Miracle-dz/UniFAR-FTUs huggingface dataset:
Hybrid Pathogenicity Island PAGI-5 Contributes to the Highly Virulent Phenotype of a Pseudomonas aeruginosa Isolate in Mammals

ABSTRACT Most known virulence determinants of Pseudomonas aeruginosa are remarkably conserved in this bacterium's core genome, yet individual strains differ significantly in virulence. One explanation for this discrepancy is that pathogenicity islands, regions of DNA found in some strains but not in others, contribute to the overall virulence of P. aeruginosa. Here we employed a strategy in which the virulence of a panel of P. aeruginosa isolates was tested in mouse and plant models of disease, and a highly virulent isolate, PSE9, was chosen for comparison by subtractive hybridization to a less virulent strain, PAO1. The resulting subtractive hybridization sequences were used as tags to identify genomic islands found in PSE9 but absent in PAO1. One 99-kb island, designated P. aeruginosa genomic island 5 (PAGI-5), was a hybrid of the known P. aeruginosa island PAPI-1 and novel sequences. Whereas the PAPI-1-like sequences were found in most tested isolates, the novel sequences were found only in the most virulent isolates. Deletional analysis confirmed that some of these novel sequences contributed to the highly virulent phenotype of PSE9. These results indicate that targeting highly virulent strains of P. aeruginosa may be a useful strategy for identifying pathogenicity islands and novel virulence determinants.
A High-Efficiency Current-Fed Semi-Dual-Active Bridge DC–DC Converter for Low Input Voltage Applications

A current-fed semi-dual-active bridge (S-DAB) dc-dc converter with symmetrical dual-pulse width modulation (PWM) and phase shifted control was proposed. All the power switches can achieve zero voltage switching (ZVS) and the output side diodes can achieve zero current switching (ZCS) naturally. The converter has lower conduction loss, lower peak current, and higher efficiency. The typical operating modes were analyzed. The parameter optimal design criterion was given to achieve soft switching and circulation loss reduction. Simulation and experimental results for a 1-kW prototype were made to verify the effectiveness of the proposed topology employing the proposed control.
PRELIMINARY RESULTS IN MEASURING THE HARDINESS OF PLANTS.

The injury of plants occasioned by winter conditions has been a subject of great interest and importance to plant breeders and agriculturists. The development of hardy strains has been, and is, one of the principal means of comiibating losses caused by injury from cold, although cultural methods, as well, lhave been adapted to help the plant survive the rigors of its climatic environiment. Recog,nition of the degree of hardiness has necessitated field trials commonly requiring extended periods of time, during which weather conditions may be too mild to test the relative hardiness in one season, while so severe in the next that hardy as well as tender varieties and strains are severely injured. It is quite evident that a rapid means of measuring relative degrees of resistance to cold of strains and varieties of plants, grown with various cultural procedures, would hasten progress in the work of plant breeders, as well as facilitate investigations of the physical and chemical nature of the hardening process, and its relation to the resistance of plants to low temperatures and other climatic conditions. No attempt will be made to review the literature on hardiness or reactions of plants to freezing in reference to changes in permeability, colloidal structure or compositional variations. It seems to be generally accepted that the inijury, or killing of tissue, by cold, or by any other means, involves the disorganization of the substances essential for carrying on the processes of life. With such disorganization, it is well recognized that the cell loses its capacity to regulate the diffusion of its soluble contents. Upon this basis, it was assumed that the degree of injury from low temperature, to overwintering and other plant structures might be correlated with the exosmosis of electrolytes and other materials following exposure to cold. Such outiward diffusion of electrolytes can readily be estimated by conductivity measurements. Other investigators have applied conductivity metlhods to problems involving the viability of seeds, and the injury of plant and animal tissues. To test this hypothesis, alfalfa roots of three varieties of known hardiness (Grimm, Utah Common, and Hairy Peruvian) were frozen under con-
Community Detection in Networks

The problem of community detection is relevant in many disciplines of science. A community is usually defined, in a qualitative way, as a subset of nodes of a network which are more connected among themselves than to the rest of the network. In this article, we introduce a new method for community detection in complex networks. We define new merit factors based on the weak and strong community definitions formulated by Radicchi et al. [2004] and we show that this local definition properly describes the communities observed experimentally in two typical social networks.
Neuropsychological comparisons of Spanish-speaking participants from the U.S.–Mexico border region versus Spain

Two samples of participants from the U.S.–Mexico Borderland (N = 185) versus Spain (N = 205) were compared on 16 Spanish-language neuropsychological measures. In most measures the two samples obtained similar results. There were some significant main effects of place of birth and some significant interactions between education and place of birth. Differences between the samples diminished with increasing levels of education. Within the Borderland sample, percent of life span spent in the U.S. and bilingual status were correlated with performance in some tests. Increased percent of life span spent in the U.S. was negatively correlated with performance on a Spanish word-generation task, and positively correlated with performance on the Wisconsin Card Sorting Test. Bilingual Borderland participants performed significantly better than monolingual speakers in learning a list of words. We suggest that the most likely causes for the observed interaction effects are documented regional differences in early SES-related nutrition, medical care, quality of educational experiences, and general socioeconomic conditions. (JINS, 1998, 4, 363–379.)
Seed Dispersal Distances by Ants Increase in Response to Anthropogenic Disturbances in Australian Roadside Environments

Ants provide a common dispersal vector for a variety of plants in many environments through a process known as myrmecochory. The efficacy of this dispersal mechanism can largely determine the ability of species to track changes in habitat availability caused by ongoing land-use and associated disturbances, and can be critical for population gene flow and persistence. Field studies were conducted in a typical fragmented agricultural landscape in southern NSW, Australia, to investigate the extent to which dispersal services by ants are influenced by anthropogenic disturbances associated with roadwork activities (i.e. soil disturbance as the result of grading of roads). Observational experiments were performed in road segments that were divided into disturbed and non-disturbed zones, where Acacia pycnantha seeds were offered at multiple bait stations and monitored. For combined species, the mean dispersal distance recorded in the disturbed zone (12.2m) was almost double that recorded in the non-disturbed zone (5.4m) for all roadside sites. Our findings show that myrmecochory is an unevenly diffuse mutualism, where few ant species contributed to much of the dispersal of seeds. Iridomyrmex purpureus was responsible for all seed dispersal distances > 17m, where a maximum of 120m in disturbed, versus 69m in non-disturbed zones, was recorded. Rhytidoponera metallica and Melophorus bruneus were important seed dispersers in non-disturbed and disturbed zones, respectively. In general, large bodied ants tended to move more seeds to longer distances in disturbed zones, as opposed to non-disturbed zones, where smaller bodied species carried out a greater percentage of short distance dispersals (< 1m). We also recorded secondary dispersal events from nests by I. purpureus, a phenomenon previously not quantified. Infrequent, long distance dispersal to suitable sites may be highly important for seedling recruitment in disturbed or modified habitats in otherwise highly fragmented rural environments.
HITS vs . Non-negative Matrix Factorization

Ranking algorithms have been widely used for web and other networks to infer quality/popularity. Both PageRank and HITS were developed for ranking web pages from a web reference graph. Nevertheless, these algorithms have also been applied extensively for a variety of other applications such as question-answer services, author-paper graphs, and others where a graph can be deduced from the data set. The intuition behind HITS has been explained in terms of hubs and spokes as two values are inferred for each node. HITS has also been used extensively for ranking in other applications although it is not clear whether the same intuition carries over. It would be beneficial if we can understand these algorithms mathematically in a general manner so that the results can be interpreted and understood better for different applications. This paper provides such as understanding for applying HITS algorithm to other applications. In this paper, we generalize the graph semantics in terms two underlying concepts: in-link probability (ILP) and out-link probability (OLP). Using these two, the rank scores of nodes in a graph are computed. We propose the standard non-negative matrix factorization (NMF) approach to calculate ILP and OLP vectors. We also establish a relationship between HITS vectors and ILP/OLP vectors which enables us to better understand HITS vectors associated with any graph in terms of these two probabilities. Finally, we illustrate the versatility of our approach using different graph types (representing different application areas) and validate the results. This work provides an alternative way of understanding HITS algorithm for a variety of applications.
Capacity Theorem and Optimal Power Allocation for Frequency Division Multiple-Access Relay Channels

The capacity region of general Multiple-Access Relay Channel (MARC) has long been an open question. In this paper, we consider MARC with orthogonal components, where the channel from the source senders to the relay node is orthogonal to the channel from the source senders and relay to the destination. We give the capacity theorem for the discrete memoryless MARC with orthogonal components. Based on the result, we obtain the capacity region of frequency-division Gaussian MARC. The optimal power allocation for the source nodes to allocate power on different frequencies is investigated. Numerical results show that the optimal allocation of power can achieve the maximum sum rate.
Inhibitor-Sensitive FGFR 2 and FGFR 3 Mutations in Lung Squamous Cell Carcinoma

A comprehensive description of genomic alterations in lung squamous cell carcinoma (lung SCC) has recently been reported, enabling the identification of genomic events that contribute to the oncogenesis of this disease. In lung SCC, one of the most frequently altered receptor tyrosine kinase families is the fibroblast growth factor receptor (FGFR) family, with amplification or mutation observed in all four family members. Here, we describe the oncogenic nature of mutations observed in FGFR2 and FGFR3, each of which are observed in 3% of samples, for a mutation rate of 6% across both genes. Using cell culture and xenograft models, we show that several of these mutations drive cellular transformation. Transformation can be reversed by small-molecule FGFR inhibitors currently being developed for clinical use. We also show that mutations in the extracellular domains of FGFR2 lead to constitutive FGFR dimerization. In addition, we report a patient with an FGFR2-mutated oral SCC who responded to the multitargeted tyrosine kinase inhibitor pazopanib. These findings provide new insights into driving oncogenic events in a subset of lung squamous cancers, and recommend future clinical studies with FGFR inhibitors in patients with lung and head and neck SCC. Cancer Res; 73(16); 5195–205. 2013 AACR.
Disabled children’s services: how do we measure family-centred care?

Family-centred care has been defined as a philosophy of care where families are supported in their decision-making roles in an equal partnership with professionals. The research question was ‘How ‘‘family centred’’ do staff and parents perceive their work with disabled children and young people? ’ A questionnaire, the Measure of Processes of Care for Service Providers (MPOC-SP), was used as a basis for designing focus groups and interview questions. Staff and parents took part in these and data were analysed using an editing approach. Staff described how they adapted their service to meet parental needs and empowered and enabled parents despite receiving no specific training in FCC. Parents spoke highly of the staff input and gave varied descriptions of the attributes they most valued, including feeling supported and being in an equal partnership. Investigation of the influence of focused FCC training on parental experiences is warranted.
Treatment of panic disorder with bupropion in a patient with Parkinson’s disease

We report on a 57‐year‐old woman, diagnosed with Parkinson’s disease, whose panic disorder showed marked improvement after introduction of bupropion, a norepinephrine–dopamine reuptake inhibitor. Additionally a comorbid major depression disappeared under this treatment. Bupropion may be useful for the treatment of patients with both panic disorder and Parkinson’s disease.
The autonomous platoon driving system of the on line electric vehicle

Since there are traffic and environment problem in the downtown center, we suggest an autonomous platoon driving system based on infrastructure to solve these problem. This paper considers three parts: 1) Sensing electric magnetic field on the power supply line that is installed under the road to supply power to the electric vehicle wirelessly and controlling steering motor and driving motors of the electric vehicle for the autonomous driving. 2) Laying RFID tags under the power supply line and estimating the position of the electric vehicle based on it. 3) Calculating a distance between electric vehicles based on each vehicle's position information which is acquired from the vehicle to vehicle communication and controlling the velocity of the electric vehicle to maintain the distance between the electric vehicles. Developed the autonomous platoon driving system is set on electric vehicles and is confirmed through analytical and experimental performance evaluation.
A digital-control sensorless current-mode boost converter with non-zero error bin compensation and seamless mode transition

A digital-control sensorless current-mode boost DC-DC converter is presented in this paper. By using the proposed sensorless current-mode control, the requirement for implementation of current sensor for conventional current-mode dc-dc converter is relaxed. Moreover, the converter can seamlessly switch between CCM and DCM operation as in conventional current-mode control. With this method, the non-limited-cycle for digital-control current-mode converter is realized. Lower resolution of DPWM can be used to avoid the appearance of limited cycle, regardless of loading condition.
Physical Activity, Media Time, and Body Composition in Young Children.

BACKGROUND It is uncertain as to whether physical activity (PA) may influence the body composition of young children. PURPOSE To determine the association between PA, media time, and body composition in children age 4 to 7 y. METHODS 100 children (52 girls, 48 boys) were assessed for body-mass index (BMI), body fat, fat mass (FM), and fat-free mass using dual energy x-ray absorbtiometryptiometry (DXA). PA was monitored using accelerometers and media time was reported by parental proxy. RESULTS In general, correlations were low to moderate at best (r < 0.51), but in the expected direction. Total media time and TV were significantly associated with BMI (r = 0.51, P < 0.05) and FM (r = 0.29 to 0.30, P < 0.05) in girls. In boys, computer usage was significantly associated with FM in boys (r = 0.31, P < 0.05). CONCLUSION The relatively low correlations suggest that other factors may influence the complex, multi-factorial body composition phenotype of young children.
Crystal Structures of Type II Restriction Endonuclease EcoO109I and Its Complex with Cognate DNA*

EcoO109I is a type II restriction endonuclease that recognizes the DNA sequence of RGGNCCY. Here we describe the crystal structures of EcoO109I and its complex with DNA. A comparison of the two structures shows that the catalytic domain moves drastically to capture the DNA. One metal ion and two water molecules are observed near the active site of the DNA complex. The metal ion is a Lewis acid that stabilizes the pentavalent phosphorus atom in the transition state. One water molecule, activated by Lys-126, attacks the phosphorus atom in an SN2 mechanism, whereas the other water interacts with the 3′-leaving oxygen to donate a proton to the oxygen. EcoO109I is similar to EcoRI family enzymes in terms of its DNA cleavage pattern and folding topology of the common motif in the catalytic domain, but it differs in the manner of DNA recognition. Our findings propose a novel classification of the type II restriction endonucleases and lead to the suggestion that EcoO109I represents a new subclass of the EcoRI family.
Up–down Asymmetry in Vertical Induced Motion

Induced motion (IM) is the illusory movement of an object in the direction opposite to the real motion of adjacent detail. One theory of IM suggests that it results, in part, from suppression of optokinetic nystagmus (OKN) by fixational (smooth-pursuit) effort. In several studies an asymmetry in human vertical OKN has been reported, with upward optokinetic stimulation eliciting higher OKN gain than downward motion. This provides a test of the nystagmus-suppression theory of IM. If suppression of OKN contributes significantly to IM, upward inducing stimuli should result in a greater magnitude of the illusion than should downward stimulus motion. Additionally, the asymmetry of vertical OKN should become more pronounced at higher stimulus velocities. Therefore, the asymmetry of vertical IM should be greater at higher inducing-stimulus velocities. Twelve subjects viewed a large, random-dot stimulus, which moved either upward or downward at a velocity of 10, 40, or 70 deg s−1. Subjects fixated a horizontally moving laser spot and adjusted a rod to match the apparent slope of the motion path of the spot. IM magnitude was derived from these measures. Mean IM velocity was significantly higher with upward than with downward stimulation, and the difference was maximal at velocities of 40 and 70 deg s−1. The results are discussed within the context of the nystagmus-suppression theory and other theories of IM.
The impulses produced by sensory nerve‐endings

THE present investigation deals with the analysis of the impulses set up in cutaneous nerves by painful stimuli and compares the pain discharge with that of other receptors. The older view that pain resulted from excessive stimulation of any cutaneous receptor has been largely abandoned in favour of the idea of special pain receptors and conductors. The specific character of " pain " suggests that these receptors and conductors may differ considerably from those of the other types of cutaneous sensation. For instance, the "protopathic and epicritic" hypothesis of Head and Rivers demands that the nerve fibres concerned with pain must belong to a system phylogenetically distinct from those concerned with touch and the histological work of R ans o n has added the view that the pain fibres may be non-medullated. Again, the pain receptor probably differs from many others in the absence of a capsule surrounding the axon termination and for this reason it has been suggested that the discharge of impulses from the pain endings may have some characteristic frequency or grouping of its own. These and similar possibilities can evidently be tested by recording the impulses produced in the afferent nerve fibres by a painful stimulus. Preliminary observations (1) with the capillary electrometer and amplifier showed that it was possible to record the action currents set up in afferent nerves when the skin was pinched or pricked. The next step was to secure that not more than a few nerve fibres should be in action together so that each impulse might be recorded without interference. Apart from the use of nerves with very few fibres two general methods may be applied in any research of this character, namely (1) to restrict the stimulus to a very small area so that only a few receptors are stimulated; (2) to destroy or put out of action all but a few of the receptors or nerve fibres which will be affected by the stimulus. The former method is suited to the present case since a prick with a very fine needle will produce sensation which is clearly painful, but will scarcely stimulate
Multicommodity flow models, failure propagation, and reliable loss network design

Multicommodity flow (MF) models are well known and have been widely used in the design of packet-switched networks. They have also been used as approximations in the design of circuit-switched networks with reliability constraints. We investigate the usefulness of multicommodity models both as routing models and as an integral part of design models conceived under the failure propagation strategy. First, we compare the performance measures calculated by the models with results produced by a real-time technique. Next, we study the performance of networks dimensioned with flow models and with known adaptive models under failures of transmission facilities when a real-time routing technique is used. Results obtained using realistic data show that the MF models compare favorably with exact dimensioning algorithms when failures are considered.
Antagonistic control of the Escherichia coli bgl promoter by FIS and CAP in vitro

The wild‐type Escherichia coli bgl promoter is silent in vivo but active in vitro. Silencing in vivo is directed by silencer sequences that flank the promoter, and requires nucleoid‐associated protein H‐NS and other unidentified cellular factors. Here we show that the DNA bending protein FIS is a repressor of the bgl promoter. Two FIS binding sites, centred at positions −52 and −27, overlap the CAP binding site and the −35 box respectively. FIS efficiently competes with CAP for binding to the wild‐type promoter. However, FIS does not prevent binding of RNA polymerase. It interferes with the formation of a heparin‐resistant complex and represses transcription initiation up to 40‐fold. The presence of CAP has very little effect on the FIS‐mediated repression of the wild‐type bgl promoter in vitro. However, when a bgl promoter allele was tested that carries an improved CAP binding site (which leads to activation in vivo) CAP effectively counteracted repression by FIS in vitro. These results suggest that FIS contributes to silencing of the wild‐type bgl promoter in vivo, presumably in the early exponential phase when FIS is predominantly expressed.