bluuebunny/crossref_metadata_2025 huggingface dataset:
Relation between clinical mature and immature lymphocyte cells in human peripheral blood and their spatial label free scattering patterns
Authors: Zhang Lu , Zhao Xin , Zhang Zhenxi , Zhao Hong , Chen Wei , Yuan Li
Published: July 2016

A single living cell’s light scattering pattern (LSP) in the horizontal plane, which has been denoted as the cell’s “2D fingerprint,” may provide a powerful label-free detection tool in clinical applications. We have recently studied the LSP in spatial scattering planes, denoted as the cell’s “3D fingerprint,” for mature and immature lymphocyte cells in human peripheral blood. The effects of membrane size, morphology, and the existence of the nucleus on the spatial LSP are discussed. In order to distinguish clinical label-free mature and immature lymphocytes, the special features of the spatial LSP are studied by statistical method in both the spatial and frequency domains. Spatial LSP provides rich information on the cell’s morphology and contents, which can distinguish mature from immature lymphocyte cells and hence ultimately it may be a useful label-free technique for clinical leukemia diagnosis.
Spatially resolved Thomson scattering measurements of the transition from the collective to the non-collective regime in a laser-produced plasma
Authors: Schaeffer D. B. , Constantin C. G. , Bondarenko A. S. , Everson E. T. , Niemann C.
Published: July 2016

We present optical Thomson scattering results that image for the first time in a single measurement the spatial transition from collective to non-collective scattering. Data were taken in the Phoenix laser laboratory at the University of California, Los Angeles. The Raptor laser was used to ablate a carbon plasma, which was diagnosed with the frequency-doubled Phoenix laser serving as a Thomson scattering probe. Scattered light was collected from the laser plasma up to 10 cm from the target surface and up to 10 us after ablation, and imaged with high spatial and spectral resolutions. The results show a strong Thomson collective feature close to the target surface that smoothly transitions to a non-collective feature over several mm.
Operation of a quantum dot in the finite-state machine mode: Single-electron dynamic memory
Authors: Klymenko M. V. , Klein M. , Levine R. D. , Remacle F.
Published: July 2016

A single electron dynamic memory is designed based on the non-equilibrium dynamics of charge states in electrostatically defined metallic quantum dots. Using the orthodox theory for computing the transfer rates and a master equation, we model the dynamical response of devices consisting of a charge sensor coupled to either a single and or a double quantum dot subjected to a pulsed gate voltage. We show that transition rates between charge states in metallic quantum dots are characterized by an asymmetry that can be controlled by the gate voltage. This effect is more pronounced when the switching between charge states corresponds to a Markovian process involving electron transport through a chain of several quantum dots. By simulating the dynamics of electron transport we demonstrate that the quantum box operates as a finite-state machine that can be addressed by choosing suitable shapes and switching rates of the gate pulses. We further show that writing times in the ns range and retention memory times six orders of magnitude longer, in the ms range, can be achieved on the double quantum dot system using experimentally feasible parameters, thereby demonstrating that the device can operate as a dynamic single electron memory.
The role of interstitial binding in radiation induced segregation in W-Re alloys
Authors: Gharaee Leili , Marian Jaime , Erhart Paul
Published: July 2016

Due to their high strength and advantageous high-temperature properties, tungsten-based alloys are being considered as plasma-facing candidate materials in fusion devices. Under neutron irradiation, rhenium, which is produced by nuclear transmutation, has been found to precipitate in elongated precipitates forming thermodynamic intermetallic phases at concentrations well below the solubility limit. Recent measurements have shown that Re precipitation can lead to substantial hardening, which may have a detrimental effect on the fracture toughness of W alloys. This puzzle of sub-solubility precipitation points to the role played by irradiation induced defects, specifically mixed solute-W interstitials. Here, using first-principles calculations based on density functional theory, we study the energetics of mixed interstitial defects in W-Re, W-V, and W-Ti alloys, as well as the heat of mixing for each substitutional solute. We find that mixed interstitials in all systems are strongly attracted to each other with binding energies of −2.4 to −3.2 eV and form interstitial pairs that are aligned along parallel first-neighbor 〈111〉 strings. Low barriers for defect translation and rotation enable defect agglomeration and alignment even at moderate temperatures. We propose that these elongated agglomerates of mixed-interstitials may act as precursors for the formation of needle-shaped intermetallic precipitates. This interstitial-based mechanism is not limited to radiation induced segregation and precipitation in W–Re alloys but is also applicable to other body-centered cubic alloys.
A phenomenological model for self-rippling energy of free graphene monolayers
Authors: Wu Bingjie , Ru C. Q.
Published: July 2016

Several candidate phenomenological expressions are studied for self-rippling energy that drives ripple formation of free single-layer graphene sheets. One phenomenological expression is admitted, while all others are rejected because they cannot admit stable periodic ripple mode. The admitted phenomenological expression contains two terms: one quadratic term which acts like a compressive force and has a destabilizing effect, and another fourth-order term which acts like a nonlinear elastic foundation and has a stabilizing effect. The two associated coefficients depend on specific mechanism of self-rippling and can be determined based on observed wavelength and amplitude of ripple mode. Based on the admitted expression, the effect of an applied force on ripple formation is studied. The present model predicts that the rippling can be controlled or even suppressed with an applied tensile force or collapsed into narrow wrinkles (of deformed wavelengths down to around 2 nm) under an applied compressive force, and the estimated minimum tensile strain to suppress rippling is in remarkable agreement with some known data. Our results show that self-rippling energy dominates ripple formation of sufficiently long free graphene ribbons, although it cannot drive self-rippling of sufficiently short free graphene ribbons. Consequently, a critical length is estimated so that self-rippling occurs only when the length of free single-layer graphene ribbons is much longer than the critical length. The estimated critical length is reasonably consistent with the known fact that self-rippling cannot occur in shorter free graphene sheets (say, of length below 20 nm).
Towards strong light-matter coupling at the single-resonator level with sub-wavelength mid-infrared nano-antennas
Authors: Malerba M. , Ongarello T. , Paulillo B. , Manceau J.-M. , Beaudoin G. , Sagnes I. , De Angelis F. , Colombelli R.
Published: July 2016

We report a crucial step towards single-object cavity electrodynamics in the mid-infrared spectral range using resonators that borrow functionalities from antennas. Room-temperature strong light-matter coupling is demonstrated in the mid-infrared between an intersubband transition and an extremely reduced number of sub-wavelength resonators. By exploiting 3D plasmonic nano-antennas featuring an out-of-plane geometry, we observed strong light-matter coupling in a very low number of resonators: only 16, more than 100 times better than what reported to date in this spectral range. The modal volume addressed by each nano-antenna is sub-wavelength-sized and it encompasses only ≈4400 electrons.
Effective ionization coefficients, limiting electric fields, and electron energy distributions in CF3I + CF4 + Ar ternary gas mixtures
Authors: Tezcan S. S. , Dincer M. S. , Bektas S.
Published: July 2016

This paper reports on the effective ionization coefficients, limiting electric fields, electron energy distribution functions, and mean energies in ternary mixtures of (Trifluoroiodomethane) CF3I + CF4 + Ar in the E/N range of 100–700 Td employing a two-term solution of the Boltzmann equation. In the ternary mixture, CF3I component is increased while the CF4 component is reduced accordingly and the 40% Ar component is kept constant. It is seen that the electronegativity of the mixture increases with increased CF3I content and effective ionization coefficients decrease while the limiting electric field values increase. Synergism in the mixture is also evaluated in percentage using the limiting electric field values obtained. Furthermore, it is possible to control the mean electron energy in the ternary mixture by changing the content of CF3I component.
Research on structural design and test technologies for a three-chamber launching device
Authors: Jun Wu , Qiushi Yan , Ling Xiao , Tieshuan Zhuang , Chengyu Yang
Published: July 2016

A three-chamber launching device with improved acceleration is proposed and developed. As indicated by the damage generated during the pill and engineering protection tests, the proposed device is applicable as a high-speed launching platform for pills of different shapes and quality levels. Specifically, it can be used to investigate kinetic energy weapons and their highly destructive effects due to the resulting large bomb fragments. In the horizontal direction of the barrel, two auxiliary chambers are set at a certain distance from the main chamber. When the pill reaches the mouth of the auxiliary chambers, the charges in the auxiliary chambers are ignited by the high-temperature, high-pressure combustible gas trailing the pill. The combustible gas in the auxiliary chambers can resist the rear pressure of the pill and thus maintain the high pressure of the pill base. In this way, the required secondary acceleration of the pill is met. The proposed device features the advantage of launching a pill with high initial velocity under low bore pressure. Key techniques are proposed in the design of the device to address the problems related to the angle between the main chamber axis and the ancillary chamber axis, the overall design of a three-chamber barrel, the structural design of auxiliary propellant charge, the high-pressure combustible gas sealing technology, and the sabot and belt design. Results from the launching test verify the reasonable design of this device and its reliable structural sealing. Additionally, the stiffness and the strength of the barrel meet design requirements. Compared with the single-chamber launching device with the same caliber, the proposed device increases the average launching velocity by approximately 15% and the amount of muzzle kinetic energy by approximately 35%. Therefore, this equipment is capable of carrying out small-caliber, high-speed pill firing tests.
Engineering the switching dynamics of TiOx-based RRAM with Al doping
Authors: Trapatseli Maria , Khiat Ali , Cortese Simone , Serb Alexantrou , Carta Daniela , Prodromakis Themistoklis
Published: July 2016

Titanium oxide (TiOx) has attracted a lot of attention as an active material for resistive random access memory (RRAM), due to its versatility and variety of possible crystal phases. Although existing RRAM materials have demonstrated impressive characteristics, like ultra-fast switching and high cycling endurance, this technology still encounters challenges like low yields, large variability of switching characteristics, and ultimately device failure. Electroforming has been often considered responsible for introducing irreversible damage to devices, with high switching voltages contributing to device degradation. In this paper, we have employed Al doping for tuning the resistive switching characteristics of titanium oxide RRAM. The resistive switching threshold voltages of undoped and Al-doped TiOx thin films were first assessed by conductive atomic force microscopy. The thin films were then transferred in RRAM devices and tested with voltage pulse sweeping, demonstrating that the Al-doped devices could on average form at lower potentials compared to the undoped ones and could support both analog and binary switching at potentials as low as 0.9 V. This work demonstrates a potential pathway for implementing low-power RRAM systems.
Enhanced hydrogen storage by using lithium decoration on phosphorene
Authors: Yu Zhiyuan , Wan Neng , Lei Shuangying , Yu Hong
Published: July 2016

The hydrogen storage characteristics of Li decorated phosphorene were systematically investigated based on first-principle density functional theory. It is revealed that the adsorption of H2 on pristine phosphorene is relatively weak with an adsorption energy of 0.06 eV. While this value can be dramatically enhanced to ∼0.2 eV after the phosphorene was decorated by Li, and each Li atom can adsorb up to three H2 molecules. The detailed mechanism of the enhanced hydrogen storage was discussed based on our density functional theory calculations. Our studies give a conservative prediction of hydrogen storage capacity to be 4.4 wt. % through Li decoration on pristine phosphorene. By comparing our calculations to the present molecular dynamic simulation results, we expect our adsorption system is stable under room temperature and hydrogen can be released after moderate heating.
Critical thickness of 2D to 3D transition in GexSi1−x/Si(001) system
Authors: Lozovoy K. A. , Kokhanenko A. P. , Voitsekhovskii A. V.
Published: July 2016

In this paper, Stranski–Krastanov growth of GexSi1−x epitaxial layers on the Si(001) surface is considered. Experimental investigations show that the moment of transition from 2D to 3D growth and the critical thickness of 2D layer at which this transition occurs play a key role during the synthesis of such materials. Among the most important parameters determining the peculiarities of the growth process and characteristics of emerging island ensembles are growth temperature and surface conditions (for example, the presence of surfactants). But existing theoretical models are not able to predict the values of the critical thickness in the whole range of growth temperatures and compositions x of solution for these systems. For the calculations of the critical thickness of transition from 2D to 3D growth, in this paper, a theoretical model based on general nucleation theory is proposed. This model is specified by taking into account dependencies of elastic modulus, lattices mismatch, and surface energy of the side facet on the composition x. As a result, dependencies of the critical thickness of Stranski–Krastanov transition on composition x and temperature are obtained. This allows one to determine conditions of transition from 2D to 3D growth mode in these systems. The simulated results explain experimentally observed results on temperature dependencies of the critical thickness for different germanium contents.
Epitaxial growth and electrochemical transfer of graphene on Ir(111)/α-Al2O3(0001) substrates
Authors: Koh Shinji , Saito Yuta , Kodama Hideyuki , Sawabe Atsuhito
Published: July 2016

Low-pressure chemical vapor deposition growth of graphene on Iridium (Ir) layers epitaxially deposited on α-Al2O3 (0001) substrates was investigated. The X-ray diffraction, Raman and reflection high energy electron diffraction characterizations revealed that graphene films were epitaxially grown on Ir(111) layers, and the in-plane epitaxial relationship between graphene, Ir(111), and α-Al2O3(0001) was graphene ⟨11¯00⟩//Ir⟨112¯⟩//α-Al2O3⟨112¯0⟩. The graphene on Ir(111) was electrochemically transferred onto SiO2/Si substrates. We also demonstrated the reuse of the Ir(111)/α-Al2O3(0001) substrates in multiple growth and transfer cycles.
Embedding objects during 3D printing to add new functionalities
Authors: Yuen Po Ki
Published: July 2016

A novel method for integrating and embedding objects to add new functionalities during 3D printing based on fused deposition modeling (FDM) (also known as fused filament fabrication or molten polymer deposition) is presented. Unlike typical 3D printing, FDM-based 3D printing could allow objects to be integrated and embedded during 3D printing and the FDM-based 3D printed devices do not typically require any post-processing and finishing. Thus, various fluidic devices with integrated glass cover slips or polystyrene films with and without an embedded porous membrane, and optical devices with embedded Corning® Fibrance™ Light-Diffusing Fiber were 3D printed to demonstrate the versatility of the FDM-based 3D printing and embedding method. Fluid perfusion flow experiments with a blue colored food dye solution were used to visually confirm fluid flow and/or fluid perfusion through the embedded porous membrane in the 3D printed fluidic devices. Similar to typical 3D printed devices, FDM-based 3D printed devices are translucent at best unless post-polishing is performed and optical transparency is highly desirable in any fluidic devices; integrated glass cover slips or polystyrene films would provide a perfect optical transparent window for observation and visualization. In addition, they also provide a compatible flat smooth surface for biological or biomolecular applications. The 3D printed fluidic devices with an embedded porous membrane are applicable to biological or chemical applications such as continuous perfusion cell culture or biocatalytic synthesis but without the need for any post-device assembly and finishing. The 3D printed devices with embedded Corning® Fibrance™ Light-Diffusing Fiber would have applications in display, illumination, or optical applications. Furthermore, the FDM-based 3D printing and embedding method could also be utilized to print casting molds with an integrated glass bottom for polydimethylsiloxane (PDMS) device replication. These 3D printed glass bottom casting molds would result in PDMS replicas with a flat smooth bottom surface for better bonding and adhesion.
Globin X is a six-coordinate globin that reduces nitrite to nitric oxide in fish red blood cells
Authors: Corti Paola , Xue Jianmin , Tejero Jesús , Wajih Nadeem , Sun Ming , Stolz Donna B. , Tsang Michael , Kim-Shapiro Daniel B. , Gladwin Mark T.
Published: July 2016

Significance

Hemoglobin is generally assumed to be the only globin in vertebrate RBCs. In addition to its foremost role as an oxygen carrier, mammalian hemoglobin can also operate as a nitrite reductase, producing the signaling molecule nitric oxide (NO) from nitrite. Over the last 15 yr, several novel globins have been identified with six-coordinate heme geometry and uncertain physiological functions. Here we report that a six-coordinate globin of ancient origin, named Globin X, is present in fish RBCs. We establish that Globin X is a fast nitrite reductase, and this activity can regulate NO production from fish RBCs and modulate platelet activation. Thus we provide evidence that the ancestral globins in blood were efficient nitrite reductases.
COP1 is required for UV-B–induced nuclear accumulation of the UVR8 photoreceptor
Authors: Yin Ruohe , Skvortsova Mariya Y. , Loubéry Sylvain , Ulm Roman
Published: July 2016

Significance

Plant tissues are resistant to the potentially damaging UV-B radiation intrinsic to sunlight. UV-B photoreception by a UV RESISTANCE LOCUS 8 (UVR8) photoreceptor regulates gene expression in plants associated with UV-B acclimation and stress tolerance and with morphological changes. Mechanistically, UV-B photon reception by specific tryptophan residues of UVR8 homodimers results in monomerization and enhanced nuclear accumulation of UVR8. Active UVR8 monomers interact with the key signaling protein CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1). This UV-B–dependent interaction is a crucial step in signal propagation, but the link between this mechanism and UVR8 nuclear accumulation and gene expression remains ill defined. Our results emphasize the importance of nuclear-localized UVR8 and highlight a previously unknown activity of COP1 in mediating UVR8 nuclear accumulation in response to UV-B.
Researching norms, narratives, and transitional justice: focus group methodology in post-conflict Croatia
Authors: Sokolić Ivor
Published: July 2016

This article is based on the assumption that norms can help better understand one of the expressivist aims of transitional justice, that of building a new narrative about the past. The main argument is that focus groups, as an interactive method of inquiry, are well suited to investigating how this “judicial” narrative interacts with the official and dominant war narrative in Croatia. Focus groups are more adept at this than other methodological approaches since they can effectively reflect independence of opinion; they lead to more truthful answers through spontaneity; they effectively probe taken-for-granted concepts; and they can more easily overcome distrust in post-conflict societies, especially with ex-combatants. The approach faces new challenges in such a situation since recruitment problems, insider/outsider status, and posttraumatic stress disorder, among other ethical concerns, present problems that often arise due to the group process. The powerful and unpredictable effect of the group dynamic can, therefore, provide a deep exploration of social norms, but it can also cause significant upset among participants. In this instance the methodology explores how widely accepted the war narrative is, how it is constructed, and how important the public believes it is not to question it.
Growth mechanism and adhesion of PEO coatings on 2024Al alloy
Authors: Li Q. B. , Liu C. C. , Yang W. B. , Liang J.
Published: July 2016

In this work, the growth mechanism and adhesion of plasma electrolytic oxidation (PEO) coatings on 2024Al alloy were studied under different cathodic voltages. It is found that the growth of PEO coatings is characterised by both the inward growth and outward growth, which result from the oxidation of the substrate and the deposition of electrolyte-borne compounds. Moreover, the growth mechanism and adhesion of PEO coatings are closely related and significantly influenced by the applied cathodic voltages. When the cathodic voltage increases, the oxidation of the substrate becomes more predominant, causing more inward growth. And the increase of inward growth results in more compact structure and higher adhesion of PEO coatings.
A non-radioactive assay for selenophosphate synthetase activity using recombinant pyruvate pyrophosphate dikinase from Thermus thermophilus HB8
Authors: Kamada Saho , Okugochi Takahiro , Asano Kaori , Tobe Ryuta , Mihara Hisaaki , Nemoto Michiko , Inagaki Kenji , Tamura Takashi
Published: July 2016

Biosynthesis of selenocysteine-containing proteins requires monoselenophosphate, a selenium-donor intermediate generated by selenophosphate synthetase (Sephs). A non-radioactive assay was developed as an alternative to the standard [8-14C] AMP-quantifying assay. The product, AMP, was measured using a recombinant pyruvate pyrophosphate dikinase from Thermus thermophilus HB8. The KM and kcat for Sephs2-Sec60Cys were determined to be 26 μM and 0.352 min−1, respectively.
Expression of PR-protein genes and induction of defense-related enzymes by Bacillus subtilis CBR05 in tomato (Solanum lycopersicum) plants challenged with Erwinia carotovora subsp. carotovora
Authors: Chandrasekaran Murugesan , Chun Se Chul
Published: July 2016

The present study was aimed to evaluate the effectiveness of a biocontrol agent Bacillus subtilis CBR05 for control of soft rot disease (Erwinia carotovora subsp. carotovora) in tomato, and the possible mechanisms of its resistance induction have been investigated under pot conditions. Results showed that plants inoculated with B. subtilis CBR05 had lower disease incidence (36%). A significant increase in superoxide dismutase, catalase, peroxidase, and polyphenol oxidase activities was observed in plants inoculated with B. subtilis between 48 and 72 hpi. Also, the transcript profiles of Glu and Phenyl ammonia lyase (PAL) showed a significant up-regulation following inoculation. The most significant up-regulation was observed in transcript profile of PAL that showed 0.49 Fold Expression, at 72 hpi as compared to its expression at 12 hpi. These results suggest that systemic induction of defense-related genes expression and antioxidant enzyme activity by B. subtilis could play a pivotal role in disease resistance against soft rot disease.
Serum pharmacokinetics of choline, trimethylamine, and trimethylamine-N-oxide after oral gavage of phosphatidylcholines with different fatty acid compositions in mice
Authors: Gao Xiang , Jiang Chengzi , Xu Jie , Yanagita Teruyoshi , Xue Changhu , Wang Yuming
Published: July 2016

Little is known about the pharmacokinetics of phosphatidylcholine (PC)-derived choline, trimethylamine (TMA), and trimethylamine-N-oxide (TMAO). We therefore aim to investigate serum choline, TMA, and TMAO pharmacokinetics following different PCs gavage and compare the difference between PC emulsions and liposomes (SOL). Serum choline, TMA, and TMAO levels were measured after orally gavaged egg yolk PC emulsion (EGE), squid PC emulsion (SQE), soybean PC emulsion (SOE), and SOL in fasted mice. Time to reach peak concentration (Tmax) and productions for TMA and TMAO were more slow and less in SQE group compared with EGE and SOE groups. Tmax for choline, TMA, and TMAO prolonged, and the productions of them were significantly declined in SOL group compared to SOE group. These findings indicated that marine source squid PC could counter-regulate the potential risks of TMAO generation, and the use of liposome as the form of PC supplementary may eliminate TMAO production.
Friction stir lap joining of aluminium alloy to polypropylene sheets
Authors: Shahmiri H. , Movahedi M. , Kokabi A. H.
Published: July 2016

Joining feasibility of aluminium alloy to polypropylene sheets via friction stir lap joining was examined. Effects of heat-input on microstructure and mechanical behaviour of the joints were investigated. A covering plate was used to confine flow of molten polymer. The results showed a distinctive interaction layer at polymer/aluminium interface, consisted mainly of C, O and Al. Shear strength of the joints decreased by enhancement of the heat-input due to increase in the thickness of the interaction layer as well as the gap width between this layer and both aluminium and polymer matrices. Maximum shear-tensile strength of 5.1 MPa (∼20% of polymer shear strength) was obtained, which was higher than or comparable to that of the joints produced by other processes.
Electron beam welding of thick-walled copper components
Authors: Enzinger N. , Loidolt P. , Wiednig C. , Stütz M. , Sommitsch C.
Published: July 2016

Electron beam welding facilitates a very high energy density, which is a significant advantage when welding materials with a high thermal conductivity like copper. Nevertheless, in EBW of copper, unique root defects are observed in full penetration welding of thick components. Therefore, it is of scientific interest and relevant for applications to determine the reason and to develop countermeasures. A novel attempt to address this problem is using filler material. First, with a copper–tin alloy filler metal in form of sheets, a sufficient solidification range can be established. Second, a pure tin plasma-sprayed layer is applied to achieve an alloyed weld zone. With these approaches and in combination with proper welding parameters, defect free joints are established.
Assessing Sustainable Development Goals from the standpoint of equity for children
Authors: Minujin Alberto , Ferrer Mildred
Published: July 2016

The article develops a discourse about equality for children and their recent evolution from adult-centred consideration to definition as a separate, critical constituency as stated in the Sustainable Development Goals (SDGs), with their child-focused goals and targets. Challenges implementing equality and fairness are discussed, from the World Summit for Children (WSC) in 1990 to the nearly simultaneous ratification of the Convention on the Rights of the Child (CRC), which gives children agency through its legally binding clauses, and the Millennium Development Goals (MDGs). The article reviews past lessons learned and the post-2015 agenda debate, from which worldwide agreement evolved about multidimensional poverty and an equality roadmap. The article suggests social accountability processes to achieve lasting SDG targets. It provides a methodology for implementing social accountability actions, accompanied by examples to mobilise communities and encourage child and youth participation at the local level.
Survey of period variations of superhumps in SU UMa-type dwarf novae. VIII. The eighth year (2015–2016)
Authors: Kato Taichi , Hambsch Franz-Josef , Monard Berto , Vanmunster Tonny , Maeda Yutaka , Miller Ian , Itoh Hiroshi , Kiyota Seiichiro , Isogai Keisuke , Kimura Mariko , Imada Akira , Tordai Tamás , Akazawa Hidehiko , Tanabe Kenji , Otani Noritoshi , Ogi Minako , Ando Kazuko , Takigawa Naoki , Dubovsky Pavol A. , Kudzej Igor , Shugarov Sergey Yu. , Katysheva Natalia , Golysheva Polina , Gladilina Natalia , Chochol Drahomir , Starr Peter , Kasai Kiyoshi , Pickard Roger D. , Miguel Enrique de , Kojiguchi Naoto , Sugiura Yuki , Fukushima Daiki , Yamada Eiji , Uto Yusuke , Kamibetsunawa Taku , Tatsumi Taiki , Takeda Nao , Matsumoto Katsura , Cook Lewis M. , Pavlenko Elena P. , Babina Julia V. , Pit Nikolaj V. , Antonyuk Oksana I. , Antonyuk Kirill A. , Sosnovskij Aleksei A. , Baklanov Aleksei V. , Kafka Stella , Stein William , Voloshina Irina B. , Ruiz Javier , Sabo Richard , Dvorak Shawn , Stone Geoff , Andreev Maksim V. , Antipin Sergey V. , Zubareva Alexandra M. , Zaostrojnykh Anna M. , Richmond Michael , Shears Jeremy , Dubois Franky , Logie Ludwig , Rau Steve , Vanaverbeke Siegfried , Simon Andrei , Oksanen Arto , Goff William N. , Bolt Greg , Dębski Bartłomiej , Kochanek Christopher S. , Shappee Benjamin , Stanek Krzysztof Z. , Prieto José L. , Stubbings Rod , Muyllaert Eddy , Hiraga Mitsutaka , Horie Tsuneo , Schmeer Patrick , Hirosawa Kenji
Published: July 2016

Continuing the project described by Kato et al. (2009, PASJ, 61, S395), we collected times of superhump maxima for 128 SU UMa-type dwarf novae observed mainly during the 2015–2016 season and characterized these objects. The data have improved the distribution of orbital periods, the relation between the orbital period and the variation of superhumps, and the relation between period variations and the rebrightening type in WZ Sge-type objects. Coupled with new measurements of mass ratios using growing stages of superhumps, we now have a clearer and statistically greatly improved evolutionary path near the terminal stage of evolution of cataclysmic variables. Three objects (V452 Cas, KK Tel, and ASASSN-15cl) appear to have slowly growing superhumps, which is proposed to reflect the slow growth of the 3 : 1 resonance near the stability border. ASASSN-15sl, ASASSN-15ux, SDSS J074859.55+312512.6, and CRTS J200331.3−284941 are newly identified eclipsing SU UMa-type (or WZ Sge-type) dwarf novae. ASASSN-15cy has a short (∼0.050 d) superhump period and appears to belong to EI Psc-type objects with compact secondaries having an evolved core. ASASSN-15gn, ASASSN-15hn, ASASSN-15kh, and ASASSN-16bu are candidate period bouncers with superhump periods longer than 0.06 d. We have newly obtained superhump periods for 79 objects and 13 orbital periods, including periods from early superhumps. In order that future observations will be more astrophysically beneficial and rewarding to observers, we propose guidelines on how to organize observations of various superoutbursts.
Song discrimination by nestling collared flycatchers during early development
Authors: McFarlane S. Eryn , Söderberg Axel , Wheatcroft David , Qvarnström Anna
Published: July 2016

Pre-zygotic isolation is often maintained by species-specific signals and preferences. However, in species where signals are learnt, as in songbirds, learning errors can lead to costly hybridization. Song discrimination expressed during early developmental stages may ensure selective learning later in life but can be difficult to demonstrate before behavioural responses are obvious. Here, we use a novel method, measuring changes in metabolic rate, to detect song perception and discrimination in collared flycatcher embryos and nestlings. We found that nestlings as early as 7 days old respond to song with increased metabolic rate, and, by 9 days old, have increased metabolic rate when listening to conspecific when compared with heterospecific song. This early discrimination between songs probably leads to fewer heterospecific matings, and thus higher fitness of collared flycatchers living in sympatry with closely related species.
Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)
Authors: Bapst D. W. , Wright A. M. , Matzke N. J. , Lloyd G. T.
Published: July 2016

Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian ‘tip-dating’ methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative
a posteriori
approaches including via the probabilistic
cal3
method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from
cal3
and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.
Costly learning: preference for familiar food persists despite negative impact on survival
Authors: Costa Thaiany M. , Hebets Eileen A. , Melo Diogo , Willemart Rodrigo H.
Published: July 2016

Animals often rely on events in their environment that provide information (i.e. experience) to alter their future decision-making in ways that are presumed to be beneficial. Such experience-based learning, however, does not always lead to adaptive decision-making. In this study, we use the omnivorous harvestman
Heteromitobates discolor
to explore the role of past diet on subsequent food choice and survival. We first tested whether a short-term homogeneous diet (rotten crickets, fresh crickets or dog food) influenced subsequent food choice (rotten cricket versus fresh cricket). We next examine the impact of diet on survival. We found that following experience with a homogeneous cricket diet, adult harvestmen displayed a learned preference for familiar food, regardless of whether it was rotten or fresh crickets; individuals experiencing dog food were equally likely to choose rotten versus fresh crickets. We additionally found that individuals that ate rotten crickets suffered shorter survival than those that ate fresh crickets. Together, our results suggest that the diet an individual experiences can lead to maladaptive food preferences—preferences that ultimately result in reduced longevity.
Developmental plasticity evolved according to specialist–generalist trade-offs in experimental populations ofDrosophila melanogaster
Authors: Le Vinh Thuy Jacqueline , VandenBrooks John M. , Angilletta Michael J.
Published: July 2016

We studied the evolution of developmental plasticity in populations ofDrosophila melanogasterthat evolved at either constant or fluctuating temperatures. Consistent with theory, genotypes that evolved at a constant 16°C or 25°C performed best when raised and tested at that temperature. Genotypes that evolved at fluctuating temperatures performed well at either temperature, but only when raised and tested at the same temperature. Our results confirm evolutionary patterns predicted by theory, including a loss of plasticity and a benefit of specialization in constant environments.
SOX7-enforced expression promotes the expansion of adult blood progenitors and blocks B-cell development
Authors: Cuvertino Sara , Lacaud Georges , Kouskoff Valerie
Published: July 2016

During embryogenesis, the three SOXF transcription factors, SOX7, SOX17 and SOX18, regulate the specification of the cardiovascular system and are also involved in the development of haematopoiesis. The ectopic expression of SOX17 in both embryonic and adult blood cells enhances self-renewal. Likewise, the enforced expression of SOX7 during embryonic development promotes the proliferation of early blood progenitors and blocks lineage commitment. However, whether SOX7 expression can also affect the self-renewal of adult blood progenitors has never been explored. In this study, we demonstrate using an inducible transgenic mouse model that the enforced expression ofSox7 ex vivoin bone marrow/stroma cell co-culture promotes the proliferation of blood progenitors which retain multi-lineage short-term engrafting capacity. Furthermore, SOX7 expression induces a profound block in the generation of B lymphocytes. Correspondingly, the ectopic expression of SOX7in vivoresults in dramatic alterations of the haematopoietic system, inducing the proliferation of blood progenitors in the bone marrow while blocking B lymphopoiesis. In addition, SOX7 expression induces extra-medullary haematopoiesis in the spleen and liver. Together, these data demonstrate that the uncontrolled expression of the transcription factor SOX7 in adult haematopoietic cells has dramatic consequences on blood homeostasis.
Rates of ecological divergence and body size evolution are correlated with species diversification in scaly tree ferns
Authors: Ramírez-Barahona Santiago , Barrera-Redondo Josué , Eguiarte Luis E.
Published: July 2016

Variation in species richness across regions and between different groups of organisms is a major feature of evolution. Several factors have been proposed to explain these differences, including heterogeneity in the rates of species diversification and the age of clades. It has been frequently assumed that rapid rates of diversification are coupled to high rates of ecological and morphological evolution, leading to a prediction that remains poorly explored for most species: the positive association between ecological niche divergence, morphological evolution and species diversification. We combined a time-calibrated phylogeny with distribution, ecological and body size data for scaly tree ferns (Cyatheaceae) to test whether rates of species diversification are predicted by the rates at which clades have evolved distinct ecological niches and body sizes. We found that rates of species diversification are positively correlated with rates of ecological and morphological evolution, with rapidly diversifying clades also showing rapidly evolving ecological niches and body sizes. Our results show that rapid diversification of scaly tree ferns is associated with the evolution of species with comparable morphologies that diversified into similar, yet distinct, environments. This suggests parallel evolutionary pathways opening in different tropical regions whenever ecological and geographical opportunities arise. Accordingly, rates of ecological niche and body size evolution are relevant to explain the current patterns of species richness in this ‘ancient’ fern lineage across the tropics.
Whole genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom
Authors: Chheda Himanshu , Palta Priit , Pirinen Matti , McCarthy Shane , Walter Klaudia , Koskinen Seppo , Salomaa Veikko , Daly Mark , Durbin Richard , Palotie Aarno , Aittokallio Tero , Ripatti Samuli ,   Sequencing Initiative Suomi (SISu) Project
Published: July 2016

Isolated populations with enrichment of variants due to recent population bottlenecks provide a powerful resource for identifying disease-associated genetic variants and genes. As a model of an isolate population, we sequenced the genomes of 1463 Finnish individuals as part of the Sequencing Initiative Suomi (SISu) Project. We compared the genomic profiles of the 1463 Finns to a sample of 1463 British individuals that were sequenced in parallel as part of the UK10K Project. Whereas there were no major differences in the allele frequency of common variants, a significant depletion of variants in the rare frequency spectrum was observed in Finns when comparing the two populations. On the other hand, we observed >2.1 million variants that were twice as frequent among Finns compared to Britons and 800,000 variants that were more than 10 times more frequent in Finns. Furthermore, in Finns we observed a relative proportional enrichment of variants in the minor allele frequency range between 2 - 5% (p < 2.2×10−16). When stratified by their functional annotations, loss-of-function (LoF) variants showed the highest proportional enrichment in Finns (p = 0.0291). In the noncoding part of the genome, variants in conserved regions (p = 0.002) and promoters (p = 0.01) were also significantly enriched in the Finnish samples. These functional categories represent the highesta prioripower for downstream association studies of rare variants using population isolates.
discoal: flexible coalescent simulations with selection
Authors: Kern Andrew D. , Schrider Daniel R.
Published: July 2016

Here we describediscoal, a coalescent simulator able to generate population samples that include selective sweeps in a feature-rich, flexible manner.discoalcan perform simulations conditioning on the fixation of an allele due to drift or either hard or soft selective sweeps—even those occurring a large genetic distance away from the simulated locus.discoalcan simulate sweeps with recurrent mutation to the adaptive allele, recombination, and gene conversion, under nonequilibrium demographic histories and without specifying an allele frequency trajectory in advance.

Availability and Implementation

Availability and implementation: discoal is implemented in the C programming language. Source code is freely available on GitHub (https://github.com/kernlab/discoal_multipop) under a GNU General Public License.

Contact

kern@dls.rutgers.edu

Supplementary information

Supplementary Figures and Text are appended below
Parallel Evolution of Cold Tolerance WithinDrosophila melanogaster
Authors: Pool John E. , Braun Dylan T. , Lack Justin B.
Published: July 2016

Drosophila melanogasteroriginated in tropical Africa before expanding into strikingly different temperate climates in Eurasia and beyond. Here, we show that elevated cold tolerance has arisen at least three times within this species: beyond the well-studied non-African case, we show that populations from the highlands of Ethiopia and South Africa have significantly increased cold tolerance as well. We observe greater cold tolerance in outbred versus inbred flies, but only in populations with higher inversion frequencies. Each cold-adapted population shows lower inversion frequencies than a closely-related warm-adapted population, suggesting that inversion frequencies may decrease with altitude in addition to latitude. Using theFST-based “Population Branch Excess” statistic (PBE), we found only limited evidence for parallel genetic differentiation at the scale of ~4 kb windows, specifically between Ethiopian and South African cold-adapted populations. And yet, when we looked for single nucleotide polymorphisms (SNPs) with codirectional frequency change in two or three cold-adapted populations, strong genomic enrichments were observed from all comparisons. These findings could reflect an important role for selection on standing genetic variation leading to “soft sweeps”. One SNP showed sufficient codirectional frequency change in all cold-adapted populations to achieve experiment-wide significance: an intronic variant in the synaptic geneProsap. More generally, proteins involved in neurotransmission were enriched as potential targets of parallel adaptation. The ability to study cold tolerance evolution in a parallel framework will enhance this classic study system for climate adaptation.
Novel features of telomere biology revealed by the absence of telomeric DNA methylation
Authors: Vega-Vaquero Alejandro , Bonora Giancarlo , Morselli Marco , Vaquero-Sedas María I. , Rubbi Liudmilla , Pellegrini Matteo , Vega-Palas Miguel A.
Published: July 2016

Cytosine methylation regulates the length and stability of telomeres, which can affect a wide variety of biological features, including cell differentiation, development, or illness. Although it is well established that subtelomeric regions are methylated, the presence of methylated cytosines at telomeres has remained controversial. Here, we have analyzed multiple bisulfite sequencing studies to address the methylation status of Arabidopsis thaliana telomeres. We found that the levels of estimated telomeric DNA methylation varied among studies. Interestingly, we estimated higher levels of telomeric DNA methylation in studies that produced C-rich telomeric strands with lower efficiency. However, these high methylation estimates arose due to experimental limitations of the bisulfite technique. We found a similar phenomenon for mitochondrial DNA: The levels of mitochondrial DNA methylation detected were higher in experiments with lower mitochondrial read production efficiencies. Based on experiments with high telomeric C-rich strand production efficiencies, we concluded that Arabidopsis telomeres are not methylated, which was confirmed by methylation-dependent restriction enzyme analyses. Thus, our studies indicate that telomeres are refractory to de novo DNA methylation by the RNA-directed DNA methylation machinery. This result, together with previously reported data, reveals that subtelomeric DNA methylation controls the homeostasis of telomere length.
Malonate in the nucleotide-binding site traps human AKAP18γ/δ in a novel conformational state
Authors: Bjerregaard-Andersen Kaare , Østensen Ellen , Scott John D. , Taskén Kjetil , Morth Jens Preben
Published: July 2016

A-kinase anchoring proteins (AKAPs) are a family of proteins that provide spatiotemporal resolution of protein kinase A (PKA) phosphorylation. In the myocardium, PKA and AKAP18γ/δ are found in complex with sarcoendoplasmic reticulum Ca2+-ATPase 2 (SERCA2) and phospholamban (PLB). This macromolecular complex provides a means by which anchored PKA can dynamically regulate cytoplasmic Ca2+release and re-uptake. For this reason, AKAP18γ/δ presents an interesting drug target with therapeutic potential in cardiovascular disease. The crystal structure of the central domain of human AKAP18γ has been determined at the atomic resolution of 1.25 Å. This first structure of human AKAP18γ is trapped in a novel conformation by a malonate molecule bridging the important R-loop with the 2H phosphoesterase motif. Although the physiological substrate of AKAP18γ is currently unknown, a potential proton wire deep in the central binding crevice has been indentified, leading to bulk solvent below the R-loop. Malonate complexed with AKAP18γ at atomic resolution provides an excellent starting point for structure-guided drug design.