Miracle-dz/UniFAR-FTUs huggingface dataset:
The Planetary Nebula NGC 1360: A Test Case of Magnetic Collimation and Evolution after the Fast Wind

The central star of this nebula has an observed intense magnetic field and the fast wind is no longer present, indicating that a back flow process has probably developed. Long-slit, spatially resolved echelle spectra have been obtained across the main body of NGC 1360 and over its system of bipolar jets. Deep images of the knotty structures of the jets have also been obtained. The data allow a detailed study of the structure and kinematics of this object and the results are modeled considering the effects of a magnetic collimation process in the development of the nebula and then switching off the fast stellar wind to follow its evolution to its current state. The model is able to successfully reproduce many key features of NGC 1360 under these premises.
p300-mediated Acetylation of Histone H3 Lysine 56 Functions in DNA Damage Response in Mammals

The packaging of newly replicated and repaired DNA into chromatin is crucial for the maintenance of genomic integrity. Acetylation of histone H3 core domain lysine 56 (H3K56ac) has been shown to play a crucial role in compaction of DNA into chromatin following replication and repair in Saccharomyces cerevisiae. However, the occurrence and function of such acetylation has not been reported in mammals. Here we show that H3K56 is acetylated and that this modification is regulated in a cell cycle-dependent manner in mammalian cells. We also demonstrate that the histone acetyltransferase p300 acetylates H3K56 in vitro and in vivo, whereas hSIRT2 and hSIRT3 deacetylate H3K56ac in vivo. Further we show that following DNA damage H3K56 acetylation levels increased, and acetylated H3K56, which is localized at the sites of DNA repair. It also colocalized with other proteins involved in DNA damage signaling pathways such as phospho-ATM, CHK2, and p53. Interestingly, analysis of occurrence of H3K56 acetylation using ChIP-on-chip revealed its genome-wide spread, affecting genes involved in several pathways that are implicated in tumorigenesis such as cell cycle, DNA damage response, DNA repair, and apoptosis.
Aerobic exercise training reduces epicardial fat in obese men.

The purpose of this study was to determine the effects of exercise training on ventricular epicardial fat thickness in obese men and to investigate the relationship of the change in epicardial fat thickness to changes in abdominal fat tissue following exercise training. Twenty-four obese middle-aged men [age, 49.4 +/- 9.6 yr; weight, 87.7 +/- 11.2 kg; body mass index (BMI), 30.7 +/- 3.3 kg/m(2); peak oxygen consumption, 28.4 +/- 7.2 ml.kg(-1). min(-1); means +/- SD] participated in this study. Each participant completed a 12-wk supervised exercise training program (60-70% of the maximal heart rate; 60 min/day, 3 days/wk) and underwent a transthoracic echocardiography. The epicardial fat thickness on the free wall of the right ventricle was measured from both parasternal long- and short-axis views. The visceral adipose tissue (VAT) and subcutaneous adipose tissues were measured by computed tomography. Following exercise training, the epicardial fat thickness was significantly decreased (P < 0.001). The percentage change of epicardial fat thickness was twice as high compared with those of waist, BMI, and body weight of original values (P <0.05). There was a significant relationship (r = 0.525, P = 0.008) between changes in the epicardial fat thickness and VAT with exercise training. Stepwise multiple regression analysis revealed that the change in VAT, change in systolic blood pressure, and change in quantitative insulin sensitivity check index were independently related to the change epicardial fat thickness (P < 0.05). The ventricular epicardial fat thickness is reduced significantly after aerobic exercise training and is associated with a decrease in VAT. These results suggest that aerobic exercise training may be an effective nonpharmacological strategy for decreasing the ventricular epicardial fat thickness and visceral fat area in obese middle-aged men.
Decisional tool to assess current and future process robustness in an antibody purification facility

Increases in cell culture titers in existing facilities have prompted efforts to identify strategies that alleviate purification bottlenecks while controlling costs. This article describes the application of a database‐driven dynamic simulation tool to identify optimal purification sizing strategies and visualize their robustness to future titer increases. The tool harnessed the benefits of MySQL to capture the process, business, and risk features of multiple purification options and better manage the large datasets required for uncertainty analysis and optimization. The database was linked to a discrete‐event simulation engine so as to model the dynamic features of biopharmaceutical manufacture and impact of resource constraints. For a given titer, the tool performed brute force optimization so as to identify optimal purification sizing strategies that minimized the batch material cost while maintaining the schedule. The tool was applied to industrial case studies based on a platform monoclonal antibody purification process in a multisuite clinical scale manufacturing facility. The case studies assessed the robustness of optimal strategies to batch‐to‐batch titer variability and extended this to assess the long‐term fit of the platform process as titers increase from 1 to 10 g/L, given a range of equipment sizes available to enable scale intensification efforts. Novel visualization plots consisting of multiple Pareto frontiers with tie‐lines connecting the position of optimal configurations over a given titer range were constructed. These enabled rapid identification of robust purification configurations given titer fluctuations and the facility limit that the purification suites could handle in terms of the maximum titer and hence harvest load. © 2012 American Institute of Chemical Engineers Biotechnol. Prog. , 28: 1019–1028, 2012
Evaluation of antimicrobial treatment in a bovine model of acute Chlamydia psittaci infection: tetracycline versus tetracycline plus rifampicin.

Antimicrobial treatment of chlamydial infections is known to be of limited efficacy. In this study, effects of doxycycline (D), usually the drug of choice, were compared with the combined therapy of doxycycline and rifampicin (R) in a bovine model of respiratory Chlamydia psittaci infection. After intrabronchial inoculation of the pathogen, 30 animals were assigned to five groups (n = 6 per group): untreated controls, monotherapy with D (5 mg kg(-1)day(-1) or 10 mg kg(-1)day(-1)), and combination therapy of D and R (600 mg day(-1)). Treatment continued until day 14 post inoculation (d.p.i.). Clinical signs, inflammatory markers, and pathological findings confirmed successful infection in all animals. Reisolation of the pathogen was possible in 4/6 untreated animals and in 4/12 animals treated with D alone until 4 d.p.i. , but in none of the calves of the two D + R groups. Pathogen detection was possible in all animals without significant differences among groups. Severity of disease and time course of its resolution, assessed by clinical and pathological findings as well as inflammatory parameters, were not significantly different between untreated controls and calves receiving D alone or in combination with R. Regardless of the treatment regimen, all groups recovered clinically and cleared the infection within 2 weeks.
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses

For a very long time, Type II restriction enzymes (REases) have been a paradigm of ORFans: proteins with no detectable similarity to each other and to any other protein in the database, despite common cellular and biochemical function. Crystallographic analyses published until January 2008 provided high-resolution structures for only 28 of 1637 Type II REase sequences available in the Restriction Enzyme database (REBASE). Among these structures, all but two possess catalytic domains with the common PD-(D/E)XK nuclease fold. Two structures are unrelated to the others: R.BfiI exhibits the phospholipase D (PLD) fold, while R.PabI has a new fold termed ‘half-pipe’. Thus far, bioinformatic studies supported by site-directed mutagenesis have extended the number of tentatively assigned REase folds to five (now including also GIY-YIG and HNH folds identified earlier in homing endonucleases) and provided structural predictions for dozens of REase sequences without experimentally solved structures. Here, we present a comprehensive study of all Type II REase sequences available in REBASE together with their homologs detectable in the nonredundant and environmental samples databases at the NCBI. We present the summary and critical evaluation of structural assignments and predictions reported earlier, new classification of all REase sequences into families, domain architecture analysis and new predictions of three-dimensional folds. Among 289 experimentally characterized (not putative) Type II REases, whose apparently full-length sequences are available in REBASE, we assign 199 (69%) to contain the PD-(D/E)XK domain. The HNH domain is the second most common, with 24 (8%) members. When putative REases are taken into account, the fraction of PD-(D/E)XK and HNH folds changes to 48% and 30%, respectively. Fifty-six characterized (and 521 predicted) REases remain unassigned to any of the five REase folds identified so far, and may exhibit new architectures. These enzymes are proposed as the most interesting targets for structure determination by high-resolution experimental methods. Our analysis provides the first comprehensive map of sequence-structure relationships among Type II REases and will help to focus the efforts of structural and functional genomics of this large and biotechnologically important class of enzymes.
Roux-en-Y Gastric Bypass Surgery Induces Early Plasma Metabolomic and Lipidomic Alterations in Humans Associated with Diabetes Remission

Roux-en-Y gastric bypass (RYGB) is an effective method to attain sustained weight loss and diabetes remission. We aimed to elucidate early changes in the plasma metabolome and lipidome after RYGB. Plasma samples from 16 insulin-resistant morbidly obese subjects, of whom 14 had diabetes, were subjected to global metabolomics and lipidomics analysis at pre-surgery and 4 and 42 days after RYGB. Metabolites and lipid species were compared between time points and between subjects who were in remission and not in remission from diabetes 2 years after surgery. We found that the variables that were most discriminatory between time points were decanoic acid and octanoic acid, which were elevated 42 days after surgery, and sphingomyelins (18:1/21:0 and 18:1/23:3), which were at their lowest level 42 days after surgery. Insulin levels were lower at 4 and 42 days after surgery compared with pre-surgery levels. At 4 days after surgery, insulin levels correlated positively with metabolites of branched chain and aromatic amino acid metabolism and negatively with triglycerides with long-chain fatty acids. Of the 14 subjects with diabetes prior to surgery, 7 were in remission 2 years after surgery. The subjects in remission displayed higher pre-surgery levels of tricarboxylic acid cycle intermediates and triglycerides with long-chain fatty acids compared with subjects not in remission. Thus, metabolic alterations are induced soon after surgery and subjects with diabetes remission differ in the metabolic profiles at pre- and early post-surgery time points compared to patients not in remission.
Stimulus Typicality Determines How Broadly Fear Is Generalized

The ability to represent knowledge at the category level promotes the transfer of learning. How this ability integrates with basic forms of conditioned learning is unknown but could explain why conditioned fear is overgeneralized after aversive experiences. We examined the impact of stimulus typicality—an important determinant of category-based induction—on fear learning and generalization. Typicality is known to affect the strength of categorical arguments; a premise involving typical exemplars (e.g., sparrow) is believed to apply to other members, whereas a premise about atypical exemplars (e.g., penguin) generalizes more narrowly to similar items. We adopted this framework to human fear conditioning and found that fear conditioned to typical exemplars generalized more readily to atypical members than vice versa, despite equal feature overlap across conditions. These findings have implications for understanding why some fearful events lead to broad overgeneralization of fear whereas others are regarded as isolated episodes.
Rheology of molten blends of polyoxymethylene and ethylene‐vinyl acetate copolymer and the microstructure of extrudates as a function of their melt viscosities

Blends of polyoxymethylene (POM) with a copolymer of ethylene and vinyl acetate (CEVAc) have been studied. The effect of viscosity ratio for melts of the components on the processes of fiber formation in extrudates and on the rheological properties of the molten blend has been tested. The viscosity ratio of the fiber-forming POM and the matrix varied in the range 0.35-27.7. POM ultrathin fibers of unlimited length can be formed in the CEVAc only at a viscosity ratio close to unity. For ratios much greater than unity, the extrudate is found to contain short fibers and a finely dispersed powder or no fibers at all. If the viscosity of the POM melt is lower than that of the matrix, films are formed in addition to fibers. The second factor that governs fiber formation is the extrusion shear stress. An optimum shear stress exists at which the amount of ultrathin fibers is a maximum.
Signal aware multi-path TCP

Mobile devices have been augmented by Multi-path TCP (MPTCP), enabling them to exploit the path diversity. Signal aware MPTCP (SA-MPTCP) takes the signal quality, playing a significant role in energy waste, into account to enhance MPTCP energy consumption. The problem is formulated as a decision making problem under uncertainty, endeavoring to optimize energy efficiency by selecting the best policy. The simulation results for bulk data transfer show that 42% and 17% energy have been saved in uploading and downloading compared to the base MPTCP, respectively.
Penetration of gentamicin into the alveolar lining fluid of critically ill patients with ventilator-associated pneumonia.

STUDY OBJECTIVES To estimate the penetration of gentamicin into lung tissue by measuring its concentrations in alveolar lining fluid (ALF) and blood in critically ill patients with ventilator-associated pneumonia (VAP). PATIENTS AND INTERVENTIONS The study population consisted of 24 patients who were admitted to an ICU for respiratory failure and developed VAP. Patients were scheduled to undergo bronchoscopy with BAL after IV administration of a once-daily, 240-mg schedule of gentamicin for the treatment of VAP. Patients were assigned at random to one of four groups of six patients each according to the scheduled time for bronchoscopy (1, 2, 4, or 6 h, respectively). A serum sample was obtained at 0.5 h (n = 24), and both serum and ALF samples (n = 6) were collected at each of the above specified times for measurement of antibiotic concentrations. MEASUREMENTS AND RESULTS Mean +/- SEM gentamicin concentrations in the ALF were 2.95 +/- 0.37, 4.24 +/- 0.42, 3.10 +/- 0.39, and 2.65 +/- 0.35 microg/mL at 1, 2, 4, and 6 h, respectively, after the start of antibiotic infusion. Maximum gentamicin concentrations in serum (13.39 +/- 0.91 mug/mL, n = 24) and ALF (4.24 +/- 0.42 microg/mL, n = 6) were achieved at 0.5 h and 2 h, respectively, giving a penetration ratio of 0.32. The mean ratios of ALF/serum concentrations between 1 h and 6 h ranged from 0.30 to 1.14. After completion of the distribution phase, a significant positive correlation (p = 0.02) was found between gentamicin concentrations in the serum and ALF. CONCLUSIONS Once-daily IV administration of 240-mg gentamicin achieved average peak antibiotic concentrations of 4.24 microg/mL in the ALF 2 h after administration, and an ALF/serum penetration ratio of 32%. Higher gentamicin doses to produce higher peak blood levels than those found with the study dose are necessary to obtain active alveolar concentrations against less sensitive microorganisms in the treatment of VAP in ICU patients.
Decentralized, adaptive resource allocation for sensor networks

This paper addresses the problem of resource allocation in sensor networks. We are concerned with how to allocate limited energy, radio bandwidth, and other resources to maximize the value of each node's contribution to the network. Sensor networks present a novel resource allocation challenge: given extremely limited resources, varying node capabilities, and changing network conditions, how can one achieve efficient global behavior? Currently, this is accomplished by carefully tuning the behavior of the low-level sensor program to accomplish some global task, such as distributed event detection or in-network data aggregation. This manual tuning is difficult, error-prone, and typically does not consider network dynamics such as energy depletion caused by bursty communication patterns. We present Self-Organizing Resource Allocation (SORA), a new approach for achieving efficient resource allocation in sensor networks. Rather than manually tuning sensor resource usage, SORA defines a virtual market in which nodes sell goods (such as sensor readings or data aggregates) in response to prices that are established by the programmer. Nodes take actions to maximize their profit, subject to energy budget constraints. Nodes individually adapt their operation over time in response to feedback from payments, using reinforcement learning. The behavior of the network is determined by the price for each good, rather than by directly specifying local node programs. SORA provides a useful set of primitives for controlling the aggregate behavior of sensor networks despite variance of individual nodes. We present the SORA paradigm and a sensor network vehicle tracking application based on this design, as well as an extensive evaluation demonstrating that SORA realizes an efficient allocation of network resources that adapts to changing network conditions.
Essential requirement of reduced glutathione (GSH) for the anti-oxidant effect of the flavonoid quercetin

We have analyzed the anti- or pro-oxidant effects of the flavonoid quercetin (QU) by evaluating, in U937 cell line, hydrogen peroxide (H2O2), superoxide anion reduced glutathione (GSH) content, mitochondrial membrane potential, DNA content, phosphatidylserine exposure on the outer face of the plasma membrane and cell viability. Polychromatic flow cytometry was used to evaluate in the same cells several functional parameters. For short periods of treatment QU exerted an anti-oxidant effect (decrease in H2O2 levels), whereas for long periods it showed a pro-oxidant activity (increase in ). In these conditions, GSH content was reduced, and this correlated with a lack of anti-oxidant activity of QU, which in turn could be correlated with proapoptotic activity of this molecule. Thus, QU can exert different effects (anti-/prooxidant) depending on exposure times and oxidative balance, and in particular on stores of GSH.
Elastic uplift in southeast Greenland due to rapid ice mass loss

The rapid unloading of ice from the southeastern sector of the Greenland ice sheet between 2001 and 2006 caused an elastic uplift of ∼35 mm at a GPS site in Kulusuk. Most of the uplift results from ice dynamic‐induced volume losses on two nearby outlet glaciers. Volume loss from Helheim Glacier, calculated from sequential digital elevation models, contributes about ∼16 mm of the observed uplift, with an additional ∼5 mm from volume loss of Kangerdlugssuaq Glacier. The remaining uplift signal is attributed to significant melt‐induced ice volume loss from the ice sheet margin along the southeast coast between 62°N and 66°N.
The relationship between morphology, escape behaviour and microhabitat occupation in the lizard clade Liolaemus (Iguanidae: Tropidurinae * : Liolaemini)

Phenotypic differences among species are known to have functional consequences that in turn allow species to use different habitats. However, the role of behaviour in this ecomorphological paradigm is not well defined. We investigated the relationship between morphology, ecology and escape behaviour among 25 species of the lizard clade Liolaemus in a phylogenetic framework. We demonstrate that the relationship between morphology and characteristics of habitat structure shows little or no association, consistent with a previous study on this group. However, a significant relationship was found between morphology and escape behaviour with the distance a lizard moved from a potential predator correlated with body width, axilla‐groin length, and pelvis width. A significant relationship between escape behaviour and habitat structure occupation was found; lizards that occupied tree trunks and open ground ran longer distances from predators and were found greater distances from shelter. Behavioural strategies used by these lizards in open habitats appear to have made unnecessary the evolution of limb morphology that has occurred in other lizards from other clades that are found in open settings. Understanding differences in patterns of ecomorphological relationships among clades is an important component for studying adaptive diversification.
Controlled Flooding Search in a Large Network

In this paper, we consider the problem of searching for a node or an object (i.e., piece of data, file, etc.) in a large network. Applications of this problem include searching for a destination node in a mobile ad hoc network, querying for a piece of desired data in a wireless sensor network, and searching for a shared file in an unstructured peer-to-peer network. We consider the class of controlled flooding search strategies where query/search packets are broadcast and propagated in the network until a preset time-to-live (TTL) value carried in the packet expires. Every unsuccessful search attempt, signified by a timeout at the origin of the search, results in an increased TTL value (i.e., larger search area) and the same process is repeated until the object is found. The primary goal of this study is to find search strategies (i.e., sequences of TTL values) that will minimize the cost of such searches associated with packet transmissions. Assuming that the probability distribution of the object location is not known a priori, we derive search strategies that minimize the search cost in the worst-case, via a performance measure in the form of the competitive ratio between the average search cost of a strategy and that of an omniscient observer. This ratio is shown in prior work to be asymptotically (as the network size grows to infinity) lower bounded by 4 among all deterministic search strategies. In this paper, we show that by using randomized strategies (i.e., successive TTL values are chosen from certain probability distributions rather than deterministic values), this ratio is asymptotically lower bounded by e. We derive an optimal strategy that achieves this lower bound, and discuss its performance under other criteria. We further introduce a class of randomized strategies that are sub-optimal but potentially more useful in practice