Miracle-dz/UniFAR-FTUs huggingface dataset:
RadD Contributes to R-Loop Avoidance in Sub-MIC Tobramycin

Bacteria frequently encounter low concentrations of antibiotics. Active antibiotics are commonly detected in soil and water at concentrations much below lethal concentration. Although sub-MICs of antibiotics do not kill bacteria, they can have a major impact on bacterial populations by contributing to the development of antibiotic resistance through mutations in originally sensitive bacteria or acquisition of DNA from resistant bacteria. It was shown that concentrations as low as 100-fold below the MIC can actually lead to the selection of antibiotic-resistant cells. We seek to understand how bacterial cells react to such antibiotic concentrations using E. coli, the Gram-negative bacterial paradigm, and V. cholerae, the causative agent of cholera. Our findings shed light on the processes triggered at the DNA level by antibiotics targeting translation, how damage occurs, and what the bacterial strategies are to respond to such DNA damage. ABSTRACT We have previously identified Vibrio cholerae mutants in which the stress response to subinhibitory concentrations of aminoglycoside is altered. One gene identified, VC1636, encodes a putative DNA/RNA helicase, recently named RadD in Escherichia coli. Here we combined extensive genetic characterization and high-throughput approaches in order to identify partners and molecular mechanisms involving RadD. We show that double-strand DNA breaks (DSBs) are formed upon subinhibitory tobramycin treatment in the absence of radD and recBCD and that formation of these DSBs can be overcome by RNase H1 overexpression. Loss of RNase H1, or of the transcription-translation coupling factor EF-P, is lethal in the radD deletion mutant. We propose that R-loops are formed upon sublethal aminoglycoside treatment, leading to the formation of DSBs that can be repaired by the RecBCD homologous recombination pathway, and that RadD counteracts such R-loop accumulation. We discuss how R-loops that can occur upon translation-transcription uncoupling could be the link between tobramycin treatment and DNA break formation. IMPORTANCE Bacteria frequently encounter low concentrations of antibiotics. Active antibiotics are commonly detected in soil and water at concentrations much below lethal concentration. Although sub-MICs of antibiotics do not kill bacteria, they can have a major impact on bacterial populations by contributing to the development of antibiotic resistance through mutations in originally sensitive bacteria or acquisition of DNA from resistant bacteria. It was shown that concentrations as low as 100-fold below the MIC can actually lead to the selection of antibiotic-resistant cells. We seek to understand how bacterial cells react to such antibiotic concentrations using E. coli, the Gram-negative bacterial paradigm, and V. cholerae, the causative agent of cholera. Our findings shed light on the processes triggered at the DNA level by antibiotics targeting translation, how damage occurs, and what the bacterial strategies are to respond to such DNA damage.
CHOICE OF REFERENCE IN CART APPLICATIONS USING PMU DATA

Classification and Regression trees (CART) are being used for various applications in Power Systems. PMU phasor data is used in most of these applications to build decision trees. A noticeable difference in results may be seen by changing the reference bus in CART simulations. Recently studies on PMU placement for security- dependability based adaptive relay protection scheme using data mining were proposed. Using this topic as a case study, with the help of CART simulations we have investigated the effects of changing the reference bus. In addition to this the issues related to CART simulation in representing phasor data as a single complex number attribute or as two different attributes i.e. a number associated with the real part of the complex number as one attribute and a number associated with imaginary part of the complex number as a different attribute are also discussed. Keywords— PMUs, Adaptive relaying, security- dependability, decision trees, CART.
Transporting Children in Autonomous Vehicles: An Exploratory Study

Objective Identify factors that impact parents’ decisions about allowing an unaccompanied child to ride in an autonomous vehicle (AV). Background AVs are being tested in several U.S. cities and on highways in multiple states. Meanwhile, suburban parents are using ridesharing services to shuttle children from school to extracurricular activities. Parents may soon be able to hire AVs to transport children. Method Nineteen parents of 8- to 16-year-old children, and some of their children, rode in a driving simulator in autonomous mode, then were interviewed. Parents also participated in focus groups. Topics included minimum age for solo child passengers, types of trips unaccompanied children might take, and vehicle features needed to support child passengers. Results Parents would require two-way audio communication and prefer video feeds of vehicle interiors, seatbelt checks, automatic locking, secure passenger identification, and remote access to vehicle information. Parents cited convenience as the greatest benefit and fear that AVs could not protect passengers during unplanned trip interruptions as their greatest concern. Conclusion Manufacturers have an opportunity to design family-friendly AVs from the outset, rather than retrofit them to be safe for child passengers. More research, especially usability studies where families interact with technology prototypes, is needed to understand how AV design impacts child passengers. Application Potential applications of this research include not only designing vehicles that can be used to safely transport children, seniors who no longer drive, and individuals with disabilities but also developing regulations, policies, and societal infrastructure to support safe child transport via AVs.
Validation of a death assay for Angiostrongylus cantonensis larvae (L3) using propidium iodide in a rat model (Rattus norvegicus)

Abstract Angiostrongylus cantonensis is a pathogenic nematode and the cause of neuroangiostrongyliasis, an eosinophilic meningitis more commonly known as rat lungworm disease. Transmission is thought to be primarily due to ingestion of infective third stage larvae (L3) in gastropods, on produce, or in contaminated water. The gold standard to determine the effects of physical and chemical treatments on the infectivity of A. cantonensis L3 larvae is to infect rodents with treated L3 larvae and monitor for infection, but animal studies are laborious and expensive and also raise ethical concerns. This study demonstrates propidium iodide (PI) to be a reliable marker of parasite death and loss of infective potential without adversely affecting the development and future reproduction of live A. cantonensis larvae. PI staining allows evaluation of the efficacy of test substances in vitro, an improvement upon the use of lack of motility as an indicator of death. Some potential applications of this assay include determining the effectiveness of various anthelmintics, vegetable washes, electromagnetic radiation and other treatments intended to kill larvae in the prevention and treatment of neuroangiostrongyliasis.
Histone Deacetylase 6 Regulates Endothelial MyD88-dependent canonical TLR signaling, Lung inflammation, and Alveolar Remodeling in the developing lung.

Lung endothelial cell (EC) immune activation during bacterial sepsis contributes to acute lung injury and bronchopulmonary dysplasia in premature infants. The epigenetic regulators of sepsis-induced endothelial immune activation, lung inflammation and alveolar remodeling remain unclear. Herein, we examined the role of the cytoplasmic histone deacetylase, HDAC6, in regulating EC Toll-Like Receptor 4 (TLR4) signaling and modulating sepsis-induced lung injury in a neonatal model of sterile sepsis. In human primary microvascular endothelial cells (HPMEC), lipopolysaccharide (LPS)-induced MAPK, IKK-β, and p65 phosphorylation as well as inflammatory cytokine expression was exaggerated with the HDAC6 inhibitor tubastatin A, and by dominant negative HDAC6 with a mutated catalytic domain 2. Expression of HDAC6 wild-type protein suppressed LPS-induced MyD88 acetylation, p65 (Lys310) acetylation, MyD88/TRAF6 co-immunoprecipitation, and pro-inflammatory TLR4 signaling in HPMEC. In a neonatal mouse model of sepsis, the HDAC6 inhibitor tubastatin A, amplified lung EC TLR4 signaling and vascular permeability. HDAC6-inhibition augmented LPS-induced MyD88 acetylation, MyD88/TRAF6 binding, p65 acetylation, canonical TLR4 signaling, and inflammation in the developing lung. Sepsis-induced decreases in the fibroblast growth factors FGF-2 and FGF-7, and increase in matrix metalloproteinase 9 was worsened with HDAC6-inhbition, while elastin expression was equally suppressed. Exaggerated sepsis-induced acute lung inflammation observed with HDAC6-inhibition worsened alveolar simplification evidenced by increases in mean linear intercepts and decreased radial alveolar counts. Our studies reveal that HDAC6 is a constitutive, negative regulator of cytoplasmic TLR4 signaling in EC and the developing lung. The therapeutic efficacy of augmenting HDAC6 activity in neonatal sepsis to prevent lung injury needs to be evaluated.
Phytochelatin database: a resource for phytochelatin complexes of nutritional and environmental metals

Abstract Phytochelatins (PyCs) are a diverse set of plant compounds that chelate metals, protect against metal toxicity and function in metal homeostasis. PyCs are present in plants consumed as food by humans and could, in principle, impact absorption and utilization of essential and toxic metals such as selenium and cadmium, respectively. PyCs vary in terminal amino acid composition and chain length, exist in multiple oxidation states and reversibly bind multiple metals; consequently, PyCs include a large set of possible structures. Although individual PyC-metal complexes have been studied, no resource exists to characterize the diversity of PyCs and PyC-metal complexes. We used the scientific literature to develop a database of elemental formulas for polymer forms varying in chain length from 2 to 11 glutamyl-cysteine repeats. Using elemental formulas, we calculated monoisotopic masses using the most abundant isotopes of each element and calculated masses for complexes with 13 metals of nutritional and toxicological significance. The resulting phytochelatin database (PyCDB) contains 46 260 unique elemental formulas for PyC and PyC-metal complexes. The database is available online for download as well as for direct mass queries for mass spectrometry using an accurate mass annotation tool for user-selected PyC types, metals and adducts of interest. We performed studies of a commonly consumed food—onion—to validate the database and test utility of the tool. Onion samples were analyzed using ultra-high resolution mass spectrometry-based metabolomics. Mass spectral features were annotated using the PyCDB web tool and the R package, xMSannotator; annotated features were further validated by collision-induced dissociation mass spectrometry. The results establish use and a workflow for PyCDB as a resource for characterization of PyCs and PyC-metal complexes.
The PRIAMO study: active sexual life is associated with better motor and non‐motor outcomes in men with early Parkinson's disease

Data suggest a relationship between sexual dysfunction, mainly erectile dysfunction in men, and worse disease progression in Parkinson's disease (PD). There is scant evidence on the correlates of sexual activity in PD patients. By involving a subgroup of 355 patients from the PRIAMO (Parkinson Disease Non Motor Symptoms) study, the present 24‐month longitudinal prospective analysis aims to demonstrate that the presence of active sexual life is associated with disease progression in early PD.
The Use of Operational Cash Flow in the Estimation of Accrual-Based Earnings Management

Abstract One of the most important analytical spheres enabling the diagnostic estimation of intentional changes in a company’s financial result is the area of accrual adjustments of net profit, separated in the cash flow statement prepared using the indirect method. The special cognitive value of accrual differences can be seen when the structure of total accruals is separated by those adjustments that are not directly related to the real activity of the enterprise, and are the result of subjective accounting choices. The main objective of the article is to present the selected econometric models used for examining accrual-based earnings management phenomenon in Poland. The analysis includes following regression models, namely: the Jones model, the Kasznik model, the Dechow-Dichev model and the McNichols model. The empirical studies were conducted among listed companies qualified for the Warsaw Stock Exchange indices: WIG-20 and mWIG-40, whose shares were traded for at least ten years in 1998-2017.
Dimensionless characterization of the non-linear soil consolidation problem of Davis and Raymond. Extended models and universal curves

Abstract The dimensionless groups that govern the Davis and Raymond non-linear consolidation model, and its extended versions resulting from eliminating several restrictive hypotheses, were deduced. By means of the governing equations nondimensionalization technique and introducing the characteristic time concept, both in terms of settlement and pressures, was obtained (for the most general model) that the average degree of settlement only depends on the dimensionless time while the average degree of pressure dissipation does it, additionally, on the loading ratio. These results allowed the construction of universal curves expressing the solutions of the unknowns of interest in a direct and simple way.
Spectrum management, pricing, and efficiency control in broadband wireless communications

The radio spectrum is a unique, ubiquitous natural resource shared by various types of services. Unlike many other natural resources, it can be repeatedly reused. In practice, though, it remains a finite resource, and it can only accommodate a limited number of simultaneous users. This restriction requires careful planning and management for maximizing its value for all services. This is especially true since the demand for communication spectrum worldwide is rapidly increasing. As the pressure on spectrum increases with a generalized image of radio techniques, traditional ways to assess the merits of new technical solutions and to allocate as well as to tax frequencies appear to be adapted less and less. This paper reviews the present situation and stresses the need for more proactive, harmonized, and dynamic approaches linking technical and regulatory aspects in order to introduce broadband wireless communications systems.
Prediction of Zero Shear Viscosity of Poly (Vinyl Chloride) Plastisols

Abstract The rheological behaviour of PVC plastisols composed of a blend of suspension and micro-suspension resins in different proportions was investigated. The present work was mainly focused on the variation of the zero shear viscosity versus the concentration of the extender resin. Hence, the packing fraction Fm was evaluated using the Krieger-Dougherty equation. These experiments confirmed the major influence of particle size distribution concerning the decrease of viscosity for concentrated suspensions. In addition, a model based on the porosity model developed by Ouchiyama et al. (Ouchiyama N, Tanaka T: Porosity estimation for random packings of spherical particle”, Ind. Eng. Chem. Fundam. 23 (1984) 490-493) to predict the packing fraction in the case of multimodal lattices was successfully applied to our PVC plastisols formulations.
Evaluating Software Sensors for Actively Profiling Windows 2000 Computer Users

We report on a new, on-going intrusion-detection project that empirically investigates the usefulness of "stealing" a small amount of CPU cycles (1%), main memory (16MB), and disk memory (100 MB) in order to continually gather and analyze dozens of fine-grained system measurements, such as network traffic, identity of the current programs executing, and the user’s typing speed. The underlying scientific hypothesis is that a properly chosen set of measurements can provide a "fingerprint" that is unique to each user. Hence, such measurements could serve to help distinguish appropriate use of a given computer from misuse, especially by insiders.
Determine the Required Log Reductions of Human Intestinal Helminth Eggs by Waste Stabilization Pond: A Simulation for Wastewater Recycling in Agriculture

Abstract This paper investigates the determined the required log reductions for human intestinal helminth eggs by waste stabilization ponds as simulation as assessing of mitigating health risk to satisfy practice WHO, 2006 guidelines for the safe use of wastewater in agriculture (≤ 0.1 helminth egg/L) to protect the health of children under 15 years was the development of MATLAB, a computer program based waste stabilization ponds design based on parameter uncertainty and 10,000-trial Monte Carlo simulations were developed for a series of anaerobic, facultative and maturation ponds based on 95%-ile of effluent (≤ 0.1 helminth egg/L) which the result in a health-based target. Whereas the influent of the helminth eggs (Nematode) was (932.500 eggs/L). While the treatment provided (100 % reduction/removal) for the overall treatment process with total hydraulic retention time in climatic conditions of Libya it took 36.207 days in the anaerobic pond, facultative pond, first maturation pond and one of the subsequent maturation pond.
A Review of Hashing based Image Copy Detection Techniques

Abstract Images are considered to be natural carriers of information, and a large number of images are created, exchanged and are made available online. Apart from creating new images, the availability of number of duplicate copies of images is a critical problem. Hashing based image copy detection techniques are a promising alternative to address this problem. In this approach, a hash is constructed by using a set of unique features extracted from the image for identification. This article provides a comprehensive review of the state-of-the-art image hashing techniques. The reviewed techniques are categorized by the mechanism used and compared across a set of functional & performance parameters. The article finally highlights the current issues faced by such systems and possible future directions to motivate further research work.
A GaAs ASIC chip set for NASAs deep space network

A new GaAs chip set is the core of a new ground-based digital receiver to be installed in NASA's deep space network. GaAs technology is needed to handle the high-precision carrier demodulation process at the data rate of 160 million samples per second. The chip set architecture and design strategy are discussed. The capabilities of the digital signal processor printed wiring assembly which contains the ASIC chip set are described, together with design verification techniques for the chip set itself. <<ETX>>
Finding Hidden Structures, Hierarchies, and Cores in Networks via Isospectral Reduction

Abstract The method of isospectral network reduction allows one the ability to reduce a network while preserving the network’s spectral structure. In this paper we describe a number of recent applications of the theory of isospectral reductions. This includes finding hidden structures, specifically latent symmetries, in networks, uncovering different network hierarchies, and simultaneously determining different network cores. We also specify how such reductions can be interpreted as dynamical systems and describe the type of dynamics such systems have. Additionally, we show how the recent theory of equitable decompositions can be paired with the method of isospectral reductions to decompose networks.
Payments for Forest Ecosystem Services Across Europe – Main Approaches and Examples from Slovakia

Abstract Payments for ecosystem services (PES) are flexible, financial mechanisms for utilisation of available finances for environmental improvement. Payments for forest ecosystem services (PFES) have gained increasing policy acceptance at national and international levels. However, evidence about their implementation is limited and rather mixed. PES design is a complex task. There are a number of PES design features that need careful understanding of the specific ecological and socio-economic context. The aim of this article is to analyse main approaches to PFES and types of PES schemes or financial arrangements with the emphasis on three basic schemes: (i) public schemes or government-financed PES (Pigouvian type), (ii) private schemes or user-financed PES (Coasean type) and (iii) public–private schemes (a mixed type). The empirical part is based on the review of PES schemes implemented in different Forest Europe signatory countries. The main features of PES schemes are described on chosen examples from Slovakia.
Traffic Flow Variables Estimation: An Automated Procedure Based on Moving Observer Method. Potential Application for Autonomous Vehicles

Abstract The estimation of traffic flow variables (flow, space mean speed and density) plays a fundamental role in highways planning and designing, as well as in traffic control strategies. Moving Observer Method (MOM) allows traffic surveys in a road, or in a road network. This paper proposes a novel automated procedure, called MOM-AP based on Moving Observer Method and Digital Image Processing (DIP) Technique able to automatically detect (without human observers) and calculate flow q, space mean speed vs and density k in case of stationary and homogeneous traffic conditions. In order to evaluate how reliable is the MOM-AP, an experiment has been carried out in a segment of one two-lane single carriageway road, in Italy. 30 datasets for the segment have been collected (in total 30 round trips). A comparative analysis between MOM-AP and traditional MOM has been carried out. First results show that the current MOM-AP algorithms underestimate the local mean flow variable values of around 10%. Nowadays MOM-AP may be implemented in smartphone apps. Instead, in the near future, it is realistic expecting the increase in the use of automated procedures for calculating the traffic flow variables (based on the “moving observer method”), due to the amount of sensors and digital cameras employed in the new autonomous vehicles (AVs). Considering such technical advances, the MOM-AP is a feasible model for real-time traffic analyses of road networks.