Miracle-dz/UniFAR-FTUs huggingface dataset:
Analytical estimation of common mode conducted EMI in PWM inverter

In PWM inverter system, the high dv/dt and di/dt due to the fast switching of IGBT could bring serious EMI issues. How conducted emission measurement should be made are specified. Based on the study of mechanisms on common mode conducted electromagnetic interference (CM EMI) associated with a single phase PWM inverter, the origin and propagation path of CM EMI noise are highlighted. Compared with buck converter, a simple equivalent circuit is proposed to study the CM EMI. Time and frequency domain analysis is conducted to obtain CM current waveforms and noise spectra in 10 KHz-30 MHz frequencies. The simulated CM EMI waveforms are compared with the actual experiments to verify the validity of the proposed model. The modeling method described can be readily extended to a three-phase PWM inverter.
Use of Natural mRNAs in the Cell-Free Protein-Synthesizing Systems of the Moderate Halophile Vibrio costicola

In vitro protein synthesis was studied in extracts of the moderate halophile Vibrio costicola by using as mRNAs the endogenous mRNA of V. costicola and the RNA of the R17 bacteriophage of Escherichwa coli. Protein synthesis (amino acid incorporation) was dependent on the messenger, ribosomes, soluble cytoplasmic factors, energy source, and tRNAmet (in the R17 RNA system) and was inhibited by certain antibiotics. These properties indicated de novo protein synthesis. In the V. costicola system directed by R17 RNA, a protein of the same electrophoretic mobility as the major coat protein of the R17 phage was synthesized. Antibiotic action and the response to added tRNA4et showed that protein synthesis in the R17 RNA system, but not in the endogenous messenger system, absolutely depended on initiation. Optimal activity of both systems was observed in 250 to 300mM NH4' (as glutamate). Higher salt concentrations, especially those with Clas anion, were generally inhibitory. The R17 RNA-directed system was more sensitive to Clions than the endogenous system was. Glycine betaine stimulated both systems and partly overcame the toxic effects of Clions. Both systems required Mg2+, but in lower concentrations than the polyuridylic acid-directed system previously studied. Initiation factors were removed from ribosomes by washing with 3.0 to 3.5 M NH4C1, concentrations about three times as high as that needed to remove initiation factors from E. coli ribosomes. Washing with 4.0 M NH4Cl damaged V. costicola ribosomes, although the initiation factors still functioned. Clions inhibited the attachment of initiation factors to tRNAmet but had little effect on binding of initiation factors to R17 RNA.
Combining Formal Concept Analysis and semantic information for building ontological structures from texts : an exploratory study

This work studies conceptual structures based on the Formal Concept Analysis method. We build these structures based on lexico-semantic information extracted from texts, among which we highlight the semantic roles. In our research, we propose ways to include semantic roles in concepts produced by this formal method. We analyze the contribution of semantic roles and verb classes in the composition of these concepts through structural measures. In these studies, we use the Penn Treebank Sample and SemLink 1.1 corpora, both in English.
Occurrence of Staphylococcus lugdunensis in consecutive clinical cultures and relationship of isolation to infection

Consecutive record review over a 63-month period revealed 229 Staphylococcus lugdunensis isolates, or 10.1% of the staphylococcal species that were not Staphylococcus aureus or Staphylococcus epidermidis. A total of 155 S. lugdunensis specimens were isolated from sites over the entire bodies of the 143 patients studied. The most common clinical diagnoses were skin and skin structure infections (55.4%) and blood and vascular catheter infections (17.4%). For 40% of the reviewed specimens, S. lugdunensis was the sole agent isolated, and for 60% of specimens, S. lugdunensis was isolated as part of mixed flora. In only 15.4% of clinically reviewed specimens was S. lugdunensis clearly a culture contaminant or colonizing organism. The pattern of human infection identified in this study emphasizes the predominance of skin and soft tissue S. lugdunensis infections over deep serious infections such as endocarditis, peritonitis, infected hip prosthesis, and osteomyelitis and vascular-associated infections. S. lugdunensis should be included along with S. epidermidis, Staphylococcus haemolyticus, and Staphylococcus saprophyticus as a coagulase-negative species of Staphylococcus pathogenic for humans.
Host Specificity and Phylogenetic Relationships of Chicken and Turkey Parvoviruses

SUMMARY Inoculation of specific-pathogen-free chickens and turkeys with five chicken parvoviruses (ChPV) and five turkey parvoviruses (TuPV) resulted in productive virus replication only in the homologous host species. A phylogenetic tree based on nucleotide sequences of the VP1 gene segment revealed a host-specific clustering of the virus strains. These results suggest that the VP1 gene plays an essential role in host specificity of ChPV and TuPV strains and could be a relevant target sequence for strain classification. RESUMEN Nota de Investigación- Especificidad de hospedador y relaciones filogenéticas de parvovirus de pollos y pavos. La inoculación de pollos y pavos libres de patógenos específicos con cinco parvovirus de pollo (ChPV) y cinco parvovirus de pavo (TuPV) dio lugar a la replicación viral productiva únicamente en la especie hospedadora homóloga. El árbol filogenético basado en las secuencias de nucleótidos del segmento del gene VP1 reveló una agrupación de las cepas virales específica de hospedador. Estos resultados sugieren que el gene VP1 juega un papel esencial en la especificidad del hospedador de las cepas de parvovirus de pollo y de pavo y podría ser una secuencia blanco relevante para la clasificación de las cepas.
Transferable Resistance to Aminoglycosides by Methylation of G1405 in 16S rRNA and to Hydrophilic Fluoroquinolones by QepA-Mediated Efflux in Escherichia coli

ABSTRACT Plasmid pIP1206 was detected in Escherichia coli strain 1540 during the screening of clinical isolates of Enterobacteriaceae for high-level resistance to aminoglycosides. The sequence of this IncFI conjugative plasmid of ca. 100 kb was partially determined. pIP1206 carried the rmtB gene for a ribosome methyltransferase that was shown to modify the N7 position of nucleotide G1405, located in the A site of 16S rRNA. It also contained the qepA (quinolone efflux pump) gene that encodes a 14-transmembrane-segment putative efflux pump belonging to the major facilitator superfamily of proton-dependent transporters. Disruption of membrane proton potential by the efflux pump inhibitor carbonyl cyanide m-chlorophenylhydrazone in a transconjugant harboring the qepA gene resulted in elevation of norfloxacin accumulation. The transporter conferred resistance to the hydrophilic quinolones norfloxacin and ciprofloxacin.
Characteristics of growth, morphology, contractility, and protein expression of fibroblasts derived from keloid

Phenotypic alterations of keloid‐derived fibroblasts were characterized by comparison with the phenotypes of normal fibroblasts from the same patient. Explant cultures of keloids showed unique features. Keloid explants contracted considerably and reduced their size during culture, whereas the size of normal skin explants remained unchanged. Enlarged cells were found among fibroblasts which had grown out of all the explants and were morphologically distinct from fibroblasts; however, keloid explants produced many more of them than did the normal tissues. The growth rate of fibroblast colonies formed from normal explants was five times higher than keloid explants. Keloid fibroblasts which had been serially cultivated contracted lattices of collagen gels at a rate similar to normal fibroblasts. Proteins extracted from serially cultivated fibroblasts were mapped on polyacrylamide two‐dimensional electrophoretic gels. No significant qualitative alterations in protein expression in keloid cells were found as compared with normal fibroblasts. However, some quantitative changes were found between the two. A computer‐assisted image analyzer detected 151 polypeptide spots—50 spots (33%) of which increased their amounts in keloid cells, whereas 34 spots (22.5%) decreased in comparison with normal fibroblasts. Sixteen major polypeptides were identified as known proteins with the aid of time‐of‐flight mass spectrometry. The level of expression of these identified proteins was similar between normal and keloid cells, except stathmin whose expression was suppressed in keloid fibroblasts.
A One-Size-Fits-All Indexing Method Does Not Exist: Automatic Selection Based on Meta-Learning

We present a methodology that automatically selects indexing algorithms for each heading in Medical Subject Headings (MeSH), National Library of Medicine’s vocabulary for indexing MEDLINE. While manually comparing indexing methods is manageable with a limited number of MeSH headings, a large number of them make automation of this selection desirable. Results show that this process can be automated, based on previously indexed MEDLINE citations. We find that AdaBoostM1 is better suited to index a group of MeSH hedings named Check Tags, and helps improve the micro F-measure from 0.5385 to 0.7157, and the macro F-measure from 0.4123 to 0.5387 (both p < 0.01). Category: Convergence computing
Evolutionary Origin and Conserved Structural Building Blocks of Riboswitches and Ribosomal RNAs: Riboswitches as Probable Target Sites for Aminoglycosides Interaction.

PURPOSE Riboswitches, as noncoding RNA sequences, control gene expression through direct ligand binding. Sporadic reports on the structural relation of riboswitches with ribosomal RNAs (rRNA), raises an interest in possible similarity between riboswitches and rRNAs evolutionary origins. Since aminoglycoside antibiotics affect microbial cells through binding to functional sites of the bacterial rRNA, finding any conformational and functional relation between riboswitches/rRNAs is utmost important in both of medicinal and basic research. METHODS Analysis of the riboswitches structures were carried out using bioinformatics and computational tools. The possible functional similarity of riboswitches with rRNAs was evaluated based on the affinity of paromomycin antibiotic (targeting "A site" of 16S rRNA) to riboswitches via docking method. RESULTS There was high structural similarity between riboswitches and rRNAs, but not any particular sequence based similarity between them was found. The building blocks including "hairpin loop containing UUU", "peptidyl transferase center conserved hairpin A loop"," helix 45" and "S2 (G8) hairpin" as high identical rRNA motifs were detected in all kinds of riboswitches. Surprisingly, binding energies of paromomycin with different riboswitches are considerably better than the binding energy of paromomycin with "16S rRNA A site". Therefore the high affinity of paromomycin to bind riboswitches in comparison with rRNA "A site" suggests a new insight about riboswitches as possible targets for aminoglycoside antibiotics. CONCLUSION These findings are considered as a possible supporting evidence for evolutionary origin of riboswitches/rRNAs and also their role in the exertion of antibiotics effects to design new drugs based on the concomitant effects via rRNA/riboswitches.
Analysis of bacterial RM-Systems through genome-scale analysis and related taxonomic issues

Recognition sites for type II restriction and modification enzymes in genomes of several bacteria are recognized as semi-palindromic motifs and are avoided at a significant degree. The key idea of contrast word analysis with respect to RMS recognition sites, is that under-represented words are likely to be selected against. Starting from over- or underrepresented words corresponding to RMS recognition sites in specific clades, the specificity of unknown R-M systems can be highlighted. Among the known restriction enzymes, that are described in the REBASE database of restriction and modification systems, many of their recognition sites are still uncharacterized. Eventually, this motivates studies aimed at assessing horizontal transferring events of RMS in micro-organisms through the analysis of word usage biases in well-determined genomic regions. A probabilistic model is built on a first-order Markovian chain. Statistics on the k-neighborhood of a word is carried out to assess the biological significance of a genomic motif. Efficient word counting procedures have been implemented and statistics are used for the assessment of the significance of individual words in large sequences. On the basis of the set of most avoided words, and in accordance to the IUPAC coding standards, suggestions are made regarding potential recognition sequences. In certain cases, a comparison of avoided palindromic words in taxonomically related bacteria shows a pattern of relatedness of their R-M systems. For strengthening this analysis, the primary protein structure of all type II R-M systems known in REBASE have been blasted against the nr-GENBANK database. The combination of these analyses has revealed some interesting examples of possible horizontal transfer events of R-M systems.
Improving the physiological realism of experimental models

The Virtual Physiological Human (VPH) project aims to develop integrative, explanatory and predictive computational models (C-Models) as numerical investigational tools to study disease, identify and design effective therapies and provide an in silico platform for drug screening. Ultimately, these models rely on the analysis and integration of experimental data. As such, the success of VPH depends on the availability of physiologically realistic experimental models (E-Models) of human organ function that can be parametrized to test the numerical models. Here, the current state of suitable E-models, ranging from in vitro non-human cell organelles to in vivo human organ systems, is discussed. Specifically, challenges and recent progress in improving the physiological realism of E-models that may benefit the VPH project are highlighted and discussed using examples from the field of research on cardiovascular disease, musculoskeletal disorders, diabetes and Parkinson's disease.
In vitro studies on the control of trophoblast outgrowth in the mouse.

When placed in serum-free medium on reconstituted collagen surfaces re-implantation mouse embryos are capable of producing characteristic trophoblast outgrowths. Previously this pattern of differentiation has been considered to be essentially dependent on the presence of serum macromolecules. Such activity is expressed only at the late blastocyst stage and is qualitatively different from the adhesive interactions between blastomeres earlier in development. The development of the properties responsible for outgrowth is intrinsic to the blastocyst, being independent of stimulation by exposure either to the uterine environment or to whole serum. The significance of these observations related to implantation control in vivo is discussed.
Of inflammasomes and pathogens – sensing of microbes by the inflammasome

Inflammasomes are signalling platforms that sense a diverse range of microbial products and also a number of stress and damage associated endogenous signals. Inflammasome complexes can be formed by members of the Nod‐like receptor family or the PYHIN family member AIM2. Upon formation, inflammasomes trigger proteolysis of caspase‐1, which subsequently leads to a potent inflammatory response through the maturation and secretion of IL‐1 family cytokines, which can be accompanied by an inflammatory cell death termed pyroptosis. Here, we review the sensing mechanisms of the currently characterized inflammasome complexes and discuss how they are involved in the innate immune response against microbial pathogens. We especially highlight recent advances in the molecular understanding of how microbial patterns are detected and discriminated from endogenous compounds by inflammasome sensors. Further, we review how inflammasomes contribute to the anti microbial host defense by cytokine‐dependent and cell autonomous mechanisms.
Effect of Family Support on the Success of Translocated Black‐Tailed Prairie Dogs

Abstract: Translocation has become a widely used conservation tool but remains only marginally successful. High mortality is often attributed to predation, but for highly social species, founder group composition may also play a critical role in postrelease survival. I compared the fitness of black‐tailed prairie dogs translocated with or without their family groups. Animals in the family translocated groups were individually marked and observed until coterie membership was determined. Nonfamily translocated animals were trapped without regard to family membership. I measured fitness by retrapping all marked animals remaining at release sites in the summer following release. Family translocated animals were five times more likely to survive and had significantly higher reproductive success than those translocated without families. Predation was an important impediment of translocation success, but family translocation significantly reduced the success of predators on newly established prairie dog colonies. Postrelease survival was also affected by the timing of release, but appeared to be more important for juveniles than adults. These results demonstrate the importance of considering familiarity when translocations are required. More broadly, these results illustrate the value of applying animal behavior to conservation efforts and suggest that other species dependent on social interactions for survival and reproduction may benefit substantially from the maintenance of social groups during translocations.
A New Approach to the Characterization of Subtle Errors in Everyday Action: Implications for Mild Cognitive Impairment

Mild functional difficulties have been associated with early cognitive decline in older adults and increased risk for conversion to dementia in mild cognitive impairment, but our understanding of this decline has been limited by a dearth of objective methods. This study evaluated the reliability and validity of a new system to code subtle errors on an established performance-based measure of everyday action and described preliminary findings within the context of a theoretical model of action disruption. Here 45 older adults completed the Naturalistic Action Test (NAT) and neuropsychological measures. NAT performance was coded for overt errors, and subtle action difficulties were scored using a novel coding system. An inter-rater reliability coefficient was calculated. Validity of the coding system was assessed using a repeated-measures ANOVA with NAT task (simple versus complex) and error type (overt versus subtle) as within-group factors. Correlation/regression analyses were conducted among overt NAT errors, subtle NAT errors, and neuropsychological variables. The coding of subtle action errors was reliable and valid, and episodic memory breakdown predicted subtle action disruption. Results suggest that the NAT can be useful in objectively assessing subtle functional decline. Treatments targeting episodic memory may be most effective in addressing early functional impairment in older age.
Lossless compression of video using temporal information

In this paper, we consider the problem of lossless compression of video by taking into account temporal information. Video lossless compression is an interesting possibility in the line of production and contribution. We propose a compression technique which is based on motion compensation, optimal three-dimensional (3-D) linear prediction and context based Golomb-Rice entropy coding. The proposed technique is compared with 3-D extensions of the JPEG-LS standard for still image compression. A compression gain of about 0.8 bit/pel with respect to static JPEG-LS, applied on a frame-by-frame basis, is achievable at a reasonable computational complexity.
Variation in inbreeding depression and plasticity across native and non-native field environments.

BACKGROUND AND AIMS Since the early 1990s, research on genetic variation of phenotypic plasticity has expanded and empirical research has emphasized the role of the environment on the expression of inbreeding depression. An emerging question is how these two evolutionary ecology mechanisms interact in novel environments. Interest in this area has grown with the need to understand the establishment of populations in response to climate change, and to human-assisted transport to novel environments. METHODS We compare performance in the field of outcrossed (O) and inbred lines (S1, S2) from 20 maternal families from each of two native populations of Mimulus guttatus. The experiment was planted in California in each population's home site, in the other populations's home site, in a novel site within the native range of M. guttatus, and in a novel site within the non-native range in North America. The experiment included nearly 6500 individuals. Survival, sexual reproduction and above-ground biomass were examined in order to evaluate inbreeding depression, and stem diameter and plant height were examined in order to evaluate phenotypic plasticity. KEY RESULTS Across all field sites, approx. 36 % of plants survived to flowering. Inbreeding depression differed among sites and outcrossed offspring generally outperformed selfed offspring. However, in the native-novel site, self-progeny performed better or equally well as outcross progeny. Significant phenotypic plasticity and genetic variation in plasticity was detected in the two architectural traits measured. The absolute value of plasticity showed the most marked difference between home and non-native novel site or non-native-novel site. Evidence was detected for an interaction between inbreeding and plasticity for stem diameter. CONCLUSIONS The results demonstrate that during initial population establishment, both inbreeding depression and phenotypic plasticity vary among field sites, and may be an important response to environments outside a species' currently occupied range. However, the interaction between inbreeding and plasticity may be limited and environment-dependent.