Miracle-dz/UniFAR-FTUs huggingface dataset:
DOA Estimation of Near-field Passive Sources with Acoustic Array Based on Fractional Fourier Transform

In this paper, we propose an efficient near-field source DOA estimation method based on the Fractional Fourier transform. In this method, the received data of the sensor array for the near-field source is modeled as a linear-frequencymodulated (LFM) signal in spatial domain after the Fresnel approximation. Then the Fractional Fourier transform is employed to estimate the modulated frequency rate, which stands for the influence of quadratic phase of near-field source. After compensating this quadratic phase term, the received signal can subsequently be converted into a far-field expression. Finally, classical DOA estimation methods for far-field can be applied to find the direction of the source. In addition, for multiple sources, a CLEAN technique is proposed to extract the sources iteratively. Simulations are finally carried out to demonstrate its validity.
Pathoadaptive Mutations That Enhance Virulence: Genetic Organization of the cadA Regions ofShigella spp

ABSTRACT Pathoadaptive mutations improve the fitness of pathogenic species by modification of traits that interfere with factors (virulence and ancestral) required for survival in host tissues. A demonstrated pathoadaptive mutation is the loss of lysine decarboxylase (LDC) expression in Shigella species that have evolved from LDC-expressing Escherichia coli. Previous studies demonstrated that the product of LDC activity, cadaverine, blocks the action of Shigella enterotoxins and that the gene encoding LDC, cadA, was abolished by large chromosomal deletions in each Shigella species. To better understand the nature and evolution of these pathoadaptive mutations, remnants of thecad region were sequenced from the fourShigella species. These analyses reveal novel gene arrangements in this region of the pathogens' chromosomes. Insertion sequences, a phage genome, and/or loci from different positions on the ancestral E. coli chromosome displaced the cadAlocus to form distinct genetic linkages that are unique to eachShigella species. Hybridization studies, using an E. coli K-12 microarray, indicated that the genes displaced to form the novel linkages still remain in the Shigella genomes. None of these novel gene arrangements were observed in representatives of all E. coli phylogenies. Collectively, these observations indicate that inactivation of the cadAantivirulence gene occurred independently in each Shigellaspecies. The convergent evolution of these pathoadaptive mutations demonstrates that, following evolution from commensal E. coli, strong pressures in host tissues selectedShigella clones with increased fitness and virulence through the loss of an ancestral trait (LDC). These observations strongly support the role of pathoadaptive mutation as an important pathway in the evolution of pathogenic organisms.
An improved discontinuous modulation for three-level inverter

This paper proposes an optimized space vector modulation method for the switching loss reduction of the Neutral-Point-Clamped Three-Level Inverter (NPC-TLI). The main contributions are: 1) several different sequence patterns of the space vectors are compared and an optimized sequence pattern with low switching loss and low current THD is selected; 2) a new Discontinuous Pulse-Width-Modulation clamped to Zero (DPWMZ) is proposed for the switching loss reduction in low modulation ratio; 3) a fast detection method for the load power factor angle φ is designed with cle φ can be calculated in only one sampling period, and the no-switching duration is in the center of the peak value region of the load current. The loss can be reduced further. The simulation and experiment is presented to verify the concept proposed in the paper.
Monolayer ice.

We report results from molecular dynamics simulations of water under confinement and at ambient conditions that predict a first-order freezing transition from a monolayer of liquid water to a monolayer of ice induced by increasing the distance between the confining parallel plates. Since a slab geometry is incompatible with a tetrahedral arrangement of the sp(3) hybridized oxygen of water, the freezing is coupled to a linear buckling transition. By exploiting the ordered out-of-plane displacement of the molecules in the buckled phase the distortion of the hydrogen bonds is minimized.
Placement of tRNA primer on the primer-binding site requires pol gene expression in avian but not murine retroviruses

In an early step in the retroviral infectious process, reverse transcriptase copies the genomic RNA of the virus into complementary minus-strand DNA. The primer for this synthetic event is a molecule of cellular tRNA, which is annealed by its 3' 18 nucleotides to a region of the genomic RNA termed the primer-binding site (PBS); the sequence of the PBS and hence the identity of the tRNA depend upon the retrovirus species. In addition to the primer tRNA, retrovirus particles contain a substantial number of other tRNA molecules. The latter tRNA population is enriched for the tRNA species which serves as primer for the virus. While there is considerable evidence that the enrichment for the primer species can be attributed to the pol gene product, nothing is known regarding mechanisms of annealing the primer to the PBS. We have analyzed pol- mutants of avian leukosis virus (ALV) and murine leukemia virus (MuLV) for the presence of primer at the PBS in virion genomic RNA. Remarkably, the results were different for the two viruses: the PBS was substantially occupied by primer in MuLV but not in ALV. Previous data indicates that the Pol-dependent enrichment of the primer within the virion is much greater in ALV than in MuLV. We therefore propose that the absence of primer at the PBS in pol- ALV is due to the deficiency of the primer species within the particle. The results suggest that, at least in MuLV, the tRNA is unwound by either the Gag protein or a cellular protein for annealing to the PBS. Further, the C-terminal 17 amino acids of Gag are unnecessary for this function in MuLV.
Proteasome Dysfunction Activates Autophagy and the Keap1-Nrf2 Pathway*

Background: Malfunctions in the ubiquitin-proteasome system cause accumulation of non-functional, potentially toxic protein aggregates. Results: The protein aggregates activate Nrf2 and are then excluded by autophagy in vivo. Conclusion: Both Nrf2 and autophagy serve as in vivo cellular adaptations to impaired proteasome. Significance: Cells contain networks of cellular defense mechanisms against defective proteostasis. The ubiquitin-proteasome system and autophagy are crucially important for proteostasis in cells. These pathways are interdependent, and dysfunction in either pathway causes accumulation of ubiquitin-positive aggregates, a hallmark of human pathological conditions. To elucidate in vivo compensatory action(s) against proteasomal dysfunction, we developed mice with reduced proteasome activity in their livers. The mutant mice exhibited severe liver damage, accompanied by formation of aggregates positive for ubiquitin and p62/Sqstm1, an adaptor protein for both selective autophagy and the anti-oxidative Keap1-Nrf2 pathway. These aggregates were selectively entrapped by autophagosomes, and pathological features of livers with impaired proteasome activity were exacerbated by simultaneous suppression of autophagy. In contrast, concomitant loss of p62/Sqstm1 had no apparent effect on the liver pathology though p62/Sqstm1 was indispensable for the aggregates formation. Furthermore, defective proteasome function led to transcriptional activation of the Nrf2, which served as a physiological adaptation. Our in vivo data suggest that cells contain networks of cellular defense mechanisms against defective proteostasis.
SPIROCHETES IN TICKS AND ANTIBODIES TO BORRELIA BURGDORFERI IN WHITE-TAILED DEER FROM CONNECTICUT, NEW YORK STATE, AND NORTH CAROLINA

Ticks were screened for spirochetes and serum samples from white-tailed deer (Odocoileus virginianus) were assayed for antibodies to Borrelia burgdorferi during 1983–1984. Using fluorescein isothiocyanate-labeled rabbit antibodies produced to B. burgdorferi, the etiologic agent of Lyme disease, spirochetes were detected in Ixodes dammini (10.5% of 1,193) and Dermacentor albipictus (0.6% of 157) adults from Connecticut, I. dammini nymphs (49.1% of 108) and adults (64.7% of 99) from Armonk, New York, and in I. scapularis (0.4% of 531) and Amblyomma americanum (3.5% of 173) adults from North Carolina. Infected ticks were either seeking hosts or feeding on deer during the summer and fall. Direct fluorescent antibody staining also revealed spirochetes in two larvae of I. scapularis that emerged from eggs deposited by separate females in the laboratory. Using indirect immunofluorescence tests, antibodies to B. burgdorferi were identified in white-tailed deer living in tick-infested areas of all three states. Aside from minor cross-reactivity, there was no serologic evidence of Treponema or Leptospira infections. Ixodes dammini is a primary vector of B. burgdorferi in northeastern United States, but in North Carolina, other ixodid ticks may transmit this spirochete to humans and wildlife.
Nonaffine displacements in crystalline solids in the harmonic limit.

A systematic coarse graining of microscopic atomic displacements generates a local elastic deformation tensor D as well as a positive definite scalar χ measuring nonaffinity, i.e., the extent to which the displacements are not representable as affine deformations of a reference crystal. We perform an exact calculation of the statistics of χ and D and their spatial correlations for solids at low temperatures, within a harmonic approximation and in one and two dimensions. We obtain the joint distribution P(χ,D) and the two-point spatial correlation functions for χ and D. We show that nonaffine and affine deformations are coupled even in a harmonic solid, with a strength that depends on the size of the coarse-graining volume Ω and dimensionality. As a corollary to our work, we identify the field h(χ) conjugate to χ and show that this field may be tuned to produce a transition to a state where the ensemble average and the correlation length of χ diverge. Our work should be useful as a template for understanding nonaffine displacements in realistic systems with or without disorder and as a means for developing computational tools for studying the effects of nonaffine displacements in melting, plastic flow, and the glass transition.
Functional interaction of c-Ets-1 and GHF-1/Pit-1 mediates Ras activation of pituitary-specific gene expression: mapping of the essential c-Ets-1 domain

The mechanism by which activation of common signal transduction pathways can elicit cell-specific responses remains an important question in biology. To elucidate the molecular mechanism by which the Ras signaling pathway activates a cell-type-specific gene, we have used the pituitary-specific rat prolactin (rPRL) promoter as a target of oncogenic Ras and Raf in GH4 rat pituitary cells. Here we show that expression of either c-Ets-1 or the POU homeo-domain transcription factor GHF-1/Pit-1 enhance the Ras/Raf activation of the rPRL promoter and that coexpression of the two transcription factors results in an even greater synergistic Ras response. By contrast, the related GHF-1-dependent rat growth hormone promoter fails to respond to Ras or Raf, indicating that GHF-1 alone is insufficient to mediate the Ras/Raf effect. Using amino-terminal truncations of c-Ets-1, we have mapped the c-Ets-1 region required to mediate the optimal Ras response to a 40-amino-acid segment which contains a putative mitogen-activated protein kinase site. Finally, dominant-negative Ets and GHF constructs block Ras activation of the rPRL promoter, and each blocks the synergistic activation mediated by the other partner protein, further corroborating that a functional interaction between c-Ets-1 and GHF-1 is required for an optimal Ras response. Thus, the functional interaction of a pituitary-specific transcription factor, GHF-1, with a widely expressed nuclear proto-oncogene product, c-Ets-1, provides one important molecular mechanism by which the general Ras signaling cascade can be interpreted in a cell-type-specific manner.
Cell Density-Dependent Gene Contributes to Efficient Seed Colonization by Pseudomonas putida KT2440

ABSTRACT We have characterized the expression pattern of a gene, ddcA, involved in initial colonization of corn seeds by Pseudomonas putida KT2440. The ddcA gene codes for a putative membrane polypeptide belonging to a family of conserved proteins of unknown function. Members of this family are widespread among prokaryotes and include the products of a Salmonella enterica serovar Typhimurium gene expressed during invasion of macrophages and psiE, an Escherichia coli phosphate starvation-inducible gene. Although its specific role is undetermined, the presence of ddcA in multicopy restored the seed adhesion capacity of a KT2440 ddcA mutant. Expression of ddcA is growth phase regulated, being maximal at the beginning of stationary phase. It is independent of RpoS, nutrient depletion, or phosphate starvation, and it is not the result of changes in the medium pH during growth. Expression of ddcA is directly dependent on cell density, being also stimulated by the addition of conditioned medium and of seed exudates. This is the first evidence suggesting the existence of a quorum-sensing system in P. putida KT2440. The potential implication of such a signaling process in seed adhesion and colonization by the bacterium is discussed.
Analysis of data pre-processing influence on intrusion detection using NSL-KDD dataset

Data pre-processing for machine learning methods is key step for knowledge discovery process. Depending on nature of the data, pre-processing might take the majority time of data analysis. Correctly prepared data for processing guarantees precise and reliable results of data analysis. This paper analyses initial data pre-processing influence to attack detection accuracy by using Decision Trees, Naïve Bayes and Rule-Based classifiers with NSL-KDD dataset. In addition, the results of detected attacks accuracy dependency by selecting different attacks grouping options and using ensembles of various classifiers are presented.
Iodinated contrast media‐induced nephropathy: pathophysiology, clinical aspects and prevention

Summary— Administration of iodinated contrast media (CM) for radiographic purposes is a preoccupying cause of acute renal failure. This review of the literature deals with what is known about physiopathology, clinical course, risk factors and prevention. Factors involved in the pathophysiology of CM‐induced acute renal failure are vasoconstriction, direct tubular cell injury and tubular obstruction by casts. In the case of pre‐existing renal hypoperfusion, CM may disturb the complex interaction between factors which modulate renal haemodynamics by increasing vasoconstrictor factors, notably endothelin peptides. The renal medulla, a zone characterized by a high metabolic activity and a low oxygen tension, may be a specific target for CM‐induced effects. CM‐induced nephropathy (CMN) is essentially observed in patients with one or more associated risk factors (chronic renal failure, dehydration, diabetes mellitus with impaired renal function, multiple myeloma, large CM volume, intra‐arterial rather than intravenous route, etc). There is much debate as to whether newer low osmolar CM (LOCM) are better tolerated than conventional high osmolar CM (HOCM). Most of the animal studies clearly demonstrate the advantages of LOCM over HOCM. Clinical literature is far more confusing, although some recent studies and one meta‐analysis demonstrate that LOCM are better tolerated in patients with impaired renal function. The low number of comparative clinical trials carried out in high risk patients, wide variability in CMN definitions, limited number of patients enrolled and inadequacy of various selected endpoints may explain difficulties experienced in demonstrating this advantage. Furthermore, while hydration is correctly maintained during clinical trials, this is not always true in clinical practice. Such a discrepancy could lead to underestimation of the potential advantage of LOCM over HOCM. Effective prevention should associate the correct hydration of patients, identification and, when possible, optimal correction of risk factors, avoidance of repeated CM injections within a short period of time and temporary disruption of treatment with other nephrotoxic drugs (non steroidal antiinflammatory drugs, aminoglycosides, etc).
Inhibition of P2X Receptors Protects Human Monocytes against Damage by Leukotoxin from Aggregatibacter actinomycetemcomitans and α-Hemolysin from Escherichia coli

ABSTRACT α-Hemolysin (HlyA) from Escherichia coli and leukotoxin A (LtxA) from Aggregatibacter actinomycetemcomitans are important virulence factors in ascending urinary tract infections and aggressive periodontitis, respectively. The extracellular signaling molecule ATP is released immediately after insertion of the toxins into plasma membranes and, via P2X receptors, is essential for the erythrocyte damage inflicted by these toxins. Moreover, ATP signaling is required for the ensuing recognition and phagocytosis of damaged erythrocytes by the monocytic cell line THP-1. Here, we investigate how these toxins affect THP-1 monocyte function. We demonstrate that both toxins trigger early ATP release and a following increase in the intracellular Ca2+ concentration ([Ca2+]i) in THP-1 monocytes. The HlyA- and LtxA-induced [Ca2+]i response is diminished by the P2 receptor antagonist in a pattern that fits the functional P2 receptor expression in these cells. Both toxins are capable of lysing THP-1 cells, with LtxA being more aggressive. Either desensitization or blockage of P2X1, P2X4, or P2X7 receptors markedly reduces toxin-induced cytolysis. This pattern is paralleled in freshly isolated human monocytes from healthy volunteers. Interestingly, only a minor fraction of the toxin-damaged THP-1 monocytes eventually lyse. P2X7 receptor inhibition generally prevents cell damage, except from a distinct cell shrinkage that prevails in response to the toxins. Moreover, we find that preexposure to HlyA preserves the capacity of THP-1 monocytes to phagocytose damaged erythrocytes and may induce readiness to discriminate between damaged and healthy erythrocytes. These findings suggest a new pharmacological target for protecting monocytes during exposure to pore-forming cytolysins during infection or injury.
Race as a predictor of job satisfaction and turnover in US nurses

AIM The purpose of this analysis is to determine US minority nurses' job satisfaction and turnover using three outcome variables: job dissatisfaction; change of jobs; and intent to quit. BACKGROUND A balanced nursing workforce is essential for supporting a racially diverse nation. Understanding minority nurses' job satisfaction is the first step in achieving this balance. METHODS A secondary data analysis was conducted using the 2008 National Sample Survey of Registered Nurses. The association between race and job satisfaction was examined using logistic regression. RESULTS Black nurses were more likely to intend to quit than white ones (OR = 1.46, 95% CI = 1.31-1.64), as were Hispanics (OR = 1.35, 95% CI = 1.18-1.55). Asians were less dissatisfied (OR = 0.69, 95% CI = 0.57-0.84), and less likely to have changed jobs (OR = 0.71, 95% CI = 0.60-85) or intend to quit (OR = 0.84, 95% CI = 0.75-0.95) than white nurses. CONCLUSIONS This analysis demonstrated that black and Hispanic nurses are more likely to intend to quit, even while controlling for dissatisfaction. The reasons for this, and the increased job satisfaction demonstrated by Asian nurses, are directions for future research. IMPLICATIONS FOR NURSING MANAGEMENT Nurse managers should endeavour to create a workplace free of discrimination. Efforts to increase the job satisfaction of all nurses are of equal importance.
Requirements analysis of weapons and equipment based on QFD and SPA methods

Aiming at the problem how to get the importance of measures of performance(MOP) in requirements demonstration of weapons and equipment,an approach based on quality function deployment(QFD) and set pair analysis(SPA) methods was proposed and applied in this paper.As a computation framework, house of quality(HOQ) was used to set interrelationship between operation requirements and MOP.Requirements satisfaction of the same type of equipments was evaluated by multivariate connection number. Application result shows that by the provided approach different opinions of experts are centralized and the importance of MOP are quantified.In addition,the persuasion of MOP analysis result is also enhanced in the process of requirements demonstration of weapons and equipment.
A simple remedy for the exaggerated extrinsic information produced by the SOVA algorithm

In this paper, we propose a novel and simple approach for dealing with the exaggerated extrinsic information produced by the soft-output Viterbi algorithm (SOVA). The proposed remedy is based on mathematical analysis and it involves using two attenuators, one applied to the immediate output of the SOVA and another applied to the extrinsic information before it is passed to the other decoder (assuming iterative decoding). The use of these attenuators aims at reducing the inherent strong correlation between the intrinsic information (input to the SOVA) and extrinsic information (output of the SOVA). We examine the modified SOVA (MSOVA) on additive white Gaussian noise (AWGN) and flat fading channels for parallel concatenated codes (PCCs) and serial concatenated codes (SCCs). We show that the MSOVA provides substantial performance improvements over both channels. For example, it provides improvements of about 0.8 to 1.0 dB at P/sub b/ = 10/sup -5/ in AWGN, and about 1.4 to 2.0 dB at P/sub b/ = 10/sup -5/ on fading channels. We also show that there are cases where the MSOVA is superior to the a posteriori probability (APP) algorithm. With this motivation, we extend the proposed modification to the APP algorithm with favorable results. We demonstrate that the modified APP (MAPP) provides performance improvements between 0.3 to 0.6 dB at P/sub b/ = 10/sup -5/ relative to the APP. We lastly mention that the proposed modifications, while they provide considerable performance improvements, keep the complexity of these decoders almost the same, which is remarkable.
Histone Phosphorylation: Its Role during Cell Cycle and Centromere Identity in Plants

As the main protein components of chromatin, histones can alter the structural/functional capabilities of chromatin by undergoing extensive post-translational modifications (PTMs) such as phosphorylation, methylation, acetylation, ubiquitination, sumoylation, and so on. These PTMs are thought to transmit signals from the chromatin to the cell machinery to regulate various processes. Histone phosphorylation is associated with chromosome condensation/segregation, activation of transcription, and DNA damage repair. In this review, we focus on how different histone phosphorylations mark for chromatin change during the cell cycle, the relationship between histone phosphorylation and functional centromeres, and the candidate kinases that trigger and the phosphatase or kinase inhibitors that alter histone phosphorylation. Finally, we review the crosstalk between different PTMs.