Miracle-dz/UniFAR-FTUs huggingface dataset:
The Catabolism of Phenanthrene and Naphthalene by Bacteria

SUMMARY: Thirteen strains of bacteria able to grow on phenanthrene were isolated from soil; they included fluorescent and non-fluorescent pseudomonads, vibrios and unidentified bacteria. Two of the pseudomonads, like Aeromonas sp. s45p1, also grew on naphthalene. In all strains, growth on phenanthrene induced the enzyme responsible for the conversion of 1-hydroxy-2-naphthoate to 2-carboxybenzaldehyde, NAD-dependent 2-carboxybenzalde-hyde dehydrogenase and protocatechuate oxygenase, but not salicylate hydroxylase, catechol oxygenase or NAD(P)H-dependent 1-hydroxy-2-naphthoate hydroxylase. Growth on naphthalene induced salicylate hydroxylase and catechol oxygenase. It is suggested that the catabolism of phenanthrene occurs via protocatechuate in all these bacteria, and that the pathways for degradation of phenanthrene and naphthalene are separate.
A randomized comparison of group cognitive-behavioral therapy and group interpersonal psychotherapy for the treatment of overweight individuals with binge-eating disorder.

BACKGROUND Cognitive-behavioral therapy (CBT) has documented efficacy for the treatment of binge eating disorder (BED). Interpersonal psychotherapy (IPT) has been shown to reduce binge eating but its long-term impact and time course on other BED-related symptoms remain largely unknown. This study compares the effects of group CBT and group IPT across BED-related symptoms among overweight individuals with BED. METHODS One hundred sixty-two overweight patients meeting DSM-IV criteria for BED were randomly assigned to 20 weekly sessions of either group CBT or group IPT. Assessments of binge eating and associated eating disorder psychopathology, general psychological functioning, and weight occurred before treatment, at posttreatment, and at 4-month intervals up to 12 months following treatment. RESULTS Binge-eating recovery rates were equivalent for CBT and IPT at posttreatment (64 [79%] of 81 vs 59 [73%] of 81) and at 1-year follow-up (48 [59%] of 81 vs 50 [62%] of 81). Binge eating increased slightly through follow-up but remained significantly below pretreatment levels. Across treatments, patients had similar significant reductions in associated eating disorders and psychiatric symptoms and maintenance of gains through follow-up. Dietary restraint decreased more quickly in CBT but IPT had equivalent levels by later follow-ups. Patients' relative weight decreased significantly but only slightly, with the greatest reduction among patients sustaining recovery from binge eating from posttreatment to 1-year follow-up. CONCLUSIONS Group IPT is a viable alternative to group CBT for the treatment of overweight patients with BED. Although lacking a nonspecific control condition limits conclusions about treatment specificity, both treatments showed initial and long-term efficacy for the core and related symptoms of BED.
Scale dependence of the primordial spectrum from combining the three-year WMAP, galaxy clustering, supernovae, and Lyman-alpha forests

We probe the scale dependence of the primordial spectrum in the light of the three-year WMAP (WMAP3) alone and WMAP3 in combination with the other cosmological observations such as galaxy clustering and type Ia supernova (SNIa). We pay particular attention to the combination with the Lyman-α (Lyα) forest. In contrast to the first-year WMAP (WMAP1), WMAP3’s preference for the running of the scalar spectral index on large scales is now fairly independent of the low CMB multipoles . A combination with the galaxy power spectrum from the Sloan Digital Sky Survey (SDSS) prefers a negative running to larger than 2σ, regardless of the presence of the low- CMB () or not. On the other hand, if we focus on the power law ΛCDM cosmology with only six parameters (matter density Ωmh2, baryon density Ωbh2, Hubble constant H0, optical depth τ, the spectral index, ns, and the amplitude, As, of the scalar perturbation spectrum) when we drop the low- CMB contributions WMAP3 is consistent with the Harrison–Zel’dovich–Peebles scale-invariant spectrum (ns = 1 and no tensor contributions) at ∼1σ. When assuming a simple power-law primordial spectral index or a constant running, in the case when one drops the low- contributions () WMAP3 is more consistent with the other observations, such as the inferred value of σ8.
How Does the Architect&#146;s Role Change as the Software Ages?

It is widely recognized that a good and appropriate architecture is critical to the success of a software product or system [5]. However, neither the system nor its architecture is static, and a good architecture anticipates and guides the evolution of the system over time. As the system evolves over time, the role of the software architect evolves as well, and skills that enabled an architect to be successful during one phase of a system’s lifetime may not enable success in later phases. This paper proposes a three-phase model to describe the evolution of software systems, and describes the contributions of the software architect which are necessary for success in each phase. This topic is of interest to practicing architects, and to software development managers responsible for selecting and hiring architects to contribute to a software system.
Design Space Exploration of the Violacein Pathway in Escherichia coli Based Cell-Free System

In this study, an Escherichia coli (E. coli) based transcription translation cell-free system (TX-TL) was employed to sample various enzyme expression levels of the violacein pathway. The pathway was successfully reconstructed in TX-TL. Its variation produced different metabolites as evident from the extracts’ assorted colors. Analysis of the violacein product via UV-Vis absorption and liquid chromatography-mass spectrometry (LC-MS) detected 68 ng of violacein per μl reaction volume. Significant buildup of prodeoxyviolacein intermediate was also detected in the equimolar TX-TL reaction. Finally, design space exploration experiments suggested an improvement in violacein production at high VioC and VioD DNA concentrations.
Steady state analysis of P-MIP mobility management

Paging extensions for Mobile IP (P-MIP) was proposed to avoid unnecessary registration signaling overhead of Mobile IP (MIP) and there is a tradeoff between registration and paging signaling based on the probability that a mobile node (MN) is in active or idle state. This probability varies from MN to MN and changes even for a given MN as time goes by. It is, however, assumed to be a fixed value in P-MIP for simplicity. In this letter, the steady-state probability of active and idle states is derived using a semi-Markov chain approach and the performance of P-MIP is compared with MIP based on session-to-mobility ratio.
Correlation decay and deterministic FPTAS for counting list-colorings of a graph

We propose a deterministic algorithm for approximately counting the number of list colorings of a graph. Under the assumption that the graph is triangle free, the size of every list is at least αΔ, where α is an arbitrary constant bigger than α = 2.8432 . , the solution of αe-1/α = 2, and α is the maximum degree of the graph, we obtain the following results. For the case when the size of the each list is a large constant, we show the existence of a deterministic FPTAS for computing the total number of list colorings. The same deterministic algorithm has complexity 2O(log2 n) without any assumptions on the sizes of the lists, where n is the size of the instance. Our results are not based on the most powerful existing counting technique - rapidly mixing Markov chain method. Rather we build upon concepts from statistical physics, in particular, the decay of correlation phenomena and its implication for the uniqueness of Gibbs measures in infinite graphs. This approach was proposed in two recent papers [BG06] and [Wei05]. The principle insight of the present work is that the correlation decay property can be established with respect to certain computation tree, as opposed to the conventional correlation decay property which is typically established with respect to graph theoretic neighborhoods of a given node. This allows truncation of computation at a logarithmic depth in order to obtain polynomial accuracy in polynomial time. While the analysis conducted in this paper is limited to the problem of counting list colorings, the proposed algorithm can be extended to an arbitrary constraint satisfaction problem in a straightforward way.
DWT Based Blind Digital Video Watermarking Scheme for Video Authentication

Digital video is one of the popular multimedia data exchanged in the internet. Due to their perfectly replicable nature many illegal copies of the original video can be made. Methods are needed to protect copyrights of the owner and prevent illegal copying. A video can also undergo several intentional attacks like frame dropping, averaging, cropping and median filtering and unintentional attacks like addition of noise and compression which can compromise the owner information thereby denying authentication. In this paper, a robust Discrete Wavelet Transform (DWT)-based blind digital video watermarking scheme with scrambled watermarks based on scene changes has been proposed for authentication of digital video, which embeds different parts of a single watermark into different scenes of a video. The video watermarking algorithm is robust against the attacks of frame dropping, averaging and compression, which are considered as some of the common types of attacks applied particularly on the video and due to the use of DWT it can also withstand geometrical attacks making the watermark perceptually invisible. Furthermore, it allows blind retrieval of embedded watermark which does not need the original video. The proposed algorithm has been compared with an existing DWT based watermarking scheme and is found to exhibit better robustness.
Thiadiazines, N,N-Heterocycles of Biological Relevance

The 3,5-disubstituted tetrahydro-2H-1,3,5-thiadiazine-2-thione scaffold has found many applications in recent years. This review is aimed at highlighting the most important aspects of these compounds: Synthesis, spectroscopic characterization and biological activities. How the chemical nature of N-substituents influences the overall activity and cytotoxicity profile will also be discussed.
Lipopolysaccharide Adsorbed to the Bio-Corona of TiO2 Nanoparticles Powerfully Activates Selected Pro-inflammatory Transduction Pathways

It is known that the adsorption of bioactive molecules provides engineered nanoparticles (NPs) with novel biological activities. However, the biological effects of the adsorbed molecules may also be modified by the interaction with NP. Bacterial lipopolysaccharide (LPS), a powerful pro-inflammatory compound, is a common environmental contaminant and is present in several body compartments such as the gut. We recently observed that the co-incubation of LPS with TiO2 NPs markedly potentiates its pro-inflammatory effects on murine macrophages, suggesting that, when included in a NP bio-corona, LPS activity is enhanced. To distinguish the effects of adsorbed LPS from those of the free endotoxin, a pellet fraction, denominated P25/LPS, was isolated by centrifugation from a mixture of P25 TiO2 NP (128 µg/ml) and LPS (10 ng/ml) in the presence of fetal bovine serum. Western blot analysis of the pellet eluate indicated that the P25/LPS fraction contained, besides proteins, also LPS, pointing to the presence of LPS-doped NP. The effects of adsorbed or free LPS were then compared in Raw264.7 murine macrophages. RT-PCR was used to evaluate the induction of cytokine genes, whereas active, phosphorylated isoforms of proteins involved in signaling pathways were assessed with western blot. At a nominal LPS concentration of 40 pg/ml, P25/LPS induced the expression of both NF-κB and IRF3-dependent cytokines at levels comparable with those observed with free LPS (10 ng/ml), although with different time courses. Moreover, compared to free LPS, P25/LPS caused a more sustained phosphorylation of p38 MAPK and a more prolonged induction of STAT1-dependent genes. Cytochalasin B partially inhibited the induction of Tnfa by P25/LPS, but not by free LPS, and suppressed the induction of IRF3-dependent genes by either P25/LPS or free LPS. These data suggest that, when included in the bio-corona of TiO2 NP, LPS exhibits enhanced and time-shifted pro-inflammatory effects. Thus, in assessing the hazard of NP in real life, the enhanced effects of adsorbed bioactive molecules should be taken into account.
Pheochromocytoma in Italy: a multicentric retrospective study.

OBJECTIVE To conduct an epidemiological study on pheochromocytoma in Italy. METHODS Data on 284 patients with pheochromocytoma observed between 1978 and 1997 were collected from 18 Italian centers through a questionnaire reporting epidemiological, clinical, laboratory, radiological and surgical data. RESULTS 53.6% of the patients were females and 46.4% were males. Thirty-two tumors were discovered as incidental adrenal masses. The most frequent referred symptoms were palpitations (58.1%), headache (51.9%), sweating (48. 8%) and anxiety (35.3%). Their association was present only in 15.5% of patients. Paroxysmal symptoms were reported in 67.1% and hypertensive crises in 59.7% of patients. Normal blood pressure (systolic and diastolic) was present both in the supine and upright positions in 21.1% of patients. Among laboratory assays, urinary vanylmandelic acid (VMA) was the most widely used (58.1%) and was the least sensitive (25% of false negative results). Basal plasma catecholamines were found to be normal in 11.3% of patients but were always elevated when sampled during a hypertensive paroxysm. A clonidine suppression test was performed in 38 patients with no adverse side effects. It gave a false negative response in 2 patients. A glucagon test was performed in 21 patients. It was interrupted for acute hypertension in 52.4% of patients. Only 5/21 patients were normotensive and had normal basal plasma catecholamines. In these patients the test gave a positive response in four (80%). CT (79.6%) and I-MIBG scintigraphy (68.5%) were the most widely used methods for tumor localization. CT sensitivity was 98.9% for intra-adrenal and 90.9% for extra-adrenal tumors. MIBG sensitivity was 88.5%. In the 263 patients who underwent surgery, the tumor was intra-adrenal in 89.4%, extra-adrenal in 8.5%, intra- and extra-adrenal in 2.1%, and bilateral in 11.0% of patients. Malignancy was reported in 9.9% of cases. Surgery caused remission of hypertension in 59.3%, improvement in 26.8%, and no changes in 13. 9% of patients. In the last group the interval between initial symptoms and diagnosis was significantly longer. CONCLUSIONS The present study confirms that the clinical presentation of pheochromocytoma is variable and aspecific. Normotension is often present and often the tumor is discovered incidentally. An indication for the routine use of screening methods more sensitive than urinary VMA is strongly suggested. The clonidine test was found to be safe and should be preferred to the glucagon test which has to be restricted to very selected patients. CT and MIBG scintigraphy are almost always successful in localizing the tumor. Reversal of hypertension by surgery seems to depend on an early diagnosis.
Consumption of cereal fiber, mixtures of whole grains and bran, and whole grains and risk reduction in type 2 diabetes, obesity, and cardiovascular disease.

BACKGROUND Studies of whole grain and chronic disease have often included bran-enriched foods and other ingredients that do not meet the current definition of whole grains. Therefore, we assessed the literature to test whether whole grains alone had benefits on these diseases. OBJECTIVE The objective was to assess the contribution of bran or cereal fiber on the impact of whole grains on the risk of type 2 diabetes (T2D), obesity and body weight measures, and cardiovascular disease (CVD) in human studies as the basis for establishing an American Society for Nutrition (ASN) position on this subject. DESIGN We performed a comprehensive PubMed search of human studies published from 1965 to December 2010. RESULTS Most whole-grain studies included mixtures of whole grains and foods with ≥25% bran. Prospective studies consistently showed a reduced risk of T2D with high intakes of cereal fiber or mixtures of whole grains and bran. For body weight, a limited number of prospective studies on cereal fiber and whole grains reported small but significant reductions in weight gain. For CVD, studies found reduced risk with high intakes of cereal fiber or mixtures of whole grains and bran. CONCLUSIONS The ASN position, based on the current state of the science, is that consumption of foods rich in cereal fiber or mixtures of whole grains and bran is modestly associated with a reduced risk of obesity, T2D, and CVD. The data for whole grains alone are limited primarily because of varying definitions among epidemiologic studies of what, and how much, was included in that food category.
Neuroprotection by Exendin-4 Is GLP-1 Receptor Specific but DA D3 Receptor Dependent, Causing Altered BrdU Incorporation in Subventricular Zone and Substantia Nigra

Glucagon-like peptide-1 receptor (GLP-1R) activation by exendin-4 (EX-4) is effective in preclinical models of Parkinson's disease (PD) and appears to promote neurogenesis even in severely lesioned rats. In the present study, we determined the effects of EX-4 on cellular BrdU incorporation in the rat subventricular zone (SVZ) and substantia nigra (SN). We also determined the specificity of this effect with the GLP-1R antagonist EX-(9-39) as well as the potential role of dopamine (DA) D3 receptors. Rats were administered 6-OHDA and 1 week later given EX-4 alone, with EX-(9-39) or nafadotride (D3 antagonist) and BrdU. Seven days later, rats were challenged with apomorphine to evaluate circling. Extracellular DA was measured using striatal microdialysis and subsequently tissue DA measured. Tyrosine hydroxylase and BrdU were verified using immunohistochemistry. Apomorphine circling was reversed by EX-4 in lesioned rats, an effect reduced by EX-4, while both EX-(9-39) and NAF attenuated this. 6-OHDA decreased extracellular and tissue DA, both reversed by EX-4 but again attenuated by EX-(9-39) or NAF. Analysis of BrdU+ cells in the SVZ revealed increases in 6-OHDA-treated rats which were reversed by EX-4 and antagonised by either EX-(9-39) or NAF, while in the SN the opposite profile was seen.
Exploiting the synthetic lethality between terminal respiratory oxidases to kill Mycobacterium tuberculosis and clear host infection

Significance New drugs are needed to combat multidrug-resistant tuberculosis. The electron transport chain (ETC) maintains the electrochemical potential across the cytoplasmic membrane and allows production of ATP, the energy currency of any living cell. The ETC of the tubercle bacilli contains two terminal oxidases, the cytochrome bc1:aa3 and the cytochrome bd oxidase. In this study, we used genetics and chemical biology approaches to demonstrate that simultaneous inhibition of both terminal oxidases stops respiration, kills nonreplicating drug-tolerant Mycobacterium tuberculosis, and eradicates infection in vivo at an extraordinarily fast rate. Exploiting this potent synthetic lethal interaction with new drugs promises to shorten tuberculosis chemotherapy. The recent discovery of small molecules targeting the cytochrome bc1:aa3 in Mycobacterium tuberculosis triggered interest in the terminal respiratory oxidases for antituberculosis drug development. The mycobacterial cytochrome bc1:aa3 consists of a menaquinone:cytochrome c reductase (bc1) and a cytochrome aa3-type oxidase. The clinical-stage drug candidate Q203 interferes with the function of the subunit b of the menaquinone:cytochrome c reductase. Despite the affinity of Q203 for the bc1:aa3 complex, the drug is only bacteriostatic and does not kill drug-tolerant persisters. This raises the possibility that the alternate terminal bd-type oxidase (cytochrome bd oxidase) is capable of maintaining a membrane potential and menaquinol oxidation in the presence of Q203. Here, we show that the electron flow through the cytochrome bd oxidase is sufficient to maintain respiration and ATP synthesis at a level high enough to protect M. tuberculosis from Q203-induced bacterial death. Upon genetic deletion of the cytochrome bd oxidase-encoding genes cydAB, Q203 inhibited mycobacterial respiration completely, became bactericidal, killed drug-tolerant mycobacterial persisters, and rapidly cleared M. tuberculosis infection in vivo. These results indicate a synthetic lethal interaction between the two terminal respiratory oxidases that can be exploited for anti-TB drug development. Our findings should be considered in the clinical development of drugs targeting the cytochrome bc1:aa3, as well as for the development of a drug combination targeting oxidative phosphorylation in M. tuberculosis.
Nonlinear Phase Shift Compensator for Pilot-Induced Oscillations Prevention

The pilot-induced oscillation (PIO) is denoted as unintended steady fluctuation of the piloted aircraft, generated due to the efforts of the pilot to control the aircraft. The main non-linear factor leading to the PIO is, generally, rate limitations of the aircraft control surfaces, resulting in a delay in the response of the aircraft to pilot commands. Due to the tight relationship between magnitude and phase frequency responses for linear systems, applicability of the linear compensator for mentioned aim is highly restricted. This leads to the idea of employing the nonlinear phase shift compensator. In the control theoretic literature, various nonlinear corrective devices (NCD) are elaborated, which make it possible to change the phase-frequency and amplitude-frequency responses independently on each other. In the paper, a novel phase shift compensator based on nonlinear correction technique is presented and numerical comparative study for two models of a pilot for PIO prevention during the flight is given. The results obtained demonstrate that the proposed method in several times increases the admissible gain of the "airplane-pilot" loop as compared with non-corrected system.
NLOS Identification for UWB Body Communications

the last few years, a great attention has been paid to wireless communications for body area networks especially since the IEEE 802.15. 6 standard. The main objective of this work is to present a good technique for identifying between both Line-Of-Sight (LOS) and Non-Line-Of-Sight (NLOS) propagation schemes for UWB both of both on-body and off- body communication. Our work is focalize in the first to extract the information using traditional features compared with our proposed methods and secondly to classify it using Support Vector Machine for objective to given a good recognition rate of identification between LOS and NLOS phenomena. This characterized was applied for UWB measurement by the antenna Electromagnetics Group (Body WiSeR). Keywords-wideband (UWB), Line-of-sight (LOS), Non-line-of- sight (NLOS), Stable distribution, Support Vector Machine (SVM), On-body, Off-body.
Learn more by training less: systematicity in sentence processing by recurrent networks

Connectionist models of sentence processing must learn to behave systematically by generalizing from a small training set. To what extent recurrent neural networks manage this generalization task is investigated. In contrast to Van der Velde et al. (Connection Sci., 16, pp. 21–46, 2004), it is found that simple recurrent networks do show so-called weak combinatorial systematicity, although their performance remains limited. It is argued that these limitations arise from overfitting in large networks. Generalization can be improved by increasing the size of the recurrent layer without training its connections, thereby combining a large short-term memory with a small long-term memory capacity. Performance can be improved further by increasing the number of word types in the training set.