Miracle-dz/UniFAR-FTUs huggingface dataset:
Glucose availability controls ATF4-mediated MITF suppression to drive melanoma cell growth

It is well know that cancer cells have adopted an altered metabolism and that glucose is a major source of energy for these cells. In melanoma, enhanced glucose usage is favoured through the hyper-activated MAPK pathway, which suppresses OXPHOS and stimulates glycolysis. However, it has not been addressed how glucose availability impacts on melanoma specific signaling pathways that drive melanoma cell proliferation. Here we show that melanoma cells are dependent on high glucose levels for efficient growth. Thereby, glucose metabolism controls the expression of the melanoma fate transcription factor MITF, a master regulator of melanoma cell survival and proliferation, invasion and therapy resistance. Restriction of glucose availability to physiological concentrations induces the production of reactive oxygen species (ROS). Increased ROS levels lead to the up-regulation of AFT4, which in turn suppresses MITF expression by competing with CREB, an otherwise potent inducer of the MITF promoter. Our data give new insight into the complex regulation of MITF, a key regulator of melanoma biology, and support previous findings that link metabolic disorders such as hyperglycemia and diabetes with increased melanoma risk.
Intelligent compressive data gathering using data ferries for wireless sensor networks

The latest research progress of the theory of compressed sensing (CS) over graphs makes it possible that the advantage of CS can be utilized by data ferries to gather data in WSNs. In this paper, we leverage the non-uniform distribution of the sensing data field to significantly reduce the required number of data ferries, yet ensuring the recovered data quality. Specially, we propose an intelligent compressive data gathering scheme consisting of an efficient stopping criterion and a novel learning strategy. The proposed stopping criterion is based only on the gathered data, without relying on the priori knowledge on the sparsity of unknown sensing data. Our strategy minimizes the number of data ferries while guaranteeing the data quality by learning the statistical distribution of gathered data. Simulation results show that the proposed scheme improves the reconstruction quality compared to the existing ones.
Modulation of Metabolism and Switching to Biofilm Prevail over Exopolysaccharide Production in the Response of Rhizobium alamii to Cadmium

Heavy metals such as cadmium (Cd2+) affect microbial metabolic processes. Consequently, bacteria adapt by adjusting their cellular machinery. We have investigated the dose-dependent growth effects of Cd2+ on Rhizobium alamii, an exopolysaccharide (EPS)-producing bacterium that forms a biofilm on plant roots. Adsorption isotherms show that the EPS of R. alamii binds cadmium in competition with calcium. A metabonomics approach based on ion cyclotron resonance Fourier transform mass spectrometry has showed that cadmium alters mainly the bacterial metabolism in pathways implying sugars, purine, phosphate, calcium signalling and cell respiration. We determined the influence of EPS on the bacterium response to cadmium, using a mutant of R. alamii impaired in EPS production (MSΔGT). Cadmium dose-dependent effects on the bacterial growth were not significantly different between the R. alamii wild type (wt) and MSΔGT strains. Although cadmium did not modify the quantity of EPS isolated from R. alamii, it triggered the formation of biofilm vs planktonic cells, both by R. alamii wt and by MSΔGT. Thus, it appears that cadmium toxicity could be managed by switching to a biofilm way of life, rather than producing EPS. We conclude that modulations of the bacterial metabolism and switching to biofilms prevails in the adaptation of R. alamii to cadmium. These results are original with regard to the conventional role attributed to EPS in a biofilm matrix, and the bacterial response to cadmium.
Fault Current Limiting Characteristics of Transformer-Type Superconducting Fault Current Limiter Due to Winding Direction of Additional Circuit

In this paper, the transformer-type superconducting fault current limiter (SFCL) with additional circuit, which could limit the fault current through twice quench operations, was suggested. The suggested SFCL includes one primary winding, two nonisolated secondary windings wound on the same iron core, and two high-TC superconducting elements connected with each secondary winding. The advantage of the suggested SFCL is that it can perform the twice current limiting operations due to the transient amplitude of the fault current. Among its design parameters, the winding direction of another secondary winding comprising the additional circuit of the transformer-type SFCL or the nonisolated secondary winding is expected to affect its fault current limiting characteristics. To analyze the dependence of the fault current limiting operation on the winding direction of two nonisolated secondary windings, two limiting operational currents from its electrical equivalent circuit were derived. Through the fault current limiting tests for the suggested SFCL, the fault current limiting characteristics of the SFCL were discussed.
Irreversible bonding of polyimide and polydimethylsiloxane (PDMS) based on a thiol-epoxy click reaction

Polyimide is one of the most popular substrate materials for the microfabrication of flexible electronics, while polydimethylsiloxane (PDMS) is the most widely used stretchable substrate/encapsulant material. These two polymers are essential in fabricating devices for microfluidics, bioelectronics, and the internet of things; bonding these materials together is a crucial challenge. In this work, we employ click chemistry at room temperature to irreversibly bond polyimide and PDMS through thiol-epoxy bonds using two different methods. In the first method, we functionalize the surfaces of the PDMS and polyimide substrates with mercaptosilanes and epoxysilanes, respectively, for the formation of a thiol-epoxy bond in the click reaction. In the second method, we functionalize one or both surfaces with mercaptosilane and introduce an epoxy adhesive layer between the two surfaces. When the surfaces are bonded using the epoxy adhesive without any surface functionalization, an extremely small peel strength (<0.01 N mm−1) is measured with a peel test, and adhesive failure occurs at the PDMS surface. With surface functionalization, however, remarkably higher peel strengths of ~0.2 N mm−1 (method 1) and >0.3 N mm−1 (method 2) are observed, and failure occurs by tearing of the PDMS layer. We envision that the novel processing route employing click chemistry can be utilized in various cases of stretchable and flexible device fabrication.
Decline in Topsoil Microbial Quotient, Fungal Abundance and C Utilization Efficiency of Rice Paddies under Heavy Metal Pollution across South China

Agricultural soils have been increasingly subject to heavy metal pollution worldwide. However, the impacts on soil microbial community structure and activity of field soils have been not yet well characterized. Topsoil samples were collected from heavy metal polluted (PS) and their background (BGS) fields of rice paddies in four sites across South China in 2009. Changes with metal pollution relative to the BGS in the size and community structure of soil microorganisms were examined with multiple microbiological assays of biomass carbon (MBC) and nitrogen (MBN) measurement, plate counting of culturable colonies and phospholipids fatty acids (PLFAs) analysis along with denaturing gradient gel electrophoresis (DGGE) profile of 16S rRNA and 18S rRNA gene and real-time PCR assay. In addition, a 7-day lab incubation under constantly 25°C was conducted to further track the changes in metabolic activity. While the decrease under metal pollution in MBC and MBN, as well as in culturable population size, total PLFA contents and DGGE band numbers of bacteria were not significantly and consistently seen, a significant reduction was indeed observed under metal pollution in microbial quotient, in culturable fungal population size and in ratio of fungal to bacterial PLFAs consistently across the sites by an extent ranging from 6% to 74%. Moreover, a consistently significant increase in metabolic quotient was observed by up to 68% under pollution across the sites. These observations supported a shift of microbial community with decline in its abundance, decrease in fungal proportion and thus in C utilization efficiency under pollution in the soils. In addition, ratios of microbial quotient, of fungal to bacterial and qCO2 are proved better indicative of heavy metal impacts on microbial community structure and activity. The potential effects of these changes on C cycling and CO2 production in the polluted rice paddies deserve further field studies.
Android permission system and user privacy — A review of concept and approaches

Use of smartphones in our everyday life has become widely popular. A large proportion of smartphones use Android OS, which supports third party software development, so there is increasing number of developers developing applications for the android platform. But this means there are significant privacy risks associated with the use of android based smartphone applications. In this paper the process through which different apps gain access to sensitive device permissions when installed on an android devices is studied. More specifically we emphasize the difficulty for the user to understand how different device permissions can affect its privacy. The context and use-case for each permission affects its impact and when multiple permissions are granted determining the potential impact on the privacy of users becomes a much more complex problem. In this work we quantify the potential impact of the most important individual permissions and take some first steps towards an evaluation of privacy impact of multiple device permissions. It is also noted that many ‘free’ apps tend to request unnecessary or redundant permissions, often with the aim to gather valuable user data. This is discussed and some strategies to discourage such permission requesting are outlined. Some ideas for further development of this research are provided in the concluding discussion.
High Gradient Nb3Sn Quadrupole Demonstrator MKQXF Engineering Design

The future upgrades of the CERN accelerator chain along with the future high-energy colliders, notably the future circular collider (FCC), will require high gradient quadrupoles. As part of the High Luminosity Large Hadron Collider (HL-LHC) project, the 11 T dipole was designed to be compatible with accelerator requirements and industrial production. It is based on the “pole-loading” concept. This allows shimming at the pole and uses the collars more efficiently for creating the coil prestress. MKQXF is a further application of the “pole-loading” concept for Nb3Sn quadrupoles. The pole region of the coils is identical to the 11 T dipole and the collared coil is based on dipole-type collars. This concept can be extended to any length and applied on both 1-in-1 and 2-in-1 configurations. For benchmarking purposes and to compare with the present base-line design of the HL-LHC IR quadrupole MQXF, based on the bladder-and-key concept, this conceptual study was made with identical coils and quasi-identical magnetic characteristics. The design features 140 T/m gradient in 150 mm coil aperture. This paper describes the design concept of MKQXF and the multiphysics finite element model, including the end regions. The design is described and the optimized assembly parameters and the effect of the manufacturing tolerances are presented.
A Reliability-Generalization Study of Journal Peer Reviews: A Multilevel Meta-Analysis of Inter-Rater Reliability and Its Determinants

Background This paper presents the first meta-analysis for the inter-rater reliability (IRR) of journal peer reviews. IRR is defined as the extent to which two or more independent reviews of the same scientific document agree. Methodology/Principal Findings Altogether, 70 reliability coefficients (Cohen's Kappa, intra-class correlation [ICC], and Pearson product-moment correlation [r]) from 48 studies were taken into account in the meta-analysis. The studies were based on a total of 19,443 manuscripts; on average, each study had a sample size of 311 manuscripts (minimum: 28, maximum: 1983). The results of the meta-analysis confirmed the findings of the narrative literature reviews published to date: The level of IRR (mean ICC/r2 = .34, mean Cohen's Kappa = .17) was low. To explain the study-to-study variation of the IRR coefficients, meta-regression analyses were calculated using seven covariates. Two covariates that emerged in the meta-regression analyses as statistically significant to gain an approximate homogeneity of the intra-class correlations indicated that, firstly, the more manuscripts that a study is based on, the smaller the reported IRR coefficients are. Secondly, if the information of the rating system for reviewers was reported in a study, then this was associated with a smaller IRR coefficient than if the information was not conveyed. Conclusions/Significance Studies that report a high level of IRR are to be considered less credible than those with a low level of IRR. According to our meta-analysis the IRR of peer assessments is quite limited and needs improvement (e.g., reader system).
Antibacterial activity of selected glass ionomer cements Aktywność przeciwbakteryjna wybranych cementów szkłojonomerowych

Summary The aim of the paper was to determine the antibacterial activity of four glass ionomer cements against bacteria of the genera Streptococcus and Lactobacillus. Four capsulated glass ionomer cements were applied in the study: Fuji Triage (GC), Fuji IX (GC), Ketac Molar (3M Espe) and Ketac Silver (3M Espe). Four standard bacterial strains were used to assess the antibacterial activity of the studied cements: Streptococcus mutans, S. sanguis, S. salivarius and Lactobacillus casei. The antibacterial activity was determined by the agar diffusion method. The bacterial suspension was spread with a cotton swab on TSA plates. For each material six wells (7 mm diameter, 5 mm deep) were made with a cork borer. Each well was then filled with freshly prepared cements. The results were obtained by measuring the bacterial growth inhibition zone after 1, 2, 3 and 7 days. Fuji Triage cement inhibited the growth of all bacterial strains. Fuji IX cement demonstrated the most potent antibacterial activity against S. sanguis. Ketac Molar showed antibacterial activity against S. sanguis and S. salivarius, whereas Ketac Silver was efficient against S. mutans as well. Neither of the Ketac cements inhibited growth of the standard L. casei strain. Antibacterial activity of glass ionomer cements has attracted the interest of scientists in recent years. Most authors, including us, carried out experiments using the agar diffusion method and demonstrated antibacterial activity of glass ionomer cements. Different antibacterial activity of glass ionomer cements, observed in our study and studies of other authors, depended on the evaluated cement, bacterial strain and period of evaluation.
A low power temperature sensor for IOT applications in CMOS 65nm technology

This paper describes the architecture of a smart temperature sensor designed in CMOS 65nm technology node, intended for IOT and RFID applications. The shift of the trimming circuitry and of a portion of the readout operations into the digital domain, combined with a reduced design complexity in the sensor analog front-end, allow the minimization of the power consumption. The maximum inaccuracy of the sensor, obtained by means of a two point calibration, is ±0.3°C over the [−40°C÷125°C] temperature range, with an average power consumption of 375 nW at a conversion speed of 1 Sa/s.
What Is New for an Old Molecule? Systematic Review and Recommendations on the Use of Resveratrol

Background Resveratrol is a natural compound suggested to have beneficial health effects. However, people are consuming resveratrol for this reason without having the adequate scientific evidence for its effects in humans. Therefore, scientific valid recommendations concerning the human intake of resveratrol based on available published scientific data are necessary. Such recommendations were formulated after the Resveratrol 2010 conference, held in September 2010 in Helsingør, Denmark. Methodology Literature search in databases as PubMed and ISI Web of Science in combination with manual search was used to answer the following five questions: 1Can resveratrol be recommended in the prevention or treatment of human diseases? ; 2Are there observed “side effects” caused by the intake of resveratrol in humans? ; 3What is the relevant dose of resveratrol? ; 4What valid data are available regarding an effect in various species of experimental animals? ; 5Which relevant (overall) mechanisms of action of resveratrol have been documented? Conclusions/Significance The overall conclusion is that the published evidence is not sufficiently strong to justify a recommendation for the administration of resveratrol to humans, beyond the dose which can be obtained from dietary sources. On the other hand, animal data are promising in prevention of various cancer types, coronary heart diseases and diabetes which strongly indicate the need for human clinical trials. Finally, we suggest directions for future research in resveratrol regarding its mechanism of action and its safety and toxicology in human subjects.
Stripe to Spot Transition in a Plant Root Hair Initiation Model

A generalised Schnakenberg reaction-diffusion system with source and loss terms and a spatially dependent coefficient of the nonlinear term is studied both numerically and analytically in two spatial dimensions. The system has been proposed as a model of hair initiation in the epidermal cells of plant roots. Specifically the model captures the kinetics of a small G-protein ROP, which can occur in active and inactive forms, and whose activation is believed to be mediated by a gradient of the plant hormone auxin. Here the model is made more realistic with the inclusion of a transverse co-ordinate. Localised stripe-like solutions of active ROP occur for high enough total auxin concentration and lie on a complex bifurcation diagram of single and multi-pulse solutions. Transverse stability computations, confirmed by numerical simulation show that, apart from a boundary stripe, these 1D solutions typically undergo a transverse instability into spots. The spots so formed typically drift and undergo secondary instabilities such as spot replication. A novel 2D numerical continuation analysis is performed that shows the various stable hybrid spot-like states can coexist. The parameter values studied lead to a natural singularly perturbed, so-called semi-strong interaction regime. This scaling enables an analytical explanation of the initial instability, by describing the dispersion relation of a certain non-local eigenvalue problem. The analytical results are found to agree favourably with the numerics. Possible biological implications of the results are discussed.
Seascape Genetics of a Globally Distributed, Highly Mobile Marine Mammal: The Short-Beaked Common Dolphin (Genus Delphinus)

Identifying which factors shape the distribution of intraspecific genetic diversity is central in evolutionary and conservation biology. In the marine realm, the absence of obvious barriers to dispersal can make this task more difficult. Nevertheless, recent studies have provided valuable insights into which factors may be shaping genetic structure in the world's oceans. These studies were, however, generally conducted on marine organisms with larval dispersal. Here, using a seascape genetics approach, we show that marine productivity and sea surface temperature are correlated with genetic structure in a highly mobile, widely distributed marine mammal species, the short-beaked common dolphin. Isolation by distance also appears to influence population divergence over larger geographical scales (i.e. across different ocean basins). We suggest that the relationship between environmental variables and population structure may be caused by prey behaviour, which is believed to determine common dolphins' movement patterns and preferred associations with certain oceanographic conditions. Our study highlights the role of oceanography in shaping genetic structure of a highly mobile and widely distributed top marine predator. Thus, seascape genetic studies can potentially track the biological effects of ongoing climate-change at oceanographic interfaces and also inform marine reserve design in relation to the distribution and genetic connectivity of charismatic and ecologically important megafauna.
The relBE2Spn Toxin-Antitoxin System of Streptococcus pneumoniae: Role in Antibiotic Tolerance and Functional Conservation in Clinical Isolates

Type II (proteic) chromosomal toxin-antitoxin systems (TAS) are widespread in Bacteria and Archaea but their precise function is known only for a limited number of them. Out of the many TAS described, the relBE family is one of the most abundant, being present in the three first sequenced strains of Streptococcus pneumoniae (D39, TIGR4 and R6). To address the function of the pneumococcal relBE2Spn TAS in the bacterial physiology, we have compared the response of the R6-relBE2Spn wild type strain with that of an isogenic derivative, ΔrelB2Spn under different stress conditions such as carbon and amino acid starvation and antibiotic exposure. Differences on viability between the wild type and mutant strains were found only when treatment directly impaired protein synthesis. As a criterion for the permanence of this locus in a variety of clinical strains, we checked whether the relBE2Spn locus was conserved in around 100 pneumococcal strains, including clinical isolates and strains with known genomes. All strains, although having various types of polymorphisms at the vicinity of the TA region, contained a functional relBE2Spn locus and the type of its structure correlated with the multilocus sequence type. Functionality of this TAS was maintained even in cases where severe rearrangements around the relBE2Spn region were found. We conclude that even though the relBE2Spn TAS is not essential for pneumococcus, it may provide additional advantages to the bacteria for colonization and/or infection.
Enhanced immune activation linked to endotoxemia in HIV-1 seronegative men who have sex with men

This study assessed cellular and soluble markers of immune activation in HIV-1-seronegative men who have sex with men (MSM). MSM immune profiles were characterized by increased expression of CD57 on T cells and endotoxemia. Endotoxin presence was linked to recent highrisk exposure and associated with elevated cytokine levels and decreased CD4/CD8 T cell ratios. Taken together, these data show elevated levels of inflammation linked to periods of endotoxemia resulting in a significantly different immune phenotype in a subset of MSM at high risk of HIV-1 acquisition.