Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution and Regulation of the Mobile Genetic Element-Encoded Phenol-Soluble Modulin PSM-mec in Methicillin-Resistant Staphylococcus aureus

The phenol-soluble modulin PSM-mec is the only known staphylococcal toxin that is encoded on a mobile antibiotic resistance determinant, namely the staphylococcal cassette chromosome (SCC) element mec encoding resistance to methicillin. Here we show that the psm-mec gene is found frequently among methicillin-resistant Staphylococcus aureus (MRSA) strains of SCCmec types II, III, and VIII, and is a conserved part of the class A mec gene complex. Controlled expression of AgrA versus RNAIII in agr mutants of all 3 psm-mec-positive SCCmec types demonstrated that expression of psm-mec, which is highly variable, is controlled by AgrA in an RNAIII-independent manner. Furthermore, psm-mec isogenic deletion mutants showed only minor changes in PSMα peptide production and unchanged (or, as previously described, diminished) virulence compared to the corresponding wild-type strains in a mouse model of skin infection. This indicates that the recently reported regulatory impact of the psm-mec locus on MRSA virulence, which is opposite to that of the PSM-mec peptide and likely mediated by a regulatory RNA, is minor when analyzed in the original strain background. Our study gives new insight in the distribution, regulation, and role in virulence of the PSM-mec peptide and the psm-mec gene locus.
Tree and Graph Mining

During the past decade, we have witnessed an explosive growth in our capabilities to both generate and collect data. Various data mining techniques have been proposed and widely employed to discover valid, novel and potentially useful patterns in these data. Data mining involves the discovery of patterns, associations, changes, anomalies, and statistically significant structures and events in huge collections of data. One of the key success stories of data mining research and practice has been the development of efficient algorithms for discovering frequent itemsets – both sequential (Srikant & Agrawal, 1996) and non-sequential (Agrawal & Srikant, 1994). Generally speaking, these algorithms can extract co-occurrences of items (taking or not taking into account the ordering of items) in an efficient manner. Although the use of sets (or sequences) has effectively modeled many application domains, like market basket analysis, medical records, a lot of applications have emerged whose data models do not fit in the traditional concept of a set (or sequence), but require the deployment of richer abstractions, like graphs or trees. Such graphs or trees arise naturally in a number of different application domains including network intrusion, semantic Web, behavioral modeling, VLSI reverse engineering, link analysis and chemical compound classification. Thus, the need to extract complex tree-like or graphlike patterns in massive data collections, for instance, in bioinformatics, semistructured or Web databases, became a necessity. The class of exploratory mining tasks, which deal with discovering patterns in massive databases representing complex interactions among entities, is called Frequent Structure Mining (FSM) (Zaki, 2002). In this article we will highlight some strategic application domains where FSM can help provide significant results and subsequently we will survey the most important algorithms that have been proposed for mining graph-like and tree-like substructures in massive data collections.
The Efficiency of Discrete Convolution Method on Solving Exact String Matching Problem

In this paper, we first derived an equation which can approach the probability of appearing of a pattern string in a text string. From this equation, we see that the probability that a pattern string appears in a text string reduces to 0 quickly as the length of the pattern string increases. Because of this observation, we introduce an algorithm based on the discrete convolution method with an early termination. The algorithm stops as soon as it discovers that a prefix of the pattern string does not appear in the text string. In this paper, we show that the discrete convolution method with an early termination is quite efficient to solve exact string matching problem.
Sonification Of A Virtual Model Of The Old Rare Musical Instrument

The paper describes a project whose goal was to enable users realistically interact with a 3D virtual model of a historical musical instrument – the clavichord attributed to the famous 18th century maker. A challenge of enabling the user to play the virtual copy of the instrument was resolved by using the dynamic MIDI keyboard. The prerecorded clavichord sound samples are controlled by the software using the MIDI commands. Playing the real keyboard is synchronized with the movement of virtual keys and other parts of sound generating mechanism. The sound effects, characteristic for the clavichord Tragen der Tonne and Bebung may be imitated, which gives the user the impression of playing the real instrument.
Fluency or Similarities? Cognitive Abilities that Contribute to Creative Metaphor Generation

This study focused on the cognitive abilities that contribute to creative metaphor generation. A concept explanation task was used to test conventional and novel (creative) metaphor generation. Conceptual fluency and similarities were measured using the Tel-Aviv Creativity Test (TACT). The main goal was to investigate how fluency of ideas and similarities contribute to creative metaphor generation. Fifty-four children (M = 12.59, SD = 2.05) participated in the study. The findings demonstrated that fluency of ideas contributed to the prediction of creative potential, but not conventional metaphor generation, beyond similarities, cognitive abilities, executive functions, verbal abilities, and age. The results thus show that novel metaphor generation is unique and separate estimate of creative potential, which is reciprocally related to conceptual fluency.
Nutrients and cyclical interdigestive pancreatic enzyme secretion in humans.

BACKGROUND AND AIMS: It is hypothesised that nutrients increase pancreatic enzyme secretion by converting cyclical interdigestive secretion to a non-cyclical pattern. This study tested the hypotheses that nutrients do not interrupt cycles and determined the relation of nutrients, calories, and osmotic load to the rate of pancreatic secretion. METHODS: Twenty six healthy persons were intubated with oroduodenal and orogastric tubes. Each had one of four different solutions containing 12 to 36% of calories as protein, 24 to 48% as fat, and 40 to 64% as carbohydrate infused into the duodenum at 40, 90, or 160 kcal/h for 300 minutes. Nine g/l sodium chloride (290 mOsm) was added to 16 infusates; osmolality of the other 10 infusates was 24 to 98 mOsm. Pancreatic enzyme outputs were measured every 15 minutes and peaks of enzyme secretion were identified. RESULTS: The number of enzyme peaks was similar for the different infusates and the proportion of nutrients in the infusates did not affect secretion of individual enzymes. The nadir, but not the peak of the cycles of enzyme outputs correlated with increasing the caloric load (r = 0.55, p < 0.003 for nadir:peak ratio). Increasing osmolality did not affect cycling but reduced (p < 0.001) enzyme output. CONCLUSION: Nutrients entering the duodenum do not abolish cycles of enzyme secretion; instead they modulate cycles by increasing the nadir. Forty and 90 kcal infusions submaximally stimulate pancreatic secretion and might be used in patients with pancreatitis without producing pain; adding sodium chloride to solutions should increase this effect.
Seasonal Migration and Improving Living Standards in Vietnam

We use panel data methods to explore whether households in Vietnam used seasonal migration to increase their living standards during the 1990s. Using per capita expenditures as our primary measure of living standards and historical and latent network variables as instruments for migration, we can attribute 5.2 percentage points of annualized expenditure growth to increased migration. The results are robust to several alternative measures of living standards. As the estimates suggest migration accounts for a 3 percentage point decrease in the poverty headcount, we conclude migration played an important role in the improvement of living standards observed in Vietnam.
Applied Psychometrics: The 3-Faced Construct Validation Method, a Routine for Evaluating a Factor Structure

The “3-faced construct validation method” is a routine for establishing the validity and reliability of an existing scale when adapted in a different cultural context from the context initially developed. This routine can also be used for the initial validation of a newly developed scale. This is essentially a construct validation procedure based on a sample-splitting. The sample is randomly split into three parts, 20% for EFA, 40% for an exploratory CFA and 40% for a cross-validating CFA. The cases per variable threshold is set above 5:1, preferably above 10:1 (minimum conditions) and the first approximately 20% subsample emerges (adequate conditions) to evaluate EFA and Bifactor EFA models. Then the cases per variable threshold is set above 10:1, preferably above 20:1 (minimum conditions) and the 40% subsample emerges (adequate conditions) to examine alternative CFA models (ICM-CFA, Bifactor CFA, ESEM and Bifactor ESEM models). The optimal model(s) is cross-validated by a second CFA in yet another 40% subsample (equal-power CFA sample) as a protection against overfitting (over-optimization) to safeguard model replicability. Measurement invariance follows and is essentially another cross-check of the optimal model over the entire sample because the optimal model is used as the baseline model.
A comparison of linguistically and statistically enhanced models for speech-to-speech machine translation

The goal of this work is to improve current translation models by taking into account additional knowledge sources such as semantically motivated segmentation or statistical categorization. Speciﬁcally, two different approaches are discussed. On the one hand, phrase-based approach, and on the other hand, categorization. For both approaches, both statistical and linguistic alternatives are explored. As for translation framework, ﬁnite-state transducers are considered. These are versatile models that can be easily integrated on-the-ﬂy with acoustic models for speech translation purposes. In what the experimental framework concerns, all the models presented were evaluated and compared taking conﬁdence intervals into account.
Correlation of paleotectonic fracture and microfracture orientations in cores with seismic anisotropy at Cajon Pass Drill Hole, southern California

Fractures and microfractures in oriented cores from the Cajon Pass drill hole, southern California, have strong preferred orientations. There are two major sets of extensional fractures and microfractures that have northwest and northeast strikes and vertical dips. Relative and absolute densities of both sets vary greatly within a single core. The regional tectonic history implies that these fractures and microfractures probably formed before late Miocene-Pliocene. Vertical seismic profiling experiments in the drill hole show shear wave splitting with polarization directions parallel to the fracture and microfracture orientations. The measured seismic anisotropy is due to these inherited deformation fabrics and does not appear to be caused by the current local stress field.
The Angiopoietin-1 Variant COMP-Ang1 Enhances BMP2-Induced Bone Regeneration with Recruiting Pericytes in Critical Sized Calvarial Defects

Craniofacial bone defects are observed in a variety of clinical situations, and their reconstructions require coordinated coupling between angiogenesis and osteogenesis. In this study, we explored the effects of cartilage oligomeric matrix protein-angiopoietin 1 (COMP-Ang1), a synthetic and soluble variant of angiopoietin 1, on bone morphogenetic protein 2 (BMP2)-induced cranial bone regeneration, and recruitment and osteogenic differentiation of perivascular pericytes. A critical-size calvarial defect was created in the C57BL/6 mouse and COMP-Ang1 and/or BMP2 proteins were delivered into the defects with absorbable collagen sponges. After 3 weeks, bone regeneration was evaluated using micro-computed tomography and histologic examination. Pericyte recruitment into the defects was examined using immunofluorescence staining with anti-NG2 and anti-CD31 antibodies. In vitro recruitment and osteoblastic differentiation of pericyte cells were assessed with Boyden chamber assay, staining of calcified nodules, RT-PCR and Western blot analyses. Combined administration of COMP-Ang1 and BMP2 synergistically enhanced bone repair along with the increased population of CD31 (an endothelial cell marker) and NG2 (a specific marker of pericyte) positive cells. In vitro cultures of pericytes consistently showed that pericyte infiltration into the membrane pore of Boyden chamber was more enhanced by the combination treatment. In addition, the combination further increased the osteoblast-specific gene expression, including bone sialoprotein (BSP), osteocalcin (OCN) and osterix (OSX), phosphorylation of Smad/1/5/8, and mineralized nodule formation. COMP-Ang1 can enhance BMP2-induced cranial bone regeneration with increased pericyte recruitment. Combined delivery of the proteins might be a therapeutic strategy to repair cranial bone damage.
Economic inequality in nutritional knowledge, attitude and practice of Iranian households: The NUTRI-KAP study

Background: Improper nutritional knowledge is one of the most important causes of nutritional problems, which can affect practice and cause more complications. The aim of this study was to assess the association between nutritional knowledge, attitude and practice (KAP) of Iranian households with socioeconomic status (SES). Methods: The study population was 14,136 households (57 clusters of 8 individuals in each province) who lived in urban and rural regions of 31 provinces of Iran. The sample size of the study was selected using multistage cluster sampling technique. A structured questionnaire and interview with the qualified person in each family was used to collect data. The questionnaire included demographic, SES and nutritional KAP questions. Using principle component analysis, some variables including household assets, occupation and education level of the heads of the families and respondents and the number of family members were used to construct family SES. The SES was categorized as good, moderate and weak. Pearson’s Chi-square test was used to analyze categorical variables. Results: The percentage of knowledge about growing up, acquiring energy and being healthy as reasons for eating food was 24.1%, 44.8% and 54.7%, respectively. Only 69.7%, 60.5% and 52.5% of the participants had knowledge of identification of meat and legumes, grain and dairy group, respectively. More than 97% of the participants had a favorable attitude toward importance of nutrition in health. The nutritional knowledge linearly increased with increasing SES. Families with good SES significantly consumed more fruit, vegetable, dairy group, red meat, chicken and poultry, fish and egg while sugar consumption was significantly higher in families with weak SES (p<0.05). Conclusion: SES can influence the rate of nutritional KAP. Some policies should be considered to increase nutritional KAP especially in lower SES group in the society.
Comparison of different impulse response measurement techniques

The impulse response of an acoustical space or transducer is one of its most important characterizations. In order to perform the measurement of their impulse responses, four of the most suitable methods are compared: MLS (maximum-length sequence), IRS (inverse repeated sequence), time-stretched pulses, and SineSweep. These methods have already been described in the literature. Nevertheless, the choice of one of them depending on the measurement conditions is critical. Therefore an extensive comparison has been realized. This comparison was done through the implementation and realization of a complete, fast, reliable, and cheap measurement system. Finally, a conclusion for the use of each method according to the principal measurement conditions is presented. It is shown that in the presence of nonwhite noise, the MLS and IRS techniques seem to be more accurate. On the contrary, in quiet environments the logarithmic SineSweep method seems to be the most appropriate.
Multivariate Algorithmics for Finding Cohesive Subnetworks

Community detection is an important task in the analysis of biological, social or technical networks. We survey different models of cohesive graphs, commonly referred to as clique relaxations, that are used in the detection of network communities. For each clique relaxation, we give an overview of basic model properties and of the complexity of the problem of finding large cohesive subgraphs under this model. Since this problem is usually NP-hard, we focus on combinatorial fixed-parameter algorithms exploiting typical structural properties of input networks.
The effects of modulator shape and methods for expressing modulation depth on spectral modulation detection thresholds

The detection of sinusoidal modulation is commonly used for assessing the auditory perception of temporal, spectral, and spectro-temporal acoustic features. For temporal (amplitude) modulation, the sinusoidal modulator usually is expressed on a linear amplitude scale. For spectral modulation, the sinusoidal modulator has been specified on a linear amplitude scale, consistent with temporal modulation, or on a logarithmic amplitude scale, with the notion of approximating a sinusoidal excitation pattern. The definition of modulation depth depends on the measurement points (i.e., midpoint to peak or peak to peak) and order of operations when expressing depth in dB. Such differences can make it difficult to compare results for similar tasks among investigations. Here we quantify differences among methods and provide a complete matrix for translating among methods. Spectral modulation detection was measured for 9 normal-hearing listeners in ten conditions (linear vs. logarithmic shape at 0.5, 1, 2, 4, and 8 cycles/octave). Peak-to-peak values of the modulation envelope were equalized, thus only modulation waveform shape differed. Noise carriers had a passband from 400 to 3200 Hz. Thresholds revealed statistically significant effects of both spectral shape and spectral modulation frequency. Several methods for expressing threshold modulation depth were compared to highlight differences among the methods. The detection of sinusoidal modulation is commonly used for assessing the auditory perception of temporal, spectral, and spectro-temporal acoustic features. For temporal (amplitude) modulation, the sinusoidal modulator usually is expressed on a linear amplitude scale. For spectral modulation, the sinusoidal modulator has been specified on a linear amplitude scale, consistent with temporal modulation, or on a logarithmic amplitude scale, with the notion of approximating a sinusoidal excitation pattern. The definition of modulation depth depends on the measurement points (i.e., midpoint to peak or peak to peak) and order of operations when expressing depth in dB. Such differences can make it difficult to compare results for similar tasks among investigations. Here we quantify differences among methods and provide a complete matrix for translating among methods. Spectral modulation detection was measured for 9 normal-hearing listeners in ten conditions (linear vs. logarithmic shape at 0.5, 1, 2, 4, and 8 cyc.
A DEAD-box-family protein is required for nucleocytoplasmic transport of yeast mRNA

An enormous variety of primary and secondary mRNA structures are compatible with export from the nucleus to the cytoplasm. Therefore, there seems to be a mechanism for RNA export which is independent of sequence recognition. There nevertheless is likely to be some relatively uniform mechanism which allows transcripts to be packaged as ribonucleoprotein particles, to gain access to the periphery of the nucleus and ultimately to translocate across nuclear pores. To study these events, we and others have generated temperature-sensitive recessive mRNA transport (mtr) mutants of Saccharomyces cerevisiae which accumulate poly(A)+ RNA in the nucleus at 37 degrees C. Several of the corresponding genes have been cloned. Upon depletion of one of these proteins, Mtr4p, conspicuous amounts of nuclear poly(A)+ RNA accumulate in association with the nucleolus. Corresponding dense material is also seen by electron microscopy. MTR4 is essential for growth and encodes a novel nuclear protein with a size of approximately 120 kDa. Mtr4p shares characteristic motifs with DEAD-box RNA helicases and associates with RNA. It therefore may well affect RNA conformation. It shows extensive homology to a human predicted gene product and the yeast antiviral protein Ski2p. Critical residues of Mtr4p, including the mtr4-1 point mutation, have been identified. Mtr4p may serve as a chaperone which translocates or normalizes the structure of mRNAs in preparation for export.
New bounds for the sum capacity of binary and nonbinary synchronous CDMA systems

Lower and upper bounds are derived for the sum capacity of synchronous CDMA where the signature matrix and input alphabets are binary or (2p + 1)-ary, in two cases of noiseless and noisy channels. The bounds are very tight in some regions. Interestingly, simulations show that the formulas for noisy systems tend to the ones for noiseless system as noise tends to 0 while it cannot be deduced easily from the formulas. The results give good insights about the extent of the number of users in which errorless communication is possible for a system with a given chip rate.
Mass Spectrometric Analysis of Whole Secretome and Amylase-precipitated Secretome Proteins from Streptococcus gordonii

Oral biofilm (dental plaque) is formed by the initial adhesion of “pioneer species” to salivary proteins that form the dental pellicle on the tooth surface. One such pioneer species, Streptococcus gordonii, is known to bind salivary amylase through specific amylase-binding proteins such as amylase-binding protein A (AbpA). Recent studies have demonstrated that once bound, salivary amylase appears to modulate gene expression in S. gordonii. However, it is not known if this amylase-induced gene expression leads to secretion of proteins that play a role in plaque biofilm formation. In this study we examined the differences in secreted proteomes between S. gordonii KS1 (wild type) and AbpA-deficient (ΔAbpA) strains. We also examined the differentially precipitated secretome proteins following incubation with salivary amylase. The culture supernatants from KS1 and ΔAbpA were analyzed by nano-LC/MS/MS to characterize the whole secreted proteomes of the KS1 and ΔAbpA. A total of 107 proteins were identified in the KS1 and ΔAbpA secretomes of which 72 proteins were predicted to have an N-terminal signal peptide for secretion. Five proteins were differentially expressed between the KS1 and ΔAbpA secretomes; AbpA and sortase B were expressed exclusively by KS1, whereas Gdh, AdcA and GroEL were expressed only by ΔAbpA. Incubation of culture supernatants from KS1 and ΔAbpA with amylase (50 μg/ml) at room temperature for 2 h resulted in the differential precipitation of secretome proteins. Hypothetical protein (SGO_0483), cation-transporting ATPase YfgQ (Aha1), isocitrate dehydrogenase (Icd), sortase A (SrtA), beta-N-acetylhexosaminidase (SGO_0405), peptide chain release factor 1(PrfA) and cardiolipin synthase (SGO_2037) were precipitated by amylase from the KS1 culture supernatant. Among the identified secreted proteins and amylase-precipitated proteins, transcriptional regulator LytR (SGO_0535) and cation-transporting ATPase YfgQ (Aha1) are potential signaling proteins.