Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Bacillus subtilis
 σW‐dependent genes that provide intrinsic resistance to antimicrobial compounds produced by Bacilli

Bacillus subtilis produces many antibiotics of varying structures and specificity. Here we identify a prominent role for σW, an extracytoplasmic function (ECF) sigma factor, in providing intrinsic resistance to antimicrobial compounds produced by other Bacilli. By using a panel of B. subtilis mutants disrupted for each of the 30 known σW‐dependent operons we identified resistance genes for at least three different antimicrobial compounds. The ydbST and fosB genes contribute to resistance to antimicrobial compound(s) produced by B. amyloliquefaciens FZB42, the yqeZyqfAB operon provides resistance to the SPβ prophage‐encoded bacteriocin sublancin, and the yknWXYZ operon and yfhL provide resistance to the antimicrobial peptide SdpC. YfhL encodes a paralogue of SdpI, a membrane protein that provides immunity to SdpC. In competition experiments, we identify σW as a key factor in allowing B. subtilis to resist antibiotic killing and encroachment by competing strains. Together with the previous observation that σW provides inducible resistance against the Streptomyces antibiotic fosfomycin, these studies support the notion that σW controls an antibiosis regulon important in the microbial ecology of soil bacteria.
3D Cultures of Prostate Cancer Cells Cultured in a Novel High-Throughput Culture Platform Are More Resistant to Chemotherapeutics Compared to Cells Cultured in Monolayer

Despite monolayer cultures being widely used for cancer drug development and testing, 2D cultures tend to be hypersensitive to chemotherapy and are relatively poor predictors of whether a drug will provide clinical benefit. Whilst generally more complicated, three dimensional (3D) culture systems often better recapitulate true cancer architecture and provide a more accurate drug response. As a step towards making 3D cancer cultures more accessible, we have developed a microwell platform and surface modification protocol to enable high throughput manufacture of 3D cancer aggregates. Herein we use this novel system to characterize prostate cancer cell microaggregates, including growth kinetics and drug sensitivity. Our results indicate that prostate cancer cells are viable in this system, however some non-cancerous prostate cell lines are not. This system allows us to consistently control for the presence or absence of an apoptotic core in the 3D cancer microaggregates. Similar to tumor tissues, the 3D microaggregates display poor polarity. Critically the response of 3D microaggregates to the chemotherapeutic drug, docetaxel, is more consistent with in vivo results than the equivalent 2D controls. Cumulatively, our results demonstrate that these prostate cancer microaggregates better recapitulate the morphology of prostate tumors compared to 2D and can be used for high-throughput drug testing.
Influence of Aging in the Warm Forming of 6xxx series Aluminum Alloys

Tese de doutoramento em cotutela, na area de Engenharia Mecânica, no ramo de Tecnologias de Producao, apresentada ao Departamento de Engenharia Mecânica da Faculdade de Ciencias e Tecnologia da Universidade de Coimbra e a Universite de Bretagne-Sud, Franca
An optimizer for hardware synthesis

A description is given of a process-graph analyzer, i.e. a program that optimizes an algorithmic hardware description while endeavoring to attain maximum speed with the minimum commitment to resources. The analyzer is part of the V-Synth system. The four major subsystems of the analyzer-the decomposer, the optimizer, the control-state generator, and the translator-are discussed. Because both its input and output are in VHDL, VHDL itself is discussed. Preliminary test results for the analyzer are presented. <<ETX>>
A Complete Lipopolysaccharide Inner Core Oligosaccharide Is Required for Resistance of Burkholderia cenocepacia to Antimicrobial Peptides and Bacterial Survival In Vivo

ABSTRACT Burkholderia cenocepacia is an important opportunistic pathogen of patients with cystic fibrosis. This bacterium is inherently resistant to a wide range of antimicrobial agents, including high concentrations of antimicrobial peptides. We hypothesized that the lipopolysaccharide (LPS) of B. cenocepacia is important for both virulence and resistance to antimicrobial peptides. We identified hldA and hldD genes in B. cenocepacia strain K56-2. These two genes encode enzymes involved in the modification of heptose sugars prior to their incorporation into the LPS core oligosaccharide. We constructed a mutant, SAL1, which was defective in expression of both hldA and hldD, and by performing complementation studies we confirmed that the functions encoded by both of these B. cenocepacia genes were needed for synthesis of a complete LPS core oligosaccharide. The LPS produced by SAL1 consisted of a short lipid A-core oligosaccharide and was devoid of O antigen. SAL1 was sensitive to the antimicrobial peptides polymyxin B, melittin, and human neutrophil peptide 1. In contrast, another B. cenocepacia mutant strain that produced complete lipid A-core oligosaccharide but lacked polymeric O antigen was not sensitive to polymyxin B or melittin. As determined by the rat agar bead model of lung infection, the SAL1 mutant had a survival defect in vivo since it could not be recovered from the lungs of infected rats 14 days postinfection. Together, these data show that the B. cenocepacia LPS inner core oligosaccharide is needed for in vitro resistance to three structurally unrelated antimicrobial peptides and for in vivo survival in a rat model of chronic lung infection.
Russian blues reveal effects of language on color discrimination

English and Russian color terms divide the color spectrum differently. Unlike English, Russian makes an obligatory distinction between lighter blues (“goluboy”) and darker blues (“siniy”). We investigated whether this linguistic difference leads to differences in color discrimination. We tested English and Russian speakers in a speeded color discrimination task using blue stimuli that spanned the siniy/goluboy border. We found that Russian speakers were faster to discriminate two colors when they fell into different linguistic categories in Russian (one siniy and the other goluboy) than when they were from the same linguistic category (both siniy or both goluboy). Moreover, this category advantage was eliminated by a verbal, but not a spatial, dual task. These effects were stronger for difficult discriminations (i.e., when the colors were perceptually close) than for easy discriminations (i.e., when the colors were further apart). English speakers tested on the identical stimuli did not show a category advantage in any of the conditions. These results demonstrate that (i) categories in language affect performance on simple perceptual color tasks and (ii) the effect of language is online (and can be disrupted by verbal interference).
Evaluation of a pre-existing, 3-year household water treatment and handwashing intervention in rural Guatemala.

BACKGROUND The promotion of household water treatment and handwashing with soap has led to large reductions in child diarrhoea in randomized efficacy trials. Currently, we know little about the health effectiveness of behaviour-based water and hygiene interventions after the conclusion of intervention activities. METHODS We present an extension of previously published design (propensity score matching) and analysis (targeted maximum likelihood estimation) methods to evaluate the behavioural and health impacts of a pre-existing but non-randomized intervention (a 3-year, combined household water treatment and handwashing campaign in rural Guatemala). Six months after the intervention, we conducted a cross-sectional cohort study in 30 villages (15 intervention and 15 control) that included 600 households, and 929 children <5 years of age. RESULTS The study design created a sample of intervention and control villages that were comparable across more than 30 potentially confounding characteristics. The intervention led to modest gains in confirmed water treatment behaviour [risk difference = 0.05, 95% confidence interval (CI) 0.02-0.09]. We found, however, no difference between the intervention and control villages in self-reported handwashing behaviour, spot-check hygiene conditions, or the prevalence of child diarrhoea, clinical acute lower respiratory infections or child growth. CONCLUSIONS To our knowledge this is the first post-intervention follow-up study of a combined household water treatment and handwashing behaviour change intervention, and the first post-intervention follow-up of either intervention type to include child health measurement. The lack of child health impacts is consistent with unsustained behaviour adoption. Our findings highlight the difficulty of implementing behaviour-based household water treatment and handwashing outside of intensive efficacy trials.
Phase equilibrium calculations for confined fluids, including surface tension prediction models

Phase equilibrium calculations for fluids confined inside capillary tubes or porous media are formulated using the isofugacity equations. In this situation, the phase pressures are not equal and it is assumed that they are related by the Laplace equation. With this formulation, existing procedures for phase equilibrium calculations can be readily modified to include capillary effects. In this paper, we review some of the main authors who have studied the behavior of fluids inside porous media and perform bubble- and dew-point calculations for pure components and mixtures, using the Peng-Robinson equation of state to model the coexisting phases and several planar surface tension models. Comparisons with results from the literature indicate that the proposed formulation is adequate for representing phase equilibrium inside capillary tubes.
A Visual Constraint Specifying Approach for Adaptive Software

Monitoring sensitive events is of great significance for adaptive software. Specifying a sufficient set of constraints prior to software deployment is necessary to detect the presence of such events during execution. Here we propose a visual constraint specifying approach, which can generate monitoring code automatically, so as to make the constraint specification easy, and the adaptation of software easy. The detailed representing approach, generating algorithm, and a typical implementation are introduced also
Effect of boundary on controlled memristor-based oscillator

Recently, the applications of memristors have spread into many fields and especially in the circuit theory. Many models have been proposed for the HP-memristor based on the window functions. In this paper, we introduce a complete mathematical analysis of the controlled reactance-less oscillator for two different window functions of Joglekar's model (linear and nonlinear dopant drift) to discuss the effect of changing the window function on the oscillator's behavior. The generalized necessary and sufficient conditions based on the circuit elements and control voltages for both the linear and nonlinear models are introduced. Moreover, closed form expressions for the oscillation frequency and duty cycle are derived for these models and verified using PSPICE simulations showing an excellent matching. Finally a comparison between the linear and nonlinear models which shows their effect on the oscillation frequency and conditions of oscillation is introduced.
Smallholder milk market participation, dietary diversity and nutritional status among young children in Ethiopia

This study examines the effects of smallholder milk market participation on household and intra-household dietary diversity and on nutritional status of young children in Ethiopia. Using the FAO dietary diversity questionnaire, 164 households were followed for two consecutive days and all food items consumed by five household members were recorded. T-test and propensity score matching were used to analyze the data. Milk market participant households have significantly higher levels of milk production, household income, dietary diversity and nutritional status of young children. Despite significant differences in milk production between market participant and non-participant households, no significant differences were found with regard to animal source food consumption in general and milk consumption in particular. However, dietary diversity and nutritional status of children under five is better in participant households, thus indicating that smallholder market participation is positively associated with food security and nutritional status of farm households in rural Ethiopia.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1463 Efficient Simulation of Wave Phenomena

Almquist, M. 2017. Efficient Simulation of Wave Phenomena. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1463. 42 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-9777-4. Wave phenomena appear in many fields of science such as acoustics, geophysics, and quantum mechanics. They can often be described by partial differential equations (PDEs). As PDEs typically are too difficult to solve by hand, the only option is to compute approximate solutions by implementing numerical methods on computers. Ideally, the numerical methods should produce accurate solutions at low computational cost. For wave propagation problems, highorder finite difference methods are known to be computationally cheap, but historically it has been difficult to construct stable methods. Thus, they have not been guaranteed to produce reasonable results. In this thesis we consider finite difference methods on summation-by-parts (SBP) form. To impose boundary and interface conditions we use the simultaneous approximation term (SAT) method. The SBP-SAT technique is designed such that the numerical solution mimics the energy estimates satisfied by the true solution. Hence, SBP-SAT schemes are energy-stable by construction and guaranteed to converge to the true solution of well-posed linear PDE. The SBPSAT framework provides a means to derive high-order methods without jeopardizing stability. Thus, they overcome most of the drawbacks historically associated with finite difference methods. This thesis consists of three parts. The first part is devoted to improving existing SBP-SAT methods. In Papers I and II, we derive schemes with improved accuracy compared to standard schemes. In Paper III, we present an embedded boundary method that makes it easier to cope with complex geometries. The second part of the thesis shows how to apply the SBP-SAT method to wave propagation problems in acoustics (Paper IV) and quantum mechanics (Papers V and VI). The third part of the thesis, consisting of Paper VII, presents an efficient, fully explicit time-integration scheme well suited for locally refined meshes.
Ensuring Correctness of Dynamic Reconfiguration in SOA Based Software

SOA based software is typically based on dynamic reconfiguration, since it is the composition of services. Then ensuring the correctness of dynamic reconfiguration is an important challenge. But few work focuses on it, this paper gives a better answer to solve the problem. It uses services-behavioral type discipline extended the Martin-Löf’s Type Theory (for short, MLTT) which supports a type-theoretic formulation of services behavior structured patterns, so that services can be formally constructed by type services-behavioral type. Then, the type rules for subtype, duality, and correctness of dynamic reconfiguration are discussed. In our case study, the deductions are gave to show that how to verify the correctness of the dynamic reconfiguration. Finally, the implement of our approach is discussed.
A universal microcontroller circuit and firmware design and implementation for IoT-based realtime measurement and control applications

This paper presents a design and implementation techniques to construct a universal microcontroller board based on realtime measurement and control applications. It is not only designed for realtime applications, but is also designed for supporting many modern WiFi devices that utilize TCP/IP protocol over internet networks. It means the proposed system fully supports many Internet-of-Things (IoT) applications. Furthermore, it can also be used for computer based monitoring and control applications and many other industrial applications, including Industrial Internet-of-Things (IIoTs) as well. In addition, the universal microcontroller board is designed for flexibility of use, meaning the users can custom the board to reduce and expand their applications. The system is composed of all necessary components including analog and digital input/output ports, WiFi communication based on TCP/IP. The realtime operating system (RTOS) and communication protocol drivers, e.g., UART, I2C, and SPI, are also embedded in the microcontroller firmware. The system is evaluated and examined in web-based realtime monitoring to prove that it can be used in IoT based realtime applications. The experimental results show that the proposed system appropriately exchanges data over internet networks to web-browser with high speed data transfer rate as expected.
Do nucleic acids moonlight as molecular chaperones?

Abstract Organisms use molecular chaperones to combat the unfolding and aggregation of proteins. While protein chaperones have been widely studied, here we demonstrate that DNA and RNA exhibit potent chaperone activity in vitro. Nucleic acids suppress the aggregation of classic chaperone substrates up to 300-fold more effectively than the protein chaperone GroEL. Additionally, RNA cooperates with the DnaK chaperone system to refold purified luciferase. Our findings reveal a possible new role for nucleic acids within the cell: that nucleic acids directly participate in maintaining proteostasis by preventing protein aggregation.
Impact of Infection Dose and Previous Serum Antibodies against the Locus of Enterocyte Effacement Proteins on Escherichia coli O157:H7 Shedding in Calves following Experimental Infection

Escherichia coli O157:H7 is the main causative agent of haemolytic uremic syndrome. Cattle are the main reservoir of these bacteria, and have been shown to develop immune response to colonization. Our aim was to investigate the faecal shedding pattern of E. coli O157:H7 in calves challenged intragastrically with either 108 or 1010 CFU, as well as the ability of specific preexisting antibodies to reduce shedding of the pathogen. Shedding was analysed by direct counting as well as enrichment of rectoanal mucosal swabs. Statistical analysis was performed using a linear model for repeated measures with and without the inclusion of preexisting antibodies against the carboxy-terminal fraction of intimin-γ (γ-intimin C280) as a covariable. Results suggest that there is a statistical difference in the area under the shedding curves between both doses for 14 as well as 28 days after challenge (p = 0.0069 and 0.0209, resp.). This difference is increased when the prechallenge antibodies are taken into account (p = 0.0056 and 0.0185). We concluded that the bacterial dose influences shedding on calves experimentally challenged and that preexisting antibodies against E. coli O157:H7 γ-intimin C280 could partially reduce faecal excretion.
Dynamical multilayer neural networks that learn continuous trajectories

The feed-forward multilayer networks (perceptrons, radial basis func tion networks (RBF), probabilistic networks, etc.) are currently used as „static syst ems“ in pattern recognition, speech generation, identification and control, prediction, etc. (see, e. g. [1]). The oretical works by several researchers, including [2] and [3] have proved that, even with one idden layer, a perceptron neural network can uniformly approximate any continuous function over a compact domain, provided that this perceptron has a sufficient number of neur ns in the hidden layer. Recently, interest has increased to apply the neural networks in le ar ing continuous trajectories, identification and/or control of dynamical systems. I n such a case it is natural to use the networks involving dynamical elements in the form of feedback connections whi ch are known as recurrent neural networks. Although a huge amount of work and studies in th field of feed-forward neural networks has been done, only few of the results c oncern learning continuous trajectories by means of dynamical recurrent neural networks. Pearlmutter [4], [5], Werbos [6], Toomarian and Barhen [7] have developed a n algorithm using gradient-descent-based methods which is known as back-propagation throug h time (BPTT); it learns time-varying external inputs and produces eithe r desired temporal behaviours over a bounded time interval or trains non-fixed-point attractors . Williams and Zipser [8], Meert and Ludik [9] have constructed a gradient descent le ar ing rule which they call real-time recurrent learning (RTRL) and which can deal w ith time sequences of arbitrary length. A stochastic search method based on an adaptive simulated anneal ing algorithm has been used by Cohen et al. [10] to efficiently train recurrent neural networks with time delays (TDRNN). An effort was made in the above investigation to implement s veral benchmark tasks using minimum size networks. In all the above investigations, a dynamical neural network evolves in a ccordance with the following general equations
Reliable PPG-based algorithm in atrial fibrillation detection

Atrial Fibrillation (AF) is the most common type of arrhythmia. Since AF is a risk factor for stroke, automatic detection of AF is an important public health issue. Currently, the most useful and accurate tool for diagnosing AF is electrocardiography (EKG). On the other hand, PPG-based AF detection desires exploration. Photoplethysmogram (PPG) is an alternative technique to obtain the heart rate information by pulse oximetry. Convenience makes PPG promising in identifying arrhythmia like AF. The aim of this study is to investigate the potential of analyzing PPG waveforms to identify patients with AF. With the extracted features from multiple parameters, including interval and amplitude of PPG signals, patients were classified into AF and non-AF by support vector machine (SVM). The receiver operating characteristic curve (ROC) and statistical measures were applied to evaluate model performances. Among 468 patients' signals recorded in clinic environments, we achieve ROC area under curve, sensitivity and accuracy of 0.971, 0.942, and 0.957, respectively. The result suggests that the PPG-based AF detection algorithm is a promising pre-screening tool to help doctors monitoring patient with arrhythmia.
Arterial Wall Vibration Distal to Stenoses in Isolated Arteries of Dog and Man

It has been suggested that poststenotic weakening of arterial walls is caused by arterial wall vibration and structural fatigue initiated by pressure disturbances in turbulent blood flow. We examined the frequency spectra of wall vibration downstream from experimental arterial stenoses and compared them with the natural resonant vibration characteristics of the artery walls. Spectra of arterial wall displacement of isolated perfused dog and human arteries were measured with a noncontacting capacitance transducer during conditions of fluid flow through the artery; resonant vibration characteristics were determined during pure sine and random sound stimulation of the artery walls in the absence of flow. It is concluded that fluid flow through isolated arteries with an experimental stenosis excites the artery wall to vibrate over a wide range of frequencies within which are discrete frequencies that coincide with the resonant frequencies of the artery wall.