Miracle-dz/UniFAR-FTUs huggingface dataset:
Erosion, deposition and material migration in the JET divertor with carbon and ITER-like walls

This study investigates erosion, deposition and material migration in the divertor of the fusion tokamak JET. Nuclear fusion provides a potential method for sustainable energy generation without large carbon emissions or long-term radioactive waste. Toroidal chambers with magnetic field coils known as tokamaks are used to contain the plasma of hydrogen fuel. The fuel ions can erode the plasma-facing materials, leading to degradation of plasma performance, limitation of vessel lifetimes and fuel retention. Plasma-material interaction is particularly significant in the divertor region of the tokamak. The carbon walls of JET-C have been replaced with the beryllium/tungsten walls of JET-ILW in anticipation of their use in the larger ITER tokamak. Determination and analysis of the different erosion/deposition characteristics provides vital information for the efficient, economic and safe operation of ITER. A combination of diagnostics and modelling techniques have been applied to produce a detailed study of the important processes and results. Rotating collectors provide time-resolved deposition measurements through varying the surfaces deposited on; quartz microbalances (QMBs) use piezoelectric crystals to measure changes in deposited mass. A simple, geometrical model is used to describe the rotating collector depositions over long timescales, incorporating experimental data from sources such as spectroscopy. More detailed, higher time resolution modelling of erosion, deposition and transport in the JET-ILW divertor is performed with a Monte Carlo code written for this study. The rotating collectors demonstrate a replacement of carbon by beryllium as the dominant impurity deposit in JET-ILW relative to JET-C and an associated reduction in deuterium retention. The total deposition rate on the JET-ILW collectors is reduced by an order of magnitude. In general, time-dependent modelled and experimental collector deposition profiles show good qualitative agreement. A lack of carbon deposition in the remote JET-C outer divertor for corner strike points is determined from the collector modelling and QMB measurements; similar behaviour is not observed for beryllium in JET-ILW. Additionally, there is a reversal of deposition asymmetry between the inner and outer divertor corners in JET-ILW. These different distributions of deposits are attributed to the different chemical properties of carbon and beryllium and their associated responses to elevated temperatures. Local beryllium surface coverages have a considerable impact on erosion and deposition behaviour in JET-ILW due to reduced impurity concentrations. Monte Carlo modelling is used to assess the impact of varying strike points, beryllium fluxes, beryllium coverages and plasma temperatures/densities. Further insight is gained through comparison of modelling and experimental results. Peaking of the beryllium influx is investigated using divertor spectroscopy and modelling, revealing the importance of the limiter phase and initial divertor phase for beryllium erosion, deposition and transport.
FlyBase at 25: looking to the future

Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interactions, and reagents such as stocks and cDNAs. Access to data is provided through a number of tools, reports, and bulk-data downloads. Looking to the future, FlyBase is expanding its focus to serve a broader scientific community. In this update, we describe new features, datasets, reagent collections, and data presentations that address this goal, including enhanced orthology data, Human Disease Model Reports, protein domain search and visualization, concise gene summaries, a portal for external resources, video tutorials and the FlyBase Community Advisory Group.
Molecular Signatures of a TLR4 Agonist-Adjuvanted HIV-1 Vaccine Candidate in Humans

Systems biology approaches have recently provided new insights into the mechanisms of action of human vaccines and adjuvants. Here, we investigated early transcriptional signatures induced in whole blood of healthy subjects following vaccination with a recombinant HIV-1 envelope glycoprotein subunit CN54gp140 adjuvanted with the TLR4 agonist glucopyranosyl lipid adjuvant-aqueous formulation (GLA-AF) and correlated signatures to CN54gp140-specific serum antibody responses. Fourteen healthy volunteers aged 18–45 years were immunized intramuscularly three times at 1-month intervals and whole blood samples were collected at baseline, 6 h, and 1, 3, and 7 days post first immunization. Subtle changes in the transcriptomic profiles were observed following immunization, ranging from over 300 differentially expressed genes (DEGs) at day 1 to nearly 100 DEGs at day 7 following immunization. Functional pathway analysis revealed blood transcription modules (BTMs) related to general cell cycle activation, and innate immune cell activation at early time points, as well as BTMs related to T cells and B cell activation at the later time points post-immunization. Diverse CN54gp140-specific serum antibody responses of the subjects enabled their categorization into high or low responders, at early (<1 month) and late (up to 6 months) time points post vaccination. BTM analyses revealed repression of modules enriched in NK cells, and the mitochondrial electron chain, in individuals with high or sustained antigen-specific antibody responses. However, low responders showed an enhancement of BTMs associated with enrichment in myeloid cells and monocytes as well as integrin cell surface interactions. Flow cytometry analysis of peripheral blood mononuclear cells obtained from the subjects revealed an enhanced frequency of CD56dim NK cells in the majority of vaccines 14 days after vaccination as compared with the baseline. These results emphasize the utility of a systems biology approach to enhance our understanding on the mechanisms of action of TLR4 adjuvanted human vaccines.
Neural Avalanches at the Critical Point between Replay and Non-Replay of Spatiotemporal Patterns

We model spontaneous cortical activity with a network of coupled spiking units, in which multiple spatio-temporal patterns are stored as dynamical attractors. We introduce an order parameter, which measures the overlap (similarity) between the activity of the network and the stored patterns. We find that, depending on the excitability of the network, different working regimes are possible. For high excitability, the dynamical attractors are stable, and a collective activity that replays one of the stored patterns emerges spontaneously, while for low excitability, no replay is induced. Between these two regimes, there is a critical region in which the dynamical attractors are unstable, and intermittent short replays are induced by noise. At the critical spiking threshold, the order parameter goes from zero to one, and its fluctuations are maximized, as expected for a phase transition (and as observed in recent experimental results in the brain). Notably, in this critical region, the avalanche size and duration distributions follow power laws. Critical exponents are consistent with a scaling relationship observed recently in neural avalanches measurements. In conclusion, our simple model suggests that avalanche power laws in cortical spontaneous activity may be the effect of a network at the critical point between the replay and non-replay of spatio-temporal patterns.
Towards industrial exploitation of innovative and harmonized production systems

Industrial competitiveness today means shorter product lifecycles, increased product variety and shorter time-to-market. To face this challenge, the manufacturing industry is forced by different initiatives, namely Internet of Things, Industrie 4.0 and Cyber-Physical System to move from traditional control approaches towards intelligent manufacturing control systems that are dynamically adaptable to changing production environment and flexible to different processing tasks. For years several emergent intelligent approaches such as Multi-Agent Systems, Service-oriented Architecture, Plug-and-Produce systems and Cloud technologies have been developed in a variety of research fields. This paper reviews the state-of-the-art methodologies and technologies of flexible and reconfigurable manufacturing systems outlining the differences between them and arising benefits within the vision of the PERFoRM (Production harmonizEd Reconfiguration of Flexible Robots and Machinery) project. Current trends and challenges in industrial implementation of these methodologies are reported and research opportunities are described.
Differences in Relationship Between Macular Inner Retinal Layer Thickness and Retinal Sensitivity in Eyes With Early and Progressed Glaucoma.

PURPOSE To determine if the relationship between retinal sensitivity and macular inner retinal layer thickness differs between primary open-angle glaucoma (POAG) with mild and advanced central visual field (VF) damage. METHODS One eye of 153 POAG patients was included. Using spectral-domain optical coherence tomography, we measured the average thickness of the macular ganglion cell-inner plexiform layers (GCIPLT) and the macular nerve fiber layer/GCIPL (ganglion cell complex [GCCT]) in a 0.9-mm-diameter ganglion cell displacement-adjusted circular area corresponding to the four central test points of the Humphrey Perimeter 24-2 program and correlated the results with the average retinal sensitivity (1/Lambert) at the corresponding test points, with adjustment for other confounding factors. RESULTS Ninety-three eyes had mild central and 60 eyes advanced central VF damage with an average total deviation (TD) of the four test points of greater than or equal to -4 decibels (dB) (mild group) and less than -4 dB (more severe group), respectively; the average mean deviations were -3.0 and -9.8 dB, respectively. In the mild group, the GCCT and GCIPLT were correlated significantly and positively with the average retinal sensitivity with partial regression coefficient of 0.007 and 0.005, respectively, and in the more severe group with partial regression coefficient of 0.019 = 0.007 + 0.012 (P = 0.007) and 0.010 = 0.005 + 0.005 (P = 0.078), respectively. The axial length and disc size were correlated with GCIPLT with marginal significance (P = 0.052 and P = 0.042). CONCLUSIONS The relationship between the macular GCC and GCIPL thickness and retinal sensitivity at the corresponding retinal areas differed between POAG with mild and advanced central VF damage.
Osteoblast-Specific Transcription Factor Osterix Increases Vitamin D Receptor Gene Expression in Osteoblasts

Osterix (Osx) is an osteoblast-specific transcription factor required for osteoblast differentiation from mesenchymal stem cells. In Osx knock-out mice, no bone formation occurs. The vitamin D receptor (VDR) is a member of the nuclear hormone receptor superfamily that regulates target gene transcription to ensure appropriate control of calcium homeostasis and bone development. Here, we provide several lines of evidence that show that the VDR gene is a target for transcriptional regulation by Osx in osteoblasts. For example, calvaria obtained from Osx-null embryos displayed dramatic reductions in VDR expression compared to wild-type calvaria. Stable overexpression of Osx stimulated VDR expression in C2C12 mesenchymal cells. Inhibition of Osx expression by siRNA led to downregulation of VDR. In contrast, Osx levels remained unchanged in osteoblasts in VDR-null mice. Mechanistic approaches using transient transfection assays showed that Osx directly activated a 1 kb fragment of the VDR promoter in a dose-dependent manner. To define the region of the VDR promoter that was responsive to Osx, a series of VDR promoter deletion mutants were examined and the minimal Osx-responsive region was refined to the proximal 120 bp of the VDR promoter. Additional point mutants were used to identify two GC-rich regions that were responsible for VDR promoter activation by Osx. Chromatin immunoprecipitation assays demonstrated that endogenous Osx was associated with the native VDR promoter in primary osteoblasts in vivo. Cumulatively, these data strongly support a direct regulatory role for Osx in VDR gene expression. They further provide new insight into potential mechanisms and pathways that Osx controls in osteoblasts and during the process of osteoblastic cell differentiation.
Predictive modeling of nanomaterial exposure effects in biological systems

Background Predictive modeling of the biological effects of nanomaterials is critical for industry and policymakers to assess the potential hazards resulting from the application of engineered nanomaterials. Methods We generated an experimental dataset on the toxic effects experienced by embryonic zebrafish due to exposure to nanomaterials. Several nanomaterials were studied, such as metal nanoparticles, dendrimer, metal oxide, and polymeric materials. The embryonic zebrafish metric (EZ Metric) was used as a screening-level measurement representative of adverse effects. Using the dataset, we developed a data mining approach to model the toxic endpoints and the overall biological impact of nanomaterials. Data mining techniques, such as numerical prediction, can assist analysts in developing risk assessment models for nanomaterials. Results We found several important attributes that contribute to the 24 hours post-fertilization (hpf) mortality, such as dosage concentration, shell composition, and surface charge. These findings concur with previous studies on nanomaterial toxicity using embryonic zebrafish. We conducted case studies on modeling the overall effect/impact of nanomaterials and the specific toxic endpoints such as mortality, delayed development, and morphological malformations. The results show that we can achieve high prediction accuracy for certain biological effects, such as 24 hpf mortality, 120 hpf mortality, and 120 hpf heart malformation. The results also show that the weighting scheme for individual biological effects has a significant influence on modeling the overall impact of nanomaterials. Sample prediction models can be found at http://neiminer.i-a-i.com/nei_models. Conclusion The EZ Metric-based data mining approach has been shown to have predictive power. The results provide valuable insights into the modeling and understanding of nanomaterial exposure effects.
Stabilization of protein-protein interactions in drug discovery

ABSTRACT Introduction: PPIs are involved in every disease and specific modulation of these PPIs with small molecules would significantly improve our prospects of developing therapeutic agents. Both industry and academia have engaged in the identification and use of PPI inhibitors. However in comparison, the opposite strategy of employing small-molecule stabilizers of PPIs is underrepresented in drug discovery. Areas covered: PPI stabilization has not been exploited in a systematic manner. Rather, this concept validated by a number of therapeutically used natural products like rapamycin and paclitaxel has been shown retrospectively to be the basis of the activity of synthetic molecules originating from drug discovery projects among them lenalidomide and tafamidis. Here, the authors cover the growing number of synthetic small-molecule PPI stabilizers to advocate for a stronger consideration of this as a drug discovery approach. Expert opinion: Both the natural products and the growing number of synthetic molecules show that PPI stabilization is a viable strategy for drug discovery. There is certainly a significant challenge to adapt compound libraries, screening techniques and downstream methodologies to identify, characterize and optimize PPI stabilizers, but the examples of molecules reviewed here in our opinion justify these efforts.
Hydrogen Stark Broadening by Different Kinds of Model Microfields

The “method of model microfields (MMM)”, which has been employed successfully especially for the calculation of hydrogen Stark profiles, is based on the assumption that reliable line shapes may be obtained from just the probability density of the plasma microfield and its autocorrelation function. To test the influence of higher order statistical features two different model microfields have been used to investigate Stark broadening of hydrogen Lyman lines by either electrons or ions. Corresponding profiles computed in this way lie close together over the full intensity range, but systematic relative deviations of about 20% show up at frequency separations from the unperturbed line of approximately three times the plasma frequency (for electrons or ions, respectively), i.e., in the “transition region” where neither the impact nor the static approximation holds. Though the joint action of electrons and ions as well as Doppler broadening will tend to diminish these deviations, the present form of the MMM cannot be expected to yield an accuracy better than some 10% throughout the line profile.
An Authentication Protocol for Future Sensor Networks

Authentication is one of the essential security services in Wireless Sensor Networks (WSNs) for ensuring secure data sessions. Sensor node authentication ensures the confidentiality and validity of data collected by the sensor node, whereas user authentication guarantees that only legitimate users can access the sensor data. In a mobile WSN, sensor and user nodes move across the network and exchange data with multiple nodes, thus experiencing the authentication process multiple times. The integration of WSNs with Internet of Things (IoT) brings forth a new kind of WSN architecture along with stricter security requirements; for instance, a sensor node or a user node may need to establish multiple concurrent secure data sessions. With concurrent data sessions, the frequency of the re-authentication process increases in proportion to the number of concurrent connections. Moreover, to establish multiple data sessions, it is essential that a protocol participant have the capability of running multiple instances of the protocol run, which makes the security issue even more challenging. The currently available authentication protocols were designed for the autonomous WSN and do not account for the above requirements. Hence, ensuring a lightweight and efficient authentication protocol has become more crucial. In this paper, we present a novel, lightweight and efficient key exchange and authentication protocol suite called the Secure Mobile Sensor Network (SMSN) Authentication Protocol. In the SMSN a mobile node goes through an initial authentication procedure and receives a re-authentication ticket from the base station. Later a mobile node can use this re-authentication ticket when establishing multiple data exchange sessions and/or when moving across the network. This scheme reduces the communication and computational complexity of the authentication process. We proved the strength of our protocol with rigorous security analysis (including formal analysis using the BAN-logic) and simulated the SMSN and previously proposed schemes in an automated protocol verifier tool. Finally, we compared the computational complexity and communication cost against well-known authentication protocols.
Situation Awareness Information Dominance & Information Warfare.

Abstract : Information warfare and its primary objective of achieving information dominance over enemy forces have arisen as a major area of emphasis for future military actions. The concept of information dominance and the issues involved in attaining it are explored through a model of situation awareness within the context of the type of complex, distributed crews (or military units) envisioned in future military operations. Achieving information dominance involves far more than having more data than the enemy. It will require that available data be transformed into relevant information in a timely manner for a multitude of forces, each with varied and dynamically changing but inter-related information needs. Further, the information must be properly understood by each within the context of a joint mission. The difficulty of accomplishing this task is not to be underestimated, however. This is exactly where an understanding of situation awareness and the factors that impact it are essential. By examining what is known about how people access, assimilate and interpret information to develop situation awareness as well as how this fits within the decision making and action cycle, clear directions for the development of systems to support the goal of information dominance can be established.
Influenza Vaccination and Intention to Receive the Pandemic H1N1 Influenza Vaccine among Healthcare Workers of British Columbia, Canada: A Cross-Sectional Study

Objective. To assess healthcare workers' attitudes and concerns regarding seasonal and pandemic influenza vaccines in order to improve vaccination campaign communications. Design. Cross-sectional survey. Setting. All 6 health authorities in British Columbia, Canada. Methods. An anonymous, self-administered online survey was conducted from August 30 through September 30, 2009. Question topics included demographic characteristics, factors influencing acceptance of seasonal influenza vaccine, factors influencing intentions to accept pandemic H1N1 influenza vaccine, and knowledge and concerns regarding the effect of the influenza pandemic. Participants. All 96,217 British Columbia healthcare workers were eligible to participate. Results. A volunteer sample of 4,046 healthcare workers returned the survey; 3,563 (88%) were women, 58% were under 50 years old (mean age ± standard deviation, 45.3 ± 10.9 years), 3,152 of 4,023 (79%) had 5 or more years of experience in their profession, 1,853 of 4,023 (46%) were nurses, and 2,833 (70%) had been vaccinated against seasonal influenza the previous year. Two thousand eight hundred (69%) respondents reported intending to receive the pandemic H1N1 vaccine. The most important predictor of this intention was having received the seasonal vaccine the previous year (odds ratio [OR], 6.25 [95% confidence interval {CI}, 5.39-7.26]). Worry about making loved ones ill was the only attitude associated with intention to receive the pandemic H1N1 vaccine (adjusted OR, 1.38 [95% CI, 1.27-1.50]). Concerns with vaccine safety (adjusted OR, 0.31 [95% CI, 0.25-0.39]) and belief “that H1N1 is not severe enough” (adjusted OR, 0.29 [95% CI, 0.26-0.32]) were independently associated with the intention to reject the pandemic H1N1 vaccine. Conclusions. Vaccination campaigns for pandemic H1N1 vaccine should use messages that emphasize the risk of illness among younger people and the opportunity to protect loved ones by getting the vaccine and should address concerns about the safety and effectiveness of the vaccine.