bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of light irradiation timing on the efficacy of nanoformula-based photo/chemo combination therapy
Authors: Xiao Yafang , An Fei-Fei , Chen Jiaxiong , Xiong Shiyun , Zhang Xiao-Hong
Published: April 2018

This research found that the light irradiation timing has a significant impact on the efficacy of nanoformula-based photo/chemo combination therapy.
Polymeric chemosensor for the detection and quantification of chloride in human sweat. Application to the diagnosis of cystic fibrosis
Authors: Vallejos Saúl , Hernando Elsa , Trigo Miriam , García Félix C. , García-Valverde María , Iturbe David , Cabero María Jesús , Quesada Roberto , García José M.
Published: April 2018

We have developed a new extremely hydrophilic polymeric film suitable for the detection and quantification of chloride in human sweat directly on the skin.
Laser-irradiated inclined metal nanocolumns for selective, scalable, and room-temperature synthesis of plasmonic isotropic nanospheres
Authors: Noh Myoung-Sub , Han Soo Deok , Chae Songhwa , Back Seung Hyuk , Kim Sangtae , Baek Seung-Hyub , Kim Seong Keun , Choi Ji-Won , Kim Jin-Sang , Ahn Dong June , Choi Dukhyun , Kang Chong-Yun
Published: April 2018

Isotropic gold nanospheres were fabricated on wafer-scale rigid and flexible substrates at room temperature by a selective laser irradiation process.
A search for OB stars in the field of the galactic OB association Bochum 7
Authors: Corti M. A. , Orellana R. B. , Bosch G. L.
Published: April 2018

Aims. We plan to identify the members of the Bochum 7 association by performing simultaneous astrometric and spectrophotometric analyses, and estimate its distance and evolutionary stage.

Methods. We used our own visual spectroscopic and UBV photometric data of a 30′ × 30′ region centered at = 8h44m47.2s, = −45°58′55.5″. This information enabled us to estimate the spectral classification and distance of all stars present in the region. The proper motion was analyzed with data of the UCAC 5 catalog and was used to identify the members of this association. We added JHK data from 2MASS and IRAS catalogs to check for the presence of infrared (IR) excess stars.

Results. We found that Bochum 7 is an OB association with at least 27 identified stellar members (l = 265°.12, b = − 2°) at a distance of ≃5640 pc. Its proper motion is μαcos δ = −4.92 ± 0.08 mas yr−1, μδ = 3.26 ± 0.08 mas yr−1. We derived an average heliocentric radial velocity of ~35 km s−1 and were able to confirm the binary nature of the (ALS 1135) system and detect four new binary star candidates. Analysis of data for massive Bo 7 star candidates points towards a young age (≤ 3 × 106 years old) for the association, although the presence of a previous episode of star formation remains to be analyzed.
The structuring role of artificial structure on fish assemblages in a dammed river of the Pearl River in China
Authors: Zhou Lei , Guo Dingli , Zeng Lei , Xu Peng , Tang Qindong , Chen Zhi , Zhu Qiaoying , Wang Gongpei , Chen Qiaofei , Chen Luoan , Luo Yong , Li Guifeng
Published: April 2018

To address the fish use patterns of artificial structures mimicking floating macrophytes deployed in a impounded tributary of the Pearl River, China, field experiments were performed from December 2014 to June 2016 using multi-mesh gillnet. The fish assemblages using artificial structures differ in terms of species richness, abundance, body size, diversity indices, and ecological traits from fish assemblages on natural barren habitats of this river. Overall, fish abundance, species richness, Shannon diversity index, and functional richness were higher at the artificial structures than at the control sites, while fish length and functional evenness was greater at the control sites in comparison to artificial structures. The introduction of artificial structures did not result in statistically significant effects on fish biomass as artificial structures attracted more individuals with smaller size. Seasonal changes of chlorophyll-a and transparency may affect the efficiency of artificial structure in harboring fishes. This study revealed that artificial structures, as synthesized habitats, are effective in acting as a “fish attractor” and an alternative tool to provide new habitats for smaller individuals in a dammed river like the Youjiang River which is a structure-less ecosystem.
Branch-and-Cut-and-Price algorithms for the preemptive RCPSP
Authors: Fouilhoux Pierre , Mahjoub A.Ridha , Quilliot Alain , Toussaint Hélène
Published: April 2018

In this article, we address the preemptive Resource-Constrained Precedence Scheduling Problem. We propose two mixed integer formulations containing an exponential number of variables and inequalities. An antichain is a set of pairwise incomparable elements with respect to the precedence constraints. In the first formulation, the integer variables are associated with the antichains. For the second, the integer variables are limited to a particular subset of antichains. We propose two Branch-and-Cut-and-Price algorithms for each of these formulations. We introduce some valid inequalities in order to reinforce the second formulation. Finally, we give some computational results on instances of the PSPLIB and compare the formulations.
Production-inventory and emission reduction investment decision under carbon cap-and-trade policy
Authors: Fan Yuyao , Wang Min , Zhao Lindu
Published: April 2018

The increasing amount of carbon emissions has caused global warming and challenged the sustainable development of environment. Governments around the world have implemented carbon policies including carbon cap-and-trade policy. In this paper, we focus on how a two-echelon supply chain manages its carbon footprints in production and inventory under carbon cap-and-trade policy. We extend the classical EOQ (economic order quantity) model and study decisions on production-inventory, carbon trading and emission reduction investment in the decentralized and centralized situations. The results show that emission permit sharing can effectively reduce the total cost and total carbon emissions of the supply chain. Moreover, the manufacturer’s emission reduction effort rises with the increase of the buying and selling prices of emission permits under centralized decision-making. In addition, a compensation mechanism is proposed for the centralized supply chain with emission permit sharing. It is observed that the buying and selling prices of emission permits have a positive influence on the permit sharing price in the compensation mechanism. Meanwhile, the retailer pays less for using the emission permits if it has a higher carbon cap, while the manufacturer with a higher carbon cap is more capable to provide a high compensation for the retailer.
A guide to conic optimisation and its applications
Authors: Letchford Adam N. , Parkes Andrew J.
Published: April 2018

Most OR academics and practitioners are familiar with linear programming (LP) and its applications. Many are however unaware of conic optimisation, which is a powerful generalisation of LP, with a prodigious array of important real-life applications. In this invited paper, we give a gentle introduction to conic optimisation, followed by a survey of applications in OR and related areas. Along the way, we try to help the reader develop insight into the strengths and limitations of conic optimisation as a tool for solving real-life problems.
Pediatric Endoscopic Endonasal Approaches for Skull Base Lesions in the Very Young: Is It Safe and Effective?
Authors: Schupper Alexander , Deconde Adam , Levy Michael , Nation Javan
Published: April 2018

Introduction The fully endoscopic expanded endonasal approach (EEA) has been shown to be safe and efficacious in pediatric patients. However, in the very young patient (ages six and under), the anatomical challenge of working through a small nasal corridor is problematic. The ability to repair the skull base and use a nasoseptal flap (NSF) has also been called into question. Here, we review skull base resections using EEA in patients aged 6 years and younger.

Methods A retrospective chart review was conducted on pediatric patients age 6 years and younger who underwent EEA skull base resections over a 3-year period (June 2014 through June 2017).

Results Eight children aged 6 and under with seven tumor pathologies underwent an EEA for the resection of their skull base tumors, with a mean follow-up of 1.45 years. Only chordoma cases required multiple-staged resections. There are no tumor recurrences to date. A high-flow intraoperative cerebrospinal fluid (CSF) leak was encountered in three cases, and there were no postoperative CSF leaks. CSF leaks were effectively repaired with NSFs. One patient suffered from postoperative hypopituitarism, one patient experienced recurrent epistaxis secondary to turbinate destruction by the tumor, and one patient expired 8 months postresection secondary to metastatic disease.

Conclusion In our case series, EEA for skull base tumors in children aged 6 and under was a safe and effective surgical approach. Skull base defects are able to be effectively addressed with typical repairs including NSFs. Larger studies are warranted to further investigate this technique in this pediatric population.
Energetic-particle-modified global Alfvén eigenmodes
Authors: Lestz J. B. , Belova E. V. , Gorelenkov N. N.
Published: April 2018

Fully self-consistent hybrid MHD/particle simulations reveal strong energetic particle modifications to sub-cyclotron global Alfvén eigenmodes (GAEs) in low-aspect ratio, NSTX-like conditions. Key parameters defining the fast ion distribution function—the normalized injection velocity v0/vA and central pitch—are varied in order to study their influence on the characteristics of the excited modes. It is found that the frequency of the most unstable mode changes significantly and continuously with beam parameters, in accordance with the Doppler-shifted cyclotron resonances which drive the modes, and depending most substantially on v0/vA. This unexpected result is present for both counter-propagating GAEs, which are routinely excited in NSTX, and high frequency co-GAEs, which have not been previously studied. Large changes in frequency without clear corresponding changes in the mode structure are signatures of an energetic particle mode, referred to here as an energetic-particle-modified GAE. Additional simulations conducted for a fixed MHD equilibrium demonstrate that the GAE frequency shift cannot be explained by the equilibrium changes due to energetic particle effects.
Effects of gravity on the thermo-hydrodynamics of moving contact lines
Authors: Mondal Pranab Kumar , Chaudhry Shubham
Published: April 2018

In this paper, we demonstrate the effects of gravity on the interfacial thermo-hydrodynamics as modulated by the patterned wettability gradients placed on the surfaces of a narrow fluidic channel. We investigate the dynamics of contact line motion of two-component incompressible immiscible liquid mixtures under the framework of a thermodynamically consistent phase field model. We validate our model with the experimental results available in the literature in the purview of thermocapillary-actuated microscale transport. We show that the gravity-induced forces in the presence of the thermocapillarity effect play a unique role on the interfacial dynamics at small scales, leading to a uniform movement of the interface in the channel, and offer a greater degree of controllability in the filling/wetting rate in the capillary. We show that the change in patch width, placed on the walls of the channel, leads to a change in the filling dynamics into the capillary. Also, we investigate the rate of different dissipations during the movement of the contact line along the channel and show that the kinetic energy modulated dissipation provides maximum energy to the motion of the contact line.
Free energy study of H2O, N2O5, SO2, and O3 gas sorption by water droplets/slabs
Authors: Li Wentao , Pak Chi Yuen , Tse Ying-Lung Steve
Published: April 2018

Understanding gas sorption by water in the atmosphere is an active research area because the gases can significantly alter the radiation and chemical properties of the atmosphere. We attempt to elucidate the molecular details of the gas sorption of water and three common atmospheric gases (N2O5, SO2, and O3) by water droplets/slabs in molecular dynamics simulations. The system size effects are investigated, and we show that the calculated solvation free energy decreases linearly as a function of the reciprocal of the number of water molecules from 1/215 to 1/1000 in both the slab and the droplet systems. By analyzing the infinitely large system size limit by extrapolation, we find that all our droplet results are more accurate than the slab results when compared to the experimental values. We also show how the choice of restraints in umbrella sampling can affect the sampling efficiency for the droplet systems. The free energy changes were decomposed into the energetic ΔU and entropic −TΔS contributions to reveal the molecular details of the gas sorption processes. By further decomposing ΔU into Lennard-Jones and Coulombic interactions, we observe that the ΔU trends are primarily determined by local effects due to the size of the gas molecule, charge distribution, and solvation structure around the gas molecule. Moreover, we find that there is a strong correlation between the change in the entropic contribution and the mean residence time of water, which is spatially nonlocal and related to the mobility of water.
Role of internal motions and molecular geometry on the NMR relaxation of hydrocarbons
Authors: Singer P. M. , Asthagiri D. , Chen Z. , Valiya Parambathu A. , Hirasaki G. J. , Chapman W. G.
Published: April 2018

The role of internal motions and molecular geometry on 1H NMR relaxation rates in liquid-state hydrocarbons is investigated using MD (molecular dynamics) simulations of the autocorrelation functions for intramolecular and intermolecular 1H–1H dipole-dipole interactions. The effects of molecular geometry and internal motions on the functional form of the autocorrelation functions are studied by comparing symmetric molecules such as neopentane and benzene to corresponding straight-chain alkanes n-pentane and n-hexane, respectively. Comparison of rigid versus flexible molecules shows that internal motions cause the intramolecular and intermolecular correlation-times to get significantly shorter, and the corresponding relaxation rates to get significantly smaller, especially for longer-chain n-alkanes. Site-by-site simulations of 1H’s across the chains indicate significant variations in correlation times and relaxation rates across the molecule, and comparison with measurements reveals insights into cross-relaxation effects. Furthermore, the simulations reveal new insights into the relative strength of intramolecular versus intermolecular relaxation as a function of internal motions, as a function of molecular geometry, and on a site-by-site basis across the chain.
Deviation from equilibrium conditions in molecular dynamic simulations of homogeneous nucleation
Authors: Halonen Roope , Zapadinsky Evgeni , Vehkamäki Hanna
Published: April 2018

We present a comparison between Monte Carlo (MC) results for homogeneous vapour-liquid nucleation of Lennard-Jones clusters and previously published values from molecular dynamics (MD) simulations. Both the MC and MD methods sample real cluster configuration distributions. In the MD simulations, the extent of the temperature fluctuation is usually controlled with an artificial thermostat rather than with more realistic carrier gas. In this study, not only a primarily velocity scaling thermostat is considered, but also Nosé-Hoover, Berendsen, and stochastic Langevin thermostat methods are covered. The nucleation rates based on a kinetic scheme and the canonical MC calculation serve as a point of reference since they by definition describe an equilibrated system. The studied temperature range is from T = 0.3 to 0.65 ϵ/k. The kinetic scheme reproduces well the isothermal nucleation rates obtained by Wedekind et al. [J. Chem. Phys. 127, 064501 (2007)] using MD simulations with carrier gas. The nucleation rates obtained by artificially thermostatted MD simulations are consistently lower than the reference nucleation rates based on MC calculations. The discrepancy increases up to several orders of magnitude when the density of the nucleating vapour decreases. At low temperatures, the difference to the MC-based reference nucleation rates in some cases exceeds the maximal nonisothermal effect predicted by classical theory of Feder et al. [Adv. Phys. 15, 111 (1966)].
Automatic selection of atomic fingerprints and reference configurations for machine-learning potentials
Authors: Imbalzano Giulio , Anelli Andrea , Giofré Daniele , Klees Sinja , Behler Jörg , Ceriotti Michele
Published: April 2018

Machine learning of atomic-scale properties is revolutionizing molecular modeling, making it possible to evaluate inter-atomic potentials with first-principles accuracy, at a fraction of the costs. The accuracy, speed, and reliability of machine learning potentials, however, depend strongly on the way atomic configurations are represented, i.e., the choice of descriptors used as input for the machine learning method. The raw Cartesian coordinates are typically transformed in “fingerprints,” or “symmetry functions,” that are designed to encode, in addition to the structure, important properties of the potential energy surface like its invariances with respect to rotation, translation, and permutation of like atoms. Here we discuss automatic protocols to select a number of fingerprints out of a large pool of candidates, based on the correlations that are intrinsic to the training data. This procedure can greatly simplify the construction of neural network potentials that strike the best balance between accuracy and computational efficiency and has the potential to accelerate by orders of magnitude the evaluation of Gaussian approximation potentials based on the smooth overlap of atomic positions kernel. We present applications to the construction of neural network potentials for water and for an Al–Mg–Si alloy and to the prediction of the formation energies of small organic molecules using Gaussian process regression.
A surface impedance-based three-channel acoustic metasurface retroreflector
Authors: Shen Chen , Díaz-Rubio Ana , Li Junfei , Cummer Steven A.
Published: April 2018

We propose the design and measurement of an acoustic metasurface retroreflector that works at three discrete incident angles. An impedance model is developed such that for acoustic waves impinging at −60°, the reflected wave is defined by the surface impedance of the metasurface, which is realized by a periodic grating. At 0° and 60°, the retroreflection condition can be fulfilled by the diffraction of the surface. The thickness of the metasurface is about half of the operating wavelength and the retroreflector functions without parasitic diffraction associated with conventional gradient-index metasurfaces. Such highly efficient and compact retroreflectors open up possibilities in metamaterial-based acoustic sensing and communications.
Correlation dimension and phase space contraction via extreme value theory
Authors: Faranda Davide , Vaienti Sandro
Published: April 2018

We show how to obtain theoretical and numerical estimates of correlation dimension and phase space contraction by using the extreme value theory. The maxima of suitable observables sampled along the trajectory of a chaotic dynamical system converge asymptotically to classical extreme value laws where: (i) the inverse of the scale parameter gives the correlation dimension and (ii) the extremal index is associated with the rate of phase space contraction for backward iteration, which in dimension 1 and 2, is closely related to the positive Lyapunov exponent and in higher dimensions is related to the metric entropy. We call it the Dynamical Extremal Index. Numerical estimates are straightforward to obtain as they imply just a simple fit to a univariate distribution. Numerical tests range from low dimensional maps, to generalized Henon maps and climate data. The estimates of the indicators are particularly robust even with relatively short time series.
Motion behavior of water droplets driven by triboelectric nanogenerator
Authors: Nie Jinhui , Jiang Tao , Shao Jiajia , Ren Zewei , Bai Yu , Iwamoto Mitsumasa , Chen Xiangyu , Wang Zhong Lin
Published: April 2018

By integrating a triboelectric nanogenerator (TENG) and a simple circuit board, the motion of water droplets can be controlled by the output of the TENG, which demonstrates a self-powered microfluidic system toward various practical applications in the fields of microfluidic system and soft robotics. This paper describes a method to construct a physical model for this self-powered system on the basis of electrostatic induction theory. The model can precisely simulate the detailed motion behavior of the droplet under driving of TENG, and it can also reveal the influences of surface hydrophobicity on the motion of the droplet, which can help us to better understand the key parameters that decide the performance of the system. The experimental observation of the dynamic performance of the droplet has also been done with a high speed camera system. A comparison between simulation results and real measurements confirms that the proposed model can predict the velocity and position of the water droplet driven by high voltage source as well as TENG. Hence, the proposed model in this work could serve as a guidance for optimizing the self-powered systems in future studies.
Differences in abundance and diversity of diurnal invertebrates among three Fijian forests, and a comparison of two trapping methods for rapid assessments
Authors: Westwood Nathan , Pearson Mollie , Mustafa Erdem , Scanlon Annette T.
Published: April 2018

Apart from some high-profile exceptions (e.g. charismatic long-horned beetles), the ecology and conservation of Fijian invertebrates have received little research attention, and their potential as biodiversity surrogates or indicators is poorly understood. We surveyed diurnal terrestrial invertebrates within three Fijian forest types (lowland, upland, and coastal) using Malaise traps and beating trays to compare invertebrate abundance and diversity among forests. We also evaluated the efficiency of the two trapping methods for rapid invertebrate assessments. Overall, we collected 2584 invertebrates representing 321 morphospecies within 22 arthropod orders. We found significant differences in the abundance and diversity of invertebrates among forest sites for beating-tray samples, but not for Malaise-trap samples. Upland forest had the greatest diversity (Simpsons diversity index, D = 0.98); coastal forest recorded the lowest diversity (D = 0.14), but the greatest abundance of invertebrates. Several orders of invertebrates were relatively abundant across sites and traps (i.e. had high sampling reliability; they included Coleoptera, Hemiptera, Hymenoptera, Lepidoptera, and Diptera), so could be targeted as surrogates for broader biodiversity sampling. Given the urgency with which baseline data are needed across the South Pacific, invertebrate sampling provides a rapid biodiversity assessment tool, including for working in remote areas with few resources.
Neurosyphilis: mighty imitator forays with benign presentation and unique neuroimaging findings
Authors: Tiwana Harmanpreet , Ahmed Aiesha
Published: April 2018

Background
Common causes of temporal lobe hyper intensities are central nervous system infections like herpes simplex encephalitis, Lyme disease, limbic encephalitis and vascular pathology like Cerebral Autosomal Dominant Arteriopathy with Subcortical infarcts and Leukoencephalopathy. Methods: Personal assessment, laboratory data analysis and neuroimaging for the patient who was admitted to a central Pennsylvania tertiary care referral centre were conducted. Results: A 52-year-old male presented with a 1-year history of diffuse dysesthesia in upper and lower extremities with associated intermittent headaches and neck stiffness. Evaluation with lumbar puncture revealed increased nucleated cells (50 ul) with lymphocytic predominance (96%) and an elevated protein level of 109 mg/dl. Magnetic resonance imaging (MRI) of the brain showed T2/FLAIR hyper intensity in bilateral subcortical temporal white matter, left-greater-than-right and associated volume loss in cerebral parenchyma. Additional abnormal work up included reactive serum reactive plasma regain and Treponema pallidum antibody particle agglutination. Diagnosis of neurosyphilis was made and the patient was treated with intramuscular (IM) penicillin for 3 weeks. At the time of discharge, his headache and neck stiffness resolved and dysesthesias were decreased in intensity. Conclusions: The diagnosis of neurosyphilis is intricate, and no reference standard exists. Neuroimaging findings of neurosyphilis commonly are cerebral infarctions, leptomeningeal enhancement or non-specific white matter lesions. Less common features on fluid-attenuated inversion recovery (FLAIR) sequences are cortical atrophy and mesial temporal parenchymal signal changes. It is prudent to keep neurosyphilis in differential of mesial temporal lobe white matter changes, as early diagnosis and treatment results in better prognosis.
Very low rate of multiple paternity detected in clutches of a wild agamid lizard
Authors: Hacking Jessica , Stuart-Fox Devi , Gardner Michael
Published: April 2018

Genetic mating systems described for squamate reptiles range from primarily monogamous to completely polygynandrous. The presence of female multiple mating is almost ubiquitous among squamates and even occurs, albeit at a low rate, in socially monogamous species. Here we examine the genetic mating system of the territorial tawny dragon lizard (Ctenophorus decresii). Paternity was assigned to captive-born hatchlings using eight microsatellite loci, revealing a 4% rate of multiple paternity. One-quarter of males sired more than one clutch, although multiple mating by males is likely underestimated. The rate of multiple paternity in C. decresii represents one of the lowest among squamates and may be a result of successful male territoriality. However, the observed low rate of multiple paternity does not eliminate the possibility of widespread female multiple mating due to the potential for sperm storage and sperm competition. We conclude that the tawny dragon lizard employs a predominantly polygynous genetic mating system.
Loss of a highly conserved sterile alpha motif domain gene (
WEEP
) results in pendulous branch growth in peach trees
Authors: Hollender Courtney A. , Pascal Thierry , Tabb Amy , Hadiarto Toto , Srinivasan Chinnathambi , Wang Wanpeng , Liu Zhongchi , Scorza Ralph , Dardick Chris
Published: April 2018

Significance

Trees’ branches grow against the pull of gravity and toward light. Although gravity and light perception have been studied in model species, much is unknown about how trees detect and respond to these signals. Here, we report the identification of a gene (
WEEP
) that controls lateral branch orientations and is directly or indirectly required for gravity responses in trees. Loss or reduction of WEEP expression produced branches that grow outward and downward and did not exhibit normal gravitropism responses when displaced. WEEP is conserved throughout the plant kingdom and may be involved in gravity perception. WEEP may also be a valuable target for breeding or engineering trees with improved shapes for agricultural and landscaping applications.
Local initiation conditions for water autoionization
Authors: Moqadam Mahmoud , Lervik Anders , Riccardi Enrico , Venkatraman Vishwesh , Alsberg Bjørn Kåre , van Erp Titus S.
Published: April 2018

Significance

The dissociation of water is arguably the most fundamental chemical reaction occurring in the aqueous phase. Despite that the splitting of a water molecule very seldom occurs, the reaction is of major importance in many areas of chemistry and biology. Direct experimental probing of the event is still impossible and also simulating the event via accurate computer simulations is challenging. Here, we achieved the latter via specialized rare-event algorithms estimating rates of dissociation in agreement with indirect experimental measurements. Even more interestingly, by a rigorous analysis of our results we identified anomalies in the water structure that act as initiators of the reaction, a finding that suggests paradigms for steering and catalyzing chemical reactions.
Green function of correlated genes in a minimal mechanical model of protein evolution
Authors: Dutta Sandipan , Eckmann Jean-Pierre , Libchaber Albert , Tlusty Tsvi
Published: April 2018

Significance

Many protein functions involve large-scale motion of their amino acids, while alignment of their sequences shows long-range correlations. This has motivated search for physical links between genetic and phenotypic collective behaviors. The major challenge is the complex nature of protein: nonrandom heteropolymers made of 20 species of amino acids that fold into a strongly coupled network. In light of this complexity, simplified models are useful. Our model describes protein in terms of the Green function, which directly links the gene to force propagation and collective dynamics in the protein. This allows for derivation of basic determinants of evolution, such as fitness landscape and epistasis, which are often hard to calculate.
A comprehensive omics analysis and functional survey of cuticular proteins in the brown planthopper
Authors: Pan Peng-Lu , Ye Yu-Xuan , Lou Yi-Han , Lu Jia-Bao , Cheng Chen , Shen Yan , Moussian Bernard , Zhang Chuan-Xi
Published: April 2018

Significance

The cuticle, mainly composed of chitin and cuticular proteins (CPs), is a multifunctional structure of arthropods. CPs usually account for >1% of the total insect proteins encoded in the genome. Why does an insect need so many different CPs? In this study, we use comprehensive large-scale technologies to study the full complement of CPs and their functions in the brown planthopper (BPH). A total of 32 of the 140 BPH CP genes are found to be essential for nymph/adult development, egg production, or embryo development; in addition, redundant and complementary functions of CPs are revealed.
Symbolic emblems of the Levantine Aurignacians as a regional entity identifier (Hayonim Cave, Lower Galilee, Israel)
Authors: Tejero José-Miguel , Belfer-Cohen Anna , Bar-Yosef Ofer , Gutkin Vitaly , Rabinovich Rivka
Published: April 2018

Significance

The emergence and diffusion of Upper Paleolithic (UP) typo-technical traditions are among the most debated topics related to anatomically modern humans’ colonization of and establishment in Eurasia. The Levantine Aurignacian represents one of the UP cultural entities in the Near East, and its origins, spread, and interrelationships with other UP entities are central to the understanding of local UP dynamics. The data we present demonstrate that the notched bones from Hayonim Cave stratum D are unquestionably anthropic marks constituting an emblem of the Levantine Aurignacian. Assessment of data from Middle Stone Age and UP sites of Africa and Europe as well as other UP sites in the Levant supports the notion that this is indeed a unique feature of the Levantine Aurignacian.
Symbiotic polydnavirus of a parasite manipulates caterpillar and plant immunity
Authors: Tan Ching-Wen , Peiffer Michelle , Hoover Kelli , Rosa Cristina , Acevedo Flor E. , Felton Gary W.
Published: April 2018

Significance

The role of herbivore-associated microbes in mediating plant–herbivore interactions has gained recent attention. We show that a parasitoid associated with its caterpillar host not only suppresses the immune system of the caterpillar but also suppresses the induced defenses of the caterpillar’s host plant. Parasitoids inject eggs into their hosts but also inject polydnaviruses that suppress the caterpillar’s immunity. Immunosuppression enables eggs to hatch and develop as larvae within caterpillars. Additionally, the polydnavirus reduces salivary glucose oxidase, the primary elicitor found in the caterpillar’s oral secretions. Caterpillars injected with polydnavirus induce lower plant defenses than untreated caterpillars. Our results reveal a dimension to the complexity of plant–herbivore interactions indicating that polydnaviruses mediate the phenotypes of the parasitoid, herbivore, and plant.
Doped Kondo chain, a heavy Luttinger liquid
Authors: Khait Ilia , Azaria Patrick , Hubig Claudius , Schollwöck Ulrich , Auerbach Assa
Published: April 2018

Significance

The large effective electron mass observed in rare-earth “heavy fermion” metals, such as

C
e
A
l

3

and

C
e
C
u

6

, has challenged theorists since the discovery of the effect in 1975. In particular, the popular theory that explains the electron mass enhancement neglects important emergent magnetic interactions, which could destroy the heavy fermion phase by magnetic ordering. Here, we investigate in great detail the effect of these magnetic interactions in the 1D Kondo Lattice model, which approximates such metals. Surprisingly, we find that magnetism helps to stabilize the heavy fermion metal, albeit with different energy scales than previously predicted. These insights may help us understand the Kondo Lattice and heavy fermions in higher dimensions.
Tertiary structure of apolipoprotein A-I in nascent high-density lipoproteins
Authors: Pourmousa Mohsen , Song Hyun D. , He Yi , Heinecke Jay W. , Segrest Jere P. , Pastor Richard W.
Published: April 2018

Significance

High-density lipoprotein (HDL), popularly known as “good cholesterol,” is an assembly of lipids and proteins that is protective against cardiovascular diseases. HDL begins to develop when two copies of the protein apolipoprotein A-I (APOA1) mediate the removal of excess lipids from peripheral cells and form a nanodisc. How the proteins adjust their structures as the nanodisc increases in diameter, mediates the conversion of cholesterol to cholesteryl esters, and becomes spherical is crucial to understanding HDL maturation and relevant pathologies. This study combines multimicrosecond atomistic molecular dynamics simulations, molecular modeling, and cross-linking experiments to reveal APOA1 structure in two nascent HDLs. The structures provide a mechanistic understanding for HDL maturation and revise previous models of nascent HDL.
Hidden collapse is driven by fire and logging in a socioecological forest ecosystem
Authors: Lindenmayer David B. , Sato Chloe
Published: April 2018

Significance

Almost all descriptions of ecosystem collapse are made after it has occurred and not during the process of collapse. We describe the process of collapse in the iconic Australian Mountain Ash ecosystem. We uncovered empirical evidence for hidden collapse, which occurs when an ecosystem superficially appears to be intact but a prolonged period of decline coupled with long lag times for recovery mean that collapse is almost inevitable. This is because key ecosystem components continue to decline for long periods even after drivers of collapse are removed. Hidden collapse suggests a need for actions well before managers perceive they are required. Long-term monitoring targeting different classes of state variables can be used to provide early warnings of impending collapse.
HCMV glycoprotein B subunit vaccine efficacy mediated by nonneutralizing antibody effector functions
Authors: Nelson Cody S. , Huffman Tori , Jenks Jennifer A. , Cisneros de la Rosa Eduardo , Xie Guanhua , Vandergrift Nathan , Pass Robert F. , Pollara Justin , Permar Sallie R.
Published: April 2018

Significance

The CDC estimates that every hour, a child is born in the United States with permanent neurologic disability resulting from human cytomegalovirus (HCMV) infection—more than is caused by Down syndrome, fetal alcohol syndrome, and neural tube defects combined. A maternal vaccine to block transmission of HCMV to the developing fetus is a necessary intervention to prevent these adverse outcomes. The gB/MF59 vaccine is the most successful tested clinically to date, achieving 50% reduction in HCMV acquisition. This manuscript establishes the function and epitope specificity of the humoral response stimulated by this vaccine that may explain the partial vaccine efficacy. Understanding the mechanism of gB/MF59-elicited protective immune responses will guide rational design and evaluation of the next generation of HCMV vaccines.
Unexpected slowdown of US pollutant emission reduction in the past decade
Authors: Jiang Zhe , McDonald Brian C. , Worden Helen , Worden John R. , Miyazaki Kazuyuki , Qu Zhen , Henze Daven K. , Jones Dylan B. A. , Arellano Avelino F. , Fischer Emily V. , Zhu Liye , Boersma K. Folkert
Published: April 2018

Significance

Emissions of nitrogen oxides (NOx) have a large impact on air quality and climate change as precursors in the formation of ozone and secondary aerosols. We find that NOxemissions have not been decreasing as expected in recent years (2011–2015) when comparing top-down estimates from satellites and surface NO2measurements to the trends predicted from the US Environmental Protection Agency’s emission inventory data. The discrepancy can be explained by the growing relative contribution of industrial, area, and off-road mobile sources of emissions, decreasing relative contribution of on-road gasoline vehicles, and slower than expected decreases in on-road diesel NOxemissions, with implications for air-quality management.
Histone demethylase JMJD1A promotes alternative splicing of AR variant 7 (AR-V7) in prostate cancer cells
Authors: Fan Lingling , Zhang Fengbo , Xu Songhui , Cui Xiaolu , Hussain Arif , Fazli Ladan , Gleave Martin , Dong Xuesen , Qi Jianfei
Published: April 2018

Significance

Formation of androgen receptor splicing variant 7 (AR-V7), a constitutively active form of AR, plays a key role in the resistance of prostate cancer to hormone therapy. However, the mechanisms that regulate AR-V7 generation are poorly understood. Here, we identified a new role for histone demethylase JMJD1A (Jumonji domain containing 1A) in the formation of AR-V7 in prostate cancer cells. We found that JMJD1A facilitated recruitment of a splicing factor, heterogeneous nuclear ribonucleoprotein F, for alternative splicing and generation of AR-V7. The findings suggest that targeting JMJD1A may provide new therapeutic opportunity for prostate cancer.
Revisiting the role of IRF3 in inflammation and immunity by conditional and specifically targeted gene ablation in mice
Authors: Yanai Hideyuki , Chiba Shiho , Hangai Sho , Kometani Kohei , Inoue Asuka , Kimura Yoshitaka , Abe Takaya , Kiyonari Hiroshi , Nishio Junko , Taguchi-Atarashi Naoko , Mizushima Yu , Negishi Hideo , Grosschedl Rudolf , Taniguchi Tadatsugu
Published: April 2018

Significance

IFN regulatory factor 3 (IRF3) is one of the most well-characterized transcription factors involved in the regulation of innate immune responses. Many studies have used conventional
Irf3
-deficient mice to analyze the functions of IRF3 in immunity and other biological systems; however, these mice were found to carry another null mutation in the
Bcl2l12
gene, which has confounded the analyses of these mice. For this study, we generated conditional
Irf3
-deficient mice while leaving the
Bcl2l12
gene intact. Conditional ablation of IRF3 in myeloid cells showed increased survival when challenged with endotoxin-induced shock, indicating a myeloid cell-specific role of IRF3. The IRF3 conditional knockout mouse may be a useful tool to identify cell type-specific functions of this transcription factor.
Real self-respect and its social bases
Authors: Schemmel Christian
Published: April 2018

Many theories of social justice maintain that concern for the social bases of self-respect grounds demanding requirements of political and economic equality, as self-respect is supposed to be dependent on continuous just recognition by others. This paper argues that such views miss an important feature of self-respect, which accounts for much of its value: self-respect is a capacity for self-orientation that is robust under adversity. This does not mean that there are no social bases of self-respect that such theories ought to incorporate. It means that they are different: they consist of the motivational and epistemic resources needed to develop and maintain such robustness.
Direct bioethanol production from brown macroalgae by co-culture of two engineered Saccharomyces cerevisiae strains
Authors: Sasaki Yusuke , Takagi Toshiyuki , Motone Keisuke , Shibata Toshiyuki , Kuroda Kouichi , Ueda Mitsuyoshi
Published: April 2018

A co-culture platform for bioethanol production from brown macroalgae was developed, consisting of two types of engineered Saccharomyces cerevisiae strains; alginate- and mannitol-assimilating yeast (AM1), and cellulase-displaying yeast (CDY). When the 5% (w/v) brown macroalgae Ecklonia kurome was used as the sole carbon source for this system, 2.1 g/L of ethanol was produced, along with simultaneous consumption of alginate, mannitol, and glucans.
Uncoordinated centrosome cycle underlies the instability of non-diploid somatic cells in mammals
Authors: Yaguchi Kan , Yamamoto Takahiro , Matsui Ryo , Tsukada Yuki , Shibanuma Atsuko , Kamimura Keiko , Koda Toshiaki , Uehara Ryota
Published: April 2018

In animals, somatic cells are usually diploid and are unstable when haploid for unknown reasons. In this study, by comparing isogenic human cell lines with different ploidies, we found frequent centrosome loss specifically in the haploid state, which profoundly contributed to haploid instability through subsequent mitotic defects. We also found that the efficiency of centriole licensing and duplication changes proportionally to ploidy level, whereas that of DNA replication stays constant. This caused gradual loss or frequent overduplication of centrioles in haploid and tetraploid cells, respectively. Centriole licensing efficiency seemed to be modulated by astral microtubules, whose development scaled with ploidy level, and artificial enhancement of aster formation in haploid cells restored centriole licensing efficiency to diploid levels. The ploidy–centrosome link was observed in different mammalian cell types. We propose that incompatibility between the centrosome duplication and DNA replication cycles arising from different scaling properties of these bioprocesses upon ploidy changes underlies the instability of non-diploid somatic cells in mammals.
Extraction of ECG signal with adaptive filter for hearth abnormalities detection
Authors: Turnip Mardi , Saragih Rijois. I. E. , Dharma Abdi , Kusumandari Dwi Esti , Turnip Arjon , Sitanggang Delima , Aisyah Siti
Published: April 2018

This paper demonstrates an adaptive filter method for extraction ofelectrocardiogram (ECG) feature in hearth abnormalities detection. In particular, electrocardiogram (ECG) is a recording of the heart's electrical activity by capturing a tracingof cardiac electrical impulse as it moves from the atrium to the ventricles. The applied algorithm is to evaluate and analyze ECG signals for abnormalities detection based on P, Q, R and S peaks. In the first phase, the real-time ECG data is acquired and pre-processed. In the second phase, the procured ECG signal is subjected to feature extraction process. The extracted features detect abnormal peaks present in the waveform. Thus the normal and abnormal ECG signal could be differentiated based on the features extracted.
Particle Concentrations in Occupational Settings Measured with a Nanoparticle Respiratory Deposition (NRD) Sampler
Authors: Stebounova Larissa V , Gonzalez-Pech Natalia I , Park Jae Hong , Anthony T Renee , Grassian Vicki H , Peters Thomas M
Published: April 2018

There is an increasing need to evaluate concentrations of nanoparticles in occupational settings due to their potential negative health effects. The Nanoparticle Respiratory Deposition (NRD) personal sampler was developed to collect nanoparticles separately from larger particles in the breathing zone of workers, while simultaneously providing a measure of respirable mass concentration. This study compared concentrations measured with the NRD sampler to those measured with a nano Micro Orifice Uniform-Deposit Impactor (nanoMOUDI) and respirable samplers in three workplaces. The NRD sampler performed well at two out of three locations, where over 90% of metal particles by mass were submicrometer particle size (a heavy vehicle machining and assembly facility and a shooting range). At the heavy vehicle facility, the mean metal mass concentration of particles collected on the diffusion stage of the NRD was 42.5 ± 10.0 µg/m3, within 5% of the nanoMOUDI concentration of 44.4 ± 7.4 µg/m3. At the shooting range, the mass concentration for the diffusion stage of the NRD was 5.9 µg/m3, 28% above the nanoMOUDI concentration of 4.6 µg/m3. In contrast, less favorable results were obtained at an iron foundry, where 95% of metal particles by mass were larger than 1 µm. The accuracy of nanoparticle collection by NRD diffusion stage may have been compromised by high concentrations of coarse particles at the iron foundry, where the NRD collected almost 5-fold more nanoparticle mass compared to the nanoMOUDI on one sampling day and was more than 40% different on other sampling days. The respirable concentrations measured by NRD samplers agreed well with concentrations measured by respirable samplers at all sampling locations. Overall, the NRD sampler accurately measured concentrations of nanoparticles in industrial environments when concentrations of large, coarse mode, particles were low.
The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs
Authors: Stocks Matthew B , Mohorianu Irina , Beckers Matthew , Paicu Claudia , Moxon Simon , Thody Joshua , Dalmay Tamas , Moulton Vincent
Published: April 2018

Motivation

RNA interference, a highly conserved regulatory mechanism, is mediated via small RNAs (sRNA). Recent technical advances enabled the analysis of larger, complex datasets and the investigation of microRNAs and the less known small interfering RNAs. However, the size and intricacy of current data requires a comprehensive set of tools, able to discriminate the patterns from the low-level, noise-like, variation; numerous and varied suggestions from the community represent an invaluable source of ideas for future tools, the ability of the community to contribute to this software is essential.

Results

We present a new version of the UEA sRNA Workbench, reconfigured to allow an easy insertion of new tools/workflows. In its released form, it comprises of a suite of tools in a user-friendly environment, with enhanced capabilities for a comprehensive processing of sRNA-seq data e.g. tools for an accurate prediction of sRNA loci (CoLIde) and miRNA loci (miRCat2), as well as workflows to guide the users through common steps such as quality checking of the input data, normalization of abundances or detection of differential expression represent the first step in sRNA-seq analyses.

Availability and implementation

The UEA sRNA Workbench is available at: http://srna-workbench.cmp.uea.ac.uk. The source code is available at: https://github.com/sRNAworkbenchuea/UEA_sRNA_Workbench

Supplementary information

Supplementary data are available at Bioinformatics online.