsive materials "crowding responsive." We demonstrate that the cytosol is a stimulus for nanoemulsions, with droplet fusion occurring upon injection into cells of living zebrafish embryos. This report sets the stage for classes of thermoresponsive materials to respond to macromolecule concentration rather than temperature changes.

Powered by renewable electricity, biological | inorganic hybrids employ water-splitting electrocatalysis and generate H 2 as reducing equivalents for microbial catalysis. The approach integrates the beauty of biocatalysis with the energy efficiency of inorganic materials for sustainable chemical production. Yet a successful integration requires delicate control of the hybrid's extracellular chemical environment. Such an argument is evident in the exemplary case of O 2 because biocatalysis has a stringent requirement of O 2 but the electrocatalysis may inadvertently perturb the oxidative pressure of biological moieties. Here we report the addition of perfluorocarbon (PFC) nanoemulsions promote a biocompatible O 2 microenvironment in a O 2 -sensitive N 2 -fixing biological | inorganic hybrid. Langmuir-type nonspecific binding between bacteria and nanoemulsions facilitates O 2 transport in bacterial microenvironment and leads to a 250% increase in efficiency for organic fertilizers within 120 hours. Controlling the biological microenvironment with nanomaterials heralds a general approach accommodating the compatibility in biological | inorganic hybrids., Competing Interests: DECLARATION OF INTERESTES The authors declare no competing interests.

Perfluorocarbon (PFC) nanoemulsions, droplets of fluorous solvent stabilized by surfactants dispersed in water, are simple yet versatile nanomaterials. The orthogonal nature of the fluorous phase promotes the formation of nanoemulsions through a simple, self-assembly process while simultaneously encapsulating fluorous-tagged payloads for various applications. The size, stability, and surface chemistry of PFC nanoemulsions are controlled by the surfactant. Here, we systematically study the effect of the hydrophilic portion of polymer surfactants on PFC nanoemulsions. We find that the hydrophilic block length and identity, the overall polymer hydrophilic/lipophilic balance, and the polymer architecture are all important factors. The ability to modulate these parameters enables control over initial size, stability, payload retention, cellular internalization, and protein adsorption of PFC nanoemulsions. With the insight obtained from this systematic study of polymer amphiphiles stabilizing PFC nanoemulsions, design features required for the optimal material are obtained.

Cell migration is a fundamental process in animal development, including development of the nervous system. In C. elegans, the bilateral QR and QL neuroblasts undergo initial anterior and posterior polarizations and migrations before they divide to produce neurons. A subsequent Wnt signal from the posterior instructs QL descendants to continue their posterior migration. Nck-interacting kinases (NIK kinases) have been implicated in cell and nuclear migration as well as lamellipodia formation. Studies here show that the C. elegans MIG-15 NIK kinase controls multiple aspects of initial Q cell polarization, including the ability of the cells to polarize, to maintain polarity, and to migrate. These data suggest that MIG-15 acts independently of the Wnt signal that controls QL descendant posterior migration. Furthermore, MIG-15 affects the later migrations of neurons generated from Q cell division. Finally, a mosaic analysis indicates that MIG-15 acts cell-autonomously in Q descendant migration.