Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential degradation of polycyclic aromatic hydrocarbon mixtures by indigenous microbial assemblages in soil

Environmental contamination by polycyclic aromatic hydrocarbons (PAHs) typically occurs as mixtures of compounds. In this study, the response of indigenous soil bacterial and fungal communities to mixtures containing phenanthrene, fluoranthene and benzo(a)pyrene in various combinations was examined using molecular fingerprinting techniques and quantification of a key PAH degradative gene. Results were compared to a parallel study by Sawulski et al. (2014) which examined the effect of these PAHs on soil microbial communities when added as single contaminants. The rate of degradation of individual PAHs varied depending on whether the PAH was present as a single contaminant or in a mixture; phenanthrene was degraded most rapidly when present as a sole contaminant, fluoranthene was removed faster in the presence of the lower molecular weight phenanthrene and the rate of benzo(a)pyrene degradation was reduced in the presence of the 4‐ring PAH, fluoranthene. Bacterial and fungal assemblages differed significantly between treatments regardless of which PAH was added to soil. Although less abundant than the Gram‐negative PAH‐RHDα gene, the gene associated with Gram‐positive bacteria responded to a greater extent to the presence of PAHs, either as single compounds or as mixtures and this increase was significantly correlated with PAH degradation.
Ventral premotor cortex neuronal activity matches perceptual decisions

The relationship between neuronal activity and psychophysical judgments is central to understanding the brain mechanisms responsible for perceptual decisions. The ventral premotor cortex is known to be involved in representing different components of the decision‐making process. In this cortical area, however, neither the neuronal ability to discriminate nor the trial‐to‐trial relationship between neuronal activity and behavior have been studied during visual decision‐making. We recorded from single neurons while monkeys reported a decision based on the comparison of the orientation of two lines shown sequentially and separated by a delay. Analyses based on signal detection theory provided both the behavioral and neuronal sensitivities (d′) and the coherence between behavioral and neuronal choices. To determine the temporal evolution of neuronal sensitivity and of coherence, the optimal size and position of the encoding windows were assessed. For a subset of neurons from the premotor ventral cortex, neuronal sensitivity was close to behavioral sensitivity and the trial‐to‐trial coherence between the neuronal and behavioral choices was close to 100%. By comparing these results with those obtained in a motor control task we ruled out the possibility of this activity being explained by the motor component of the task. These results suggest that activity in the ventral premotor cortex explains behavioral performance and predicts trial‐to‐trial subject choices.
Corticosteroids in idiopathic pulmonary fibrosis

Corticosteroids were the mainstay of therapy for idiopathic pulmonary fibrosis (IPF) for more than four decades, but their efficacy is unproven and toxicities are substantial. The course of IPF is characterized by progressive respiratory insufficiency, leading to death within 3 to 8 years from the onset of symptoms. Although a subset (10–20%) of patients survives more than 10 years, there is no evidence that any form of therapy alters the natural history of the disease. Nonetheless, given the poor prognosis, a trial of corticosteroids is often given. Because of the rarity of IPF, randomized, placebo-controlled therapeutic trials have not been done. Further, no studies have compared differing dosages or duration of corticosteroid in matched patients. Interpretation of therapy efficacy is obscured by several factors including heterogeneous patient populations, inclusion of patients with histologic entities other than usual interstitial pneumonia, lack of objective, validated endpoints, different criteria for “response. ” We review published data regarding corticosteroid therapy for IPF and present a rationale for stratifying therapy based on host, demographic, and clinical factors that influence prognosis as well as risk for corticosteroid complications.
Development of ethnic disparities in internalizing and externalizing problems from adolescence into young adulthood.

BACKGROUND Little is known about changes in ethnic disparities in mental health during the development of adolescents into young adults. The aim of this study was to study the development of disparities in internalizing and externalizing problems between Dutch natives and Turkish migrant children from adolescence into adulthood. METHODS Turkish migrants (n = 217) and Dutch natives (n = 723) completed two comparable questionnaires about internalizing and externalizing problems: the Youth Self-Report at age 11-18 and the (Young) Adult Self-Report ten years later, at age 21-28. We used mixed linear regression models to model development of mental health problems and to test changes in disparities in mental health between Turkish migrants and Dutch natives. RESULTS Both in adolescence and in adulthood migrants reported more internalizing and externalizing problems than natives, most pronounced for internalizing problems. Disparities decreased from adolescence into adulthood for both internalizing problems (-52%, p < .0001) and externalizing problems (-67%, p = .01), independently of gender, age, country of birth of Turkish adolescents, and parental socio-economic position. The favorable changes in the disparities over time were due to more favorable development among Turkish migrants than among natives. CONCLUSIONS In this prospective study, ethnic disparities in internalizing and externalizing problems decreased as adolescents entered adulthood. Different explanations are discussed.
An Improved Concept Vector Space Model for Ontology Based Classification

This paper proposes an improved concept vector space (ICVS) model which takes into account the importance of ontology concepts. Concept importance shows how important a concept is in an ontology. This is reflected by the number of relations a concept has to other concepts. Concept importance is computed automatically by converting the ontology into a graph initially and then employing one of the Markov based algorithms. Concept importance is then aggregated with concept relevance which is computed using the frequency of concept occurrences in the dataset. In order to demonstrate the applicability of our proposed model and to validate its efficacy, we conducted experiments on document classification using concept based vector space model. The dataset used in this paper consists of 348 documents from the funding domain. The results show that the proposed model yields higher classification accuracy comparing to traditional concept vector space (CVS) model, ultimately giving better document classification performance. We also used different classifiers in order to check for the classification accuracy. We tested CVS and ICVS on Naive Bayes and Decision Tree classifiers and the results show that the classification performance in terms of F1 measure is improved when ICVS is used on both classifiers.
Crystal Structures of a New Class of Allosteric Effectors Complexed to Tryptophan Synthase*

Tryptophan synthase is a bifunctional α2β2 complex catalyzing the last two steps of l-tryptophan biosynthesis. The natural substrates of the α-subunit indole- 3-glycerolphosphate and glyceraldehyde-3-phosphate, and the substrate analogs indole-3-propanolphosphate anddl-α-glycerol-3-phosphate are allosteric effectors of the β-subunit activity. It has been shown recently, that the indole-3-acetyl amino acids indole-3-acetylglycine and indole-3-acetyl-l-aspartic acid are both α-subunit inhibitors and β-subunit allosteric effectors, whereas indole-3-acetyl-l-valine is only an α-subunit inhibitor (Marabotti, A., Cozzini, P., and Mozzarelli, A. (2000) Biochim. Biophys. Acta 1476, 287–299). The crystal structures of tryptophan synthase complexed with indole-3-acetylglycine and indole-3-acetyl-l-aspartic acid show that both ligands bind to the active site such that the carboxylate moiety is positioned similarly as the phosphate group of the natural substrates. As a consequence, the residues of the α-active site that interact with the ligands are the same as observed in the indole 3-glycerolphosphate-enzyme complex. Ligand binding leads to closure of loop αL6 of the α-subunit, a key structural element of intersubunit communication. This is in keeping with the allosteric role played by these compounds. The structure of the enzyme complex with indole-3-acetyl-l-valine is quite different. Due to the hydrophobic lateral chain, this molecule adopts a new orientation in the α-active site. In this case, closure of loop αL6 is no longer observed, in agreement with its functioning only as an inhibitor of the α-subunit reaction.
Dissection of the Transactivation Function of the Transcription Factor Encoded by the Eye Developmental Gene PAX6 *

PAX6 is a transcription activator that regulates eye development in animals ranging from Drosophila to human. The C-terminal region of PAX6 isproline/serine/threonine-rich (PST) and functions as a potent transactivation domain when attached to a heterologous DNA-binding domain of the yeast transcription factor, GAL4. The PST region comprises 152 amino acids encoded by four exons. The transactivation function of the PST region has not been defined and characterized in detail by in vitro mutagenesis. We dissected the PST domain in two independent systems, a heterologous system using a GAL4 DNA-binding site and the native system of PAX6. Our data consistently showed that in both systems all four constituent exons of the PST domain are responsible for the transactivation function. The four exon fragments act synergistically to stimulate transcription, although none of them can function individually as an independent transactivation domain. Combinations of two or more exon fragments can reconstitute substantial transactivation activity when fused to the DNA-binding domain of GAL4, but they surprisingly do not produce much activity in the context of native PAX6, although the mutant PAX6 proteins are stable and their DNA-binding function remains unaffected. Our data suggest that these mutants may antagonize the wild-type PAX6 activity by competing for target DNA-binding sites. We conclude that the PAX6 protein contains an unusually large transactivation domain that is evolutionarily conserved to a high degree and that its full transactivation activity relies on the synergistic action of the four exon fragments.
Trimming Mechanism of External Quality Factor in HTS Bandpass Filter Using Bulk Resonators

We investigated the usability of a trimming mechanism for varying an external quality factor (<inline-formula> <tex-math notation="LaTeX">$Q_{{\rm{e}}}$</tex-math></inline-formula>) in a high-temperature superconducting bandpass filter (BPF) using bulk resonators at around 5 GHz. The proposed trimming mechanism was composed of air space between an input port and the first resonator in a Cu cavity, a center conductor of the coaxial through the space, and a dielectric or metallic trimming rod. We decided the geometrical dimensions of the trimming mechanism and estimated the <inline-formula><tex-math notation="LaTeX">$Q_{{\rm{e}}}$</tex-math></inline-formula> by varying the height of rod (<inline-formula><tex-math notation="LaTeX">$h_{{\rm{Q}}}$</tex-math></inline-formula>) using an electromagnetic simulator. These simulated results indicate that the proposed mechanism could function for theoretical <inline-formula> <tex-math notation="LaTeX">$Q_{{\rm{e}}}$</tex-math></inline-formula> values up to those of 8-pole BPF. We then fabricated the trimming mechanism for <inline-formula><tex-math notation="LaTeX">$Q_{{\rm{e}}}$</tex-math> </inline-formula> and measured the <inline-formula><tex-math notation="LaTeX">$Q_{{\rm{e}}}$</tex-math></inline-formula> by using a vector network analyzer. The measured data almost matched the simulated data. Next, we fabricated a 5-pole BPF with the trimming mechanisms for <inline-formula><tex-math notation="LaTeX">$Q_{{\rm{e}}}$</tex-math> </inline-formula> and obtained good filtering responses.
Ecoulements granulaires sur fond meuble

Bien qu'assez repandus dans le milieu naturel et dans diverses activites industrielles, les ecoulements granulaires denses possedent des caracteristiques particulieres qui semblent dependre fortement des geometries observees. Lorsque le fond qui supporte la coulee peut etre erode, les mecanismes determinant la position de l'interface liquide-solide ou la vitesse a laquelle la pente est devalee ne sont pas encore bien compris. Ceci provient du manque de connaissance de la rheologie des ecoulements granulaires et constitue le coeur de cette these. Ce travail s'articule principalement en trois parties. Premierement, dans le but de fournir une description detaillee des ecoulements sur tas, une etude experimentale systematique des ecoulements stationnaires a ete menee dans un canal. Nous avons ainsi pu mettre en evidence l'importance des parois laterales du systeme dans le cadre des ecoulements a la surface d'un tas : les proprietes de l'ecoulement sont completement controle par la largeur du canal. Ce constat nous a ensuite conduit a la proposition d'une modelisation fondee sur une rheologie recemment developpee. Cette rheologie a ete ensuite etendue a trois dimensions et appliquee a notre configuration. Des simulations numeriques permettent de reproduire correctement les proprietes des ecoulements stationnaires. Nous avons enfin etudie un phenomene transitoire particulier afin de comprendre la maniere dont l'epaisseur coulante evolue. Malgre la presence de certaines limitations, ce travail montre qu'une description locale des ecoulements granulaire est appropriee et que la rheologie proposee ouvre la voie a des modelisations plus completes des ecoulements granulaires denses.
Meal-specific food patterns and the incidence of hyperglycemia in a Chinese adult population

Abstract This study aimed to examine the association between meal-specific food patterns and incident hyperglycaemia in a Chinese adult population. Adults aged 20 years and older (n 1056) were followed from 2002 to 2007. Dietary data were collected using a 3-d food record and meal-specific (breakfast, lunch and dinner) food patterns were independently described by factor analysis based on the consumption of thirty-five food groups at each eating occasion. Each food pattern score was recoded as quartiles. Hyperglycaemia was defined as fasting plasma glucose >5·6 mmol/l at baseline and follow-up. The associated between food patterns and incident hyperglycaemia was assessed by logistic regression. During the follow-up, 125 new cases of hyperglycaemia were identified. Traditional (wheat) breakfast was inversely associated with incident hyperglycaemia, whereas traditional (rice, vegetable and pork) lunch and dinner were positively associated with the risk of incident hyperglycaemia, even after adjustment for a number of covariates including glycaemic load, carbohydrate intake and BMI. Incident hyperglycaemia occurred in 15·9, 13·6, 11·7, 6·1 % across quartiles of traditional breakfast; and 5·3, 9·1, 15·9, 17·1 % of the quartiles of traditional lunch pattern. The adjusted OR for hyperglycaemia was 0·67 (95 % CI 0·48, 0·92), 1·83 (95 % CI 1·32, 2·53) and 1·39 (95 % CI 1·04, 1·86) for 1 sd increase of traditional breakfast, lunch and dinner pattern factor score, respectively. A traditional wheat-based breakfast is associated with a decreased risk of hyperglycaemia. A rice-based traditional lunch and dinner is associated with an increased risk of hyperglycaemia in Chinese adults.
The Study of the Antisaccade Performance and Contingent Negative Variation Characteristics in First-Episode and Chronic Schizophrenia Patients

Abstract The study tested whether the antisaccade (AS) performance and Contingent Negative Variation (CNV) measures differed between the first-episode and chronic patients to provide the evidence of PFC progressive functional deterioration. Subjects included 15 first-episode and 20 chronic schizophrenic patients (with the duration of illness more than 5 years), and 21 control subjects. The first-episode and chronic patients had significantly elevated error percent (p < .05, effect size 1.10 and p < .001, effect size 1.25), increased AS latencies (p < .01, effect size 1.18 and p < .001, effect size 1.69), and increased latencies variability (p < .01, effect size 1.52 and p < .001, effect size 1.37) compared to controls. Chronic patients had marginally significant increase of the response latency (p = .086, effect size .78) and latency variability (p < .099, effect size .63) compared to first-episode ones. Results of CNV analysis revealed that chronic patients only exhibited robustly declined frontal CNV amplitude at Fz (p < .05, effect size .70), F3 (p < .05, effect size .88), and F4 (p < .05, effect size .71) sites compared to controls. The obtained results might be related to specific changes in prefrontal cortex function over the course of schizophrenia.
Further studies on biochemical characteristics and serologic properties of the genus Aeromonas

We characterized a collection of 268 Aeromonas isolates from diverse sources (clinical, animal, and environmental sources) for their species and serogroup designations. Overall, 97% of these strains could be identified to the genomospecies level by using an expanded battery of biochemical tests. Members of the Aeromonas hydrophila complex (A. hydrophila, HG2, and A. salmonicida), a group that has previously been difficult to separate biochemically, could easily be distinguished from one another by using a number of recently described phenotypic properties which included utilization of DL-lactate and urocanic acid. Differences in species distributions on the basis of the source of isolation were noted. Serogroup analysis of these 268 isolates plus a number of reference cultures indicated that (i) each genomospecies is serologically heterogeneous and individual serogroups can be found in more than one species, (ii) most type or reference strains for each hybridization group are not serologically representative of the genomospecies at large, (iii) serogroups O:11, O:34, and O:16 predominate clinically (48%), supporting previous studies indicating their importance in human infections, and (iv) most A. trota strains do not express the O139 antigen of Vibrio cholerae. The collective results suggest that both species and serogroup designations are important factors in establishing which isolates can cause human infections when they are acquired from nonclinical sources (foods, animals, and the environment).
Combined CT venography of the lower limbs and spiral CT angiography of pulmonary arteries in acute pulmonary embolism: preliminary results of a prospective study.

PURPOSE To determine the clinical accuracy of combined CT venography (CTV) and spiral CT angiography (SCTA) in patients suspicious of acute pulmonary thrombo-embolism. MATERIALS AND METHODS 278 consecutive patients referred for SCTA for suspicion of acute pulmonary embolism (APE) underwent subsequent evaluation of the veins of the lower limbs and abdomen (CTV) within one examination without additional injection of contrast medium. Sixty-nine patients had no further study. Two hundred and nine patients were included in the study, 199 had US and 51 phlebography (PG) within 48 hours from SCTA-CTV. The investigators were blinded to the results of CT. When results of CTV and US were discordant, phlebography was indicated. RESULTS SCTA was positive in 89 patients, negative in 119 and indeterminate in 1. CTV was positive in 99 patients, negative in 103 and indeterminate in 7. US was positive in 87 patients, negative in 97 and indeterminate in 15. PG was positive in 21 patients, negative in 29 and indeterminate in 1. Excellent correlation was found between CTV and US (k = 0.84) and moderate correlation between CTV and PG, and US and PG (k = 0.53). CONCLUSIONS Combined SCTA and CTV is a rapid and accurate one-session examination in patients suspicious of acute pulmonary thrombo-embolism.
Performance evaluation of channel access protocols in overlapping ECMA-368 Wireless Personal Area Networks

Medium Access Control (MAC) protocols for Wireless Local Area Networks (WLANs) as well as Wireless Personal Area Networks (WPANs) like Carrier Sense Multiple Access with Collision Avoidance (CSMA/CA) are known to provide stable distributed channel access for multiple users. The wide acceptance of wireless systems operating in licensed-exempt frequencies demands for efficient spectrum usage of the scarce radio resources. In partially overlapping network scenarios where channel reuse becomes possible, the non-deterministic behavior prevents random access protocols from exploiting substantial reuse gain. This paper studies the performance of the Distributed Reservation Protocol (DRP) and the Prioritized Contention Access (PCA), a CSMA/CA Protocol, as specified in the Ultra Wideband (UWB) standard ECMA-368. The focus is in particular on channel reuse efficiency and the given result motivates to use DRP to substantial improve spectrum efficiency in scenarios, where a minimal reuse distance is desired. It is shown, that a gain of more than 50% is attained due to the deterministic channel access of DRP in comparison to PCA in partially overlapping network scenarios.
Noninvasive quantification of dopamine D2 receptors with iodine-123-IBF SPECT.

UNLABELLED Iodine-123-iodobenzofuran (IBF) is a potent dopamine D2 receptor ligand suited for quantitative receptor studies. The purpose of this study was to evaluate three noninvasive methods of estimating the receptor parameter k3/k4 in humans with IBF-SPECT. METHODS Scans were acquired every 5 min for 180 min using a triple-headed SPECT system following a bolus injection of IBF (296 +/- 37 MBq) in 14 normal volunteers. k3/k4 was estimated by the peak equilibrium ratio (RPE) method and two proposed methods: a variation of the graphic method that derives the ratio of ligand distribution volumes (RV) and area ratio (RA) method, in which the ratio is calculated from the areas under the specific binding and nondisplaceable activity curves. RESULTS The mean RPE, RV and RA were 2.74 +/- 0.40, 3.06 +/- 0.42 and 2.26 +/- 0.28, respectively. Both RPE and RA underestimated RV. The relationship between RPE or RA and RV was linear (p < or = 10(-5), RA showed higher correlation (r = 0.94) with RV than did RPE (r = 0.90). Simulations based on a tracer kinetic model showed that RV, unlike RPE or RA, is affected by neither regional cerebral blood flow (rCBF) nor peripheral clearance rate (CR) of IBF. All three measures showed a significant decline with increasing age (r = 0.54-0.58, p < 0.05). CONCLUSION RV is preferred because it provides a theoretically valid estimate of k3/k4, independently of rCBF or CR. Alternatively, RA might be preferred to RPE because the former is simpler than the latter to implement yet the former provides a measure that equally well correlates with k3/k4.