bluuebunny/crossref_metadata_2025 huggingface dataset:
Periodic and aperiodic bubbling in submerged gas-liquid jets through a micro-channel
Authors: Shen Yingnan , Hu Liang , Chen Wenyu , Fu Xin
Published: April 2017

The common phenomena of periodic and aperiodic bubbling, which were studied merely in single-phase gas jets, are discovered to exist in submerged gas-liquid jets through a micro-channel. Due to the participation of the liquid input flow which interacts with the gas phase, the periodic and aperiodic bubbling behaviors, as well as the regime transition mechanisms, are quite different from single-phase gas jets. Periodic bubbling is formed by injecting a regular Taylor flow into bulk liquid, in which a special motion of bubbles named “bubble bifurcation” is revealed. Bubbles move into the opposite orientation to the bubbles they touch because unequal contact angles make the bubbles tilt when they detach. The bifurcation process is described by the evolutions of the contact line, bubble centers, and the bifurcation point. The second bifurcation events cause the bubble branches to rotate simultaneously. The difference of periodicity between gas-liquid jets and single-phase gas jets is explained in a dimensionless form as a function of 1/St versus Fr. Aperiodic bubbling including double coalescence, triple, quadruple, and quintuple bubble formation is found to occur at lower gas velocities than single-phase gas jets because of the different mechanism of bubble detachment in which liquid rings make bubbles pitch off before necking. The effect of liquid rings on bubbling period, as well as the disturbance waves spreading over the bubble surface, is explained. Finally, the mechanisms of bubbling losing periodicity are figured out through analyzing the correspondence relationship between the evolutions of bubbling behaviors and the flow regime transitions in the micro-channel with regime boundaries well predicted by corresponding models.
Benchmark study of the structural and spectroscopic parameters of the hydroxymethyl peroxy (HOCH2OO) radical and its decomposition reaction to HO2 and H2CO
Authors: Linguerri Roberto , Puzzarini Cristina , Al Mogren Muneerah Mogren , Francisco Joseph S. , Hochlaf Majdi
Published: April 2017

The hydroxymethyl peroxy (HMOO) radical is a product of the oxidation of non-methane hydrocarbons. The present study provides the first accurate computational determination of critical spectroscopic features of the title radical that should aid in its experimental characterization. Structure, energetics, vibrational frequencies, and rotational parameters are reported for the three stable isomers on the ground electronic state of HMOO. While preliminary computations have been carried out using density functional theory as well as second-order Møller-Plesset perturbation theory, for the accurate structural and spectroscopic characterization we made use of coupled-cluster techniques, herewith considering both standard and explicitly correlated methods. The “CCSD(T)/CBS + CV” composite scheme, a state-of-the-art composite approach based on the coupled-cluster theory including single and double excitations together with a perturbative treatment of triples that accounts for extrapolation to the complete basis-set limit as well as core-valence correlation effects, is used to obtain accurate structural and energetic data, in particular for the decomposition reaction to HO2 and H2CO.
Modified kinetic theory applied to the shear flows of granular materials
Authors: Duan Yifei , Feng Zhi-Gang , Michaelides Efstathios E. , Mao Shaolin
Published: April 2017

Granular materials are characterized by large collections of discrete particles, where the particle-particle interactions are significantly more important than the particle-fluid interactions. The current kinetic theory captures fairly accurately the granular flow behavior in the dilute case, when only binary interactions are significant, but is not accurate at all in the dense flow regime, where multi-particle interactions and contacts must be modeled. To improve the kinetic theory results for granular flows in the dense flow regime, we propose a Modified Kinetic Theory (MKT) model that utilizes the contact duration or cutoff time to account for the complex particle-particle interactions in the dense regime. The contact duration model, also called TC model, was originally proposed by Luding and McNamara [“How to handle the inelastic collapse of a dissipative hard-sphere gas with the TC model,” Granular Matter 1, 113 (1998)] to solve the inelastic collapse issue existing in the inelastic hard sphere model. This model defines a cutoff time tc such that dissipation is not counted if the time between two consecutive contacts is less than tc. As shown in their study, the use of a cutoff time tc can also reduce the dissipation during multi-particle contacts. In this paper we relate the TC model with the Discrete Element Method (DEM) by choosing the cutoff time tc to be the duration of contact calculated from the linear-spring-dashpot soft-sphere model of the DEM. We examine two types of granular flows, simple shear flow and the plane shear flow, and compare the results of the classical kinetic theory model, the present MKT model, and the DEM model. We show that the MKT model entails a significant improvement over the kinetic theory model for simple shear flows at inertial regimes. With the MKT model the calculations are close to the DEM results at solid fractions as high as 0.57. Even for the plane shear flows, where shear rate and solid fraction are inhomogeneous, the results of the MKT model agree very well with the DEM results.
A specific absorption rate reduction method for simultaneous multislice magnetic resonance imaging
Authors: Wu Fu-Hsing , Wu Edzer L. , Tung Yi-Hang , Cheng Po-Wei , Chiueh Tzi-Dar , Chen Jyh-Horng
Published: April 2017

This study proposes a modified Shinnar–Le Roux method to synthesize the excitation radio frequency (RF) pulse for a 2D gradient echo (GRE) based simultaneous multi-slice (SMS) magnetic resonance imaging (MRI) with features of low specific absorption rate (SAR) and small out-of-slice ripple. This synthesis method for SMS RF pulses employs thinner slice bandwidth and lower multislice offset frequencies to reduce SAR values and adopts a weighted Parks–McClellan algorithm to reduce sidelobes. Formulas for estimating relative SAR values of the SMS pulses are also introduced. Relative SAR values and out-of-slice ripples of the proposed and typical RF pulses with different parameters are presented. In simultaneous 5-slice phantom and 3-slice human brain imaging, SMS pulses synthesized with the proposed method achieve 32% and 28% SAR values of standard pulses while providing similar image qualities. Typical RF pulses such as sinc x cos can also take advantage of the proposed method and offer lower SAR values for SMS imaging. The RF pulse synthesized using the proposed method features low SAR, small sidelobes, and consistent image quality for 2D GRE-based SMS MRI. This method is applicable to the synthesis of typical SMS RF pulses for significant SAR reduction.
A diabatization protocol that includes spin-orbit coupling
Authors: Zeng Tao
Published: April 2017

A diabatization protocol that combines the recently developed model space diabatization scheme and a mean-field treatment for spin-orbit coupling is presented. The protocol is highly efficient and easy to use. Its robustness is demonstrated in the calculations of the diabatic spin-orbit matrix elements of PH3+, AsH3+, and SbH3+. It captures subtle geometry-dependence of the spin-orbit couplings and provides wave function information to explain the origin of the dependence.
Study of DC Ar–CO2 mixture plasma using optical emission spectroscopy and mass spectrometry techniques
Authors: Martinez H. , Perusquía S. , Villa M. , Reyes P. G. , Yousif F. B. , Castillo F. , Contreras U.
Published: April 2017

DC generated Ar–CO2 discharge for plasma mixtures at 2.0 Torr is investigated to evaluate the variation in the electron temperature and density, electron energy distribution function, and population densities of the reactive atomic, molecular, and ionic species of CO2–Ar plasmas as a function of the Ar percentage in the mixtures. Optical emission spectroscopy and quadrupole mass spectrometry are used to determine the reactive species in the Ar–CO2 plasma in the DC discharge mode as a function of the Ar percentage. The species observed in the plasma mixtures were CO2, O2, CO, O, C2, and Ar, which agree very well with the mass spectroscopy observation. In addition, single Langmuir probes are employed to characterize the plasma. The CO species are observed to increase to 40% Ar in the mixture and then decrease. The electron temperatures and density are found to be between 1.9-3.1 eV and (0.8–2.0) × 1010 cm−3, respectively.
A developed wedge fixtures assisted high precision TEM samples pre-thinning method: Towards the batch lamella preparation
Authors: Wang Dandan , Huang Yamin , Liu Binghai , Zhu Lei , Lam Jeffrey , Mai Zhihong
Published: April 2017

Ion milling, wedge cutting or polishing, and focused ion beam (FIB) milling are widely-used techniques for the transmission electron microscope (TEM) sample preparation. Especially, the FIB milling provides a site-specific analysis, deposition, and ablation of materials in the micrometer and nanometer scale. However, the cost of FIB tools has been always a significant concern. Since it is inevitable to use the FIB technique, the improvement of efficiency is a key point. Traditional TEM sample preparation with FIB was routinely implemented on a single sample each time. Aiming at cost efficiency, a new pre-thinning technique for batch sample preparation was developed in this paper. The present proposal combines the sample preparation techniques with multi-samples thinning, cross-section scanning electron microscopy (SEM), wedge cutting, FIB and other sample pre-thinning techniques. The new pre-thinning technique is to prepare an edge TEM sample on a grinding and polishing fixture with a slant surface. The thickness of the wedges sample can be measured to 1∼2 μm under optical microscope. Therefore, this fixture is superior to the traditional optical method of estimating the membrane thickness. Moreover, by utilizing a multi-sample holding fixture, more samples can be pre-thinned simultaneously, which significantly improved the productivity of TEM sample preparation.
High performance graphene oxide-based humidity sensor integrated on a photonic crystal cavity
Authors: Gan Xuetao , Zhao Chenyang , Yuan Qingchen , Fang Liang , Li Yongjiang , Yin Jianbo , Ma Xiaoyan , Zhao Jianlin
Published: April 2017

We report a high performance relative humidity (RH) microsensor based on a few-layer graphene oxide (GO) flake coated photonic crystal (PC) cavity. Since the GO layer is highly water-reactive and interacts with the evanescent cavity mode strongly, the exposure of the GO-PC cavity in varied humidity levels results in significant resonant wavelength shifts, showing a slope of 0.68 nm/%RH in the range of 60%–85%RH. By monitoring the power variation of the cavity reflection, the microsensor presents an ultrahigh sensitivity exceeding 3.9 dB/%RH. Relying on the unimpeded permeation of water molecules through the GO interlayers and microscale distribution of the cavity mode, the integrated sensor has a response time less than 100 ms, which promises successful measurements of human breathing. Combining with the ease of fabrication, this high performance RH sensor provides great potentials in applications requiring optical access, device compactness, and fast dynamic response.
Microbranching instability in phase-field modelling of dynamic brittle fracture
Authors: Bleyer Jeremy , Molinari Jean-François
Published: April 2017

The microbranching instability occurring for rapidly propagating cracks in brittle materials has been described in various experiments as an intrinsically three-dimensional phenomenon. Using a variational phase-field model, we show that the microbranching process is, indeed, a three-dimensional instability which exhibits a strong dependence on the sample width and can be suppressed for very thin samples. We show that the phase-field internal length scale is the decisive variable governing the branching pattern, which can be either localized in the transverse direction as observed in a glass, for example, or, on the contrary, almost translational invariant with quasi-periodic structures, as observed in PMMA.
Magnetically guided Cesium interferometer for inertial sensing
Authors: Qi Lu , Hu Zhaohui , Valenzuela Tristan , Zhang Yuchi , Zhai Yueyang , Quan Wei , Waltham Nick , Fang Jiancheng
Published: April 2017

In this paper, we demonstrate a Talbot-Lau interferometer with magnetically guided Cesium atoms for inertial sensing using both three-pulse and prolonged four-pulse interferometer schemes. The recoil frequency of the Cesium atoms and the acceleration along the waveguide symmetry axis are measured. An acceleration measurement uncertainty of 7 mGal is achieved. We also realize an enclosed area of 0.018 mm2 for rotation sensing. The system limitations and its advantages are also discussed.
Screening of working fluids and metal materials for high temperature organic Rankine cycles by compatibility
Authors: Dai Xiaoye , Shi Lin , An Qingsong , Qian Weizhong
Published: April 2017

Organic Rankine Cycle (ORC) systems using high temperature (150–350 °C) heat resources have attracted much interest due to their high thermal efficiencies and outputs. However, the organic working fluids may react with the ORC system materials at high temperatures, which can lead to fluid decomposition, material corrosion, and other system safety problems. This study experimentally investigated the material compatibility for ORC systems with n-pentane, HFC245fa, hexamethyldisiloxane (MM), and HFE7100 as the test fluids with copper and aluminum. The results showed that HFC245fa and HFE7100 changed the hardness of copper samples by 2.22% and 5.79% and n-pentane and MM changed the tensile strength of copper samples by 0.59% and 0.66% at 250 °C for 100 h. HFC245fa also changed the hardness of aluminum samples by 3.84%, and HFE7100 changed the tensile strength of aluminum samples by 2.69%. Thus, n-pentane and MM with aluminum as materials are the better choices for high temperature ORC systems. Both copper and aluminum catalyzed n-pentane decomposition, and so copper and aluminum should be avoided in ORC systems when the heat resource temperatures are close to the fluid decomposition temperatures.
Broadband parametric amplifiers based on nonlinear kinetic inductance artificial transmission lines
Authors: Chaudhuri S. , Li D. , Irwin K. D. , Bockstiegel C. , Hubmayr J. , Ullom J. N. , Vissers M. R. , Gao J.
Published: April 2017

We present broadband parametric amplifiers based on the kinetic inductance of superconducting NbTiN thin films in an artificial (lumped-element) transmission line architecture. We demonstrate two amplifier designs implementing different phase matching techniques: periodic impedance loading and resonator phase shifters placed periodically along the transmission line. Our design offers several advantages over previous CPW-based amplifiers, including intrinsic 50 Ω characteristic impedance, natural suppression of higher pump harmonics, lower required pump power, and shorter total trace length. Experimental realizations of both versions of the amplifiers are demonstrated. With a transmission line length of 20 cm, we have achieved gains of 15 dB over several GHz of bandwidth.
BiFeO3-doped (K0.5,Na0.5)(Mn0.005,Nb0.995)O3 ferroelectric thin film capacitors for high energy density storage applications
Authors: Won Sung Sik , Kawahara Masami , Kuhn Lindsay , Venugopal Vineeth , Kwak Jiyeon , Kim Ill Won , Kingon Angus I. , Kim Seung-Hyun
Published: April 2017

Environmentally benign lead-free ferroelectric (K0.5,Na0.5)(Mn0.005,Nb0.995)O3 (KNMN) thin film capacitors with a small concentration of a BiFeO3 (BF) dopant were prepared by a cost effective chemical solution deposition method for high energy density storage device applications. 6 mol. % BF-doped KNMN thin films showed very slim hysteresis loops with high maximum and near-zero remanent polarization values due to a phase transition from the orthorhombic structure to the pseudo-cubic structure. Increasing the electric field up to 2 MV/cm, the total energy storage density (Jtotal), the effective recoverable energy density (Jeff), and the energy conversion efficiency (η) of lead-free KNMN-BF thin film capacitors were 31.0 J/cm3, 28.0 J/cm3, and 90.3%, respectively. In addition, these thin film capacitors exhibited a fast discharge time of a few μs and a high temperature stability up to 200 °C, proving their strong potential for high energy density storage and conversion applications.
A decision-support tool for autumn management in a spring-calving pasture-based dairy system
Authors: Neal Mark , Kay Jane , Peel Sally , McCarthy Sean
Published: April 2017

Success in a pasture-based dairy system relies on matching feed supply and feed demand in a profitable manner. Autumn is an important period for decision making to maximise current-season profitability, while ensuring key targets such as cow body condition score and the level of average pasture cover are met for the upcoming season. There are many tactical management strategies for farmers to consider during autumn to ensure that profitability is maximised in the current and next season (e.g. feeding crops, purchasing or using available supplementary feeds, reducing milking frequency, grazing off young stock, culling, or drying off cows). The complexity of trade-offs among these factors from January to calving, and the need to assess the impact of each of these on seasonal profitability led to the development of the ‘DairyNZ Autumn Management Resource’. This resource is an energy-based model that calculates the profit from different management strategies in pasture-based spring-calving systems. Feed demand is initially set to ensure that target body condition is achieved for the next season, and can then be altered using variables such as milking frequency, number of cows in milk and stock grazing on-farm. The assumption is made that energy supply comes from grazed pasture and crop first, followed by conserved forages, with the opportunity to fill remaining gaps with purchased feed. The model is a decision-support resource for farmers during the autumn that compares the economics of different management strategies in the current season, while ensuring that the performance in the next season is not compromised.
Eight-minute self-regulation intervention raises educational attainment at scale in individualist but not collectivist cultures
Authors: Kizilcec René F. , Cohen Geoffrey L.
Published: April 2017

Significance

High attrition from educational programs is a major obstacle to social mobility and a persistent source of economic inefficiency. Over two-thirds of students entering a 2-y institution fail to earn a credential in the United States. In online courses, attrition rates are even higher. In two large field experiments, we tested the conditions under which a writing activity that facilitates goal commitment and goal-directed behavior reduces attrition in online courses. The activity raised completion rates by up to 78% for members of individualist cultures and primarily for those who contended with predictable and surmountable obstacles in the form of everyday obligations, but it was ineffective in collectivist cultures and for people contending with other types of obstacles.
Tectonic controls on the long-term carbon isotope mass balance
Authors: Shields Graham A. , Mills Benjamin J. W.
Published: April 2017

Significance

The carbon isotope record has played a major role in reconstructing the oxygen and carbon dioxide content of the ancient atmosphere. However, known oxygenation events are not always reflected in the isotopic record of marine carbonate rocks, while conventional interpretations imply that less organic matter is buried when erosion rates are high, which is hard to explain. Here we show that both issues can be resolved if limestone weathering makes up a proportionately greater fraction of the global carbon cycle at high erosion rates. We argue that the link between carbon isotopes and oxygenation is more tenuous than commonly assumed, and propose a case-by-case reexamination of earth’s oxygenation history.
Plasma fibronectin stabilizes
Borrelia burgdorferi
–endothelial interactions under vascular shear stress by a catch-bond mechanism
Authors: Niddam Alexandra F. , Ebady Rhodaba , Bansal Anil , Koehler Anne , Hinz Boris , Moriarty Tara J.
Published: April 2017

Significance

Spread of bacteria via the bloodstream to vital organs causes most mortality due to bacterial infection. To exit the bloodstream and enter these organs, bacteria must be able to resist the forces generated by flowing blood so that they can adhere to the endothelial cells lining blood vessels without being washed away. This process is not yet understood for most disease-causing bacteria. Here, we show that the Lyme disease pathogen
Borrelia burgdorferi
exploits an abundant constituent of blood, plasma fibronectin, to form endothelial interactions that become stronger as forces due to blood-flow increase. The ability to recruit this highly conserved molecule may also be important for the vascular interaction mechanisms of other pathogens.
Formation of neurodegenerative aggresome and death-inducing signaling complex in maternal diabetes-induced neural tube defects
Authors: Zhao Zhiyong , Cao Lixue , Reece E. Albert
Published: April 2017

Significance

Neural tube defects in infants of women with diabetes are associated with disrupted protein folding and increased programmed cell death in embryonic cells. Misfolded proteins are ubiquitinylated and form aggregates that contain the neurodegenerative disease-associated proteins α-Synuclein, Parkin, and Huntingtin (Htt). Aggregation of Htt leads to formation of a Hip1–Hippi–Caspase-8 complex to activate Caspase-8. Treatment with chemical chaperones alleviates protein aggregation and decreases neural tube defects in the embryos of diabetic mice. Targeting misfolded proteins could be a potential approach to preventing birth defects in diabetic pregnancies.
Structural basis of Tie2 activation and Tie2/Tie1 heterodimerization
Authors: Leppänen Veli-Matti , Saharinen Pipsa , Alitalo Kari
Published: April 2017

Significance

Tie1 and Tie2 receptor tyrosine kinases are key regulators of blood and lymphatic vessel development and of pathological processes including tumor angiogenesis, atherosclerosis, and vascular leakage, e.g., in sepsis. Tie1 is essential for the Tie2 agonist activity of angiopoietins, and the activated receptors form heteromeric complexes in endothelial cell–cell junctions. However, little is known about the activation mechanisms of the Tie receptors. Here we demonstrate that the membrane-proximal domains of Tie2 mediate homotypic interactions, which occur via intermolecular β-sheet formation and are necessary for Tie2 activation. The structural analysis suggests that Tie2/Tie1 heterodimerization occurs by the same mechanism. The crystal structures provide a model for angiopoietin-stimulated Tie2 ectodomain dimerization, clustering, and activation and insights into therapeutic targeting.
Identification of a cono-RFamide from the venom of
Conus textile
that targets ASIC3 and enhances muscle pain
Authors: Reimers Catharina , Lee Cheng-Han , Kalbacher Hubert , Tian Yuemin , Hung Chih-Hsien , Schmidt Axel , Prokop Lea , Kauferstein Silke , Mebs Dietrich , Chen Chih-Cheng , Gründer Stefan
Published: April 2017

Significance

Marine cone snails provide one of the highest toxin diversities among venomous animals, the conotoxins, which often target ion channels. In addition, cone snail venoms contain short conopeptides, the molecular targets of which are mostly unknown. We identified a new conopeptide from the venom of the cone snail
Conus textile
that targets the proton-gated ion channel ASIC3, which detects painful acidosis. This peptide belongs to the subgroup of cono-RFamides and potentiates ASIC3 currents, thereby increasing the excitability of nociceptors. Injection of the cono-RFamide in mice muscle enhanced acid-induced muscle pain. Our results thus identify ASIC3 as the first molecular target of cono-RFamides. These findings underline the role of ASIC3 in pain perception and the importance of nontoxic venom components.
Molecular basis for the interaction between Integrator subunits IntS9 and IntS11 and its functional importance
Authors: Wu Yixuan , Albrecht Todd R. , Baillat David , Wagner Eric J. , Tong Liang
Published: April 2017

Significance

The Integrator complex (INT) has important functions in the 3′-end processing of noncoding RNAs and RNA polymerase II transcription. The INT contains at least 14 subunits, but its molecular mechanism of action is still poorly understood. The endonuclease activity of INT is mediated by its subunit 11 (IntS11), which forms a stable complex with Integrator complex subunit 9 (IntS9) through their C-terminal domains (CTDs). Here, we report the crystal structure of the IntS9–IntS11 CTD complex at 2.1-Å resolution and detailed, structure-based biochemical and functional studies. Highly conserved residues are located in the extensive interface between the two CTDs. Yeast two-hybrid assays and coimmunoprecipitation experiments confirm the structural observations. Functional studies demonstrate that the IntS9–IntS11 interaction is crucial for INT in snRNA 3′-end processing.
Selective entrainment of gamma subbands by different slow network oscillations
Authors: Zhong Weiwei , Ciatipis Mareva , Wolfenstetter Thérèse , Jessberger Jakob , Müller Carola , Ponsel Simon , Yanovsky Yevgenij , Brankačk Jurij , Tort Adriano B. L. , Draguhn Andreas
Published: April 2017

Significance

Theta-gamma coupling has been largely documented in hippocampal and neocortical areas and hypothesized to constitute a network mechanism for information processing. However, we identify here another global slow rhythm at near-theta frequency that also couples to gamma. By simultaneously recording respiration, we could distinguish actual theta oscillations from a respiration-entrained rhythm (RR) in the local field potential whose peak frequency may overlap with theta. We demonstrate a robust specificity for the coupling of different gamma subbands to either theta or RR depending on brain state and region. The results suggest that the brain uses different frequency channels for transferring different types of information.
Size-selective opening of the blood–brain barrier by targeting endothelial sphingosine 1–phosphate receptor 1
Authors: Yanagida Keisuke , Liu Catherine H. , Faraco Giuseppe , Galvani Sylvain , Smith Helen K. , Burg Nathalie , Anrather Josef , Sanchez Teresa , Iadecola Costantino , Hla Timothy
Published: April 2017

Significance

The blood–brain barrier (BBB) poses a major obstacle for drug delivery to the central nervous system (CNS). This study revealed that genetic or pharmacological targeting of sphingosine 1–phosphate receptor-1 (S1P
1
) facilitates a small-molecule-selective BBB opening, without major signs of CNS inflammation or injury. This size-selective BBB opening could be attributed to changes in the cytoskeletal association of tight junction proteins. Importantly, BBB opening by pharmacological blockage of S1P
1
was reversible, suggesting that targeting S1P
1
may be a promising strategy for the safe delivery of therapeutic agents into the CNS to treat neurodegenerative and neuroinflammatory diseases and neurological cancers.
Mutation in sorghum
LOW GERMINATION STIMULANT 1
alters strigolactones and causes
Striga
resistance
Authors: Gobena Daniel , Shimels Mahdere , Rich Patrick J. , Ruyter-Spira Carolien , Bouwmeester Harro , Kanuganti Satish , Mengiste Tesfaye , Ejeta Gebisa
Published: April 2017

Significance

The parasitic weed
Striga
is the greatest biological constraint to production of many crops in Africa and parts of Asia. Genetic control is the most feasible means of crop protection from this pest. We report on identification of a gene regulating
Striga
resistance in sorghum and the associated change in strigolactone chemistry. Knowing this gene and its various natural alleles, sorghum breeders can design markers within it to facilitate its transfer into improved varieties providing farmers effective control of
Striga
in infested fields. The gene could also be used to potentially improve
Striga
resistance through genome editing in crops such as maize that evolved away from
Striga
, and hence have a paucity of
Striga
resistance genes.
Formation of nucleobases in a Miller–Urey reducing atmosphere
Authors: Ferus Martin , Pietrucci Fabio , Saitta Antonino Marco , Knížek Antonín , Kubelík Petr , Ivanek Ondřej , Shestivska Violetta , Civiš Svatopluk
Published: April 2017

Significance

The study shows that Miller–Urey experiments produce RNA nucleobases in discharges and laser-driven plasma impact simulations carried out in a simple prototype of reducing atmosphere containing ammonia and carbon monoxide. We carried out a self-standing description of chemistry relevant to hypothesis of abiotic synthesis of RNA nucleobases related to early-Earth chemical evolution under reducing conditions. The research addresses the chemistry of simple-model reducing atmosphere (NH
3
+ CO + H
2
O) and the role of formamide as an intermediate of nucleobase formation in Miller–Urey experiment. The explorations combine experiments performed using modern techniques of large, high-power shock wave plasma generation by hall terawatt lasers, electric discharges, and state-of-the-art ab initio free-energy calculations.
The carbonic anhydrase CAH1 is an essential component of the carbon-concentrating mechanism in
Nannochloropsis oceanica
Authors: Gee Christopher W. , Niyogi Krishna K.
Published: April 2017

Significance

Algae account for a large proportion of global primary productivity, and the carbon that they fix supports many ecosystems and associated services used by humans. Green algae overcome various physical limitations on the rate of CO
2
supply for photosynthesis by the action of carbon-concentrating mechanisms (CCM) that deliver CO
2
to the carboxylating enzyme, Rubisco. However, marine systems are dominated by algae that contain chloroplasts of red algal origin, and we know relatively little about their biology at the molecular level. Here we characterize a carbonic anhydrase as part of a simple CCM in the oleaginous photosynthetic stramenopile,
Nannochloropsis oceanica
. This work expands our understanding of the diversity in CCMs, and may lead to biotechnological improvements in this potential biofuel-producing alga.
Automated glycan assembly using the Glyconeer 2.1 synthesizer
Authors: Hahm Heung Sik , Schlegel Mark K. , Hurevich Mattan , Eller Steffen , Schuhmacher Frank , Hofmann Johanna , Pagel Kevin , Seeberger Peter H.
Published: April 2017

Significance

Rapid access to defined, pure biomacromolecules is key to biochemical and biophysical investigations as evidenced by the impact automated solid-phase synthesis of oligonucleotides and oligopeptides had on basic research. Here, a strategy as well as a new instrument to routinely access oligosaccharides by automated synthesis is reported. The method produces glycans quickly and reliably to accelerate fundamental advances in glycobiology.
Antigenicity-defined conformations of an extremely neutralization-resistant HIV-1 envelope spike
Authors: Cai Yongfei , Karaca-Griffin Selen , Chen Jia , Tian Sai , Fredette Nicholas , Linton Christine E. , Rits-Volloch Sophia , Lu Jianming , Wagh Kshitij , Theiler James , Korber Bette , Seaman Michael S. , Harrison Stephen C. , Carfi Andrea , Chen Bing
Published: April 2017

Significance

A vaccine against HIV-1 should elicit antibodies that prevent infection (“neutralize”) by binding the viral envelope glycoprotein (Env). The extraordinary genetic diversity of Env means that protective antibodies must recognize one of a few broadly conserved sites (“epitopes”). The trimeric Env protein fluctuates among a range of conformations: Closed conformations expose only the conserved epitopes, whereas various open conformations expose many other, more variable epitopes. The latter dominate immune responses and restrict protection to a narrow range of viral strains. We describe here the properties of Env from an extremely neutralization-resistant HIV-1 variant. We find that it binds only antibodies that recognize conserved epitopes, consistent with a tightly closed conformation, and suggest that it might be a suitable vaccine template.
Intranasal MSC-derived A1-exosomes ease inflammation, and prevent abnormal neurogenesis and memory dysfunction after status epilepticus
Authors: Long Qianfa , Upadhya Dinesh , Hattiangady Bharathi , Kim Dong-Ki , An Su Yeon , Shuai Bing , Prockop Darwin J. , Shetty Ashok K.
Published: April 2017

Significance

This study demonstrated that intranasal (IN) administration of A1-exosomes alleviates multiple adverse changes that typically emerge after status epilepticus (SE), a medical crisis that presents a high propensity to evolve into chronic hippocampus dysfunction. Specifically, A1-exosome treatment after SE led to reduced neuron loss and inflammation, maintenance of normal neurogenesis, and preservation of cognitive and memory function. The results have significance for clinical application of A1-exosomes for curbing the evolution of SE-induced injury into chronic hippocampus dysfunction. The results also imply that IN administration of A1-exosomes is therapeutic for other neurological conditions that present with significant neuroinflammation.
Neuralized regulates Crumbs endocytosis and epithelium morphogenesis via specific Stardust isoforms
Authors: Perez-Mockus Gantas , Roca Vanessa , Mazouni Khalil , Schweisguth François
Published: April 2017

Crumbs (Crb) is a conserved determinant of apical membrane identity that regulates epithelial morphogenesis in many developmental contexts. In this study, we identify the Crb complex protein Stardust (Sdt) as a target of the E3 ubiquitin ligase Neuralized (Neur) in Drosophila melanogaster. Neur interacts with and down-regulates specific Sdt isoforms containing a Neur binding motif (NBM). Using a CRISPR (clustered regularly interspaced short palindromic repeats)-induced deletion of the NBM-encoding exon, we found that Sdt is a key Neur target and that Neur acts via Sdt to down-regulate Crb. We further show that Neur promotes the endocytosis of Crb via the NBM-containing isoforms of Sdt. Although the regulation of Crb by Neur is not strictly essential, it contributes to epithelium remodeling in the posterior midgut and thereby facilitates the trans-epithelial migration of the primordial germ cells in early embryos. Thus, our study uncovers a novel regulatory mechanism for the developmental control of Crb-mediated morphogenesis.
TLR sensing of bacterial spore-associated RNA triggers host immune responses with detrimental effects
Authors: Choo Min-Kyung , Sano Yasuyo , Kim Changhoon , Yasuda Kei , Li Xiao-Dong , Lin Xin , Stenzel-Poore Mary , Alexopoulou Lena , Ghosh Sankar , Latz Eicke , Rifkin Ian R. , Chen Zhijian J. , Stewart George C. , Chong Hyonyong , Park Jin Mo
Published: April 2017

The spores of pathogenic bacteria are involved in host entry and the initial encounter with the host immune system. How bacterial spores interact with host immunity, however, remains poorly understood. Here, we show that the spores of Bacillus anthracis (BA), the etiologic agent of anthrax, possess an intrinsic ability to induce host immune responses. This immunostimulatory activity is attributable to high amounts of RNA present in the spore surface layer. RNA-sensing TLRs, TLR7, and TLR13 in mice and their human counterparts, are responsible for detecting and triggering the host cell response to BA spores, whereas TLR2 mediates the sensing of vegetative BA. BA spores, but not vegetative BA, induce type I IFN (IFN-I) production. Although TLR signaling in itself affords protection against BA, spore RNA–induced IFN-I signaling is disruptive to BA clearance. Our study suggests a role for bacterial spore–associated RNA in microbial pathogenesis and illustrates a little known aspect of interactions between the host and spore-forming bacteria.
Non-local effects on pedestal kinetic ballooning mode stability
Authors: Saarelma S , Martin-Collar J , Dickinson D , McMillan B F , Roach C M
Published: April 2017

The H-mode pedestal height plays an important role in determining the global confinement of the tokamak plasma. In type I ELMy H-mode the ultimate limit for the pedestal pressure at constant width is set by the ideal MHD peeling-ballooning modes (PBMs) that are thought to be the trigger for the ELMs. However, the PBM criterion does not uniquely determine the pedestal. Increasing the width of the pedestal, the marginally peeling-ballooning stable pedestal height increases as well. The second criterion for the pedestal is set by the transport processes in the pedestal that limit the gradient between the ELMs. One candidate for driving this transport is the kinetic ballooning mode (KBM) that is driven by the pressure gradient (Snyder et al 2009 Nucl. Fusion
49 085035). The KBM growth rate increases very rapidly after the critical pressure gradient is exceeded leading to very stiff profiles with the pressure gradient clamped near to the stability limit. In the local linear gyrokinetic analysis of experimental MAST and JET plasmas we have found that, like the

n

=
∞

ideal MHD ballooning modes, the KBMs can access locally so called second stability if the magnetic shear becomes low enough (Dickinson et al 2011 Plasma Phys. Control. Fusion
53 115010; Saarelma et al 2013 Nucl. Fusion
53 123012). However, in the pedestal region the local assumption that the equilibrium can be considered radially constant for the investigated modes is no longer justified. In this paper we revisit the KBM analysis using a global code ORB5 to investigate whether second stability access exists for KBMs. We find that counter to the local analysis, the global KBM stability is not sensitive to the magnetic shear in the pedestal region. At sufficiently high β (but still below the ideal peeling-ballooning limit) the pedestal region becomes KBM unstable regardless of the amount of bootstrap current assumed in the equilibrium reconstruction. However, just as in local analysis, the mode is stabilised by reducing the pressure gradient. This suggests that KBMs can regulate the pedestal pressure gradient during the ELM cycle even when local analysis finds them stable due to high bootstrap current.
Global stability analysis of axisymmetric boundary layer over a circular cone
Authors: Bhoraniya Ramesh , Vinod Narayanan
Published: April 2017

This paper presents linear biglobal stability analysis of axisymmetric boundary layer over a circular cone. An incompressible flow over a sharp circular cone is considered with zero angle of attack. The base flow velocity profile is fully non-parallel and non-similar. Linearized Navier-Stokes (LNS) equations are derived for disturbance flow quantities using the standard procedure. The LNS equations are discretized using Chebyshev spectral collocation method. The governing equations along with boundary conditions form a general eigenvalues problem. The numerical solution of general eigenvalues problem is obtained using ARPACK subroutine, which uses Arnoldis iterative algorithm. The global temporal modes are computed for the range of Reynolds number and semi-cone angles(α)for the axisymmetric mode(N=0). The flow is found temporally and spatially stable for 1° semi-cone angle and the range of Reynolds numbers considered. However, flow becomes temporally unstable and spatially stable with the increase in semi-cone angle(α). The wave-like behaviour of the disturbances is found at small semi-cone angles (α).
Network module-based model in the differential expression analysis for RNA-seq
Authors: Lei Mingli , Xu Jia , Huang Li-Ching , Wang Lily , Li Jing
Published: April 2017

Motivation

RNA-seq has emerged as a powerful technology for the detection of differential gene expression in the transcriptome. The commonly used statistical methods for RNA-seq differential expression analysis were designed for individual genes, which may detect too many irrelevant significantly genes or too few genes to interpret the phenotypic changes. Recently network module-based methods have been proposed as a powerful approach to analyze and interpret expression data in microarray and shotgun proteomics. But the module-based statistical model has not been adequately addressed for RNA-seq data.

Result

we proposed a network module-based generalized linear model for differential expression analysis of the count-based sequencing data from RNA-seq. The simulation studies demonstrated the effectiveness of the proposed model and the improvement of the statistical power for identifying the differentially expressed modules in comparison to the existing methods. We also applied our method to tissue datasets and identified 207 significantly differentially expressed kidney-active or liver-active modules. For liver cancer datasets, significantly differentially expressed modules, including Wnt signaling pathway and VEGF pathway, were found to be tightly associated with liver cancer. Besides, in comparison with the single gene-level analysis, our method could identify more significantly biological modules, which related to the liver cancer.

Availability and Implementation

The R package SeqMADE is available at https://cran.r-project.org/web/packages/SeqMADE/.

Supplementary information

Supplementary data are available at Bioinformatics online.
SubCons: a new ensemble method for improved human subcellular localization predictions
Authors: Salvatore M , Warholm P , Shu N , Basile W , Elofsson A
Published: April 2017

Motivation

Knowledge of the correct protein subcellular localization is necessary for understanding the function of a protein. Unfortunately large-scale experimental studies are limited in their accuracy. Therefore, the development of prediction methods has been limited by the amount of accurate experimental data. However, recently large-scale experimental studies have provided new data that can be used to evaluate the accuracy of subcellular predictions in human cells. Using this data we examined the performance of state of the art methods and developed SubCons, an ensemble method that combines four predictors using a Random Forest classifier.

Results

SubCons outperforms earlier methods in a dataset of proteins where two independent methods confirm the subcellular localization. Given nine subcellular localizations, SubCons achieves an F1-Score of 0.79 compared to 0.70 of the second best method. Furthermore, at a FPR of 1% the true positive rate (TPR) is over 58% for SubCons compared to less than 50% for the best individual predictor.

Availability and Implementation

SubCons is freely available as a webserver (http://subcons.bioinfo.se) and source code from https://bitbucket.org/salvatore_marco/subcons-web-server. The golden dataset as well is available from http://subcons.bioinfo.se/pred/download.

Supplementary information

Supplementary data are available at Bioinformatics online.
HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly
Authors: Huang Shengfeng , Kang Mingjing , Xu Anlong
Published: April 2017

De novo assembly is a difficult issue for heterozygous diploid genomes. The advent of high-throughput short-read and long-read sequencing technologies provides both new challenges and potential solutions to the issue. Here, we present HaploMerger2 (HM2), an automated pipeline for rebuilding both haploid sub-assemblies from the polymorphic diploid genome assembly. It is designed to work on pre-existing diploid assemblies, which are typically created by using de novo assemblers. HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliable gap-closing method for haploid sub-assemblies. Using HM2, we demonstrate that two haploid sub-assemblies reconstructed from a real, highly-polymorphic diploid assembly show greatly improved continuity.

Availability and Implementation

Source code, executables and the testing dataset are freely available at https://github.com/mapleforest/HaploMerger2/releases/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Domain prediction with probabilistic directional context
Authors: Ochoa Alejandro , Singh Mona
Published: April 2017

Motivation

Protein domain prediction is one of the most powerful approaches for sequence-based function prediction. Although domain instances are typically predicted independently of each other, newer approaches have demonstrated improved performance by rewarding domain pairs that frequently co-occur within sequences. However, most of these approaches have ignored the order in which domains preferentially co-occur and have also not modeled domain co-occurrence probabilistically.

Results

We introduce a probabilistic approach for domain prediction that models ‘directional’ domain context. Our method is the first to score all domain pairs within a sequence while taking their order into account, even for non-sequential domains. We show that our approach extends a previous Markov model-based approach to additionally score all pairwise terms, and that it can be interpreted within the context of Markov random fields. We formulate our underlying combinatorial optimization problem as an integer linear program, and demonstrate that it can be solved quickly in practice. Finally, we perform extensive evaluation of domain context methods and demonstrate that incorporating context increases the number of domain predictions by ∼15%, with our approach dPUC2 (Domain Prediction Using Context) outperforming all competing approaches.

Availability and Implementation

dPUC2 is available at http://github.com/alexviiia/dpuc2.

Supplementary information

Supplementary data are available at Bioinformatics online.
Comment on “Bioerosion: the other ocean acidification problem”: on field studies and mechanisms
Authors: Silbiger Nyssa J , DeCarlo Thomas M
Published: April 2017

In a recent review, “Bioerosion: the other ocean acidification problem,” Schönberg et al. claim that studies of bioerosion across natural chemical gradients are “flawed” or “compromised” by co-variation among environmental factors. Their discussion falls largely on two publications, Silbiger et al. and DeCarlo et al. Here, we demonstrate that critical errors in plotting, statistical analysis, and data selection in Schönberg et al.’s reanalysis, result in a gross misrepresentation of these studies. Further, we argue three key points regarding field-based studies that require broader discussion within the bioerosion community and marine scientists in general: (1) that natural variability in field studies is not a flaw, (2) interpretations must be supported by mechanistic understanding, and (3) field-based studies play an essential role in elucidating interactions between OA and natural variability that is not captured by laboratory CO2-manipulation experiments. Our goal with this comment is to encourage open discussion of the advantages and caveats of field-based studies in general, and ultimately, advance our understanding of bioerosion patterns observed in nature.