Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning and Identification of Conjugative Transfer Origins in the Rhizobium meliloti Genome

ABSTRACT A simple approach was used to identify Rhizobium meliloti DNA regions with the ability to convert a nontransmissible vector into a mobilizable plasmid, i.e., to contain origins of conjugative transfer (oriT,mob). RecA-defective R. meliloti merodiploid populations, where each individual contained a hybrid cosmid from anR. meliloti GR4 gene library, were used as donors en masse in conjugation with another R. meliloti recipient strain, selecting transconjugants for vector-encoded antibiotic resistance. Restriction analysis of cosmids isolated from individual transconjugants resulted in the identification of 11 nonoverlapping DNA regions containing potential oriTs. Individual hybrid cosmids were confirmed to be mobilized from the originalrecA donors at frequencies ranging from 10−2to 10−5 per recipient cell. DNA hybridization experiments showed that seven mob DNA regions correspond to plasmid replicons: four on symbiotic megaplasmid 1 (pSym1), one on pSym2, and another two on each of the two cryptic plasmids harbored by R. meliloti GR4. Another three mob clones could not be located to any plasmid and were therefore preliminarily assigned to the chromosome. With this strategy, we were able to characterize theoriT of the conjugative plasmid pRmeGR4a, which confirmed the reliability of the approach to select for oriTs. Moreover, transfer of the 11 mob cosmids from R. meliloti into Escherichia coli occurred at frequencies as high as 10−1, demonstrating the R. meliloti gene transfer capacity is not limited to the familyRhizobiaceae. Our results show that the R. meliloti genome contains multiple oriTs that allow efficient DNA mobilization to rhizobia as well as to phylogenetically distant gram-negative bacteria.
Architected Cellular Materials

Additive manufacturing enables fabrication of materials with intricate cellular architecture, whereby progress in 3D printing techniques is increasing the possible configurations of voids and solids ad infinitum. Examples are microlattices with graded porosity and truss structures optimized for specific loading conditions. The cellular architecture determines the mechanical properties and density of these materials and can influence a wide range of other properties, e.g., acoustic, thermal, and biological properties. By combining optimized cellular architectures with high-performance metals and ceramics, several lightweight materials that exhibit strength and stiffness previously unachievable at low densities were recently demonstrated. This review introduces the field of architected materials; summarizes the most common fabrication methods, with an emphasis on additive manufacturing; and discusses recent progress in the development of architected materials. The review also discusses important application.
Incorporating Surrogate Species and Seascape Connectivity to Improve Marine Conservation Outcomes

Conservation focuses on maintaining biodiversity and ecosystem functioning, but gaps in our knowledge of species biology and ecological processes often impede progress. For this reason, focal species and habitats are used as surrogates for multispecies conservation, but species‐based approaches are not widely adopted in marine ecosystems. Reserves in the Solomon Islands were designed on the basis of local ecological knowledge to conserve bumphead parrotfish (Bolbometopon muricatum) and to protect food security and ecosystem functioning. Bumphead parrotfish are an iconic threatened species and may be a useful surrogate for multispecies conservation. They move across tropical seascapes throughout their life history, in a pattern of habitat use that is shared with many other species. We examined their value as a conservation surrogate and assessed the importance of seascape connectivity (i.e., the physical connectedness of patches in the seascape) among reefs, mangroves, and seagrass to marine reserve performance. Reserves were designed for bumphead parrotfish, but also enhanced the abundance of other species. Integration of local ecological knowledge and seascape connectivity enhanced the abundance of 17 other harvested fish species in local reserves. This result has important implications for ecosystem functioning and local villagers because many of these species perform important ecological processes and provide the foundation for extensive subsistence fisheries. Our findings suggest greater success in maintaining and restoring marine ecosystems may be achieved when they are managed to conserve surrogate species and preserve functional seascape connections.
GW170817: Implications for the Stochastic Gravitational-Wave Background from Compact Binary Coalescences

The LIGO Scientific and Virgo Collaborations have announced the first detection of gravitational waves from the coalescence of two neutron stars. The merger rate of binary neutron stars estimated from this event suggests that distant, unresolvable binary neutron stars create a significant astrophysical stochastic gravitational-wave background. The binary neutron star background will add to the background from binary black holes, increasing the amplitude of the total astrophysical background relative to previous expectations. In the Advanced LIGO-Virgo frequency band most sensitive to stochastic backgrounds (near 25 Hz), we predict a total astrophysical background with amplitude $\Omega_{\rm GW} (f=25 \text{Hz}) = 1. 8_{-1.3}^{+2.7} \times 10^{-9}$ with $90\%$ confidence, compared with $\Omega_{\rm GW} (f=25 \text{Hz}) = 1. 1_{-0.7}^{+1.2} \times 10^{-9}$ from binary black holes alone. Assuming the most probable rate for compact binary mergers, we find that the total background may be detectable with a signal-to-noise-ratio of 3 after 40 months of total observation time, based on the expected timeline for Advanced LIGO and Virgo to reach their design sensitivity.
SAMUEL: A Sharing-based Approach to processing Multiple SPARQL Queries with MapReduce

The volume of RDF data is now growing tremendously. It is thus considered prudent to store and process massive RDF data with distributed SPARQL engines instead of relying on a singlemachine system.Many sophisticated index and partitioning schemes have also been proposed to support SPARQL query evaluations. However, existing SPARQL engines have mainly followed oneat-a-time scheme so that query evaluation is focused only on processing each query separately. We showcase SAMUEL, a distributed SPARQL engine that simultaneously evaluates many SPARQL queries for a massive RDF dataset with MapReduce. SAMUEL provides an efficient optimization algorithm to evaluate many SPARQL queries simultaneously in a shared and balanced way. Extensive experiments present that without any sophisticated partitioning or index mechanisms, our approach significantly outperforms other MapReduce-based SPARQL engines as well as an ad-hoc query engine equipped with various indexes and partitioning tools for evaluating multiple SPARQL queries.
Nondestructive characterization of woven fabric ceramic composites

Woven fabric ceramic composites fabricated by the chemical vapor infiltration method are susceptible to high void content and inhomogeneity. The condition of such materials may be characterized nondestructively with ultrasonic methods. In this work, longitudinal and shear waves were used in the quantitative determination of elastic constants of Nicalon{trademark}/SiC composites as a function of volume percent of porosity. Elastic stiffness constants were obtained for both the in-plane and out-of-plane directions with respect to fiber fabric. The effect of porosity on the modulus of woven fabric composites was also modeled and compared to the measured results. Scan images based on the amplitude and time-of-flight of radio frequency (RF) ultrasonic pulses were used for evaluating the material homogeneity for the purpose of optimizing the manufacturing process and for correlation with the mechanical testing results.
Submitted to the EUROCAST ’ 17 Workshop on Theory and Applications of Metaheuristic Algorithms . Towards System-Aware Routes ?

Within this paper, we focus on the development of algorithms capable of providing route suggestions to multiple simultaneously traveling users such that the (negative) impacts of the routes among each other are minimized. We refer to this kind of routes as system-aware routes. E.g., if multiple travelers are concurrently following the same route in a street network, it is most likely that traffic congestion occur. If the same set of travelers is, however, distributed over multiple roads/routes, the traffic flow is maintained and negative effects like increased CO2 emissions are reduced. Today’s routing and navigation devices are, in most cases, not connected with each other, meaning that each user request is handled separately—even if the routing requests are all processed on a centrally operated infrastructure. However, dependent on the availability of traffic data, some devices adapt route suggestions based on observed (or typical) traffic conditions. This behavior leads to a so-called user equilibrium (UE) [5] where travelers cannot reduce their individual travel time by choosing another route. In contrast to an UE, a system optimum (SO) [5] consists of a traffic state where the average travel time is minimized. Obviously, this statement is equivalent to the observation that in a SO the overall travel time, i.e. the sum of all travel times, is minimized or the (overall) traffic flow is maximized. Negative environmental impacts caused by traffic congestion are reduced as well. Reaching a SO requires cooperative travelers as well as supporting technologies sharing—among others—(traffic) information with each other. First solutions to the basic underlying problem of finding a shortest route in a given network reach back to the late 50ies [2]. There were significant improvements in the last decade, especially with respect to speeding-up techniques via pre-processing, cf. [3] or [1] for a more comprehensive survey,. There is, however,
A nuclear complex of rictor and insulin receptor substrate-2 is associated with albuminuria in diabetic mice.

BACKGROUND Signaling events associated with diabetic nephropathy are not well understood. Triangulation of events triggered by unrelated bioactive peptides nephrilin and anephril, both of which inhibit albuminuria in diabetic mice, could reveal a common subset of events associated with albuminuria. METHODS db/db mice received 20 microg/day anephril or nephrilin for 7 weeks. Streptozotocin (STZ)-treated DBA/2J mice received 2 mg/kg nephrilin for 26 days. In both studies, urine albumin and creatinine, plasma glucose, and tissue proteins were measured by enzyme-linked immunosorbent assay (ELISA). In a safety study, DBA/2J mice received 20 mg/kg nephrilin for 26 days, and tissues from these mice were fixed in formalin for histological analysis. HEK293 human kidney cells were treated with glycated hemoglobin plus 20 microg/mL nephrilin or anephril for 24 h. RESULTS Both peptides reduced albuminuria in db/db mice compared to saline-treated animals without affecting plasma glucose or insulin. In kidney tissues, the immunoreactivities of insulin receptor substrate-2 (IRS2), phosphorylated protein kinase C (p-PKC), and serum- and glucocortocoid-inducible kinase (SGK1) were reduced. Nephrilin, but not anephril, lowered elevated SGK1 in spleens of db/db mice. In STZ-pretreated DBA/2J mice, nephrilin reduced albuminuria and the accumulation of nuclear Rictor, IRS2, and p-PKC in the kidney. In cultured kidney cells, nephrilin disrupted the association of Rictor with IRS2 and nuclear compartmentalization. Histopathological examination of tissues from mice treated with 20 mg/kg nephrilin daily for 26 days showed no significant pathology compared to saline-treated controls. CONCLUSIONS We define a subset of signaling markers closely associated with albuminuria. Mammalian target of rapamycin complex 2 (mTORC2)::IRS complexes may play a role in the nuclear accumulation, and possible downstream transcriptional effects, of p-PKC. The activity and apparent safety of nephrilin in rodents suggest a novel intervention strategy for diabetic kidney disease.
Temperature Cycles in the Heisenberg Spin Glass

We study numerically the nonequilibrium dynamics of the three-dimensional Heisenberg EdwardsAnderson spin glass submitted to protocols during which temperature is shifted or cycled within the spin glass phase. We show that (partial) rejuvenation and (perfect) memory effects can be numerically observed and study both effects in detail. We quantitatively characterize their dependences on parameters such as the amplitude of the temperature changes, the timescale at which the changes are performed, and the cooling rates used to vary the temperature. We contrast our results both to those found numerically in the Ising version of the model, and to experimental results in different samples. We discuss the theoretical interpretations of our findings, arguing, in particular, that ‘full’ rejuvenation can be observed in experiments even if temperature chaos is absent.
Distance-based control of K4 formation with almost global convergence

In this paper, we propose a distance-based formation control strategy that can enable four mobile agents, which are modelled by a group of single-integrators, to achieve the desired formation shape specified by using six consistent inter-agent distances in a 2-dimensional space. The control law is closely related to a gradient-based control law formed from a potential function reflecting the error between the actual inter-agent distances and the desired inter-agent distances. There are already control strategies achieving the same objective in a distance-based control manner in the literature, but the results do not yet include a global as opposed to local stability analysis. We propose a control strategy modified from the existing gradient-based control law so that we can achieve almost global convergence to the desired formation shape, and the control law uses known properties for an associated formation shape control problem involving a four-agent tetrahedron formation in 3-dimensional space. Simulation results verifying our analysis are also presented.
A prospective study of laboratory findings in dapsone treated patients with Pemphigus vulgaris and foliaceus

Background: Pemphigus is an autoimmune disorder of skin and mucous membranes that appears in the form of blistering on skin and mucous membrane and may lead to loss of life in the absence of proper treatment. Treatment is effected by using immunosuppressant drugs such as Azathioprine cyclophosphamide and some others. Objective: Our purpose of this study was to survey about blood, hepatic and renal side effects of dapsone with the patients affected by Pemphigus. Methods: The test was carried out on 37 patients who were suffering from acute Pemphigus and had undergone some therapy with dapsone amongst which 5 patients were excluded from the research because of hepatic and hematic symptoms. The study was carried on with 31 patients with an average age of 40 ± 17.5. They had no symptoms necessitating the stop of administration of the medicine. Results: Statistical analysis indicated no significant difference in the test results before and after the therapy and only platelet counts showed significant difference before and after the therapy (p<0.05). Conclusion: This study indicated that among all disagreements about dapsone treatment, dapsone can be applied as adjuvant therapy.
Novel approach to numerical measurements of the configurational entropy in supercooled liquids

Significance When liquids are cooled sufficiently fast, they remain trapped in an amorphous metastable state called a “glass. ” Due to their highly disordered structure at the microscale, however, glasses are characterized by a large multiplicity of metastable states. The configurational entropy represents a measure of their number and can be estimated in experiments and simulations via different, and sometimes inconsistent, approximations. Here we propose a novel method to compute the configurational entropy in a computer simulation. Compared with other approaches, the proposed numerical scheme allows one to obtain an observable that is conceptually closer to the theoretical definition and at the same time yields results in better agreement with experiments. The configurational entropy is among the key observables to characterize experimentally the formation of a glass. Physically, it quantifies the multiplicity of metastable states in which an amorphous material can be found at a given temperature, and its temperature dependence provides a major thermodynamic signature of the glass transition, which is experimentally accessible. Measurements of the configurational entropy require, however, some approximations that have often led to ambiguities and contradictory results. Here we implement a novel numerical scheme to measure the configurational entropy Σ(T) in supercooled liquids, using a direct determination of the free-energy cost to localize the system within a single metastable state at temperature T. For two prototypical glass-forming liquids, we find that Σ(T) disappears discontinuously above a temperature Tc, which is slightly lower than the usual estimate of the onset temperature for glassy dynamics. This observation is in good agreement with theoretical expectations but contrasts sharply with alternative numerical methods. While the temperature dependence of Σ(T) correlates with the glass fragility, we show that the validity of the Adam–Gibbs relation (relating configurational entropy to structural relaxation time) established in earlier numerical studies is smaller than previously thought, potentially resolving an important conflict between experiments and simulations.
Piezoelectric, Piezo-Phototronic, and UV Sensing Properties of Single Ultra Long Nanobelt

We present proof-of-concept of a potential new single ZnO nanobelt based sensor for converting piezoelectric effect in to visible light. Mechanical stress on ZnO ultra-long nanobelts was generated by bending at different angles and systematic color change was observed. IV curves suggested significant change in the electrical properties with applied stress. As-constructed single nanobelt UV sensor exhibit good sensitivity, indicating that these structures can be a promising candidate for miniaturization of proposed device and UV irradiation monitoring in many areas.
Reflecting on imitation in autism : Introduction

In response to our call for papers for a special issue of Journal of Experimental Child Psychology on functions and mechanisms of imitation in childhood, we received a surprisingly large number of manuscripts on a wide range of topics. We were happy and encouraged that so much interesting work is being done on imitation, and sorry that space and time constraints meant that we could not publish more of them. We ended up with two special issues, one on imitation in children with autism (the current issue) and one on imitation in typically-developing children (forthcoming). Here we provide a brief introduction to the three papers that constitute the current issue on autism and offer some speculation on how these papers might shed light on one of the more keenly debated topics in recent developmental psychopathology research: the association between autism and a dysfunctional mirror system. The identification of mirror neurons in the monkey prefrontal cortex (di Pellegrino, Fadiga, Fogassi, Gallese, & Rizzolatti, 1992; Gallese, Fadiga, Fogassi, & Rizzolatti, 1996; Rizzolatti, Fadiga, Fogassi, & Gallese 1996) and subsequent mapping of the analogue mirror system in humans (Iacoboni et al., 1999) have been hyped as being among the most important psychological discoveries in the last two decades. Indeed, it has been suggested that the mirror system may provide a unifying framework for understanding a host of human abilities including empathy, language, and theory of mind: Mirror neurons, it has been famously claimed, will do for psychology what DNA did for biology (Ramachandran, 2000). Of most relevance to the current issue, (1) the mirror system is considered to play a major role in the development and expression of imitation and (2) the symptoms associated with autism have been proposed to be directly attributable to mirror neuron dysfunction (see below). However, the papers in this issue provide information that calls some of these claims into question and that helps provide the foundation for a new perspective. Originally discovered in macaque monkeys, mirror neurons were found to fire both when the monkey performed a specific action (e.g., reaching for a peanut) and when it observed someone else performing the same action. Such direct mapping of produced and seen actions has seemingly obvious implications for imitation. Indeed, a number of theorists have linked the mirror system to imitation, typically based on the assumption that imitation fundamentally relies on a mechanism that ‘‘directly maps a pictorial or kinematic description of the observed action onto an internal motor representation of the same action” (Iacoboni et al., 1999, p. 2526). There are problems with this so-called ‘‘direct matching hypothesis,” though (Southgate, Gergely, & Csibra, in press; Southgate & Hamilton, 2008; Turella, Pierno, Tubaldi, & Castiello, in press). To begin with, monkeys, the only animal in which mirror neurons have been directly identified, are notoriously bad at imitation (Tomasello & Call, 1997). It has thus been suggested that mirror neurons are necessary but not sufficient for imitation to emerge:
Culture and group-based emotions: could group-based emotions be dialectical?

ABSTRACT Group-based emotions are experienced when individuals are engaged in emotion-provoking events that implicate the in-group. This research examines the complexity of group-based emotions, specifically a concurrence of positive and negative emotions, focusing on the role of dialecticism, or a set of folk beliefs prevalent in Asian cultures that views nature and objects as constantly changing, inherently contradictory, and fundamentally interconnected. Study 1 found that dialecticism is positively associated with the complexity of Chinese participants’ group-based emotions after reading a scenario depicting a positive intergroup experience. Study 2 found that Chinese participants experienced more complex group-based emotions compared with Dutch participants in an intergroup situation and that this cultural difference was mediated by dialecticism. Study 3 manipulated dialecticism and confirmed its causal effect on complex group-based emotions. These studies also suggested the role of a balanced appraisal of an intergroup situation as a mediating factor.
Compressed single pixel imaging in the spatial frequency domain.

We have developed compressed sensing single pixel spatial frequency domain imaging (cs-SFDI) to characterize tissue optical properties over a wide field of view ( 35 ? mm × 35 ? mm ) using multiple near-infrared (NIR) wavelengths simultaneously. Our approach takes advantage of the relatively sparse spatial content required for mapping tissue optical properties at length scales comparable to the transport scattering length in tissue ( l tr ? 1 ? mm ) and the high bandwidth available for spectral encoding using a single-element detector. cs-SFDI recovered absorption ( ? a ) and reduced scattering ( ? s ? ) coefficients of a tissue phantom at three NIR wavelengths (660, 850, and 940 nm) within 7.6% and 4.3% of absolute values determined using camera-based SFDI, respectively. These results suggest that cs-SFDI can be developed as a multi- and hyperspectral imaging modality for quantitative, dynamic imaging of tissue optical and physiological properties.