bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Basis for Lytic Bacteriophage Resistance in Enterococci
Authors: Duerkop Breck A. , Huo Wenwen , Bhardwaj Pooja , Palmer Kelli L. , Hooper Lora V.
Published: August 2016

The human intestine harbors diverse communities of bacteria and bacteriophages. Given the specificity of phages for their bacterial hosts, there is growing interest in using phage therapies to combat the rising incidence of multidrug-resistant bacterial infections. A significant barrier to such therapies is the rapid development of phage-resistant bacteria, highlighting the need to understand how bacteria acquire phage resistance
in vivo
. Here we identify novel lytic phages in municipal raw sewage that kill
Enterococcus faecalis
, a Gram-positive opportunistic pathogen that resides in the human intestine. We show that phage infection of
E. faecalis
requires a predicted integral membrane protein that we have named PIP
EF
(for phage infection protein from
E. faecalis
). We find that PIP
EF
is conserved in
E. faecalis
and harbors a 160-amino-acid hypervariable region that determines phage tropism for distinct enterococcal strains. Finally, we use a gnotobiotic mouse model of
in vivo
phage predation to show that the sewage phages temporarily reduce
E. faecalis
colonization of the intestine but that
E. faecalis
acquires phage resistance through mutations in PIP
EF
. Our findings define the molecular basis for an evolutionary arms race between
E. faecalis
and the lytic phages that prey on them. They also suggest approaches for engineering
E. faecalis
phages that have altered host specificity and that can subvert phage resistance in the host bacteria.

IMPORTANCE
Bacteriophage therapy has received renewed attention as a potential solution to the rise in antibiotic-resistant bacterial infections. However, bacteria can acquire phage resistance, posing a major barrier to phage therapy. To overcome this problem, it is necessary to understand phage resistance mechanisms in bacteria. We have unraveled one such resistance mechanism in
Enterococcus faecalis
, a Gram-positive natural resident of the human intestine that has acquired antibiotic resistance and can cause opportunistic infections. We have identified a cell wall protein hypervariable region that specifies phage tropism in
E. faecalis
. Using a gnotobiotic mouse model of
in vivo
phage predation, we show that
E. faecalis
acquires phage resistance through mutations in this cell wall protein. Our findings define the molecular basis for lytic phage resistance in
E. faecalis
. They also suggest opportunities for engineering
E. faecalis
phages that circumvent the problem of bacterial phage resistance.
Moonshot Science—Risks and Benefits
Authors: Casadevall Arturo , Fang Ferric C.
Published: August 2016

Ever since the successful Apollo 11 Moon landing in 1969, a “moonshot” has come to signify a bold effort to achieve a seemingly impossible task. The Obama administration recently called for a moonshot to cure cancer, an initiative that has elicited mixed responses from researchers who welcome additional funding but worry about raising expectations. We suggest that a successful moonshot requires a sufficient understanding of the basic science underlying a problem in question so that efforts can be focused on engineering a solution. Current gaps in our basic knowledge of cancer biology make the cancer moonshot a uniquely challenging endeavor. Nevertheless, history has shown that intensive research efforts have frequently yielded conceptual and technological breakthroughs with unanticipated benefits for society. We expect that this effort will be no different.
Growing concern following compression mammography
Authors: van Netten Johannes Pieter , Hoption Cann Stephen , Thornton Ian , Finegan Rory
Published: August 2016

A patient without clinical symptoms had a mammogram in October 2008. The procedure caused intense persistent pain, swelling and development of a haematoma following mediolateral left breast compression. Three months later, a 9×11 cm mass developed within the same region. Core biopsies showed a necrotizing high-grade ductal carcinoma, with a high mitotic index. Owing to its extensive size, the patient began chemotherapy followed by trastuzumab and later radiotherapy to obtain clear margins for a subsequent mastectomy. The mastectomy in October 2009 revealed an inflammatory carcinoma, with 2 of 3 nodes infiltrated by the tumour. The stage IIIC tumour, oestrogen and progesterone receptor negative, was highly HER2 positive. A recurrence led to further chemotherapy in February 2011. In July 2011, another recurrence was removed from the mastectomy scar. She died of progressive disease in 2012. In this article, we discuss the potential influence of compression on the natural history of the tumour.
Rapid spread ofNeisseria gonorrhoeaeciprofloxacin resistance due to a newly introduced resistant strain in Nuuk, Greenland, 2012–2015: a community-based prospective cohort study
Authors: Pedersen Michael Lynge , Poulsen Peter , Berthelsen Lene , Nørgaard Christina , Hoffmann Steen , Jensen Jørgen Skov
Published: August 2016

Objectives

To determine the antimicrobial susceptibility and genotype distribution ofNeisseria gonorrhoeaestrains isolated from a cohort of patients in Nuuk, Greenland in order to assess the risk of rapid spread in the event of introduction of new strains.

Methods

Gonococcal isolates (n=102) obtained from a prospective cohort study of ciprofloxacin resistance were collected between March 2012 and February 2013. Etest minimal inhibitory concentrations (MICs) were determined for ciprofloxacin, azithromycin, ceftriaxone, penicillin, tetracycline, spectinomycin and gentamicin. All isolates were subjected to molecular typing usingN. gonorrhoeaemultiantigen sequence typing (NG-MAST). After the introduction of a ciprofloxacin-resistant strain in early 2014, an additional 18 isolates were characterised.

Results

During the study period, all 102 isolates were fully susceptible to ciprofloxacin (≤0.03 mg/L), azithromycin, spectinomycin, gentamicin and ceftriaxone. 10 different NG-MAST types circulated in Nuuk but 7 were found as single isolates, and 3 of the 7 belonged to 1 of the 3 major genogroups (G210, G9816 and G9817) together comprising 96% of the 102 isolates. ST210 accounted for 55% of the 102 strains. The newly introduced ciprofloxacin resistant strain belonged to ST2400 and dominated the population with 59% resistant strains within 6 months after its introduction. All G2400 strains had MICs≥2 mg/L.

Conclusions

Introduction of a ciprofloxacin-resistant strain into a very homogeneousN. gonorrhoeaepopulation led to an explosive spread of the resistant clone, probably as a result of large sexual networks suggested by the strain homogeneity. Careful surveillance of antimicrobial susceptibility is essential to avoid widespread treatment failure in closed populations.
Suspected anaphylaxis from intravenous cefazolin during general anaesthesia in a dog
Authors: Pang Daniel S J , Prebble Melanie
Published: August 2016

A six‐year‐old female Shetland Sheepdog with a history of cardiorespiratory compromise during general anaesthesia was referred for ovariohysterectomy surgery. Clinical examination was unremarkable at presentation and physiological parameters under general anaesthesia were within expected ranges during preparation for surgery. Shortly after injecting intravenous cefazolin, the audible signal from the Doppler ultrasound unit stopped. Rapid survey of the patient revealed tachycardia with weak femoral pulses, tachypnoea, hyperpnoea and substantially increased resistance to manual positive pressure ventilation. Stopping inhalant anaesthesia, administering salbutamol, corticosteroids and diphenhydramine were associated with resolution of clinical signs. However, marked hypotension and resistance to ventilation recurred approximately 25 minutes later. Low dose intravenous adrenaline (5 mcg/kg) was effective at increasing arterial blood pressure and reversing respiratory dysfunction. Surgery was completed and the patient recovered uneventfully. Initial reliance on second‐line therapy and delay in administering adrenaline, the recommended treatment for anaphylaxis, may have slowed resolution of clinical signs.
Technical issues in a spherical system coupled with isotropic matter distribution and the horizon problem with higher curvature quantities
Authors: Hussain T. , Khurshudyan M.
Published: August 2016

In this paper, we explore some technical issue in the study of a spherical system coupled with isotropic matter distribution. We also study the horizon problem under the influence of higher curvature quantities. We evaluate well-known equations of motion. We also join the exterior region with an interior one by taking the well-known matching conditions. We first find total matter content within the system and then calculate black hole and cosmological horizons. We have developed a technique for determining some dynamical variables that are involved in controlling the time duration of the emergence of horizons as well as singularities.
Communicating science: Sending the right message to the right audience
Authors: Wilson Matthew J. , Ramey Tonya L. , Donaldson Michael R. , Germain Ryan R. , Perkin Elizabeth K.
Published: August 2016

For science communication to be effective, scientists must understand which sources of information their target audiences most frequently use and trust. We surveyed academic and non-academic scientists, natural resource managers, policymakers, students, and the general public about how they access, trust, and communicate scientific information. We found trust and use of information sources was related to participant age and group identity, but all groups had high levels of use and trust of personal experience and colleagues. Academic journals were the most trusted source by all groups, and social media the least trusted by most groups. The level of communication between target groups was not always bilateral, with the public generally perceiving their interaction with all other groups as low. These results provide remarkable insight into the flow of scientific information. We present these findings in the context of facilitating information flow between scientists and other stakeholders of scientific information.
The influence of the depth of k-core layers on the robustness of interdependent networks against cascading failures
Authors: Dong Zhengcheng , Fang Yanjun , Tian Meng , Kong Zhengmin
Published: August 2016

The hierarchical structure, [Formula: see text]-core, is common in various complex networks, and the actual network always has successive layers from 1-core layer (the peripheral layer) to [Formula: see text]-core layer (the core layer). The nodes within the core layer have been proved to be the most influential spreaders, but there is few work about how the depth of [Formula: see text]-core layers (the value of [Formula: see text]) can affect the robustness against cascading failures, rather than the interdependent networks. First, following the preferential attachment, a novel method is proposed to generate the scale-free network with successive [Formula: see text]-core layers (KCBA network), and the KCBA network is validated more realistic than the traditional BA network. Then, with KCBA interdependent networks, the effect of the depth of [Formula: see text]-core layers is investigated. Considering the load-based model, the loss of capacity on nodes is adopted to quantify the robustness instead of the number of functional nodes in the end. We conduct two attacking strategies, i.e. the RO-attack (Randomly remove only one node) and the RF-attack (Randomly remove a fraction of nodes). Results show that the robustness of KCBA networks not only depends on the depth of [Formula: see text]-core layers, but also is slightly influenced by the initial load. With RO-attack, the networks with less [Formula: see text]-core layers are more robust when the initial load is small. With RF-attack, the robustness improves with small [Formula: see text], but the improvement is getting weaker with the increment of the initial load. In a word, the lower the depth is, the more robust the networks will be.
Topological string theory revisited I: The stage
Authors: Jia Bei
Published: August 2016

In this paper, we reformulate topological string theory using supermanifolds and supermoduli spaces, following the approach worked out by Witten (Superstring perturbation theory revisited, arXiv:1209.5461 ). We intend to make the construction geometrical in nature, by using supergeometry techniques extensively. The goal is to establish the foundation of studying topological string amplitudes in terms of integration over appropriate supermoduli spaces.
Antiself-dual Yang–Mills, modified Faddeevs–Jackiw formalism and hidden BRS invariance
Authors: Gupta Saurabh , Roychowdhury Raju
Published: August 2016

We analyze the constraints for a system of antiself-dual Yang–Mills (ASDYM) equations by means of the modified Faddeev–Jackiw method in [Formula: see text] and [Formula: see text] gauges à la Yang. We also establish the Hamiltonian flow for ASDYM system through the hidden BRS invariance in both the gauges. Finally, we remark on the bi-Hamiltonian nature of ASDYM and the compatibility of the symplectic structures therein.
Finite width of the optical event horizon and enhancement of analog Hawking radiation
Authors: Vinish Y. , Fleurov V.
Published: August 2016

Coherent light propagating in a bulk Kerr nonlinear defocusing medium obeys nonlinear Schrödinger (NLS) equation, which is similar to the Gross–Pitaevskii equation for Bose–Einstein condensates (BECs). An equivalent hydrodynamic approach allows one to consider propagation of light as a flow of an equivalent “luminous fluid.” An analog optical event horizon can be formed when the flow velocity of this fluid equals the local sound velocity, determined by the nonlinear term in the NLS equation. The analog event horizon is characterized by a finite width, also determined by the nonlinearity length, or by the healing length in Bose–Einstein condensates. The various eigenmodes of fluctuations are found in the immediate vicinity of the event horizon and the scattering matrix due to the finite width horizon is calculated to be within the leading order corrections in the nonlinearity length. The Hawking radiation is found to be enhanced with respect to that of a Planck’s black body spectrum and is characterized by the emissivity greater than one. A procedure of paraxial quantization of the fluctuation field is discussed and its connection to the conventional quantization of the electromagnetic field is demonstrated. Quantum fluctuations of the electric field energy and those of its flow are calculated.
Higher holonomy of formal homology connections and braid cobordisms
Authors: Kohno Toshitake
Published: August 2016

We construct a representation of the homotopy 2-groupoid of a manifold by means of Chen’s formal homology connections. By using the idea of this 2-holonomy map, we describe a method to obtain a representation of the category of braid cobordisms.
Weyl n-algebras and the Kontsevich integral of the unknot
Authors: Markarian Nikita
Published: August 2016

Given a Lie algebra with a scalar product, one may consider the latter as a symplectic structure on a [Formula: see text]-scheme, which is the spectrum of the Chevalley–Eilenberg algebra. In Sec. 1 we explicitly calculate the first-order deformation of the differential on the Hochschild complex of the Chevalley–Eilenberg algebra. The answer contains the Duflo character. This calculation is used in the last section. There we sketch the definition of the Wilson loop invariant of knots, which is, hopefully, equal to the Kontsevich integral, and show that for unknot they coincide. As a byproduct, we get a new proof of the Duflo isomorphism for a Lie algebra with a scalar product.
Linking numbers in non-orientable 3-manifolds
Authors: Vassiliev Victor A.
Published: August 2016

The construction of integer linking numbers of closed curves in a three-dimensional manifold usually appeals to the orientation of this manifold. We discuss how to avoid it constructing similar homotopy invariants of links in non-orientable manifolds.
The best constants in the Wirtinger inequality
Authors: Liu Yongping , Wu Wenyan , Xu Guiqiao
Published: August 2016

This study aimed to determine the best constants in the Wirtinger inequality [Formula: see text] where [Formula: see text] is defined on [Formula: see text] with [Formula: see text]. First, we referred the computation of [Formula: see text] to the maximal eigenvalue of an integral type operator [Formula: see text]. Second, we proved that the computation of the eigenvalues of [Formula: see text] is equivalent to the solution of a Strum–Liouville problem with some boundary conditions and hence we referred the computation of [Formula: see text] to finding the minimal zero of a function with one variable. Third, by comparing with a result of Lifshits, Papageorgiou, Woźniakowski, we obtained that the strong asymptotic order of [Formula: see text]: [Formula: see text].
Multi-class ℓ2-Boost with the scoring coding
Authors: Ye Lei , Wang Can , Xu Xin , Chen Wei
Published: August 2016

Boosting, one of the best off-the-shelf classification methods, has evoked widespread interest in machine learning and statistics. However, the original algorithm was developed for binary classification problems. In this paper, we study multi-class boosting algorithms under the [Formula: see text]-loss framework, and devise two multi-class [Formula: see text]-Boost algorithms. These are based on coordinate descent and gradient descent to minimize the multi-class [Formula: see text]-loss function. We derive a scoring coding scheme using optimal scoring constraints to encode class labels and a simple decoder to recover the true class labels. Our boosting algorithms are easily implemented and their results converge to the global optimum. Experiments with synthetic and real-world datasets show that, compared with several state-of-art methods, our algorithms provide more accurate results.
Review of Recent Advances in Carbon Nanotube Biosensors Based on Field-Effect Transistors
Authors: Hou Guangfeng , Zhang Lu , Ng Vianessa , Wu Zhizhen , Schulz Mark
Published: August 2016

The extraordinary physiochemical properties of carbon nanotubes (CNTs) stimulated their wide application in biosensing research. Nanotube characteristics of fast electron transport, large surface area, high strength, excellent catalytic activity and good chemical stability contribute to ultrasensitive, highly selective and stable CNT biosensors. Among the various CNT biosensors, the field-effect transistor (FET) architecture has received tremendous attention due to the advantages of high performance, miniaturization, and capability for mass production. In this paper, we address recent advances in the development of CNT biosensors based on FETs. The synthesis and properties of CNTs are discussed, along with their integration into biosensors. Recent progress in device fabrication, including CNT functionalization, attachment, and bioreceptor immobilization in CNT-based FET biosensors are highlighted. Examples in medical, food and environmental fields are illustrated.
Structure and Self-Assembly of Multicolored Naphthalene Diimides Semiconductor
Authors: Yao Zhili , Sun Yuan , Kang Chen
Published: August 2016

The one-dimensional (1D) self-assembly of [Formula: see text]-electron molecules offers efficient strategies to enhance energy and charge transfer via highly ordered and conductive [Formula: see text] stacking of the chromophores. The chromophore rich nanostructures have great potential to serve as promising candidate materials for optoelectronic devices. However, the design and control of highly ordered nanostructures with multicolored chromophore redox gradients require finely chosen synthetic strategies and a delicate balance of supramolecular interactions. In this paper, we will introduce new strategies focused on self-assembly of nanofibers based on lysine derivatives functionalized with multi colored chromophores.
Recombination characteristics of therapeutic ion beams on ion chamber dosimetry
Authors: Matsufuji Naruhiro , Matsuyama Tetsuharu , Sato Shinji , Kohno Toshiyuki
Published: August 2016

In heavy ion radiotherapy, ionization chambers are regarded as a standard for determining the absorbed dose given to patients. In ion dosimetry, it is necessary to correct the radiation quality, which depends on the initial recombination effect. This study reveals for the radiation quality dependence of the initial recombination in air in ion dosimetry. Ionization charge was measured for the beams of protons at 40–160 MeV, carbon at 21–400 MeV/n, and iron at 23.5–500 MeV/n using two identical parallel-plate ionization chambers placed in series along the beam axis. The downstream chamber was used as a monitor operated with a constant applied voltage, while the other chamber was used for recombination measurement by changing the voltage. The ratio of the ionization charge measured by the two ionization chambers showed a linear relationship with the inverse of the voltage in the high-voltage region. The initial recombination factor was estimated by extrapolating the obtained linear relationship to infinite voltage. The extent of the initial recombination was found to increase with decreasing incident energy or increasing atomic number of the beam. This behavior can be explained with an amorphous track structure model: the increase of ionization density in the core region of the track due to decreasing kinetic energy or increasing atomic number leads to denser initial ion production and results in a higher recombination probability. For therapeutic carbon ion beams, the extent of the initial recombination was not constant but changed by 0.6% even in the target region. This tendency was quantitatively well reproduced with the track-structure based on the initial recombination model; however, the transitional change in the track structure is considered to play an important role in further understanding of the characteristics of the initial recombination.
Development of heavy-ion radiotherapy technology with HIMAC
Authors: Noda Koji
Published: August 2016

Since 1994, HIMAC has carried out clinical studies and treatments for more than 9000 cancer patients with carbon-ion beams. During the first decade of the HIMAC study, a single beam-wobbling method, adopted as the HIMAC beam-delivery technique, was improved for treatments of moving tumors and for obtaining more conformal dose distribution. During the second decade, a pencil-beam 3D scanning method has been developed toward an “adaptive cancer treatment” for treatments of both static and moving tumors. A new treatment research facility was constructed with HIMAC in order to verify the developed 3D scanning technology through a clinical study that has been successfully conducted since 2011. As the next stage, a compact heavy-ion rotating gantry with a superconducting technology has been developed for the more accurate and shorter-course treatments. The twenty-year development of the heavy-ion radiotherapy technologies including accelerator technologies with HIMAC is reviewed.
MCNPX simulations of the silicon carbide semiconductor detector response to fast neutrons from D–T nuclear reaction
Authors: Sedlačková Katarína , Šagátová Andrea , Zat'ko Bohumír , Nečas Vladimír , Solar Michael , Granja Carlos
Published: August 2016

Silicon Carbide (SiC) has been long recognized as a suitable semiconductor material for use in nuclear radiation detectors of high-energy charged particles, gamma rays, X-rays and neutrons. The nuclear interactions occurring in the semiconductor are complex and can be quantified using a Monte Carlo-based computer code. In this work, the MCNPX (Monte Carlo N-Particle eXtended) code was employed to support detector design and analysis. MCNPX is widely used to simulate interaction of radiation with matter and supports the transport of 34 particle types including heavy ions in broad energy ranges. The code also supports complex 3D geometries and both nuclear data tables and physics models. In our model, monoenergetic neutrons from D–T nuclear reaction were assumed as a source of fast neutrons. Their energy varied between 16 and 18.2 MeV, according to the accelerating voltage of the deuterons participating in D–T reaction. First, the simulations were used to calculate the optimum thickness of the reactive film composed of High Density PolyEthylene (HDPE), which converts neutral particles to charged particles and thusly enhancing detection efficiency. The dependency of the optimal thickness of the HDPE layer on the energy of the incident neutrons has been shown for the inspected energy range. Further, from the energy deposited by secondary charged particles and recoiled ions, the detector response was modeled and the effect of the conversion layer on detector response was demonstrated. The results from the simulations were compared with experimental data obtained for a detector covered by a 600 and 1300 [Formula: see text]m thick conversion layer. Some limitations of the simulations using MCNPX code are also discussed.
Burning high-level TRU waste in fusion fission reactors
Authors: Shen Yaosong
Published: August 2016

Recently, the concept of actinide burning instead of a once-through fuel cycle for disposing spent nuclear fuel seems to get much more attention. A new method of burning high-level transuranic (TRU) waste combined with Thorium–Uranium (Th–U) fuel in the subcritical reactors driven by external fusion neutron sources is proposed in this paper. The thorium-based TRU fuel burns all of the long-lived actinides via a hard neutron spectrum while outputting power. A one-dimensional model of the reactor concept was built by means of the ONESN_BURN code with new data libraries. The numerical results included actinide radioactivity, biological hazard potential, and much higher burnup rate of high-level transuranic waste. The comparison of the fusion–fission reactor with the thermal reactor shows that the harder neutron spectrum is more efficient than the soft. The Th–U cycle produces less TRU, less radiotoxicity and fewer long-lived actinides. The Th–U cycle provides breeding of [Formula: see text]U with a long operation time (>20 years), hence significantly reducing the reactivity swing while improving safety and burnup.
Detection of pulsed neutrons with solid-state electronics
Authors: Chatzakis J. , Rigakis I. , Hassan S. M. , Clark E. L. , Lee P.
Published: August 2016

Measurements of the spatial and time-resolved characteristics of pulsed neutron sources require large area detection materials and fast circuitry that can process the electronic pulses readout from the active region of the detector. In this paper, we present a solid-state detector based on the nuclear activation of materials by neutrons, and the detection of the secondary particle emission of the generated radionuclides’ decay. The detector utilizes a microcontroller that communicates using a modified SPI protocol. A solid-state, pulse shaping filter follows a charge amplifier, and it is designed as an inexpensive, low-noise solution for measuring pulses measured by a digital counter. An imaging detector can also be made by using an array of these detectors. The system can communicate with an interface unit and pass an image to a personal computer.
LiCaAlF6 scintillators in neutron and gamma radiation fields
Authors: Viererbl L. , Klupák V. , Vinš M. , Koleška M. , Šoltés J. , Yoshikawa A. , Nikl M.
Published: August 2016

Intentionally doped LiCaAlF6 (LiCAF) single crystals are prospective scintillators, especially for thermal neutron detection through the 6Li(n,t)4He nuclear reaction. Four different LiCAF scintillator samples were tested in various neutron and gamma fields. Two of the tested samples were LiCAF:Eu and LiCAF:Eu,Na single crystals, and another two samples were made of LiCAF:Eu micro crystals dispersed in transparent rubber, with different rubber dimensions. All LiCAF samples contain lithium enriched to[Formula: see text]Li. A plutonium–beryllium source was used as a neutron source. The neutron spectrum was modified by moderator and filter to get different ratios between thermal, epithermal and fast neutron fluence rates. The MCNP code was used for calculations of the fluence rates for different configurations. Radionuclides [Formula: see text]Cs and [Formula: see text]Co were applied as gamma radiation sources. The light signal from the scintillator was evaluated with a photomultiplier and a multichannel analyzer. The purpose of this work was to study the characteristics of LiCAF scintillators, especially the ability to discriminate signals from neutron and gamma radiation, which is the basic scintillator condition for neutron detection in mixed neutron-gamma radiation fields. Generally, the discrimination can be done by the pulse height and/or the pulse shape of the evaluated signals. Both methods can be used for a LiCAF scintillator. However, only the pulse height discrimination method is discussed in this paper. The possibility of fast neutron detection with LiCAF scintillators was also tested.
Radiation protection considerations along a radioactive ion beam transport line
Authors: Sarchiapone Lucia , Zafiropoulos Demetre
Published: August 2016

The goal of the SPES project is to produce accelerated radioactive ion beams for Physics studies at “Laboratori Nazionali di Legnaro” (INFN, Italy). This accelerator complex is scheduled to be built by 2016 for an effective operation in 2017. Radioactive species are produced in a uranium carbide target, by the interaction of 200 [Formula: see text]A of protons at 40 MeV. All of the ionized species in the 1+ state come out of the target (ISOL method), and pass through a Wien filter for a first selection and an HMRS (high mass resolution spectrometer). Then they are transported by an electrostatic beam line toward a charge state breeder (where the 1[Formula: see text] to n[Formula: see text] multi-ionization takes place) before selection and reacceleration at the already existing superconducting linac. The work concerning dose evaluations, activation calculation, and radiation protection constraints related to the transport of the radioactive ion beam (RIB) from the target to the mass separator will be described in this paper. The FLUKA code has been used as tool for those calculations needing Monte Carlo simulations, in particular for the evaluation of the dose rate due to the presence of the radioactive beam in the selection/interaction points. The time evolution of a radionuclide inventory can be computed online with FLUKA for arbitrary irradiation profiles and decay times. The activity evolution is analytically evaluated through the implementation of the Bateman equations. Furthermore, the generation and transport of decay radiation (limited to gamma, beta- and beta[Formula: see text] emissions) is possible, referring to a dedicated database of decay emissions using mostly information obtained from NNDC, sometimes supplemented with other data and checked for consistency. When the use of Monte Carlo simulations was not feasible, the Bateman equations, or possible simplifications, have been used directly.
WorkStream
-- A Design Pattern for Multicore-Enabled Finite Element Computations
Authors: Turcksin Bruno , Kronbichler Martin , Bangerth Wolfgang
Published: August 2016

Many operations that need to be performed in modern finite element codes can be described as an operation that needs to be done independently on every cell, followed by a reduction of these
local
results into a
global
data structure. For example, matrix assembly, estimating discretization errors, or converting nodal values into data structures that can be output in visualization file formats all fall into this class of operations. Using this realization, we identify a software design pattern that we call
WorkStream
and that can be used to model such operations and enables the use of multicore shared memory parallel processing. We also describe in detail how this design pattern can be efficiently implemented, and we provide numerical scalability results from its use in the
deal
.II software library.
Carpooling Service for Large-Scale Taxicab Networks
Authors: Zhang Desheng , He Tian , Zhang Fan , Lu Mingming , Liu Yunhuai , Lee Haengju , Son Sang H.
Published: August 2016

Carpooling has long held the promise of reducing gas consumption by decreasing mileage to deliver coriders. Although ad hoc carpools already exist in the real world through private arrangements, little research on the topic has been done. In this article, we present the first systematic work to design, implement, and evaluate a carpool service, called
coRide
, in a large-scale taxicab network intended to reduce total mileage for less gas consumption. Our
coRide
system consists of three components, a dispatching cloud server, passenger clients, and an onboard customized device, called
TaxiBox
. In the
coRide
design, in response to the delivery requests of passengers, dispatching cloud servers calculate cost-efficient carpool routes for taxicab drivers and thus lower fares for the individual passengers.

To improve
coRide
’s efficiency in mileage reduction, we formulate an NP-hard route calculation problem under different practical constraints. We then provide (1) an optimal algorithm using Linear Programming, (2) a 2-approximation algorithm with a polynomial complexity, and (3) its corresponding online version with a linear complexity. To encourage
coRide
’s adoption, we present a win-win fare model as the incentive mechanism for passengers and drivers to participate. We test the performance of
coRide
by a comprehensive evaluation with a real-world trial implementation and a data-driven simulation with 14,000 taxi data from the Chinese city Shenzhen. The results show that compared with the ground truth, our service can reduce 33% of total mileage; with our win-win fare model, we can lower passenger fares by 49% and simultaneously increase driver profit by 76%.
Neighbour-Disjoint Multipath for Low-Power and Lossy Networks
Authors: Hossain A. K. M. Mahtab , Sreenan Cormac J. , Alberola Rodolfo De Paz
Published: August 2016

In this article, we describe a neighbour disjoint multipath (NDM) scheme that is shown to be more resilient amidst node or link failures compared to the two well-known node disjoint and edge disjoint multipath techniques. A centralised NDM was first conceptualised in our initial published work utilising the spatial diversity among multiple paths to ensure robustness against localised poor channel quality or node failures. Here, we further introduce a distributed version of our NDM algorithm adapting to the low-power and lossy network (LLN) characteristics. We implement our distributed NDM algorithm in Contiki OS on top of LOADng—a lightweight On-demand Ad hoc Distance Vector Routing protocol. We compare this implementation's performance with a standard IPv6 Routing Protocol for Low power and Lossy Networks (RPL), and also with basic LOADng, running in the Cooja simulator. Standard performance metrics such as packet delivery ratio, end-to-end latency, overhead and average routing table size are identified for the comparison. The results and observations are provided considering a few different application traffic patterns, which serve to quantify the improvements in robustness arising from NDM. The results are confirmed by experiments using a public sensor network testbed with over 100 nodes.
Regex-based entity extraction with active learning and genetic programming
Authors: Bartoli Alberto , De Lorenzo Andrea , Medvet Eric , Tarlao Fabiano
Published: August 2016

We consider the long-standing problem of the automatic generation of regular expressions for text extraction, based solely on examples of the desired behavior. We investigate several active learning approaches in which the user annotates only one desired extraction and then merely answers extraction queries generated by the system.

The resulting framework is attractive because it is the system, not the user, which digs out the data in search of the samples most suitable to the specific learning task. We tailor our proposals to a state-of-the-art learner based on Genetic Programming and we assess them experimentally on a number of challenging tasks of realistic complexity. The results indicate that active learning is indeed a viable framework in this application domain and may thus significantly decrease the amount of costly annotation effort required.

We consider the long-standing problem of the automatic generation of regular expressions for text extraction, based solely on examples of the desired behavior. We investigate several active learning approaches in which the user anno- tates only one desired extraction and then merely answers extraction queries generated by the system.

The resulting framework is attractive because it is the sys- tem, not the user, which digs out the data in search of the samples most suitable to the specific learning task. We tailor our proposals to a state-of-the-art learner based on Genetic Programming and we assess them experimentally on a num- ber of challenging tasks of realistic complexity. The results indicate that active learning is indeed a viable framework in this application domain and may thus significantly decrease the amount of costly annotation effort required.
Efficient SQL querying on embedded devices using pre-compilation
Authors: Douglas Graeme , Lawrence Ramon
Published: August 2016

Microprocessors and embedded devices are used for data collection and analysis applications in infrastructure and en- vironmental monitoring, medical technology, wearable com- puting, and sensor network and mobile systems. Such appli- cations demand low energy solutions without using too much of a device's extremely limited RAM (1KB-100KB) and code space. Previously available database software for embedded devices and sensor networks relied heavily on data trans- mission across networks for centralized data processing. Re- cently, relational database systems for resource-constrained devices have been developed to execute queries on a per- device basis, which saves network transmission overhead. This work extends the applicability of such systems by lower- ing the code space and execution time requirements further through serializing queries at application build time and re- moving the query translation component from the device. By eliminating the need for complex query translation sys- tems on device, our technique can reduce ROM usage by as much as 50% while improving memory utilization. Our ex- periments demonstrate that pre-compiling can reduce query initialization times by 90% compared to typical parsing tech- niques. This translates to a further savings of up to 50% in on-device total execution times. The technique developed is applicable to a wide variety of embedded systems and
The role of proximal versus distal stomach resection in the weight loss seen after vertical sleeve gastrectomy
Authors: Kulkarni Bhushan V. , LaSance Kathleen , Sorrell Joyce E. , Lemen Lisa , Woods Stephen C. , Seeley Randy J. , Sandoval Darleen
Published: August 2016

The mechanisms involved in the weight loss seen after vertical sleeve gastrectomy (VSG) are not clear. The rat stomach has two morphologically and functionally distinct proximal and distal parts. The rat model for VSG involves complete removal of the proximal part and 80% removal of the distal part along the greater curvature. The purpose of this study was to understand the potential independent contributions of removal of these distinct gastric sections to VSG outcomes. We prepared four surgical groups of male Long-Evans rats: VSG, sham surgery (control), selective proximal section removal (PR), and selective distal section removal (DR). Gastric emptying rate (GER) was highest after VSG compared with all other groups. However, PR, in turn, had significantly greater GER compared with both DR and sham groups. The surgery-induced weight loss followed the same pattern with VSG causing the greatest weight loss and PR having greater weight loss compared with DR and sham groups. The results were robust for rats fed regular chow or a high-fat diet. Body mass analysis revealed that the weight loss was due to the loss of fat mass, and there was no change in lean mass after the surgeries. In conclusion, removal of the proximal stomach contributes to most, but not all, of the physiological impact of VSG.
Proteinuria causes dysfunctional autophagy in the proximal tubule
Authors: Nolin Angela C. , Mulhern Ryan M. , Panchenko Maria V. , Pisarek-Horowitz Anna , Wang Zhiyong , Shirihai Orian , Borkan Steven C. , Havasi Andrea
Published: August 2016

Proteinuria is a major risk factor for chronic kidney disease progression. Furthermore, exposure of proximal tubular epithelial cells to excess albumin promotes tubular atrophy and fibrosis, key predictors of progressive organ dysfunction. However, the link between proteinuria and tubular damage is unclear. We propose that pathological albumin exposure impairs proximal tubular autophagy, an essential process for recycling damaged organelles and toxic intracellular macromolecules. In both mouse primary proximal tubule and immortalized human kidney cells, albumin exposure decreased the number of autophagosomes, visualized by the autophagosome-specific fluorescent markers monodansylcadaverine and GFP-LC3, respectively. Similarly, renal cortical tissue harvested from proteinuric mice contained reduced numbers of autophagosomes on electron micrographs, and immunoblots showed reduced steady-state LC3-II content. Albumin exposure decreased autophagic flux in vitro in a concentration-dependent manner as assessed by LC3-II accumulation rate in the presence of bafilomycin, an H+-ATPase inhibitor that prevents lysosomal LC3-II degradation. In addition, albumin treatment significantly increased the half-life of radiolabeled long-lived proteins, indicating that the primary mechanism of degradation, autophagy, is dysfunctional. In vitro, mammalian target of rapamycin (mTOR) activation, a potent autophagy inhibitor, suppressed autophagy as a result of intracellular amino acid accumulation from lysosomal albumin degradation. mTOR activation was demonstrated by the increased phosphorylation of its downstream target, S6K, with free amino acid or albumin exposure. We propose that excess albumin uptake and degradation inhibit proximal tubule autophagy via an mTOR-mediated mechanism and contribute to progressive tubular injury.
Elevated PTH induces endothelial-to-chondrogenic transition in aortic endothelial cells
Authors: Wu Min , Zhang Jian-Dong , Tang Ri-Ning , Crowley Steven D. , Liu Hong , Lv Lin-Li , Ma Kun-Ling , Liu Bi-Cheng
Published: August 2016

Previous studies have shown that increased parathyroid hormone (PTH) attributable to secondary hyperparathyroidism in chronic kidney disease accelerates the arteriosclerotic fibrosis and calcification. Although the underlying mechanisms remain largely unknown, endothelial cells (ECs) have recently been demonstrated to participate in calcification in part by providing chondrogenic cells via the endothelial-to-mesenchymal transition (EndMT). Therefore, this study aimed to investigate whether elevated PTH could induce endothelial-to-chondrogenic transition in aortic ECs and to determine the possible underlying signaling pathway. We found that treatment of ECs with PTH significantly upregulated the expression of EndMT-related markers. Accordingly, ECs treated with PTH exhibited chondrogenic potential. In vivo, lineage-tracing model-subjected mice with endothelial-specific green fluorescent protein fluorescence to chronic PTH infusion showed a marked increase in the aortic expression of chondrocyte markers, and confocal microscopy revealed the endothelial origin of cells expressing chondrocyte markers in the aorta after PTH infusion. Furthermore, this in vitro study showed that PTH enhanced the nuclear localization of β-catenin in ECs, whereas β-catenin siRNA or DKK1, an inhibitor of β-catenin nuclear translocation, attenuated the upregulation of EndMT-associated and chondrogenic markers induced by PTH. In summary, our study demonstrated that elevated PTH could induce the transition of ECs to chondrogenic cells via EndMT, possibly mediated by the nuclear translocation of β-catenin.
Enhanced Simulated Annealing for Solving Aggregate Production Planning
Authors: Abu Bakar Mohd Rizam , Bakheet Abdul Jabbar Khudhur , Kamil Farah , Kalaf Bayda Atiya , Abbas Iraq T. , Soon Lee Lai
Published: August 2016

Simulated annealing (SA) has been an effective means that can address difficulties related to optimisation problems.SAis now a common discipline for research with several productive applications such as production planning. Due to the fact that aggregate production planning (APP) is one of the most considerable problems in production planning, in this paper, we present multiobjective linear programming model for APP and optimised bySA. During the course of optimising for the APP problem, it uncovered that the capability ofSAwas inadequate and its performance was substandard, particularly for a sizable controlledAPPproblem with many decision variables and plenty of constraints. Since this algorithm works sequentially then the current state will generate only one in next state that will make the search slower and the drawback is that the search may fall in local minimum which represents the best solution in only part of the solution space. In order to enhance its performance and alleviate the deficiencies in the problem solving, a modifiedSA(MSA) is proposed. We attempt to augment the search space by starting withN+1solutions, instead of one solution. To analyse and investigate the operations of the MSA with the standardSAand harmony search (HS), the real performance of an industrial company and simulation are made for evaluation. The results show that, compared toSAandHS,MSAoffers better quality solutions with regard to convergence and accuracy.
Application of Response Surface Methodology and Central Composite Inscribed Design for Modeling and Optimization of Marble Surface Quality
Authors: Cevheroğlu Çıra Sümeyra , Dağ Ahmet , Karakuş Askeri
Published: August 2016

Factors affecting the final surface quality of polished marble are not yet fully understood. Clarifying these factors for optimization of multivariate polishing process by trial and error method is difficult, time-consuming, and costly task. In this study, the empirical practices were carried out using an experimental design, specifically, a central composite inscribed (CCI) design. The factors considered in CCI design were belt speed, rotational speed, and pressure of the polishing head, and the responses were surface glossiness and roughness. Mathematical models describing responses were produced using experimental datasets, and analysis of variance (ANOVA) was used to assess the fit of the models generated with the experimental data. For process optimization, desirability function analysis (DFA) was used. This study has shown that the CCI could efficiently be applied for the modelling of polishing machine for surface quality of marble strips. Better surface quality generally resulted from lower belt speeds, which increased contact time between the abrasives and strips. Optimized surface quality for marble specimen was established.