Miracle-dz/UniFAR-FTUs huggingface dataset:
The Alkyl tert-Butyl Ether Intermediate 2-Hydroxyisobutyrate Is Degraded via a Novel Cobalamin-Dependent Mutase Pathway

ABSTRACT Fuel oxygenates such as methyl and ethyl tert-butyl ether (MTBE and ETBE, respectively) are degraded only by a limited number of bacterial strains. The aerobic pathway is generally thought to run via tert-butyl alcohol (TBA) and 2-hydroxyisobutyrate (2-HIBA), whereas further steps are unclear. We have now demonstrated for the newly isolated β-proteobacterial strains L108 and L10, as well as for the closely related strain CIP I-2052, that 2-HIBA was degraded by a cobalamin-dependent enzymatic step. In these strains, growth on substrates containing the tert-butyl moiety, such as MTBE, TBA, and 2-HIBA, was strictly dependent on cobalt, which could be replaced by cobalamin. Tandem mass spectrometry identified a 2-HIBA-induced protein with high similarity to a peptide whose gene sequence was found in the finished genome of the MTBE-degrading strain Methylibium petroleiphilum PM1. Alignment analysis identified it as the small subunit of isobutyryl-coenzyme A (CoA) mutase (ICM; EC 5.4.99.13), which is a cobalamin-containing carbon skeleton-rearranging enzyme, originally described only in Streptomyces spp. Sequencing of the genes of both ICM subunits from strain L108 revealed nearly 100% identity with the corresponding peptide sequences from M. petroleiphilum PM1, suggesting a horizontal gene transfer event to have occurred between these strains. Enzyme activity was demonstrated in crude extracts of induced cells of strains L108 and L10, transforming 2-HIBA into 3-hydroxybutyrate in the presence of CoA and ATP. The physiological and evolutionary aspects of this novel pathway involved in MTBE and ETBE metabolism are discussed.
Transgenic, an operator for evolutionary algorithms

In the 1950s and the 1960s several computer scientists independently studied evolutionary systems with the idea that evolution could be used as an optimization tool for engineering problems. For these evolutionary-computation researchers, the mechanisms of evolution seem well suited for some of the most pressing computational problems in many fields. Ideas from Genetics are usually incorporated into evolutionary algorithms, such as: haploid crossover, mutation, diploid, inversion, gene doubling, deletion, and others. In the present study, we proposed an operator, named transgenic, for evolutionary algorithms, especially designed for Genetic Algorithms (GA). This operator is inspired by genetically modified organisms (GMOs), where important features are introduced into their genome artificially. The transgenic operator uses historical information to choose the best attributes, converging to better results faster than traditional GAs. The GA, used in this study, allows the discovery of concise, yet accurate, high-level rules (from a biological and synthetic database) which can be used as a classification system. The obtained results show that transgenic operator is promising at obtaining better of the the same results with a lower number of generations and smaller populations.
The effects of systemic and intratumoral interleukin-12 treatment in C6 rat glioma model

Abstract Objective: Cytokine based immunotherapy has long been an exciting field for many investigators aiming to provide an effective alternative treatment modality for glioma management. Among these cytokines, interleukin-12 (IL-12) plays a crucial role in mediating inflammatory and antitumoral activity on the host defence. We have investigated the therapeutic role of systemic and local delivery of IL-12 in C6 rat glioma model and compared these two modalities. Methods: The donor C6 glioma cells were injected stereotactically to 32 Wistar rats and right frontal tumor formation was established in all subjects. The rats were evenly divided into four groups as intratumoral (i.t.) control group (Group IA), intraperitoneal (i.p.) control group (Group IB), i.t. treatment group (Group II) and i.p. treatment group (Group III). Magnetic resonance imaging were performed to 12 rats (three from each group) on the seventh post-inoculation day. Recombinant mouse IL-12 (rmIL-12) was administered via i.t. (0.1 μg 5 μl/day/rat) and i.p. (0.1 μg 20 μl/day/rat) routes to treatment groups between days 9 and 11 following tumor inoculation, for 3 consecutive days. The rats which were unresponsive to the external stimuli, unable to feed themselves or having severe neurological impairment were decapitated and the specimens were histopathologically examined. Results: The subjects of Group III (i.p.) showed a statistically significant prolongation in survival time (mean=39 days) when compared to the control group (mean=31.7 days) (p=0.035) and Group II (i.t.) (mean=24.5 days) (p=0.005). Histopathologic examination of Group III revealed markedly increased intratumoral and peritumoral lymphocyte infiltration compared with the other groups. Conclusion: This study demonstrated that systemic administration of IL-12 in C6 glioma model in rats prolongs the survival, probably by stimulating the cellular immunity leading to lymphocytic infiltration.
An adaptive distributed call admission control for QoS-sensitive wireless mobile networks

This paper introduces an adaptive distributed call admission control framework developed for cellular mobile networks. The main feature of the proposed framework is a more efficient support for mobile multimedia users having dynamic bandwidth requirements. This is achieved by imposing an upper bound on the experienced call dropping probability, regardless of network load changes, while maintaining a high network resource utilization. The call admission control algorithm presented in this paper involves not only the original cell (handling the new admission request) but also a cluster of neighboring cells. The neighboring cells provide significant information about their ability to support the new mobile user in the future. This distributed process allows the original cell to make a more clear-sighted admission decision for the new user. The cell changes the acceptance threshold dynamically to maintain a target call dropping probability. Simulations are provided to show the improvements obtained using our framework.
Impact of extent of surgery on survival for papillary thyroid cancer patients younger than 45 years.

CONTEXT Papillary thyroid cancer (PTC) patients <45 years old are considered to have an excellent prognosis; however, current guidelines recommend total thyroidectomy for PTC tumors >1.0 cm, regardless of age. OBJECTIVE Our objective was to examine the impact of extent of surgery on overall survival (OS) in patients <45 years old with stage I PTC of 1.1 to 4.0 cm. DESIGN, SETTING, AND PATIENTS Adult patients <45 years of age undergoing surgery for stage I PTC were identified from the National Cancer Data Base (NCDB, 1998-2006) and the Surveillance, Epidemiology, and End RESULTS dataset (SEER, 1988-2006). MAIN OUTCOME MEASURE Multivariable modeling was used to compare OS for patients undergoing total thyroidectomy vs lobectomy. RESULTS In total, 29 522 patients in NCDB (3151 lobectomy, 26 371 total thyroidectomy) and 13 510 in SEER (1379 lobectomy, 12 131 total thyroidectomy) were included. Compared with patients undergoing lobectomy, patients having total thyroidectomy more often had extrathyroidal and lymph node disease. At 14 years, unadjusted OS was equivalent between total thyroidectomy and lobectomy in both databases. After adjustment, OS was similar for total thyroidectomy compared with lobectomy across all patients with tumors of 1.1 to 4.0 cm (NCDB: hazard ratio = 1.45 [confidence interval = 0.88-2.51], P = 0.19; SEER: 0.95 (0.70-1.29), P = 0.75) and when stratified by tumor size: 1.1 to 2.0 cm (NCDB: 1.12 [0.50-2.51], P = 0.78; SEER: 0.95 [0.56-1.62], P = 0.86) and 2.1 to 4.0 cm (NCDB: 1.93 [0.88-4.23], P = 0.10; SEER: 0.94 [0.60-1.49], P = 0.80). CONCLUSIONS After adjusting for patient and clinical characteristics, total thyroidectomy compared with thyroid lobectomy was not associated with improved survival for patients <45 years of age with stage I PTC of 1.1 to 4.0 cm. Additional clinical and pathologic factors should be considered when choosing extent of resection.
Immunotherapy Markedly Increases the Effectiveness of Antimicrobial Therapy for Treatment of Burkholderia pseudomallei Infection

ABSTRACT Burkholderia pseudomallei is a soil bacterium that is endemic in southeast Asia and northern Australia and that can cause both acutely lethal pneumonia and chronic systemic infections in humans. The effective treatment of infection with B. pseudomallei requires rapid diagnosis and prolonged treatment with high doses of antimicrobials, and even with appropriate antibiotic therapy, patient relapses are common. Thus, new approaches to the treatment of B. pseudomallei infections are needed. In the present study, we asked whether active immunotherapy with gamma interferon (IFN-γ), a key cytokine regulating the intracellular replication of B. pseudomallei, could increase the effectiveness of conventional antimicrobial therapy for B. pseudomallei infection. Macrophage infection assays and in vivo pulmonary challenge models were used to assess the inhibitory effects of combined treatment with IFN-γ and ceftazidime on B. pseudomallei infection. We found that treatment with even very low doses of IFN-γ and ceftazidime elicited strong synergistic inhibition of B. pseudomallei growth within infected macrophages. In vivo, active immunotherapy markedly potentiated the effectiveness of low-dose ceftazidime therapy for the treatment of infected mice in a pulmonary challenge model of B. pseudomallei. Combined treatment was associated with a significant reduction in the bacterial burden and a significant lessening of bacterial dissemination. We concluded, therefore, that immunotherapy with either endogenous or exogenous IFN-γ could significantly increase the effectiveness of conventional antimicrobial therapy for the treatment of acute B. pseudomallei infection.
Immunolocalization of the multi‐sarco/endoplasmic reticulum Ca2+ATPase system in human platelets

We recently identified a multi‐SERCA (sarco/endoplasmic reticulum Ca2+ ATPase) system in haemopoietic cells comprising the SERCA 2b, SERCA 3 and a new monoclonal anti‐Ca2+ ATPase antibody (PL/IM 430) recognizable SERCA isoforms. We have now investigated the subcellular localization of these enzymes in human platelets by Western blotting of subcellular membrane fractions and by immunoelectron microscopy. We precisely defined the recognition specificity of the polyclonal anti‐SERCA 2b, anti‐SERCA 3, anti‐SERCA 1 antibodies as well as of the monoclonal antibody PL/IM 430 by testing their recognition of the tryptic fragments of the SERCA isoforms. The analysis of fragmented membranes enriched in plasma membrane and intracellular membrane components by Western blotting showed that the SERCA 2b and the SERCA 3 isoforms were found in both the plasma membrane and the intracellular membrane fractions, whereas the PL/IM 430 recognizable SERCA isoform was restricted to membranes associated with the plasma membrane fraction. The immunoelectron microscopical study of the SERCA isoforms in resting platelets showed that: (i) the SERCA 2b isoform was expressed in membranes associated with the plasma membrane and open canalicular system, some α‐granules and in unidentified membranes; (ii) the SERCA 3 isoform was found associated with plasma and intracellular membranes; and (iii) the PL/IM 430 recognizable SERCA isoform was observed only in structures associated with the cytoplasmic face of the plasma membranes, as confirmed by flow cytometry. Finally, since the PL/IM 430 antibody was raised against intracellular membranes, we looked for a potential membrane redistribution during the isolation procedure used for the preparation of the immunizing membranes. Neuraminidase treatment indeed induced a translocation of the PL/IM 430 recognizable SERCA isoform from plasma to intracellular membranes. Thus, the multi‐SERCA system in platelets: (i) is distributed over different platelet membranes, (ii) presents a sub‐compartmental organization with some overlapping, and (iii) is partly associated with motile membranes, reflecting an unrecognized level of complexity of Ca2+ stores in these cells.
Changes in plasma levels of 17-hydroxycorticosteroids during the intravenous administration of ACTH. I. A test of adrenocortical capacity in the human.

The recognition of the important role played by the adrenal cortex in normal physiology and its significance in withstanding "stressful situations" has led to the development of many tests to measure its functional state and capacity in the human. Most of these tests rely on measurements of phenomena which are dependent on the effect of adrenocortical secretions on some special metabolic process, and do not involve the direct measurement of adrenocortical steroids. The frequent discrepancies between the clinical picture and these indirect tests indicate that they are not always reliable indices of adrenal function. Recently, Thorn, Goetz, Streeten, Dingman, and Arons (1) have devised a test for the quantitative estimation of adrenal function based on the determination of butanol-soluble 17,21-dihydroxy-20ketosteroids in the urine. Adrenal capacity is estimated by the increase in urinary excretion of these compounds after intravenous administration of adrenocorticotrophic hormone (ACTH). While this technique is a considerable improvement over the indirect methods, measurements based on the urine have several disadvantages. If adrenal function or capacity must be determined
Facial Expressions of Emotions for Virtual Characters

The virtual character’s expressions of emotions may significantly enhance human-machine interaction. To give the capability to virtual characters to display emotions, the latter should be endowed with a repertoire of facial expressions that convey emotional meanings in conversational settings. In this chapter, we explore research works highlighting different methodologies both to identify the morphological and dynamic characteristics of emotional facial expressions and to measure the effects of the emotional expressions on the user’s perception during human-machine interaction.
Sequence conservation and region shuffling in an endoglucanase and an exoglucanase from Cellulomonas fimi

Cellulomonas fimi produces an endoglucanase and an exoglucanase which bind strongly to cellulose. Each enzyme contains three distinct regions: a short sequence of about 20 amino acids containing only proline and threonine (the ProThr box); an irregular region, rich in hydroxyamino acids, of low charge density, and which is predicted to have little secondary structure; and an ordered region of higher charge density which contains a potential active site, and which is predicted to have secondary structure; and an ordered region of higher charge density which contains a potential active site, and which is predicted to have secondary structure. The Pro‐Thr box is conserved almost perfectly in the two enzymes. The irregular regions are 50% conserved, and the conserved sequences include four Asn‐Xaa‐Ser/Thr sites. The ordered regions appear not to be conserved, but the potential active sites both have the sequence Glu‐Xaa7‐Asn‐Xaa6‐Thr; they occur at widely separated sites in the two regions. The order of the regions is reversed in the two enzymes: irregular‐Pro‐Thr box‐ordered in the endoglucanase; ordered‐Pro‐Thr box irregular in the exoglucanase. The genes for the two enzymes appear to have arisen by shuffling of two conserved sequences and either one or two other sequences.
Statistical Analysis on Manifolds : A Nonparametric Approach for Inference on Shape Spaces

This article concerns nonparametric statistics on manifolds with special emphasis on landmark based shape spaces in which a k-ad, i.e., a set of k points or landmarks on an object or a scene, is observed in 2D or 3D, for purposes of identification, discrimination, or diagnostics. Two different notions of shape are considered: reflection shape invariant under all translations, scaling and orthogonal transformations, and affine shape invariant under all affine transformations. A computation of the extrinsic mean reflection shape, which has remained unresolved in earlier works, is given in arbitrary dimensions, enabling one to extend nonparametric inference on Kendall type shape manifolds from 2D to higher dimensions. For both reflection and affine shapes, two sample test statistics are constructed based on appropriate choice of orthonormal frames on the tangent bundle and computations of differentials of projection maps with respect to them at the sample extrinsic mean. The samples in consideration can be either independent or be the outcome of a matched pair experiment. Examples are included to illustrate the theory.
Brain storm optimization algorithm in objective space

Brain storm optimization algorithm is a newly proposed swarm intelligence algorithm, which has two main operations, i.e., convergent operation and divergent operation. In the original brain storm optimization algorithm, a clustering algorithm is utilized to cluster individuals into clusters as the convergent operation which is time consuming because of distance calculation during clustering. In this paper, a new convergent operation is proposed to be implemented in the 1-dimensional objective space instead of in the solution space. As a consequence, its computation time will depend on only the population size, not the problem dimension, therefore, a big computation time saving can be obtained which makes it have good scalability. Experimental results demonstrate the effectiveness and efficiency of the proposed brain storm optimization algorithm in objective space.
INTERPRETING NEAR-INFRARED HYDROGEN LINE RATIOS IN T TAURI STARS

In accreting young stars, one of the prominent spectral features in the near-infrared is the Paschen and Brackett series in emission. We examine hydrogen line ratios for 16 classical T Tauri stars from SpeX spectra and assess the trends with veiling and accretion. The observed line ratios are compared with two theoretical models for line formation: (1) Baker & Menzel's Case B for radiative ionization and recombination and (2) a set of local line excitation calculations designed to replicate the conditions in T Tauri winds and magnetic accretion columns (KF). While the comparison between Case B and observed line ratios implies a wide range in electron density and temperature among the hydrogen line formation regions in T Tauri stars, the predictions of the local line excitation models give consistent results across multiple diagnostics. Under the assumptions of the local line excitation calculations, we find that nH in the hydrogen line formation region is constrained to 2 × 1010–2 × 1011 cm−3, where stars with higher accretion rates have densities at the higher end of this range. Because of uncertainties in extinction, temperature is not well delineated, but falls within the range expected for collisional excitation to produce the line photons. We introduce new diagnostics for assessing extinction based on near-infrared hydrogen line ratios from the local line excitation calculations.
Comparison of stress induced by manual restraint and immobilisation in the estuarine crocodile, Crocodylus porosus.

This study compared the stress induced in captive estuarine crocodiles, Crocodylus porosus, by two different handling methods: manual restraint (noosing with ropes) and immobilization by electro-stunning. To stun, a short charge (approx. 6 s) at 110 V was delivered to the back of the necks of C. porosus using a custom-built device, which immobilized the animals for 5-10 min. Immobilized and restrained animals were measured and sexed, and the condition of the skin assessed. Blood samples were taken from some animals immediately after restraint or immobilization. Other animals were returned to their pens to recover for periods of 30 min, 1, 4, 12, 24 or 48 hours after which they were stunned and blood samples taken. Individual animals (mean body length 1.96 m, N=99) were bled only once. Haematocrit and haemoglobin concentrations were measured and plasma samples were analysed for corticosterone, glucose and lactate levels. Following restraint, there were significant increases in haematocrit, haemoglobin, glucose, lactate and corticosterone concentrations in C. porosus. For restrained animals, recovery to baseline levels occurred after approximately 8 hours. The stress response of stunned animals was significantly reduced compared to manually captured and restrained crocodiles. Both groups showed a significant increase in haematocrit, haemoglobin concentration and lactate levels, however the magnitude of change was significantly reduced, and recovery was faster in stunned animals. No increase in either glucose or corticosterone levels occurred with immobilisation. The results imply that immobilization by electro-stunning is much less stressful.
A Novel Neural Network Model for Joint POS Tagging and Graph-based Dependency Parsing

We present a novel neural network model that learns POS tagging and graph-based dependency parsing jointly. Our model uses bidirectional LSTMs to learn feature representations shared for both POS tagging and dependency parsing tasks, thus handling the feature-engineering problem. Our extensive experiments, on 19 languages from the Universal Dependencies project, show that our model outperforms the state-of-the-art neural network-based Stack-propagation model for joint POS tagging and transition-based dependency parsing, resulting in a new state of the art. Our code is open-source and available together with pre-trained models at: https://github.com/datquocnguyen/jPTDP
Energy-Efficient Scheduling in Nonpreemptive Systems With Real-Time Constraints

In the past decade, the development of mobile and embedded systems has demanded energy efficiency for improving the lifetime of embedded devices. To avoid preemption overhead or ease timing verification, nonpreemptive scheduling has been deemed useful or necessary in meeting system timing requirements for certain applications built on embedded devices. In this paper, our aim is to design nonpreemptive scheduling algorithms that ensure timing correctness and optimize energy consumption on a processor with variable speeds. We propose a representative algorithm, ISA, which can produce lower speeds for a variety of nonpreemptive task sets than other comparable methods, and hence resulting in significant energy savings. When combined with a selective frequency-inheritance policy we design to efficiently determine if processor speedup can be disabled without jeopardizing any task deadlines, ISA can achieve even larger gains, up to 30% reduction in energy consumption. Finally, we propose a dynamic slack reclamation policy built on ISA, namely ISA-DR, which can result in additional energy savings when a task consumes less than its worst-case execution time.
The Impact of Economic Freedom upon Economic Growth: An Application on Different Income Groups

The objective of the study is to investigate the relationship between economic growth and economic freedom for different income groups. Therefore, the data were collected from 94 different countries belonging to five different income groups in order to cover the period from 2000 to 2010. In the study, relationship between the economic growth of the country and the level of freedom index which Fraser Institute measured and its sub-components constituting was questioned through the panel data analysis method. As a result of the analyses, it was found that there is a statistically significant positive relationship between the level of economic freedom for all income groups and economic growth. With the inclusion of sub-components of freedom index into the model, the effects of such sub-components vary depending on the income groups.