Miracle-dz/UniFAR-FTUs huggingface dataset:
Separation from parents during childhood trauma predicts adult attachment security and post-traumatic stress disorder

Background Prolonged separation from parental support is a risk factor for psychopathology. This study assessed the impact of brief separation from parents during childhood trauma on adult attachment tendencies and post-traumatic stress. Method Children (n = 806) exposed to a major Australian bushfire disaster in 1983 and matched controls (n = 725) were assessed in the aftermath of the fires (mean age 7–8 years) via parent reports of trauma exposure and separation from parents during the fires. Participants (n = 500) were subsequently assessed 28 years after initial assessment on the Experiences in Close Relationships scale to assess attachment security, and post-traumatic stress disorder (PTSD) was assessed using the PTSD checklist. Results Being separated from parents was significantly related to having an avoidant attachment style as an adult (B = −3.69, s.e. = 1.48, β = −0.23, p = 0.013). Avoidant attachment was associated with re-experiencing (B = 0.03, s.e. = 0.01, β = 0.31, p = 0.045), avoidance (B = 0.03, s.e. = 0.01, β = 0.30, p = 0.001) and numbing (B = 0.03, s.e. = 0.01, β = 0.30, p < 0.001) symptoms. Anxious attachment was associated with re-experiencing (B = 0.03, s.e. = 0.01, β = 0.18, p = 0.001), numbing (B = 0.03, β = 0.30, s.e. = 0.01, p < 0.001) and arousal (B = 0.04, s.e. = 0.01, β = 0.43, p < 0.001) symptoms. Conclusions These findings demonstrate that brief separation from attachments during childhood trauma can have long-lasting effects on one's attachment security, and that this can be associated with adult post-traumatic psychopathology.
Prediction of Protein Phosphorylation Sites by Using the Composition of k-Spaced Amino Acid Pairs

As one of the most widespread protein post-translational modifications, phosphorylation is involved in many biological processes such as cell cycle, apoptosis. Identification of phosphorylated substrates and their corresponding sites will facilitate the understanding of the molecular mechanism of phosphorylation. Comparing with the labor-intensive and time-consuming experiment approaches, computational prediction of phosphorylation sites is much desirable due to their convenience and fast speed. In this paper, a new bioinformatics tool named CKSAAP_PhSite was developed that ignored the kinase information and only used the primary sequence information to predict protein phosphorylation sites. The highlight of CKSAAP_PhSite was to utilize the composition of k-spaced amino acid pairs as the encoding scheme, and then the support vector machine was used as the predictor. The performance of CKSAAP_PhSite was measured with a sensitivity of 84.81%, a specificity of 86.07% and an accuracy of 85.43% for serine, a sensitivity of 78.59%, a specificity of 82.26% and an accuracy of 80.31% for threonine as well as a sensitivity of 74.44%, a specificity of 78.03% and an accuracy of 76.21% for tyrosine. Experimental results obtained from cross validation and independent benchmark suggested that our method was very promising to predict phosphorylation sites and can be served as a useful supplement tool to the community. For public access, CKSAAP_PhSite is available at http://59.73. 198.144/cksaap_phsite/.
Prestack multiple attenuation using the hyperbolic Radon transform A comparison of inversion schemes

I apply the iterative hyperbolic Radon transform to CMP gathers to create a velocity panel where multiples and primaries are separable. The velocity panel is created using three different inversion schemes: (1) l2 norm inversion, (2) l1 norm inversion and (3) l1 norm with l1 regularization inversion. The third technique is particularly efficient at separating primaries and multiples in the prestack domain. A comparison of the three techniques shows that some noticeable differences appear in the prestack domain after multiple attenuation and that no discrepancies emerge on the stacked sections. These conclusions are linked to convergence properties of each method, and also linked to the “quality” of the data.
Effects of vitamin E, selenium and vitamin C on various biomarkers following oxidative stress caused by diazinon exposure in rainbow trout

Biochemical parameters are appropriate biomarkers to assess the effects of pesticides on an aquatic ecosystem. Diazinon is an organophosphate pesticide whose metabolism in fish body produces reactive oxygen species that can cause oxidative stress. In this study, Oncorhynchus mykiss were allocated into four treatment groups (with three replicates): control; Diazinon; vitamin C + diazinon, and vitamin E,selenium + diazinon. Blood samples were obtained after two and four weeks and superoxide dismutase (SOD), catalase (CAT), total antioxidant capacity (TAC), and malondialdehyde (MDA) were measured. SOD activity was significantly lower in diazinon-exposed fish than in the control group. However, there were no differences between the two supplemented groups and the control group in this regard. CAT activity was significantly higher in all three diazinon-exposed groups compared to the control group. However vitamin E, selenium had the least difference with the control group. Maximum and minimum TAC were observed respectively in fish supplemented with vitamin E, selenium and those only exposed to diazinon. The diazinon group also had the highest MDA levels. The two supplemented groups and the control group had no significant differences in MDA levels. These findings highlighted the antioxidant effects of supplementation with vitamin E, selenium or vitamin C against free radical produced during the metabolism of diazinon. Meanwhile, the combination of vitamin E, selenium had higher antioxidant effects than vitamin C. Moreover, SOD, the first defensive barrier against superoxide radicals, and MDA, an index of cellular damage induced by hydroxyl radicals, are the most suitable indicators to assess the effects of diazinon.
TRAF Family Proteins Regulate Autophagy Dynamics by Modulating AUTOPHAGY PROTEIN6 Stability in Arabidopsis[OPEN]

The TRAF family proteins MUSE14/TRAF1a and MUSE13/TRAF1b regulate the dynamics of autophagy by facilitating both the proteolysis and stabilization of AUTOPHAGY PROTEIN6. Eukaryotic cells use autophagy to recycle cellular components. During autophagy, autophagosomes deliver cytoplasmic contents to the vacuole or lysosome for breakdown. Mammalian cells regulate the dynamics of autophagy via ubiquitin-mediated proteolysis of autophagy proteins. Here, we show that the Arabidopsis thaliana Tumor necrosis factor Receptor-Associated Factor (TRAF) family proteins TRAF1a and TRAF1b (previously named MUSE14 and MUSE13, respectively) help regulate autophagy via ubiquitination. Upon starvation, cytoplasmic TRAF1a and TRAF1b translocated to autophagosomes. Knockout traf1a/b lines showed reduced tolerance to nutrient deficiency, increased salicylic acid and reactive oxygen species levels, and constitutive cell death in rosettes, resembling the phenotypes of autophagy-defective mutants. Starvation-activated autophagosome accumulation decreased in traf1a/b root cells, indicating that TRAF1a and TRAF1b function redundantly in regulating autophagosome formation. TRAF1a and TRAF1b interacted in planta with ATG6 and the RING finger E3 ligases SINAT1, SINAT2, and SINAT6 (with a truncated RING-finger domain). SINAT1 and SINAT2 require the presence of TRAF1a and TRAF1b to ubiquitinate and destabilize AUTOPHAGY PROTEIN6 (ATG6) in vivo. Conversely, starvation-induced SINAT6 reduced SINAT1- and SINAT2-mediated ubiquitination and degradation of ATG6. Consistently, SINAT1/SINAT2 and SINAT6 knockout mutants exhibited increased tolerance and sensitivity, respectively, to nutrient starvation. Therefore, TRAF1a and TRAF1b function as molecular adaptors that help regulate autophagy by modulating ATG6 stability in Arabidopsis.
Is Acculturation Related to Obesity in Hispanic/Latino Adults? Results from the Hispanic Community Health Study/Study of Latinos

Background. The study examined the association of obesity with acculturation in a large and diverse sample of US Hispanic/Latino adults. Methods. The Hispanic Community Health Study (HCHS)/Study of Latinos (SOL) is a community-based cohort study of Hispanic/Latino adults aged 18–74 years (N = 16,415) from four urban areas. Height and weight were directly measured using a standardized protocol. Acculturation was assessed by the Short Acculturation Scale for Hispanics (SASH). Other immigration related variables included place of birth, length of residency in the US, and age at immigration. Odds ratios were calculated to assess the association of overweight, moderate obesity, and extreme obesity (≥40 kg/m2) with acculturation and sociodemographic variables. Results. The prevalence of obesity was 42.4% for women and 36.5% for men and varied by field center and Hispanic/Latino background. The strongest predictor of moderate and extreme obesity was length of residency in mainland US. This association was consistent across Hispanic/Latino backgrounds. Acculturation was not significantly associated with obesity. Discussion. The burden of obesity is high among Hispanic/Latino adults. The study findings suggest that prolonged exposure to the environments in these communities, rather than acculturation, is an important risk factor for obesity in this population.
Lifecourse Social Position and D-Dimer; Findings from the 1958 British Birth Cohort

The aim is to examine the association of lifecourse socioeconomic position (SEP) on circulating levels of D-dimer. Data from the 1958 British birth cohort were used, social class was determined at three stages of respondents' life: at birth, at 23 and at 42 years. A cumulative indicator score of SEP (CIS) was calculated ranging from 0 (always in the highest social class) to 9 (always in the lowest social class). In men and women, associations were observed between CIS and D-dimer (P<0.05). Thus, the respondents in more disadvantaged social classes had elevated levels of D-dimer compared to respondents in less disadvantaged social class. In multivariate analyses, the association of disadvantaged social position with D-dimer was largely explained by fibrinogen, C-reactive protein and von Willebrand Factor in women, and additionally by smoking, alcohol consumption and physical activity in men. Socioeconomic circumstances across the lifecourse at various stages also contribute independently to raised levels of D-dimer in middle age in women only. Risk exposure related to SEP accumulates across life and contributes to raised levels of D-dimer. The association of haemostatic markers and social differences in health may be mediated by inflammatory and other markers.
Emergency Centre Organization and Automated Triage System

The excessive rate of patients arriving at accident and emergency centres is a major problem facing South African hospitals. Patients are prioritized for medical care through a triage process. Manual systems allow for inconsistency and error. This paper proposes a novel system to automate accident and emergency centre triage and uses this triage score along with an artificial intelligence estimate of patient-doctor time to optimize the queue order. A fuzzy inference system is employed to triage patients and a similar system estimates the time but adapts continuously through fuzzy Q-learning. The optimal queue order is found using a novel procedure based on genetic algorithms. These components are integrated in a simple graphical user interface. Live tests could not be performed but simulations reveal that the average waiting time can be reduced by 48 minutes and priority is given to urgent patients
Bit Error Rate Reduction by Smart UWB Antenna Array in Indoor Wireless Communication

In this paper, a new ultra wideband circular antenna array (UCAA) combining genetic algorithm to minimize the bit error rate (BER) is proposed. The ultra wideband (UWB) impulse responses of the indoor channel for any transmitter-receiver location are computed by applying shooting and bouncing ray/image (SBR/Image) techniques, inverse fast Fourier transform and Hermitian processing. By using the impulse response of multipath channel, the BER performance of the binary pulse amplitude modulation (B-PAM) impulse radio (IR) UWB system with circular antenna array can be calculated. Based on the topography of the antenna and the BER formula, the array pattern synthesis problem can be reformulated into an optimization problem and solved by the genetic algorithm. Our approach is not only choosing BER as the object function instead of sidelobe level of the antenna pattern, but also considering the antenna feed length effect of each array element. The strong point of the genetic algorithm is that it can find out the solution even if the performance index cannot be formulated by simple equations. Simulation results show that the synthesized antenna array pattern is effective to focus maximum gain to the LOS path which scales as the number of array elements. In other words, the receiver can increase the received signal energy to noise ratio. The synthesized array pattern also can mitigate severe multipath fading in complex propagation environment. As a result, the BER can be reduced substantially in indoor UWB communication system.
Emergence of carbapenem resistance in Acinetobacter baumannii in the Czech Republic is associated with the spread of multidrug-resistant strains of European clone II.

OBJECTIVES The aim of this study was to analyse the emergence of carbapenem resistance among hospital strains of Acinetobacter in the Czech Republic. METHODS Acinetobacter isolates were collected prospectively in 2005-06 from 19 diagnostic laboratories. They were identified to species level by AFLP, typed using AFLP, pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing, and tested for susceptibility to 14 antimicrobials and for the presence of 20 genes associated with antimicrobial resistance. RESULTS A total of 150 Acinetobacter isolates were obtained from 56 intensive care units of 20 hospitals in 15 cities. They were identified as Acinetobacter baumannii (n = 108) or other species. A. baumannii isolates were allocated to EU clone I (n = 5), EU clone II (n = 66) or other, mostly unique genotypes. Two-thirds of the clone II isolates had nearly identical AFLP and PFGE fingerprints. As many as 85% and 88% isolates were susceptible to meropenem and imipenem (<or=4 mg/L), respectively. Carbapenem MICs of >or=8 mg/L were found in 23 A. baumannii isolates, of which 20 belonged to clone II. Isolates with bla(OXA-58-like) (n = 3)(,) bla(OXA-24-like) (n = 1) or ISAba1 adjacent to bla(OXA-51-like) (n = 34) had carbapenem MICs of 2 to >16 mg/L, while those without these elements showed MICs of <or=0.5-4 mg/L. Clone II isolates varied in susceptibility to some antibiotics including carbapenems and carried 6-12 resistance genes in 17 combinations. CONCLUSIONS The emergence of Acinetobacter carbapenem resistance in the Czech Republic is associated with the spread of A. baumannii strains of EU clone II. The variation in susceptibility in these strains is likely to result from both the horizontal spread of resistance genes and differential expression of intrinsic genes.
Immunoreactivity and Guanosine 3′,5′-Cyclic Monophosphate Activating Actions of Various Molecular Forms of Human B-Type Natriuretic Peptide

Recent studies support the speculation that different molecular forms of the cardiac hormone BNP with differential biological activity may circulate in heart failure and be detected by conventional assays. In the current study we determined the ability of 3 widely used conventional assays to detect these different forms thought to circulate in heart failure. We also evaluated the ability of pro-BNP (1-108), N-terminal peptide (NT)–pro-BNP (1-76), and BNP 3-32, the latter a cleavage product of BNP 1-32 by dipeptidyl peptidase IV, on an equimolar basis to activate cGMP in cultured cardiac fibroblasts and cardiomyocytes compared with the biologically active mature BNP 1-32. Specifically, we observed that the Roche NT–pro-BNP assay detected both NT–pro-BNP 1-76 and pro-BNP 1-108 and that Biosite Triage and Shionogi detected both mature BNP 1-32 and the shortened BNP 3-32. Moreover, in cultured cardiac fibroblasts and cardiomyocytes, BNP 1-32 (10−6 mol/L) activated cGMP. BNP 3-32 demonstrated a similar cGMP activating property in both cardiac cell types. In contrast, the cGMP response to pro-BNP 1-108 and NT–pro-BNP 1-76 was not significantly greater than no treatment alone. We conclude that widely used commercial assays for NT–pro-BNP 1-76 and BNP 1-32 cannot differentiate among pro-, processed, or degraded forms and, thus, may not thoroughly identify circulating BNP forms in heart failure patients. These findings also demonstrate differential cGMP activating properties of BNP forms and, importantly, that pro-BNP 1-108 and NT–pro-BNP 1-76 have reduced cGMP activity in vitro that may have biological relevance to human heart failure.
Examination of the Tn5 transposase overproduction phenotype in Escherichia coli and localization of a suppressor of transposase overproduction killing that is an allele of rpoH

Tn5 transposase (Tnp) overproduction is lethal to Escherichia coli. Tnp overproduction causes cell filamentation, abnormal chromosome segregation, and an increase in anucleated cell formation. There are two simple explanations for the observed phenotype: induction of the SOS response or of the heat shock response. The data presented here show that overproduction of Tnp neither induces an SOS response nor a strong heat shock response. However, our experiments do indicate that induction of some sigma32-programmed function(s) (either due to an rpoH mutation, a deletion of dnaK, or overproduction of sigma32) suppresses Tnp overproduction killing. This effect is not due to overproduction of DnaK, DnaJ, or GroELS. In addition, Tnp but not deltall Tnp (whose overproduction does not kill the host cells) associates with the inner cell membrane, suggesting a possible correlation between cell killing and Tnp membrane association. These observations will be discussed in the context of a model proposing that Tnp overproduction titrates an essential host factor(s) involved in an early cell division step and/or chromosome segregation.
CALCULATING DYNAMIC DISTURBANCE REJECTION MEASURES

Abstract A number of indicators for the determination of the disturbance rejection capability of a system have been proposed in the literature in the last two decades. These tools are useful for evaluating early stage process designs and screening regulatory control structures, since they are based on minimal modelling requirements. In previous publications (Hovd and Braatz, 2000; Hovd et al, 2003; Kookos and Perkins, 2003), it has been shown how to evaluate at steady state the disturbance rejection measures proposed by Skogestad and Wolff (1992). If acceptable values for these disturbance rejection measures are not achieved, no controller can achieve satisfactory control. In this paper, it is shown how to obtain upper and lower bounds for these disturbance rejection measures also as a function of frequency. The upper and lower bounds can be made arbitrarily accurate at the expense of increasing the size of the optimization problems involved.
Exact Top-k Nearest Keyword Search in Large Networks

Top-k nearest keyword search has been of interest because of applications ranging from road network location search by keyword to search of information on an RDF repository. We consider the evaluation of a query with a given vertex and a keyword, and the problem is to find a set of $k$ nearest vertices that contain the keyword. The known algorithms for handling this problem only give approximate answers. In this paper, we propose algorithms for top-k nearest keyword search that provide exact solutions and which handle networks of very large sizes. We have also verified the performance of our solutions compared with the best-known approximation algorithms with experiments on real datasets.
Griffith–Kelly–Sherman Correlation Inequalities: A Useful Tool in the Theory of Error Correcting Codes

It is shown that a correlation inequality of statistical mechanics can be applied to linear low-density parity-check codes. Thanks to this tool we prove that, under a natural assumption, the exponential growth rate of regular low-density parity-check (LDPC) codes, can be computed exactly by iterative methods, at least on the interval where it is a concave function of the relative weight of code words. Then, considering communication over a binary input additive white Gaussian noise channel with a Poisson LDPC code we prove that, under a natural assumption, part of the GEXIT curve (associated to MAP decoding) can also be computed exactly by the belief propagation algorithm. The correlation inequality yields a sharp lower bound on the GEXIT curve. We also make an extension of the interpolation techniques that have recently led to rigorous results in spin glass theory and in the SAT problem
A Comprehensive Reinforcement Learning Framework for Dialogue Management Optimization

Reinforcement learning is now an acknowledged approach for optimizing the interaction strategy of spoken dialogue systems. If the first considered algorithms were quite basic (like SARSA), recent works concentrated on more sophisticated methods. More attention has been paid to off-policy learning, dealing with the exploration-exploitation dilemma, sample efficiency or handling non-stationarity. New algorithms have been proposed to address these issues and have been applied to dialogue management. However, each algorithm often solves a single issue at a time, while dialogue systems exhibit all the problems at once. In this paper, we propose to apply the Kalman Temporal Differences (KTD) framework to the problem of dialogue strategy optimization so as to address all these issues in a comprehensive manner with a single framework. Our claims are illustrated by experiments led on two real-world goal-oriented dialogue management frameworks, DIPPER and HIS.