bluuebunny/crossref_metadata_2025 huggingface dataset:
Anomalous thermoelectric properties in double quantum dots coupled with Majorana bound states
Authors: Zheng Yi-Jie , Song Juntao , Li Yu-Xian
Published: December 2016

We discuss the transport properties of thermal electrons in double quantum dots that are coupled with Majorana bound states (MBSs) corresponding to two model systems with T-type structure and series connection structure. It has been found that the thermoelectric figure of merit ZT in these model systems is suppressed when we consider the effects of the Majorana bound states. Here, ZT=GS2Tκ, where G is the electric conductance, S is the thermopower, T is the temperature and κ is the thermal conductance. The sign of the thermopower S changes from negative to positive when the energy levels of the quantum dots are less than μ while the sign of the thermopower S changes from positive to negative when the energy levels of the quantum dots are above μ in the model system of T-type structure, where μ is the chemical potential. As a result, the figure of merit ZT first decreases and then increases as the temperature kBT increases. This behavior is different from what is seen in the general quantum dot structure without MBSs. It is interesting to show that in the series connection structure, the thermopower S and ZT are robustness and do not vary with changes in εM when |εd|<λ, even if κ changes with εM.
Power enhancement of partially shaded PV arrays through shade dispersion using magic square configuration
Authors: Samikannu Sarojini Mary , Namani Rakesh , Subramaniam Senthil Kumar
Published: December 2016

This paper proposes a new static reconfiguration technique to configure the modules in the Photo-Voltaic (PV) array so as to enhance the generated power from the array under partial shading conditions. In this approach, the physical location of the modules in a Total Cross Tied (TCT) connected PV array is arranged based on the Magic Square (MS) pattern so as to distribute the shading effect over the entire array. Further, this arrangement of modules is done without altering the electrical connection of the modules in the array. The MS arrangement reduces the effect of shading of modules in any row thereby enhancing the generated PV power. The MS pattern based PV array configuration has only one Global Maximum Power Point at the right most peak in the PV curve as compared to the conventional TCT configuration under partially shaded conditions. Thus, the proposed MS scheme evidently avoids the need for complex Maximum-Power-Point-Tracking algorithms. The performance of the system is investigated for different shading patterns and the results show that positioning the modules of the array according to MS pattern provides improved performance under partially shaded conditions.
Solutions based on renewable energy and technology to improve the performance of refrigeration systems
Authors: Aridhi Emna , Abbes Mehdi , Mami Abdelkader
Published: December 2016

This paper presents a review of recent studies interesting in improving the energy efficiency and cooling quality of refrigeration systems, especially, household refrigerators, air conditioners, and cold storages. They proposed solutions based on renewables such as solar, geothermal, and natural cold through designing advanced plants. Their overall improvement in energy management could bring savings of up to 95% in appropriate conditions and according to the structure of the refrigeration installation. The paper also gives statistics about the energy consumption of refrigeration systems and the interest of using renewables in this field.
Pressure-induced isostructural transition in a distorted perovskite via octahedron reconfiguration
Authors: Hong Fang , Yue Binbin , Hirao Naohisa , Ren Guohao , Chen Bin , Mao Ho-Kwang
Published: December 2016

Perovskite material studies encompass many fields such as energy harvesting, superconductivity, magnetism, and beyond. Thus, it is very important to investigate their structural varieties in external environments. Here, the pressure-induced structure change of a distorted perovskite, Y0.7Lu0.3AlO3, was examined by synchrotron x-ray diffraction. Upon compression, it underwent an isostructural transition near 22 GPa. The quenchable high-pressure phase had a much higher bulk modulus than the low-pressure phase. This work shows the flexibility of perovskite distortion and will help to understand the property anomalies in prevailing perovskite ABO3 systems and design more functional materials.
First-principles investigation on elastic and thermodynamic properties of Pnnm-CN under high pressure
Authors: Ya-Ru Zhao , Hai-Rong Zhang , Gang-Tai Zhang , Qun Wei , Yu-Quan Yuan
Published: December 2016

The elastic anisotropy and thermodynamic properties of the recently synthesized Pnnm-CN have been investigated using first-principles calculations under high temperature and high pressure. The calculated equilibrium crystal parameters and normalized volume dependence of the resulting pressure agree with available experimental and theoretical results. Within the considered pressure range of 0–90 GPa, the dependences of the bulk modulus, Young’s modulus, and shear modulus on the crystal orientation for Pnnm-CN have been systematically studied. The results show that the Pnnm-CN exhibits a well-pronounced elastic anisotropy. The incompressibility is largest along the c-axis. For tension or compression loading, the Pnnm-CN is stiffest along [001] and the most obedient along [100] direction. On the basis of the quasi-harmonic Debye model, we have explored the Debye temperature, heat capacity, thermal expansion coefficient, and Grüneisen parameters within the pressure range of 0–90 GPa and temperature range of 0–1600K.
Pseudomonas aeruginosa
sabotages the generation of host proresolving lipid mediators
Authors: Flitter Becca A. , Hvorecny Kelli L. , Ono Emiko , Eddens Taylor , Yang Jun , Kwak Daniel H. , Bahl Christopher D. , Hampton Thomas H. , Morisseau Christophe , Hammock Bruce D. , Liu Xinyu , Lee Janet S. , Kolls Jay K. , Levy Bruce D. , Madden Dean R. , Bomberger Jennifer M.
Published: December 2016

Significance

Pseudomonas aeruginosa
pulmonary infections cause prolonged and destructive inflammation for cystic fibrosis patients. Despite vigorous neutrophilic responses,
P. aeruginosa
persists in a chronic hyperinflammatory environment. We show that the
P. aeruginosa
virulence factor, cystic fibrosis transmembrane conductance regulator inhibitory factor (Cif), promotes sustained airway inflammation by reducing host pro-resolving lipid mediators. Cif hydrolyzes epithelial-derived 14,15-epoxyeicosatrienoic acid, disrupting transcellular production of the proresolving lipid 15-epi lipoxin A
4
(15-epi LXA
4
) by neutrophils. Clinical data from cystic fibrosis patients revealed that Cif abundance correlated with increased inflammation, decreased 15-epi LXA
4
, and reduced pulmonary function. Our study and the recent identification of Cif homologs in
Acinetobacter
and
Burkholderia
species suggest that bacterial epoxide hydrolases represent a novel virulence strategy shared by multiple respiratory pathogens.
Present-day African analogue of a pre-European Amazonian floodplain fishery shows convergence in cultural niche construction
Authors: McKey Doyle B. , Durécu Mélisse , Pouilly Marc , Béarez Philippe , Ovando Alex , Kalebe Mashuta , Huchzermeyer Carl F.
Published: December 2016

Significance

Erickson convincingly inferred a pre-European floodplain fishery unlike any present-day system he knew, illustrating the principle that archaeological inference should not be constrained by the range of cultural variation observed today. Our comparison of these inferences with observations from a present-day fishery in a similar environment suggests strong convergence in both the ecology of fish communities and the cultural means people have devised to exploit them, providing support for a predictive model of cultural niche construction. This conceptual framework emphasizes the synergistic action of human agency and environmental constraint in shaping patterns in the human use and management of ecosystems.
Archaeointensity results spanning the past 6 kiloyears from eastern China and implications for extreme behaviors of the geomagnetic field
Authors: Cai Shuhui , Jin Guiyun , Tauxe Lisa , Deng Chenglong , Qin Huafeng , Pan Yongxin , Zhu Rixiang
Published: December 2016

Significance

The geomagnetic field is an intriguing fundamental physical property of the Earth. Its evolution has significant implications for issues such as geodynamics, evolution of the life on the Earth, and archaeomagnetic dating. Here, we present 21 archaeointensity data points from China and establish the first archaeointensity reference curve for eastern Asia. Our results record rarely captured extreme behaviors of the geomagnetic field, with an exceptionally low intensity around ∼2200 BCE (hitherto the lowest value observed for the Holocene) and a “spike” intensity value dated at ∼1300 ± 300 BCE (either a precursor to or the same event as the Levantine spikes). These anomalous features of the geomagnetic field revealed by our data will shed light on understanding geomagnetic field during the Holocene.
Pay no attention to that man behind the curtain
Authors: Westbury Chris
Published: December 2016

There is a distinction in scientific explanation between the explanandum, statements describing the empirical phenomenon to be explained, and the explanans, statements describing the evidence that allow one to predict that phenomenon. To avoid tautology, these sets of statements must refer to distinct domains. A scientific explanation of semantics must be grounded in explanans that appeal to entities from non-semantic domains. I consider as examples eight candidate domains (including affect, lexical or sub-word co-occurrence, mental simulation, and associative learning) that could ground semantics. Following Wittgenstein (1954), I propose adjudicating between these different domains is difficult because of the reification of a word’s ‘meaning’ as an atomistic unit. If we abandon the idea of the meaning of a word as being an atomistic unit and instead think of word meaning as a set of dynamic and disparate embodied states unified by a shared label, many apparent problems associated with identifying a meaning’s ‘true’ explanans disappear. Semantics can be considered as sets of weighted constraints that are individually sufficient for specifying and labeling a subjectively-recognizable location in the high dimensional state space defined by our neural activity.
Morphological schemas
Authors: Jackendoff Ray , Audring Jenny
Published: December 2016

We propose a theory of the lexicon in which rules of grammar, encoded as declarative schemas, are lexical items containing variables. We develop a notation to encode precise relations among lexical items and show how this differs from the standard notion of inheritance. We also show how schemas can play both a generative role, acting as productive rules, and also a relational role, where they codify nonproductive but nevertheless prolific patterns within the lexicon. We then show how this theory of lexical relations can be embedded directly into a theory of lexical access and lexical processing, such that it can make direct contact with experimental findings.
Internet of Things in agriculture.
Authors: Verdouw C. , Wolfert S. , Tekinerdogan B.
Published: December 2016

This literature review on Internet of Things (IoT) in agriculture and food, provides an overview of existing applications, enabling technologies and main challenges ahead. The results of the review show that this subject received attention by the scientific community from 2010 on and the number of papers has increased since then. The literature on IoT in agriculture and food is very much dominated by Asian scientists, especially from China. In other continents, the concept of IoT was up to recently mainly adopted by non-agricultural scientists. The application area of food supply chains is addressed most frequently, followed by arable farming. Most papers report the results of explorative studies or they present IoT systems that are designed or implemented in prototypes and pilots. The literature reviewed focuses on sensing and monitoring, while actuation and remote control is much less addressed. The findings indicate that IoT is still in its infancy in the agriculture and food domain. Applications are often fragmentary, lack seamless integration and especially more advanced solutions are in an experimental stage of development. Important challenges to overcome this situation include (i) integration of existing IoT solutions by open IoT architectures, platforms and standards, (ii) upscaling the usage of interoperable IoT technologies beyond early adopters especially by the simplification of existing solutions and make it more affordable for end users, and (iii) further improvement of IoT technologies to ensure a broad usability in the diversity of the agri-food domain.
Impact of calf nutrition on overall production and productive life of cattle and buffaloes.
Authors: Garg M. R. , Bhanderi B. M. , Sachin Shankhpal Sachin Shankhpal , Ajay Goswami Ajay Goswami , Sherasia P. L.
Published: December 2016

Poor feeding during pre-natal, neonatal and post-natal stages of calves leads to higher age at first calving and overall loss of productive life. Supplying calves an optimal nutrition right from the prenatal stage is vital for their growth and development, and it also allows calves to express their full genetic potential for milk production and reproductive efficiency during the entire lifespan. Maternal nutrition during the last trimester is considered important to genetic programming
in utero
. The influence of maternal nutrition also reaches the neonatal calf through hormones, growth factors and immune-stimulants incorporated into colostrum, milk and milk replacers. The key is to accelerate the rate of maturation of the calf's ruminal papillae (rumen wall) through the provision of calf starter and grower feeds and good-quality roughages, which favour the digestion of larger proportions of fodder at an early age. Feeding and management practices to promote these processes in crossbred calves are well established; however, in most of the developing nations little is known about these processes in buffalo calves and indigenous (
Bos indicus
) cow calves. Feeding buffalo calves and indigenous cow calves on scientific lines, and rearing them using improved management practices to assist the animals reach puberty sooner, are central factors for improving their productivity and productive life in tropical and sub-tropical regions. By 2050, people living in these regions are estimated to consume about 70% of the additional milk produced.
2017 Infectious Diseases Society of America’s Clinical Practice Guidelines for Healthcare-Associated Ventriculitis and Meningitis*
Authors: Tunkel Allan R. , Hasbun Rodrigo , Bhimraj Adarsh , Byers Karin , Kaplan Sheldon L. , Scheld W. Michael , van de Beek Diederik , Bleck Thomas P. , Garton Hugh J.L. , Zunt Joseph R.
Published: December 2016

The Infectious Diseases Society of America (IDSA) Standards and Practice Guidelines Committee collaborated with partner organizations to convene a panel of 10 experts on healthcare-associated ventriculitis and meningitis. The panel represented pediatric and adult specialists in the field of infectious diseases and represented other organizations whose members care for patients with healthcare-associated ventriculitis and meningitis (American Academy of Neurology, American Association of Neurological Surgeons, and Neurocritical Care Society). The panel reviewed articles based on literature reviews, review articles and book chapters, evaluated the evidence and drafted recommendations. Questions were reviewed and approved by panel members. Subcategories were included for some questions based on specific populations of patients who may develop healthcare-associated ventriculitis and meningitis after the following procedures or situations: cerebrospinal fluid shunts, cerebrospinal fluid drains, implantation of intrathecal infusion pumps, implantation of deep brain stimulation hardware, and general neurosurgery and head trauma. Recommendations were followed by the strength of the recommendation and the quality of the evidence supporting the recommendation. Many recommendations, however, were based on expert opinion because rigorous clinical data are not available. These guidelines represent a practical and useful approach to assist practicing clinicians in the management of these challenging infections.
The young open cluster NGC 7067 using Strömgren photometry
Authors: Monguió M , Negueruela I , Marco A , González-Fernández C , Alonso-Santiago J , Costado M T , Casamiquela L , López-Corredoira M , Molgó J , Vilardell F , Alfaro E J , Antoja T , Figueras F , Garcia M , Jordi C , Romero-Gómez M
Published: December 2016

NGC 7067 is a young open cluster located in the direction between the first and the second Galactic quadrants and close to the Perseus spiral arm. This makes it useful for studies of the nature of the Milky Way spiral arms. Strömgren photometry taken with the Wide Field Camera at the Isaac Newton Telescope allowed us to compute individual physical parameters for the observed stars and hence to derive the cluster's physical parameters. Spectra from the 1.93-m telescope at the Observatoire de Haute-Provence helped to check and improve the results. We obtained photometry for 1233 stars, individual physical parameters for 515 and spectra for 9 of them. The 139 selected cluster members lead to a cluster distance of 4.4 ± 0.4 kpc, with an age below log10(t(yr)) = 7.3 and a present mass of 1260 ± 160 M⊙. The morphology of the data reveals that the centre of the cluster is at (α, δ) = (21: 24: 13.69, +48: 00: 39.2) J2000, with a radius of 6.1 arcmin. Strömgren and spectroscopic data allowed us to improve the previous parameters available for the cluster in the literature.
On the possibility (or lack thereof) of agreement between experiment and computation of flows over wings at moderate Reynolds number
Authors: Tank J. , Smith L. , Spedding G. R.
Published: December 2016

The flight of many birds and bats, and their robotic counterparts, occurs over a range of chord-based Reynolds numbers from 1 × 10
4
to 1.5 × 10
5
. It is precisely over this range where the aerodynamics of simple, rigid, fixed wings becomes extraordinarily sensitive to small changes in geometry and the environment, with two sets of consequences. The first is that practical lifting devices at this scale will likely not be simple, rigid, fixed wings. The second is that it becomes non-trivial to make baseline comparisons for experiment and computation, when either one can be wrong. Here we examine one ostensibly simple case of the NACA 0012 aerofoil and make careful comparison between the technical literature, and new experiments and computations. The agreement (or lack thereof) will establish one or more baseline results and some sensitivities around them. The idea is that the diagnostic procedures will help to guide comparisons and predictions in subsequent more complex cases.
Dynamics and flight control of a flapping-wing robotic insect in the presence of wind gusts
Authors: Chirarattananon Pakpong , Chen Yufeng , Helbling E. Farrell , Ma Kevin Y. , Cheng Richard , Wood Robert J.
Published: December 2016

With the goal of operating a biologically inspired robot autonomously outside of laboratory conditions, in this paper, we simulated wind disturbances in a laboratory setting and investigated the effects of gusts on the flight dynamics of a millimetre-scale flapping-wing robot. Simplified models describing the disturbance effects on the robot's dynamics are proposed, together with two disturbance rejection schemes capable of estimating and compensating for the disturbances. The proposed methods are experimentally verified. The results show that these strategies reduced the root-mean-square position errors by more than 50% when the robot was subject to 80 cm s−1horizontal wind. The analysis of flight data suggests that modulation of wing kinematics to stabilize the flight in the presence of wind gusts may indirectly contribute an additional stabilizing effect, reducing the time-averaged aerodynamic drag experienced by the robot. A benchtop experiment was performed to provide further support for this observed phenomenon.
Energetics in robotic flight at small scales
Authors: Karydis Konstantinos , Kumar Vijay
Published: December 2016

Recent advances in design, sensing and control have led to aerial robots that offer great promise in a range of real-world applications. However, one critical open question centres on how to improve the energetic efficiency of aerial robots so that they can be useful in practical situations. This review paper provides a survey on small-scale aerial robots (i.e. less than 1 m
2
area foot print, and less than 3 kg weight) from the point of view of energetics. The paper discusses methods to improve the efficiency of aerial vehicles, and reports on recent findings by the authors and other groups on modelling the impact of aerodynamics for the purpose of building energy-aware motion planners and controllers.
Flies compensate for unilateral wing damage through modular adjustments of wing and body kinematics
Authors: Muijres Florian T. , Iwasaki Nicole A. , Elzinga Michael J. , Melis Johan M. , Dickinson Michael H.
Published: December 2016

Using high-speed videography, we investigated how fruit flies compensate for unilateral wing damage, in which loss of area on one wing compromises both weight support and roll torque equilibrium. Our results show that flies control for unilateral damage by rolling their body towards the damaged wing and by adjusting the kinematics of both the intact and damaged wings. To compensate for the reduction in vertical lift force due to damage, flies elevate wingbeat frequency. Because this rise in frequency increases the flapping velocity of both wings, it has the undesired consequence of further increasing roll torque. To compensate for this effect, flies increase the stroke amplitude and advance the timing of pronation and supination of the damaged wing, while making the opposite adjustments on the intact wing. The resulting increase in force on the damaged wing and decrease in force on the intact wing function to maintain zero net roll torque. However, the bilaterally asymmetrical pattern of wing motion generates a finite lateral force, which flies balance by maintaining a constant body roll angle. Based on these results and additional experiments using a dynamically scaled robotic fly, we propose a simple bioinspired control algorithm for asymmetric wing damage.
Cross-species functional diversity within the PIN auxin efflux protein family
Authors: O’Connor Devin Lee , Elton Samuel , Ticchiarelli Fabrizio , Hsia Mon Mandy , Vogel John , Leyser Ottoline
Published: December 2016

In Arabidopsis, development during flowering is coordinated by transport of the hormone auxin mediated by polar-localized PIN-FORMED1 (AtPIN1). However Arabidopsis has lost a PIN clade sister to AtPIN1, Sister-of-PIN1 (SoPIN1), which is conserved in flowering plants. We previously proposed that the AtPIN1 organ initiation and vein patterning functions are split between the SoPIN1 and PIN1 clades in grasses. Here we show that in the grass Brachypodiumsopin1mutants have organ initiation defects similar to Arabidopsisatpin1, while loss ofPIN1function in Brachypodium has little effect on organ initiation but alters stem growth. Heterologous expression of Brachypodium SoPIN1 and PIN1b in Arabidopsis provides further evidence of functional specificity. SoPIN1 but not PIN1b can mediate flower formation in nullatpin1mutants, although both can complement a missense allele. The behavior of SoPIN1 and PIN1b in Arabidopsis illustrates how membrane and tissue-level accumulation, transport activity, and interaction contribute to PIN functional specificity.
Two independent modes of chromosome organization are revealed by cohesin removal
Authors: Schwarzer Wibke , Abdennur Nezar , Goloborodko Anton , Pekowska Aleksandra , Fudenberg Geoffrey , Loe-Mie Yann , Fonseca Nuno A , Huber Wolfgang , Haering Christian , Mirny Leonid , Spitz Francois
Published: December 2016

The three-dimensional organization of chromosomes is tightly related to their biological function1. Both imaging and chromosome conformation capture studies have revealed several layers of organization2-4: segregation into active and inactive compartments at the megabase scale5, and partitioning into domains (TADs)6,7and associated loops8at the sub-megabase scale. Yet, it remains unclear how these layers of genome organization form, interact with one another, and contribute to or result from genome activities. TADs seem to have critical roles in regulating gene expression by promoting or preventing interactions between promoters and distantcis-acting regulatory elements9-14, and different architectural proteins, including cohesin, have been proposed to play central roles in their formation15,16. However, experimental depletions of these proteins have resulted in marginal changes in chromosome organization17-19. Here, we show that deletion of the cohesin-loading factor,Nipbl, leads to loss of chromosome-associated cohesin and results in dramatic genome reorganization. TADs and associated loops vanish globally, even in the absence of transcriptional changes. In contrast, segregation into compartments is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the 3D organization of the genome results from the independent action of two distinct mechanisms: 1) cohesin-independent segregation of the genome into fine-scale compartment regions, defined by the underlying chromatin state; and 2) cohes-dependent formation of TADs possibly by the recently proposed loop extrusion mechanism20,21, enabling long-range and target-specific activity of promiscuous enhancers. The interplay between these mechanisms creates an architecture that is more complex than a simple hierarchy of layers and can be central to guiding normal development.
The Stone Age Plague: 1000 years of Persistence in Eurasia
Authors: Valtueña Aida Andrades , Mittnik Alissa , Key Felix M. , Haak Wolfgang , Allmäe Raili , Belinskij Andrej , Daubaras Mantas , Feldman Michal , Jankauskas Rimantas , Janković Ivor , Massy Ken , Novak Mario , Pfrengle Saskia , Reinhold Sabine , Šlaus Mario , Spyrou Maria A. , Szecsenyi-Nagy Anna , Tõrv Mari , Hansen Svend , Bos Kirsten I. , Stockhammer Philipp W. , Herbig Alexander , Krause Johannes
Published: December 2016

Molecular signatures ofYersinia pestiswere recently identified in prehistoric Eurasian individuals, thus suggestingY. pestiscaused some form of disease in humans prior to the first historically documented pandemic. Here, we present six newY. pestisgenomes spanning from the European Late Neolithic to the Bronze Age (LNBA) dating from 4,800 to 3,700 BP. We show that all currently investigated LNBA strains form a single genetic clade in theY. pestisphylogeny that appears to be extinct. Interpreting our data within the context of recent ancient human genomic evidence, which suggests an increase in human mobility during the LNBA, we propose a possible scenario for the spread ofY. pestisduring the LNBA:Y. pestismay have entered Europe from Central Eurasia during an expansion of steppe people, persisted within Europe until the mid Bronze Age, and moved back towards Central Eurasia in parallel with subsequent human population movements.
Strong and Fluctuating Sequence Constraints DriveAlu_Evolution
Authors: Wacholder Aaron C. , Pollock David D.
Published: December 2016

ThoughAluelements are the most common and well-studied transposable elements in the primate genome,Aluevolutionary dynamics remain poorly understood. To better understand these dynamics, we improved our recently introduced Bayesian transposable element ancestral reconstruction method to incorporate automated alignment and be more computationally efficient. We then used it to reconstruct the relationships among almost 800,000Aluelements in the human genome. We identified the phylogenetic network relating 154 ancestral replicativeAlusequences, and found that the aligned ancestors vary at only 56 out of ~300 sites. We show that the limited number of variable sites among replicativeAluancestors is best explained by strong sequence constraints onAlureplicative capacity. Moreover, the pattern of variation suggests that sequence constraints fluctuated over the course ofAluevolution, driving the extinction of olderAlusubfamilies and the birth of newer ones. Previous analyses have taken the tight clustering ofAlusequences with age as evidence that allAlusequences are descended from a small number of "master elements." Our results imply instead that the clustering ofAlusequences with age results from fluctuating sequence constraints, and that there were over 4,000 replicative loci during the course ofAluevolution, most of which were disabled by mutation before mutating to new replicative sequences. We also predict which sites have been functionally important for replication, and how these sites have changed over time. The newly clarified dynamics ofAluevolution invalidate assumptions used in common method of transposable element classification and phylogenetics.

Significance Statement

Transposable elements are genomic sequences that can insert copies of themselves elsewhere in the genome.Aluis the most abundant transposable element in primates, making up 10% of the human genome. Due to its ubiquity and tendency to cause genomic instability,Aluhas played a major role in shaping primate genomes. Characterizing the trajectory ofAluevolution is important for understanding how the human genome evolved.

Previous analyses ofAluconcluded that a tiny number of elements generated all copies, and existing classifications ofAlureflect that conclusion. In a whole-genome analysis, we determine that many more elements were replicative than previously understood, indicating that current classifications ofAluare flawed. We develop an alternative reconstruction ofAluevolutionary history.
A Reaction-Diffusion Model for Radiation-Induced Bystander Effects
Authors: Olobatuyi Oluwole , de Vries Gerda , Hillen Thomas
Published: December 2016

We develop and analyze a reaction-diffusion model to investigate the dynamics of the lifespan of a bystander signal emitted when cells are exposed to radiation. Experimental studies by Mothersill and Seymour 1997, using malignant epithelial cell lines, found that an emitted bystander signal can still cause bystander effects in cells even 60h after its emission. Several other experiments have also shown that the signal can persist for months and even years. Also, bystander effects have been hypothesized as one of the factors responsible for the phenomenon of low-dose hyper-radiosensitivity and increased radioresistance (HRS/IRR). Here, we confirm this hypothesis with a mathematical model, which we fit to Joiner’s data on HRS/IRR in a T98G glioma cell line. Furthermore, we use phase plane analysis to understand the full dynamics of the signal’s lifespan. We find that both single and multiple radiation exposure can lead to bystander signals that either persist temporarily or permanently. We also found that, in an heterogeneous environment, the size of the domain exposed to radiation and the number of radiation exposures can determine whether a signal will persist temporarily or permanently. Finally, we use sensitivity analysis to identify those cell parameters that affect the signal’s lifespan and the signal-induced cell death the most.
Diversity patterns across 1,800 chloroplast genomes of wild (Oryza rufipogonGriff.) and cultivated rice (O. sativaL.)
Authors: Civáň Peter , Brown Terence A.
Published: December 2016

Cultivated Asian rice(O. sativaL.) comprises several groups with distinct ecological requirements and culinary uses. While the two subspecies ofO. sativa–indicaandjaponica– have been subjected to a multitude of genetic and genomic analyses, less is known about the origins and diversity of the agronomically marginal groups –ausand aromatic rice. Here we reconstructed complete chloroplast genomes of over 1,800 accessions of wild and cultivated rice, including 240ausand 73 aromatic varieties, and analysed the haplotype diversity of the taxonomic groups. We confirm the deep phylogenetic divergence between the main chloroplast haplotypes ofjaponicaandindica,and reveal unique profiles of chloroplast diversity inausand aromatic rice. Our results indicate that the latter two groups are not simple derivatives ofindicaandjaponica,respectively, but originated from independent and/or reticulate domestication processes. Absence of phylogeographic patterns in the wild distribution of chloroplast haplogroups did not allow firm conclusions about geographic origins and the role of inter-group gene flow. Nonetheless, our results suggest that the domestication ofindica, japonica, ausand aromatic rice operated on genetically different gene pools and followed different dynamics.
Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation
Authors: Timmins-Schiffman Emma B. , Crandall Grace A. , Vadopalas Brent , Riffle Michael E. , Nunn Brook L. , Roberts Steven B.
Published: December 2016

Geoduck clams (Panopea generosa) are an increasingly important fishery and aquaculture product along the eastern Pacific coast from Baja California, Mexico to Alaska. These long-lived clams are highly fecund, though sustainable hatchery production of genetically diverse larvae is hindered by the lack of sexual dimorphism, resulting in asynchronous spawning of broodstock, unequal sex ratios, and low numbers of breeders. Development of assays of gonad physiology could indicate sex and maturation stage, as well as be used to assess the status of natural populations. Proteomic profiles were determined for three reproductive maturation stages in both male and female clams using data dependent acquisition (DDA) of gonad proteins. Gonad proteomes became increasingly divergent between males and females as maturation progressed. The DDA data was used to develop targets analyzed with selected reaction monitoring (SRM) in gonad tissue as well as hemolymph. The SRM assay yielded a suite of indicator peptides that can be used as an efficient assay to determine geoduck gonad maturation status. Application of SRM in hemolymph samples demonstrates this procedure could effectively be used to assess reproductive status in marine mollusks in a non-lethal manner.
Role of proteasome-dependent protein degradation in long-term operant memory in Aplysia
Authors: Lyons Lisa C. , Gardner Jacob S. , Gandour Catherine E. , Krishnan Harini C.
Published: December 2016

We investigated the in vivo role of protein degradation during intermediate (ITM) and long-term memory (LTM) in Aplysia using an operant learning paradigm. The proteasome inhibitor MG-132 inhibited the induction and molecular consolidation of LTM with no effect on ITM. Remarkably, maintenance of steady-state protein levels through inhibition of protein synthesis using either anisomycin or rapamycin in conjunction with proteasome inhibition permitted the formation of robust 24 h LTM. Our studies suggest a primary role for proteasomal activity in facilitation of gene transcription for LTM and raise the possibility that synaptic mechanisms are sufficient to sustain 24 h memory.
Primary auditory cortex regulates threat memory specificity
Authors: Wigestrand Mattis B. , Schiff Hillary C. , Fyhn Marianne , LeDoux Joseph E. , Sears Robert M.
Published: December 2016

Distinguishing threatening from nonthreatening stimuli is essential for survival and stimulus generalization is a hallmark of anxiety disorders. While auditory threat learning produces long-lasting plasticity in primary auditory cortex (Au1), it is not clear whether such Au1 plasticity regulates memory specificity or generalization. We used muscimol infusions in rats to show that discriminatory threat learning requires Au1 activity specifically during memory acquisition and retrieval, but not during consolidation. Memory specificity was similarly disrupted by infusion of PKMζ inhibitor peptide (ZIP) during memory storage. Our findings show that Au1 is required at critical memory phases and suggest that Au1 plasticity enables stimulus discrimination.
Crystal structure of chlorido[1-(4-nitrophenyl)thiourea-κS]bis(triphenylphosphane-κP)copper(I)
Authors: Nimthong-Roldán Arunpatcha , Promsuwhan Nichakan , Puetpaiboon Walailak , Wattanakanjana Yupa
Published: December 2016

The mononuclear mixed-ligand title complex, [CuCl(C7H7N3O2S)(C18H15P)2], displays a distorted tetrahedral coordination sphere around the CuIatom, with two P atoms from two triphenylphosphane molecules, one terminal S atom from a 1-(4-nitrophenyl)thiourea molecule and a chloride ion as ligands. An intramolecular N—H...Cl hydrogen bond stabilizes the molecular conformation [graph-set motifR22(6)]. In the crystal, further N—H...Cl hydrogen bonds connect individual molecules into zigzag chains parallel to [001]. The chains are linked by weak C—H...O hydrogen-bonding interactions into a three-dimensional network.
Crystal structure of 2-oxo-2H-chromen-3-yl 4-chlorobenzoate and Hirshfeld surface analysis
Authors: Ziki Eric , Sosso Siaka , Mansilla-Koblavi Frédérica , Djandé Abdoulaye , Kakou-Yao Rita
Published: December 2016

In the title compound, C16H9ClO4the dihedral angle between the coumarin ring system [maximum deviation = 0.023 (1) Å] and the benzene ring is 73.95 (8)°. In the crystal, π–π interactions link the dimers into a three-dimensional framework. A quantum chemical calculation is in generally good agreement with the observed structure, although the calculated dihedral angle between the ring systems (85.7%) is somewhat larger than the observed value [73.95 (8)°]. Hirshfeld surface analysis has been used to confirm and quantify the supramolecular interactions.
Crystal structure of 4-(4b,8a-dihydro-9H-pyrido[3,4-b]indol-1-yl)-7-methyl-2H-chromen-2-one
Authors: Samundeeswari S. , Kulkarni Manohar V. , Anil Kumar G. N.
Published: December 2016

The title compound, C21H14N2O2, was prepared by Pictet–Spengler cyclization of tryptamine and 4-formyl coumarin. In the molecule, the dihedral angle between the mean planes of the coumarin and β-carboline ring systems is 63.8 (2)°. In the crystal, molecules are linkedviaN—H...N hydrogen bonds, forming chains along theb-axis direction. Within the chains, there are a number of offset π–π interactions present [shortest intercentroid distance = 3.457 (2) Å].
4-Benzyl-1,2,4-triazaspiro[4.5]dec-1-ene-3-thione
Authors: Mohamed Shaaban K. , Akkurt Mehmet , Jasinski Jerry P. , Hassan Alaa A. , Abdel-Aziz Ahmed T. , Albayati Mustafa R.
Published: December 2016

In the title compound, C14H17N3S, the cyclohexane ring adopts a chair conformation. The dihedral angle between the triazole and phenyl ring is 77.2 (3)°. In the crystal structure, C—H...S hydrogen link molecules intoC(7) chains along theb-axis direction. The crystal studied was refined as as an inversion twin.
t-3-Benzyl-r-2,c-6-diphenylpiperidin-4-one oxime
Authors: Arulraj R. , Sivakumar S. , Thiruvalluvar A. , Manimekalai A.
Published: December 2016

In the title compound, C24H24N2O [systematic name: (E)-3-benzyl-2,6-diphenylpiperidin-4-one oxime], the piperidine ring adopts a slightly distorted chair conformation and the phenyl rings and the benzyl group substituents are attached equatorially. The oxime group makes a dihedral angle of 42.88 (12)° with the piperidine ring. The dihedral angle between the phenyl rings is 71.96 (8)°. The benzyl ring makes dihedral angles of 63.01 (8) and 59.35 (8)° with the two phenyl rings. In the crystal, molecules are linked by O—H...N hydrogen bonds, formingC(7) chains along thecaxis. The chains are linked by C—H...π interactions, forming slabs lying parallel to thebcplane.
Hexaaquamanganese(II) bis[hydrogen (4-aminophenyl)arsonate] tetrahydrate
Authors: Smith Graham , Wermuth Urs D.
Published: December 2016

In the structure of the complex salt formed from the reaction of manganese(II) acetate with (4-aminophenyl)arsonic acid (p-arsanilic acid), [Mn(H2O)6](C6H7AsNO3)2·4H2O, the centrosymmetric Mn(H2O)6coordination polyhedron has slightly distorted octahedral stereochemistry, with the two hydrogen (4-aminophenyl)arsonate anions and the four water molecules of solvation related by inversion. Extensive O—H...O, O—H...N and N—H...O hydrogen bonds link all species, giving an overall three-dimensional supramolecular structure, which also has weak π–π ring interactions [minimum ring-centroid separation = 3.7304 (15) Å]. The structure is isotypic with that of the Mg salt.
Effects of sublethal concentrations of silver nanoparticles on Escherichia coli and Bacillus subtilis under aerobic and anaerobic conditions
Authors: Garuglieri Elisa , Cattò Cristina , Villa Federica , Zanchi Raffaella , Cappitelli Francesca
Published: December 2016

The present work is aimed at comparing the effects of sublethal concentrations of silver nanoparticles (AgNPs) on the growth kinetic, adhesion ability, oxidative stress, and phenotypic changes of model bacteria (Escherichia coli and Bacillus subtilis) under both aerobic and anaerobic conditions. Growth kinetic tests conducted in 96-well microtiter plates revealed that sublethal concentrations of AgNPs do not affect E. coli growth, whereas 1 μg/ml AgNPs increased B. subtilis growth rate under aerobic conditions. At the same concentration, AgNPs promoted B. subtilis adhesion, while it discouraged E. coli attachment to the surface in the presence of oxygen. As determined by 2,7-dichlorofluorescein-diacetate assays, AgNPs increased the formation of intracellular reactive oxygen species, but not at the highest concentrations, suggesting the activation of scavenging systems. Finally, motility assays revealed that 0.01 and 1 μg/ml AgNPs, respectively, promoted surface movement in E. coli and B. subtilis under aerobic and anaerobic conditions. The results demonstrate that E. coli and B. subtilis react differently from AgNPs over a wide range of sublethal concentrations examined under both aerobic and anaerobic conditions. These findings will help elucidate the behavior and impact of engineered nanoparticles on microbial ecosystems.
Characterization of silver nanoparticles-alginate complexes by combined size separation and size measurement techniques
Authors: António Diana C. , Cascio Claudia , Gilliland Douglas , Nogueira António J. A. , Rossi François , Calzolai Luigi
Published: December 2016

The detection and quantification of nanoparticles is a complex issue due to the need to combine “classical” identification and quantification of the constituent material, with the accurate determination of the size of submicrometer objects, usually well below the optical diffraction limit. In this work, the authors show that one of the most used analytical methods for silver nanoparticles, asymmetric flow field-flow fractionation, can be strongly influenced by the presence of dissolved organic matter (such as alginate) and lead to potentially misleading results. The authors explain the anomalies in the separation process and show a very general way forward based on the combination of size separation and size measurement techniques. This combination of techniques results in more robust AF4-based methods for the sizing of silver nanoparticles in environmental conditions and could be generally applied to the sizing of nanoparticles in complex matrices.
Gold nanoparticles increases UV and thermal stability of human serum albumin
Authors: Capomaccio Robin , Osório Inês , Ojea-Jiménez Isaac , Ceccone Giacomo , Colpo Pascal , Gilliland Douglas , Hussain Rohanah , Siligardi Giuliano , Rossi Francois , Ricard-Blum Sylvie , Calzolai Luigi
Published: December 2016

Ultraviolet (UV) radiation, temperature, and time can degrade proteins. Here, the authors show that gold nanoparticles significantly protect human serum albumin from denaturation when exposed to “stressing” conditions such as UV irradiation and sustained exposure in suboptimal conditions. In particular, the authors show that gold nanoparticles significantly reduce the decrease in secondary structure induced by UV irradiation or extended exposure to ambient temperature.
Enhanced field emission properties from carbon nanotube emitters on the nanopatterned substrate
Authors: Kim Se Jung , Park Seol Ah , Kim Young-Cho , Ju Byeong-Kwon
Published: December 2016

The authors investigated the field emission characteristics of printed carbon nanotubes (CNTs) on KOVAR substrates with micro- and nanosize line patterns. Microsized line patterns were fabricated using photolithography techniques followed by an inductive coupled plasma-reactive ion etching process, and laser interference lithography techniques were used to fabricate uniform nanosized patterns over a relatively large area. CNTs were printed on the patterned substrate using a screen printing method. The field emission characteristics of each patterned substrate were compared to those of a nonpatterned substrate. Results revealed that varying the pattern size has an influence on the field emission characteristics. The reduction of the pattern size results in an increase in the total surface area. This surface patterning is found to provide additional areas for CNTs to adhere to the substrates, which, in turn, results in better adhesion of CNTs. As the size of the pattern is reduced, the field emission properties are improved. Specifically, substrates with nanosized patterns exhibited both the lowest turn-on field and the highest field enhancement factor (β).
Buried targets in layered media: A combined finite element/physical acoustics model and comparison to data on a half buried 2:1 cylinder
Authors: Williams Kevin L.
Published: December 2016

Previously, a combined finite element/physical acoustics model for proud targets [K. L. Williams, S. G. Kargl, E. I. Thorsos, D. S. Burnett, J. L. Lopes, M. Zampolli, and P. L. Marston, J. Acoust. Soc. Am. 127, 3356–3371 (2010)] was compared to both higher fidelity finite element models and to experimental data for a proud 2:1 aluminum cylinder. Here that expression is generalized to address the case of a target buried in a layered media. The result is compared to data acquired for the same 2:1 cylinder but half buried in a mud layer that covers the sand sediment (considered here as infinite in extent below the mud layer). The generalized expression reduces to both the previous proud result and to the result for a target buried in an infinite medium under the appropriate limiting conditions. The model/data comparisons shown include both the previous proud model and data results along with the ones for the half buried cylinder. The comparison quantifies the reduction in target strength as a function of frequency in the half buried case relative to the proud case.