Miracle-dz/UniFAR-FTUs huggingface dataset:
Electrophysiological correlates of non-stationary BOLD functional connectivity fluctuations

Spontaneous fluctuations of the BOLD (Blood Oxygen Level-Dependent) signal, measured with fMRI (functional Magnetic Resonance Imaging), display a rich and neurobiologically relevant functional connectivity structure. This structure is usually revealed using time averaging methods, which prevent the detection of functional connectivity changes over time. In this work we studied the electrophysiological correlates of dynamical BOLD functional connectivity fluctuations, by means of long (approx. 50 min) joint electroencephalographic (EEG) and fMRI recordings. We identified widespread positive and negative correlations between EEG spectral power and fMRI BOLD connectivity fluctuations in a network of 90 cortical and subcortical regions. In particular, increased alpha (8-12 Hz) and beta (15-30 Hz) power were related to decreased functional connectivity, whereas gamma (30-60 Hz) power correlated positively with BOLD connectivity between specific brain regions. Furthermore, these patterns were altered for subjects undergoing vigilance changes, with an involvement of the slow delta (0.4 - 4 Hz) band in localized positive correlations. Finally, graph theoretical indices of network structure also exhibited sharp changes over time, with average path length correlating positively with alpha power extracted from central and frontal electrodes. Our results strongly suggest that non-stationary BOLD functional connectivity has a neurophysiological origin. Positive correlations of BOLD connectivity with gamma can be interpreted as increased average binding over relatively long periods of time, possibly due to spontaneous cognition occurring during rest. Negative correlations with alpha suggest functional inhibition of local and long-range connectivity, associated with an idling state of the brain.
A Hybrid Model for Accurate Energy Analysis of WSN Nodes

Energy modeling is an important issue for designing and dimensioning low power wireless sensor networks (WSN). In order to help the developers to optimize the energy spent by WSN nodes, a pragmatic and precise hybrid energy model is proposed. This model considers different scenarios that occur during the communication and evaluates their energy consumption based on software profiling as well as the hardware components power profiles. The proposed model is a combination of analytical derivations and real-time measurements. Firstly, the analytical model provides a global view of various elements of the link and MAC layers and shows their impact on the energy consumption. Secondly, the real-time measurements provide an accurate estimate of the power consumption of the software as well as the hardware platform. These experiments are particularly useful to understand the MAC layer mechanisms, such as wake-up or data collisions for the preamble sampling category, and the energy wasted by collisions is evaluated. The presented model is validated under a specific setup with three different test cases. The results verify that the relative error is between 1 and 8%.
A novel Digital Alias-free Signal Processing method by using Weighted Periodic Nonuniform Sampling

Weighted Periodic Nonuniform Sampling (WPNS) for Digital Alias-free Signal Processing is analysed. The methodology of measuring the level of aliasing within the required range of frequencies is proposed. The optimal WPNS is found by searching a carefully selected subspace of feasible solutions and applying Lawson algorithm for weight calculation. We describe the improvements that have been made to the algorithm of searching the optimal sampling instants. It is shown that WPNS has better alias-suppression properties than traditional PNS.
Assembly of MMTV promoter minichromosomes with positioned nucleosomes precludes NF1 access but not restriction enzyme cleavage.

To generate long arrays of nucleosomes within a topologically defined chromatin domain we have assembled minichromosomes on negatively supercoiled plasmid DNA with extracts from Drosophila preblastoderm embryos. These minichromosomes are dynamic substrates for energy-dependent nucleosome remodeling machines that facilitate the binding of various transcription factors but do not exhibit nucleosome positioning. In contrast, if such minichromosomes include the mouse mammary tumour virus (MMTV) promoter we find it wrapped around a nucleosome with similar translational and rotational position as in vivo . This structure precluded binding of NF1 to its cognate site at -75/-65 at salt concentrations between 60 and 120 mM, even in the presence of ATP, which rendered the NF1 site accessible to the restriction enzyme Hin fI. However, insertion of 30 bp just upstream of the NF1 site, which moves the site to the linker DNA, allowed ATP-dependent binding of NF1 to a fraction of the minichromosomes, even in the presence ofstoichiometric amounts of histone H1. The minichromosomes assembled in the Drosophila embryo extract reproduce important features of the native MMTV promoter chromatin and reveal differences in the ability of transcription factors and restriction enzymes to access their binding sites in positioned nucleosomes.
Poincare duality complexes in dimension four

We describe an algebraic structure on chain complexes yielding algebraic models which classify homotopy types of Poincare duality complexes of dimension 4. Generalizing Turaev's fundamental triples of Poincare duality complexes of dimension 3, we introduce fundamental triples for Poincare duality complexes of dimension n > 2 and show that two Poincare duality complexes are orientedly homotopy equivalent if and only if their fundamental triples are isomorphic. As applications we establish a conjecture of Turaev and obtain a criterion for the existence of degree 1 maps between n-dimensional manifolds.
Unsupervised Word and Dependency Path Embeddings for Aspect Term Extraction

In this paper, we develop a novel approach to aspect term extraction based on unsupervised learning of distributed representations of words and dependency paths. The basic idea is to connect two words (w1 and w2) with the dependency path (r) between them in the embedding space. Specifically, our method optimizes the objective w1 + r = w2 in the low-dimensional space, where the multi-hop dependency paths are treated as a sequence of grammatical relations and modeled by a recurrent neural network. Then, we design the embedding features that consider linear context and dependency context information, for the conditional random field (CRF) based aspect term extraction. Experimental results on the SemEval datasets show that, (1) with only embedding features, we can achieve state-of-the-art results; (2) our embedding method which incorporates the syntactic information among words yields better performance than other representative ones in aspect term extraction.
Anatomical evidence for direct projections from the entorhinal area to the entire cortical mantle in the rat

The entorhinal area is the most highly differentiated cortical field of the hippocampal formation from an anatomical point of view, and is best known as the origin of the perforant pathway, a massive association projection to the molecular layer of the dentate gyrus and Ammon's horn. This pathway is important as the first link in the so-called “trisynaptic circuit,” which is thought to form the basic unit of information processing in the hippocampal formation and has been implicated in the elaboration of short-term memory and the more permanent storage of selected events in other parts of the cortical mantle. We have reexamined the efferent projections of the lateral entorhinal area with a sensitive new method that utilizes the anterograde axonal transport of a lectin, Phaseolus vulgaris leukoagglutinin (PHA-L), that is not internalized by fibers of passage, and displays labeled axons with the clarity of Golgi impregnations. The results of 5 experiments with injections confined entirely to the lateral entorhinal area suggest that this area sends fibers to innervate the entire cortical mantle, as well as to a longitudinal zone extending the length of the striatum (nucleus accumbens and medial caudoputamen) and the basolateral complex of the amygdala. In an additional series of experiments, injections of the fluorescent retrograde tracer fast blue that were centered in medial prefrontal, somatosensory, auditory, and motor areas of the cortex invariably labeled many neurons in layer IV of the lateral entorhinal area, as well as in other layers, depending on the site of injection. Finally, the results of double retrograde tracer experiments indicated that the 2 densest projections from the lateral entorhinal area--to the medial prefrontal region and to the dentate gyrus and Ammon's horn--arise from essentially separate populations of neurons. These findings serve to clarify the neural mechanisms underlying the role of the hippocampal formation in learning and memory, as well as in locomotor activity associated with goal-oriented behavior.
Identification of responders to inhaled corticosteroids in a chronic obstructive pulmonary disease population using cluster analysis

Objectives To identify clusters of patients who may benefit from treatment with an inhaled corticosteroid (ICS)/long-acting β2 agonist (LABA) versus LABA alone, in terms of exacerbation reduction, and to validate previously identified clusters of patients with chronic obstructive pulmonary disease (COPD) (based on diuretic use and reversibility). Design Post hoc supervised cluster analysis using a modified recursive partitioning algorithm of two 1-year randomised, controlled trials of fluticasone furoate (FF)/vilanterol (VI) versus VI alone, with the primary end points of the annual rate of moderate-to-severe exacerbations. Setting Global. Participants 3255 patients with COPD (intent-to-treat populations) with a history of exacerbations in the past year. Interventions FF/VI 50/25 µg, 100/25 µg or 200/25 µg, or VI 25 µg; all one time per day. Outcome measures Mean annual COPD exacerbation rate to identify clusters of patients who benefit from adding an ICS (FF) to VI bronchodilator therapy. Results Three clusters were identified, including two groups that benefit from FF/VI versus VI: patients with blood eosinophils >2.4% (RR=0.68, 95% CI 0.58 to 0.79), or blood eosinophils ≤2.4% and smoking history ≤46 pack-years, experienced a reduced rate of exacerbations with FF/VI versus VI (RR=0.78, 95% CI 0.63 to 0.96), whereas those with blood eosinophils ≤2.4% and smoking history >46 pack-years were identified as non-responders (RR=1.22, 95% CI 0.94 to 1.58). Clusters of patients previously identified in the fluticasone propionate/salmeterol (SAL) versus SAL trials of similar design were not validated; all clusters of patients tended to benefit from FF/VI versus VI alone irrespective of diuretic use and reversibility. Conclusions In patients with COPD with a history of exacerbations, those with greater blood eosinophils or a lower smoking history may benefit more from ICS/LABA versus LABA alone as measured by a reduced rate of exacerbations. In terms of eosinophils, this finding is consistent with findings from other studies; however, the validity of the 2.4% cut-off and the impact of smoking history require further investigation. Trial registration numbers NCT01009463; NCT01017952; Post-results.
Employing social gaze and speaking activity for automatic determination of the Extraversion trait

In order to predict the Extraversion personality trait, we exploit medium-grained behaviors enacted in group meetings, namely, speaking time and social attention (social gaze). The latter will be further distinguished in to attention given to the group members and attention received from them. The results of our work confirm many of our hypotheses: a) speaking time and (some forms of) social gaze are effective in automatically predicting Extraversion; b) classification accuracy is affected by the size of the time slices used for analysis, and c) to a large extent, the consideration of the social context does not add much to accuracy prediction, with an important exception concerning social gaze.
Intrusive memory quality in posttraumatic stress disorder and depression : a multimethod comparison using self-report, narrative measures and psychophysiological responding

Considerable empirical work has investigated theoretically-driven predictions about the distinctive nature of intrusive memory (IM) phenomena in PTSD. Recently, there has been increasing recognition that intrusive remembering may also play an important role in depression. The accompanying findings have been interpreted as indicating that IMs in depression and PTSD exhibit a large degree of overlap. However, much of the IM research in depression to date has been limited by a range of methodological issues (Brewin, Gregory, Lipton, & Burgess, 2010; Newby & Moulds, 2011). This dissertation attempted to address such limitations by applying a multimethod approach to the comparison of IM phenomenology across depressed, PTSD and non-clinical groups. Study 1 compared IM phenomenology using self-report and narrative data while Study 2 combined a script-driven imagery task and self-report measures to consider the role of psychophysiological arousal during trigger event recall. Results confirmed that IMs in depression and PTSD share some degree of overlap but differ on other key features. Specifically, IMs in PTSD were found to be more sensory-perceptual in nature, accompanied by more physical sensations and rated as more distressing than the IMs in depression. The IMs in PTSD were also characterised by a lack of temporal context compared to ordinary memory segments, a difference which was not observed for the depressed group. Furthermore, compared to depressed and control participants, the PTSD group exhibited significantly greater physiological arousal, particularly heart rate responses, whilst recalling trigger events. Although group differences were not found for self-reports ofIM-related "nowness",
Systematic evaluation of environmental and behavioural factors associated with all-cause mortality in the United States national health and nutrition examination survey.

BACKGROUND Environmental and behavioural factors are thought to contribute to all-cause mortality. Here, we develop a method to systematically screen and validate the potential independent contributions to all-cause mortality of 249 environmental and behavioural factors in the National Health and Nutrition Examination Survey (NHANES). METHODS We used Cox proportional hazards regression to associate 249 factors with all-cause mortality while adjusting for sociodemographic factors on data in the 1999-2000 and 2001-02 surveys (median 5.5 follow-up years). We controlled for multiple comparisons with the false discovery rate (FDR) and validated significant findings in the 2003-04 survey (median 2.8 follow-up years). We selected 249 factors from a set of all possible factors based on their presence in both the 1999-2002 and 2003-04 surveys and linkage with at least 20 deceased participants. We evaluated the correlation pattern of validated factors and built a multivariable model to identify their independent contribution to mortality. RESULTS We identified seven environmental and behavioural factors associated with all-cause mortality, including serum and urinary cadmium, serum lycopene levels, smoking (3-level factor) and physical activity. In a multivariable model, only physical activity, past smoking, smoking in participant's home and lycopene were independently associated with mortality. These three factors explained 2.1% of the variance of all-cause mortality after adjusting for demographic and socio-economic factors. CONCLUSIONS Our association study suggests that, of the set of 249 factors in NHANES, physical activity, smoking, serum lycopene and serum/urinary cadmium are associated with all-cause mortality as identified in previous studies and after controlling for multiple hypotheses and validation in an independent survey. Whereas other NHANES factors may be associated with mortality, they may require larger cohorts with longer time of follow-up to detect. It is possible to use a systematic association study to prioritize risk factors for further investigation.
Square numbers, spanning trees and invariants of achiral knots

We give constructions to realize an odd number, which is representable as sum of two squares, as determinant of an achiral knot, thus proving that these are exactly the numbers occurring as such determinants. Later we study which numbers occur as determinants of prime alternating achiral knots, and obtain a complete result for perfect squares. Using the checkerboard coloring, then an application is given to the number of spanning trees in planar self-dual graphs. Another application are some enumeration results on achiral rational knots. Finally, we describe the leading coefficients of the Alexander and skein polynomial of alternating achiral knots.
Genetic connectivity among swarming sites in the wide ranging and recently declining little brown bat (Myotis lucifugus)

Characterizing movement dynamics and spatial aspects of gene flow within a species permits inference on population structuring. As patterns of structuring are products of historical and current demographics and gene flow, assessment of structure through time can yield an understanding of evolutionary dynamics acting on populations that are necessary to inform management. Recent dramatic population declines in hibernating bats in eastern North America from white-nose syndrome have prompted the need for information on movement dynamics for multiple bat species. We characterized population genetic structure of the little brown bat, Myotis lucifugus, at swarming sites in southeastern Canada using 9 nuclear microsatellites and a 292-bp region of the mitochondrial genome. Analyses of FST, ΦST, and Bayesian clustering (STRUCTURE) found weak levels of genetic structure among swarming sites for the nuclear and mitochondrial genome (Global FST = 0.001, P < 0.05, Global ΦST = 0.045, P < 0.01, STRUCTURE K = 1) suggesting high contemporary gene flow. Hierarchical AMOVA also suggests little structuring at a regional (provincial) level. Metrics of nuclear genetic structure were not found to differ between males and females suggesting weak asymmetries in gene flow between the sexes. However, a greater degree of mitochondrial structuring does support male-biased dispersal long term. Demographic analyses were consistent with past population growth and suggest a population expansion occurred from approximately 1250 to 12,500 BP, following Pleistocene deglaciation in the region. Our study suggests high gene flow and thus a high degree of connectivity among bats that visit swarming sites whereby mainland areas of the region may be best considered as one large gene pool for management and conservation.
Mitochondrial dysfunction, impaired oxidative-reduction activity, degeneration, and death in human neuronal and fetal cells induced by low-level exposure to thimerosal and other metal compounds

Thimerosal (ethylmercurithiosalicylic acid), an ethylmercury (EtHg)-releasing compound (49.55% mercury (Hg)), was used in a range of medical products for more than 70 years. Of particular recent concern, routine administering of Thimerosal-containing biologics/childhood vaccines have become significant sources of Hg exposure for some fetuses/infants. This study was undertaken to investigate cellular damage among in vitro human neuronal (SH-SY-5Y neuroblastoma and 1321N1 astrocytoma) and fetal (nontransformed) model systems using cell vitality assays and microscope-based digital image capture techniques to assess potential damage induced by Thimerosal and other metal compounds (aluminum (Al) sulfate, lead (Pb)(II) acetate, methylmercury (MeHg) hydroxide, and mercury (Hg)(II) chloride) where the cation was reported to exert adverse effects on developing cells. Thimerosal-associated cellular damage was also evaluated for similarity to pathophysiological findings observed in patients diagnosed with autistic disorders (ADs). Thimerosal-induced cellular damage as evidenced by concentration- and time-dependent mitochondrial damage, reduced oxidative–reduction activity, cellular degeneration, and cell death in the in vitro human neuronal and fetal model systems studied. Thimerosal at low nanomolar (nM) concentrations induced significant cellular toxicity in human neuronal and fetal cells. Thimerosal-induced cytoxicity is similar to that observed in AD pathophysiologic studies. Thimerosal was found to be significantly more toxic than the other metal compounds examined. Future studies need to be conducted to evaluate additional mechanisms underlying Thimerosal-induced cellular damage and assess potential co-exposures to other compounds that may increase or decrease Thimerosal-mediated toxicity.
Quantitative real-time polymerase chain reaction for enteropathogenic Escherichia coli: a tool for investigation of asymptomatic versus symptomatic infections.

BACKGROUND Enteropathogenic Escherichia coli (EPEC) strains are pediatric pathogens commonly isolated from both healthy and sick children with diarrhea in areas of endemicity. The aim of this study was to compare the bacterial load of EPEC isolated from stool samples from children with and without diarrhea to determine whether bacterial load might be a useful tool for further study of this phenomenon. METHODS EPEC was detected by polymerase chain reaction (PCR) of colonies isolated on MacConkey plates from 53 diarrheal and 90 healthy children aged <2 years. DNA was isolated from stool samples by cetyltrimethylammonium bromide extraction. To standardize quantification by quantitative real-time PCR (qRT-PCR), the correlation between fluorescence threshold cycle and copy number of the intimin gene of EPEC E2348/69 was determined. RESULTS The detection limit of qRT-PCR was 5 bacteria/mg stool. The geometric mean load in diarrhea was 299 bacteria/mg (95% confidence interval [CI], 77-1164 bacteria/mg), compared with 29 bacteria/mg (95% CI, 10-87 bacteria/mg) in control subjects (P = .016). Bacterial load was significantly higher in children with diarrhea than in control subjects among children <12 months of age (178 vs 5 bacteria/mg; P = .006) and among children with EPEC as the sole pathogen (463 vs 24 bacteria/mg; P = .006). CONCLUSIONS EPEC load measured by qRT-PCR is higher in diarrheal than in healthy children. qRT-PCR may be useful to study the relationship between disease and colonization in settings of endemicity.