Miracle-dz/UniFAR-FTUs huggingface dataset:
Ordinary stoichiometry of extraordinary microorganisms

All life on Earth seems to be made of the same chemical elements in relatively conserved proportions (stoichiometry). Whether this stoichiometry is conserved in settings that differ radically in physicochemical conditions (extreme environments) from those commonly encountered elsewhere on the planet provides insight into possible stoichiometries for putative life beyond Earth. Here, we report measurements of elemental stoichiometry for extremophile microbes from hot springs of Yellowstone National Park (YNP). Phototrophic and chemotrophic microbes were collected in locations spanning large ranges of temperature (24 °C to boiling), pH (1.6–9.6), redox (0.1–7.2 mg L−1 dissolved oxygen), and nutrient concentrations (0.01–0.25 mg L−1 NO2− , 0.7–12.9 mg L−1 NO3− , 0.01–42 mg L−1 NH4+, 0.003–1.1 mg L−1 P mostly as phosphate). Despite these extreme conditions, the microbial cells sampled had a major and trace element stoichiometry within the ranges commonly encountered for microbes living in the more moderate environments of lakes and surface oceans. The cells did have somewhat high C:P and N:P ratios that are consistent with phosphorus (P) limitation. Furthermore, chemotrophs and phototrophs had similar compositions with the exception of Mo content, which was enriched in cells derived from chemotrophic sites. Thus, despite the extraordinary physicochemical and biological diversity of YNP environments, life in these settings, in a stoichiometric sense, remains much the same as we know it elsewhere.
Characterization of the auto-curing behavior of rapid prototyping materials for three-dimensional printing using dielectric analysis

Three-dimensional printing technology applies the high efficiency of the ink jet printer technology to manufacture functional prototypes. To optimize the printing process of PMMA powder containing an initiator and a liquid binder consisting of polymerizable monomers with activator molecules, the knowledge of the curing kinetics is required. Therefore, a methodology was developed to apply dielectric analysis measuring changes of the ion and dipole mobility in terms of a quantity called ion viscosity. Connecting time-dependent changes of ion viscosity and reaction heat determined by DSC leads to detailed insight into the curing process. The results show that the styrene concentration of the binder determines the curing kinetics—reduces thermal stresses and provides time for stress relaxation. The curing process differs significantly with respect not only to composition of the binder, but also to its aging state. The proposed approach can be implemented directly to a printer to detect dielectric changes of the materials during the manufacturing process. POLYM. ENG. SCI., 55:1485–1493, 2015. © 2015 Society of Plastics Engineers
Impact of acute cellular rejection on coagulation and fibrinolysis biomarkers within the immediate post‐operative period in pediatric liver transplantation

Mimuro J, Mizuta K, Kawano Y, Hishikawa S, Hamano A, Kashiwakura Y, Ishiwata A, Ohmori T, Madoiwa S, Kawarasaki H, Sakata Y. Impact of acute cellular rejection on coagulation and fibrinolysis biomarkers within the immediate post‐operative period in pediatric liver transplantation. Pediatr Transplantation 2010:14: 396–376. © 2009 John Wiley & Sons A/S.
Relative Humidity Measured by Wooden Stick Method in Concrete Structures: Long Term Measurements and Reduction of Humidity by Surface Treatment

The wooden stick method of measuring relative humidity (RH) is especially applicable to concrete structures with high internal humidity as with those damaged by alkali aggregate reaction (AAR) or freezing and thawing. Current findings show that the RH is stable 5 cm from the surface and that ingress of rainwater is a key source of water in most of the outdoor exposed concrete structures. Correlation tests have shown that wooden sticks are still in good condition and reliable after 7 years of continuous use. Measurements on surface-treated columns and beams in 2 structures show that the RH 5 cm from the surface decreased significantly during 4 years of monitoring, which was not the case in untreated concrete. Surface treatment seems to be able to reduce the RH in concrete structures exposed to rainwater.
Spencermartinsiella silvicola sp. nov., a yeast species isolated from rotting wood.

Three strains of a new xylanase-producing yeast species were isolated from rotting wood samples collected in the Atlantic Rain Forest of Brazil. The sequences of the internal transcribed spacer region and D1/D2 domains of the large subunit of the rRNA gene showed that this novel yeast species belongs to the genus Spencermartinsiella, and its closest relatives among recognized species are Spencermartinsiella europaea and Spencermartinsiella ligniputridi. A novel species, named Spencermartinsiella silvicola sp. nov., is proposed to accommodate these isolates. The type strain is UFMG-CM-Y274T ( = CBS 13490T). The MycoBank number is MB 813053. In addition, Candida cellulosicola is reassigned to the genus Spencermartinsiella as a new combination.
Influence of metakaolin surface area on properties of cement-based materials

Two metakaolins, with similar mineralogical composition but which vary in their surface area (11.1 versus 25.4 m2 ∕g ), were evaluated for use as supplementary cementitious materials through measurements of workability, setting time, strength, elastic modulus, heat evolution, calcium hydroxide (CH) content, and surface area. Compressive and flexural strength of concrete were greater and increased at a faster rate when the finer metakaolin was used, as expected. The addition of metakaolin increased early age (i.e., 1–3 days ) flexural strength by as much as 60%. The effect of metakaolin surface area on compressive strength was particularly evident at the lower water-to-cementitious materials ratios (w/cms) examined and generally at later ages (i.e., 7 days or later). However, although greater in the metakaolin–cement concretes than the ordinary concretes (particularly at the lowest w/cm examined, 0.40) elastic modulus measured at 28 days , was not affected by the metakaolin surface area. The greater surfac.
Remote repair of operating system state using Backdoors

Backdoors is a novel system architecture that enables remote monitoring and recovery/repair of the software state of a computer system without using its processors or relying on its OS resources. We have implemented a Backdoors prototype in the FreeBSD kernel using Myrinet NICs for remote access to the target machine. In a previous paper, we have shown how Backdoors can be used for recovery of "good" OS and application state from a failed system on other healthy systems. In this paper, we describe how Backdoors can be used to detect and repair damage to the OS state of a computer system. We present two case studies of remote repair of an OS subject to resource depletion (fork bomb and memory hog) to the point where it cannot perform useful work and local repair is impossible. We show that our prototype detects OS resource exhaustion efficiently and it successfully repairs the affected system.
Automatic Retinal Vessel Segmentation

Diabetic Retinopathy is the most common cause of blindness in the working population of the western world and is very common among people who suffer from diabetes. Fortunately, during a clinical examination an ophthalmologist is able to determine the onset of the disease by taking certain features of the retinal vessels of the fundus into account. These features include the narrowing of vessels and their general structure. The clinical examination involves retinal imaging whereby a photo of the back of the inside of the eye is taken. The ophthalmologist then usually digitises the image by manually selecting what parts of the photo constitute vessels, so that certain statistics such as the thickness of the vessels can be calculated by a computer program. Labelling all the vessels however is a tedious and time consuming process. Our work focuses on using image processing techniques in order to develop a computer program that can automatically detect and segment blood vessels in these images, thereby saving the ophthalmologist considerable time. We make use of a fast level set method without solving partial differential equations to extract the contour of the vessels in the retina and overlay the contour over the original input image. This further aids the work of an ophthalmologist because it highlights the vessel structure.
Anomaly Detection in Automobile Control Network Data with Long Short-Term Memory Networks

Modern automobiles have been proven vulnerable to hacking by security researchers. By exploiting vulnerabilities in the car's external interfaces, such as wifi, bluetooth, and physical connections, they can access a car's controller area network (CAN) bus. On the CAN bus, commands can be sent to control the car, for example cutting the brakes or stopping the engine. While securing the car's interfaces to the outside world is an important part of mitigating this threat, the last line of defence is detecting malicious behaviour on the CAN bus. We propose an anomaly detector based on a Long Short-Term Memory neural network to detect CAN bus attacks. The detector works by learning to predict the next data word originating from each sender on the bus. Highly surprising bits in the actual next word are flagged as anomalies. We evaluate the detector by synthesizing anomalies with modified CAN bus data. The synthesized anomalies are designed to mimic attacks reported in the literature. We show that the detector can detect anomalies we synthesized with low false alarm rates. Additionally, the granularity of the bit predictions can provide forensic investigators clues as to the nature of flagged anomalies.
Hypoxia decreases sclerostin expression and increases Wnt signaling in osteoblasts

Mutations in sclerostin function or expression cause sclerosing bone dysplasias, involving decreased antagonism of Wnt/Lrp5 signaling. Conversely, deletion of the VHL tumor suppressor in osteoblasts, which stabilize HIF‐α isoforms and thereby enables HIF‐α/β‐driven gene transcription, increases bone mineral content and cross‐sectional area compared to wild‐type controls. We examined the influence of cellular hypoxia (1% oxygen) upon sclerostin expression and canonical Wnt signaling. Osteoblasts and osteocytes cultured under hypoxia revealed decreased sclerostin transcript and protein, and increased expression and nuclear localization of activated β‐catenin. Similarly, both hypoxia and the hypoxia mimetic DFO increased β‐catenin gene reporter activity. Hypoxia and its mimetics increased expression of the BMP antagonists gremlin and noggin and decreased Smad‐1/5/8 phosphorylation. As a partial explanation for the mechanism of regulation of sclerostin by oxygen, MEF2 reporter assays revealed decreased activity. Modulation of VEGF signaling under normoxia or hypoxia revealed no influence upon Sost transcription. These data suggest that hypoxia inhibits sclerostin expression, through enhanced antagonism of BMP signaling independent of VEGF. J. Cell. Biochem. 110: 457–467, 2010. © 2010 Wiley‐Liss, Inc.
Combination of Origanum vulgare L. essential oil and lactic acid to inhibit Staphylococcus aureus in meat broth and meat model

This study assessed the occurrence of an enhancing inhibitory effect of the combined application of Origanum vulgare L. essential oil and lactic acid against Staphylococcus aureus by the determination of Fractional Inhibitory Concentration (FIC) index and cell viability in meat broth and meat model. Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) of the oil was 0.6 and 1.25 µL. mL-1, respectively. Lactic acid showed MIC and MBC of 2.5 and 5µL. mL-1, respectively. FIC indices of the combined application of the oil and lactic acid were 0.5 showing a synergic interaction. The essential oil and lactic acid showed similar (p>0.05) anti-S. aureus effect in meat broth over 96 h of exposure. Treatment with essential oil or lactic acid presented a smaller anti-staphylococcal effect in meat in comparison to meat broth. No significant difference (p>0.05) was found for the microbial counts in meat treated with each antimicrobial alone or in mixture. These results could arise as an interesting approach for the improvement of food preservation using more natural procedures, considering the current demand of consumer and sensory quality of foods.
Space-Time Robust Representation for Action Recognition

We address the problem of action recognition in unconstrained videos. We propose a novel content driven pooling that leverages space-time context while being robust toward global space-time transformations. Being robust to such transformations is of primary importance in unconstrained videos where the action localizations can drastically shift between frames. Our pooling identifies regions of interest using video structural cues estimated by different saliency functions. To combine the different structural information, we introduce an iterative structure learning algorithm, WSVM (weighted SVM), that determines the optimal saliency layout of an action model through a sparse regularizer. A new optimization method is proposed to solve the WSVM' highly non-smooth objective function. We evaluate our approach on standard action datasets (KTH, UCF50 and HMDB). Most noticeably, the accuracy of our algorithm reaches 51.8% on the challenging HMDB dataset which outperforms the state-of-the-art of 7.3% relatively.
Hyper-spectral camera system: acquisition and analysis

A low-cost, portable, video-camera system built by University of Bristol for the UK-DRA, Fort Halsteads, permits in-field acquisition of terrestrial hyper-spectral image sets. Each set is captured as a sequence of thirty-one images through a set of different interference filters which span the visible spectrum, at 10 nm intervals: effectively providing a spectrogram 256x256 pixels. The system is customised from of-the-shelf components. A database of twenty nine hyper-spectral images sets was acquired and analysed as a sample of natural environment. We report the manifest information capacity with respect to spatial and optical frequency drawing implications for management of hyper-spectral data and visual processing.
SLA-driven capacity planning for Cloud applications

Cloud computing paradigm has become the solution to provide good service quality and exploit economies of scale. However, the management of such elastic resources, with different Quality-of-Service (QoS) combined with on-demand self-service, is a complex issue. This paper proposes an approach driven by Service Level Agreement (SLA) for optimizing the capacity planning for Cloud applications. The main challenge for a service provider is to determine the best trade-off between profit and customer satisfaction. In order to address this issue, we follow a queueing network proposal and present an analytical performance model to predict Cloud service performance. Based on a utility function and a capacity planning method, our solution calculates the optimal configuration of a Cloud application. We rely on autonomic computing to adjust continuously the configuration. Simulation experiments indicate that our model i) faithfully captures the performance of Cloud applications for a number of workloads and configurations and ii) successfully keeps the best trade-off.
A Platform for Interoperable Domain-Specific Enterprise Modelling Based on ISO 15926

The paper shows how to describe the semantics of domain-specific enterprise and information system (IS) modelling languages using the Unified Enterprise Modelling Language (UEML). The approach is illustrated with a fragment of a domain-specific modelling language based on the new ISO 15926 standard for data integration, sharing and hand-over between computer systems. The aim is to ensure that the semantics of new domain-specific languages (DSLs) can be quickly, easily and precisely defined in relation both to one another and to existing general-purpose languages.
Mass Fabrication of Small Cell Spheroids by Using Micro‐patterned Tissue Culture Plate

A newly designed micro-patterned chamber was utilized to fabricate cell spheroids with a constant size (<200 μm) and cell number. By applying cytochalasin D as a chemical to control cell adhesion and aggregation, thousands of aggregated cells were formed in each patterned chamber. Importantly, the formed cell spheroids were collected by a simple pipetting process without using proteinase.
Solving Open Polygonals in Elastic Correction of Dead-Reckoning Errors

: - A major problem in map building is due to the imprecision of sensor measures. In a previous paper we proposed a technique, called elastic correction, for correcting the dead-reckoning errors made during the exploration of an unknown environment by a robot capable of identifying landmarks. Elastic correction is based on an analogy between the relational graph modelling the environment and a mechanical structure: the map is regarded as a truss where each route is an elastic bar and each landmark a node; errors are corrected as a result of the deformations induced from the forces arising within the structure as inconsistent measures are taken. The main weakness of this method lies in the way positional inconsistencies are solved when routes are covered for the first time. In this paper we improve first-sight elastic correction by replacing the heuristics previously adopted with a new approach which considers all the knowledge of the surrounding map acquired so far; this is achieved by calculating the minimum forces to be applied in order to restore metric consistency. The effectiveness of the new approach is demonstrated by presenting some experimental tests.
SPARQL query answering with bitmap indexes

When querying RDF data, one may use reasoning to reach intensional data, i.e., data defined by sets of rules. This is usually achieved through forward chaining, with space and maintenance overheads, or backward chaining, with high query evaluation and optimization costs. Recent approaches rely on pre-computing the terminological closure of the data rather than the full saturation. In this setting, one can even query the data without resorting to backward chaining, using a so-called semantic index. However, these techniques are limited in the type of queries they can support. In this paper, we introduce a data storage technique which mitigates the space issues of forward-chaining. We show that it can also be used with a semantic index. We propose a new structure for the index that relies on bitmaps making it resilient to updates. Our experimental results demonstrate that our storage model significantly reduces the space required to store the data. We show that the indexes can be computed quickly and fit well in memory even for very large ontologies. Finally, we analyze how query answering is affected by the data layout.
THE INERTIAL EFFECT OF ACCELERATION FIELDS ON A SELF-DECOUPLED WHEEL FORCE TRANSDUCER

WHEEL FORCE TRANSDUCER (WFT) IS A TOOL WHICH CAN MEASURE THE THREE-AXIS FORCES AND THREE-AXIS TORQUES APPLIED TO THE WHEEL IN VEHICLE TESTING APPLICATIONS. HOWEVER, THE TRANSDUCER IS GENERALLY MOUNTED ON THE WHEEL OF A MOVING VEHICLE, WHEN ABRUPTLY ACCEL-ERATING OR BRAKING, THE MASS/INERTIA OF THE TRANSDUCER ITSELF HAS EXTRA EFFECTS ON THE SENSOR RESPONSE SO THAT INERTIA/MASS LOADS WILL BE DETECTED AND COUPLED INTO THE SIGNAL OUTPUTS. THIS IS THE INERTIA COUPLING EFFECT THAT DECREASES THE SENSOR ACCURACY AND SHOULD BE AVOIDED. IN THIS PAPER, THE INERTIA COUPLING PROBLEM INDUCED BY SIX DIMENSIONAL ACCELERATIONS IS INVESTIGATED FOR A UNIVERSAL WFT. INERTIA LOAD DISTRIBUTION OF THE WFT IS SOLVED BASED ON THE PRINCIPLE OF EQUIVALENT MASS AND ROTARY INERTIA FIRST-LY, THUS THEN ITS IMPACT CAN BE IDENTIFIED WITH THE THEORETICAL DERIVATION. FEM SIMULATION AND EXPERIMENTAL VERIFICATION ARE PERFORMED AS WELL. RESULTS SHOW THAT STRAINS IN SIMULATION AGREE WELL WITH THE THEORETICAL DERIVATION. THE RELATIONSHIP BETWEEN THE APPLIED ACCELERATION AND INERTIA LOAD FOR BOTH WHEEL FORCE AND MOMENT IS THE APPROXIMATE LINEAR RESPECTIVELY. THE RELATIVE ERRORS ARE ACCEPTABLE WITHIN LESS THAN 5% AND THE MAXIMUM IMPACT OF INERTIA LOADS ON THE SIGNAL OUTPUT IS ABOUT 1.5% IN THE MEASURING RANGE.
Trained Immunity or Tolerance: Opposing Functional Programs Induced in Human Monocytes after Engagement of Various Pattern Recognition Receptors

ABSTRACT Upon priming with Candida albicans or with the fungal cell wall component β-glucan, monocytes respond with an increased cytokine production upon restimulation, a phenomenon termed “trained immunity. ” In contrast, the prestimulation of monocytes with lipopolysaccharide has long been known to induce tolerance. Because the vast majority of commensal microorganisms belong to bacterial or viral phyla, we sought to systematically investigate the functional reprogramming of monocytes induced by the stimulation of pattern recognition receptors (PRRs) with various bacterial or viral ligands. Monocytes were functionally programmed for either enhanced (training) or decreased (tolerance) cytokine production, depending on the type and concentration of ligand they encountered. The functional reprogramming of monocytes was also associated with cell shape, granulocity, and cell surface marker modifications. The training effect required p38- and Jun N-terminal protein kinase (JNK)-mediated mitogen-activated protein kinase (MAPK) signaling, with specific signaling patterns directing the functional fate of the cell. The long-term effects on the function of monocytes were mediated by epigenetic events, with both histone methylation and acetylation inhibitors blocking the training effects. In conclusion, our experiments identify the ability of monocytes to acquire adaptive characteristics after prior activation with a wide variety of ligands. Trained immunity and tolerance are two distinct and opposing functional programs induced by the specific microbial ligands engaging the monocytes.
Evaluation of pyrazole and ethanol induced S9 fraction in bacterial mutagenicity testing.

A major constitutive enzyme in the liver of the uninduced rat is cytochrome P450-2E1. This isozyme has been shown to metabolize a number of carcinogens, including low molecular weight nitrosamines and a number of compounds normally regarded as non-mutagenic in the Ames test, e.g. aniline, urethane and benzene. Using the standard induction procedures [Aroclor 1254 or a combination of phenobarbitone (PB) and beta-naphthoflavone (beta-NF)] the level of CYP2E1 in rat liver is actually suppressed and it has been suggested that this may account for the negative findings with these compounds in the Ames test. S9 fractions were prepared from rats pre-treated with pyrazole or ethanol (inducers of CYP2E1) and then used in the Ames test (or pre-incubation modification) with urethane, acetaminophen, aniline, benzene, procarbazine and N-nitrosopyrrolidine. Both pyrazole and ethanol induced S9 were superior to PB/beta-NF-S9 and uninduced-S9 for the activation of N-nitrosopyrrolidine, a known CYP2E1 substrate. However, there was no evidence of mutagenic activity with urethane, aniline, benzene, procarbazine or acetaminophen. As these compounds have demonstrated genotoxicity in vivo, additional important metabolic pathways must be required which are not present in rat liver S9 fraction.
Measurement-based effective conductivity of carbon nanotube networks for microwave design purposes

The conductivity of carbon nanotube (CNT) networks is investigated in this work. A mathematical model based on the percolation theory is developed to be implemented in simulation software to design CNT-based high-frequency components. For this purpose, two independent measurement setups are used to extract the conductivity of carbon nanotubes in its dry powder form as furnished by the manufacturer. Moreover, the radio frequency-dependent properties of CNT networks are studied experimentally for different packing densities. The effective conductivity of CNTs is extracted based on the percolation theory which provides a physical-mathematical model.