bluuebunny/crossref_metadata_2025 huggingface dataset:
Group classification of charged particle motion in stationary electromagnetic fields
Authors: Kallinikos N.
Published: November 2017

In this paper, we classify in terms of Lie point symmetries the three-dimensional nonrelativistic motion of charged particles in arbitrary time-independent electromagnetic fields. The classification is made on the ground of equivalence transformations, and when the system is nonlinear and particularly for inhomogeneous and curved magnetic fields, it is also complete. Using the homogeneous Maxwell’s equations as auxiliary conditions for consistency, in which case the system amounts to a Lagrangian of three degrees of freedom with velocity-dependent potentials, the equivalence group stays the same. Therefore, instead of the actual fields, the potentials are equally employed and their gauge invariance results in an infinite-dimensional equivalence algebra, which nevertheless projects to finite-dimensional symmetry algebras. Subsequently, optimal systems of equivalence subalgebras are obtained that lead to one-, two-, and three-parameter extended symmetry groups, besides the obvious time translations. Finally, based on symmetries of Noether type, aspects of complete integrability are discussed, as well.
Phase retrieval of an electron vortex beam using diffraction holography
Authors: Venturi Federico , Campanini Marco , Gazzadi Gian Carlo , Balboni Roberto , Frabboni Stefano , Boyd Robert W. , Dunin-Borkowski Rafal E. , Karimi Ebrahim , Grillo Vincenzo
Published: November 2017

In both light optics and electron optics, the amplitude of a wave scattered by an object is an observable that is usually recorded in the form of an intensity distribution in a real space image or a diffraction image. In contrast, retrieval of the phase of a scattered wave is a well-known challenge, which is usually approached by interferometric or numerical methods. In electron microscopy, as a result of constraints in the lens setup, it is particularly difficult to retrieve the phase of a diffraction image. Here, we use a “defocused beam” generated by a nanofabricated hologram to form a reference wave that can be interfered with a diffracted beam. This setup provides an extended interference region with the sample wavefunction in the Fraunhofer plane. As a case study, we retrieve the phase of an electron vortex beam. Beyond this specific example, the approach can be used to retrieve the wavefronts of diffracted beams from a wide range of samples.
Fe-doping effects on the structural, vibrational, magnetic, and electronic properties of ceria nanoparticles
Authors: Aragón Fermin F. H. , Aquino Juan C. R. , Ramos Jesus E. , Coaquira José A. H. , Gonzalez Ismael , Macedo Waldemar A. A. , da Silva Sebastião W. , Morais Paulo C.
Published: November 2017

In this work, we report on a single-pot synthesis route based on a polymeric precursor method used for successfully producing undoped and iron-doped CeO2 nanoparticles with iron contents up to 10.0 mol. %. The formation of high-crystalline nanoparticles with a cubic fluorite structure is determined for all the studied samples. Meanwhile, the magnetic measurements of the undoped ceria nanoparticles revealed the occurrence of ferromagnetism of bound magnetic polarons of a fraction of Ce3+ at room temperature, and only a paramagnetic behavior of Fe3+ ions was determined for Fe-doped ceria nanoparticles. A monotonous reduction of the effective magnetic moment of the Fe3+ ions was determined. It suggests a change from a high-spin to low-spin state of Fe ions as the Fe content is increased. The 3+ valence state of the iron ions has been confirmed by the Fe K-edge X-ray absorption near-edge structure (XANES) and Mössbauer spectroscopy measurements. X-ray photoelectron spectroscopy data analysis evidenced a coexistence of Ce3+ and Ce4+ ions and a decreasing tendency of the relative fraction of Ce3+ ions in the surface region of the particles as the iron content is increased. Although the coexistence of Ce3+ and Ce4+ is confirmed by results obtained via Ce L3-edge XANES measurements, any clear dependence of the relative relation of Ce3+ ions on the iron content is determined, suggesting a homogeneous distribution of Ce3+ and Ce4+-ions in the whole volume of the particles. Ce L3-edge extended X-ray absorption fine structure revealed that the Ce-O bond distance shows a monotonous decrease as the Fe content is increased, which is in good agreement with the shrinking of the unit cell volume with the iron content determined from XRD data analysis, reinforcing the substitutional solution of Ce and Fe ions in the CeO2 matrix.
Tunable multilayer submicrostructures fabricated by interference assisted two-photon polymerization
Authors: Liu Qian-Qian , Zhao Yuan-Yuan , Zheng Mei-Ling , Duan Xuan-Ming
Published: November 2017

The three-dimensional (3D) focus exhibiting pagoda-like light intensity distribution has been realized with the assistance of interference of the incident beam and the reflected beam. Benefiting from this designable laser focus tailored by the polymerization threshold, we have fabricated 3D multilayer structures with the submicron-scale by two-photon polymerization with a single scan. The light intensity distribution in the focus is simulated by the Fresnel formula, which indicates the mechanism for modulating the 3D multilayer submicrostructures with designable cross-section morphology. Furthermore, the influences of laser power and focus height on the linewidth have been investigated experimentally and theoretically. The multilayer submicrostructure fabricated by a single scan and the morphology modulation mechanism proposed in this study would be of profound importance for further applications in the fields of photonic devices, microfabrication, and biomimetic surfaces.
Determination of transport properties in optoelectronic devices by time-resolved fluorescence imaging
Authors: Bercegol Adrien , El-Hajje Gilbert , Ory Daniel , Lombez Laurent
Published: November 2017

In this article, we introduce time-resolved fluorescence imaging as an optical characterization method for optoelectronic devices. Under wide-field illumination, it allows obtaining time-resolved photoluminescence maps with a temporal resolution of 500 ps and a micrometric spatial resolution. An experiment on a GaAs-based solar cell is presented here as a proof of concept. Thanks to a model including diffusion and recombination of minority charge carriers, we fit the experimental photoluminescence transients and extract key optoelectronic properties for the considered device. For various fluence levels, we determine an intrinsic bulk recombination lifetime τn = 75 ns, a constant effective diffusion length Leff = 190 μm, which is characteristic for the lateral transport inside the solar cell, and an injection-dependent contact recombination velocity Sn, taking its values between 7 × 104 and 3 × 105 cm/s, which is explained by the saturation of defects. The wide-field illumination notably avoids lateral diffusion artefacts leading to a significant underestimation of τn.
Weakly turbulent plasma processes in the presence of inverse power-law velocity tail population
Authors: Tigik S. F. , Petruzzellis L. T. , Ziebell L. F. , Yoon P. H. , Gaelzer R.
Published: November 2017

Observations show that plasma particles in the solar wind frequently display power-law velocity distributions, which can be isotropic or anisotropic. Particularly, the velocity distribution functions of solar wind electrons are frequently modeled as a combination of a background Maxwellian distribution and a non-thermal distribution which is known as the “halo” distribution. For fast solar wind conditions, highly anisotropic field-aligned electrons, denominated as the “strahl” distribution, are also present. Motivated by these observations, the present paper considers a tenuous plasma with Maxwellian ions, and electrons described by a summation of an isotropic Maxwellian distribution and an isotropic Kappa distribution. The formalism of weak turbulence theory is utilized in order to discuss the spectra of electrostatic waves that must be present in such a plasma, satisfying the conditions of quasi-equilibrium between the processes of spontaneous fluctuations and of induced emission. The kappa index and relative density of the Kappa electron distribution are varied. By taking into account the effects due to electromagnetic waves into the weak turbulence formalism, we investigate the electromagnetic spectra that satisfy the conditions of “turbulent equilibrium,” and also the time evolution of the wave spectra and of the electron distribution, which occurs in the case of the presence of an electron beam in the electron distribution.
Solving visual correspondence between the two eyes via domain-based population encoding in nonhuman primates
Authors: Chen Gang , Lu Haidong D. , Tanigawa Hisashi , Roe Anna W.
Published: November 2017

Significance

A long-standing problem in visual depth perception is how corresponding features between the two eyes are matched (the “binocular correspondence problem”). Here, we show, using optical imaging in monkey visual cortex, that this computation occurs in the near and far disparity domains of V2, and that functional organization in V2 might facilitate the pooling of disparity signals that can reduce false matches to solve the binocular correspondence problem.
SUMOylation and ubiquitination reciprocally regulate α-synuclein degradation and pathological aggregation
Authors: Rott Ruth , Szargel Raymonde , Shani Vered , Hamza Haya , Savyon Mor , Abd Elghani Fatimah , Bandopadhyay Rina , Engelender Simone
Published: November 2017

Significance

Our work uncovers SUMOylation as a major regulator of α-synuclein fate and pathological aggregation. SUMOylation promotes α-synuclein accumulation by counteracting α-synuclein ubiquitination and inhibiting its degradation. SUMOylation also directly causes aggregation of α-synuclein in vitro and in cells, and the effects are much more prominent with the α-synuclein disease mutants. Most importantly, levels of SUMOylated α-synuclein and components of the SUMOylation machinery increase severalfold in Parkinson’s disease (PD) brains and are present in Lewy bodies. Our data indicate a major role of SUMOylation in the pathological aggregation of α-synuclein and Lewy body formation. Therefore, SUMOylation blockers provide a strategy to prevent intracellular α-synuclein accumulation, aggregation, and spreading in PD.
Def1 interacts with TFIIH and modulates RNA polymerase II transcription
Authors: Damodaren Nivedita , Van Eeuwen Trevor , Zamel Joanna , Lin-Shiao Enrique , Kalisman Nir , Murakami Kenji
Published: November 2017

Significance

All eukaryotes respond to DNA damage by polyubiquitylation and degradation of the largest subunit of RNA polymerase II (pol II), facilitated by the Elongin-Cullin ubiquitin ligase. In yeast, the recruitment of the ubiquitin ligase to pol II is dependent on Def1. We report a finding made in the course of isolating TFIIH-Def1 from yeast that suggests a potential novel function of Def1 as a transcription regulator in response to cellular stress. The function of Def1 in transcription regulation is demonstrably separable from its role in coordinating pol II stability in response to cellular stress.
Metal transporter Slc39a10 regulates susceptibility to inflammatory stimuli by controlling macrophage survival
Authors: Gao Hong , Zhao Lu , Wang Hao , Xie Enjun , Wang Xinhui , Wu Qian , Yu Yingying , He Xuyan , Ji Hongbin , Rink Lothar , Min Junxia , Wang Fudi
Published: November 2017

Significance

Zn is essential for maintaining the integrity of the immune system, and Zn homeostasis is tightly regulated by two families of ion transporters, SLC39A and SLC30A. Worldwide, an estimated two billion people have Zn deficiency, a condition that can impair immune function and increase susceptibility to a variety of infections. Despite their important roles in health and disease, the molecular mechanisms that underlie Zn transport and Zn homeostasis in macrophages are poorly understood. Here, we report that SLC39A10 plays an essential role in Zn homeostasis in macrophages, regulating the immune response following inflammatory stimuli. Specifically, we identified a role for SLC39A10 in regulating the survival of macrophages via a Zn/p53-dependent axis during the inflammatory response.
Proton movement and coupling in the POT family of peptide transporters
Authors: Parker Joanne L. , Li Chenghan , Brinth Allete , Wang Zhi , Vogeley Lutz , Solcan Nicolae , Ledderboge-Vucinic Gregory , Swanson Jessica M. J. , Caffrey Martin , Voth Gregory A. , Newstead Simon
Published: November 2017

Significance

The uptake of nutrients from the environment is an essential process that is achieved in most cells through the use of secondary active transporters. The POT family of proton-coupled peptide transporters are one of the most diverse nutrient uptake systems, recognizing amino acids, peptides, nitrate, and seed-defense compounds. A long-standing question is how this family achieves such ligand diversity. A high-resolution crystal structure combined with multiscale molecular dynamics simulations demonstrate water molecules are able to shuttle protons using a Grotthuss-type mechanism, suggesting a separation of ligand recognition from proton movement. This would have clear advantages for a transporter family that must accommodate chemically diverse ligands while retaining the ability to couple transport to the proton electrochemical gradient.
Development of self-protective biases in response to social evaluative feedback
Authors: Rodman Alexandra M. , Powers Katherine E. , Somerville Leah H.
Published: November 2017

Significance

The growing popularity of social media, especially among youth, has resulted in peer feedback (including rejection) pervading everyday life. Given that peer ostracism has been linked to depression and suicide, it is critical to understand the psychological impact of peer feedback from a developmental perspective. We demonstrate that adolescents and adults use peer feedback to inform views of themselves and of others in very different ways. Of particular interest, early adolescents internalized rejection from peers and felt worse about themselves, whereas adults exhibited evidence of self-protective biases that preserved positive self-views. This work advances theoretical insights into how development shapes social-evaluative experiences and informs sources of vulnerability that could put adolescents at unique risk for negative mental health outcomes.
Fishnet model for failure probability tail of nacre-like imbricated lamellar materials
Authors: Luo Wen , Bažant Zdeněk P.
Published: November 2017

Significance

The astonishing strength enhancement in the nacre of pearl oyster, compared with its main constituent, the aragonite, has recently been explained by the nanostructure of overlapping nanoscale platelets—but only deterministically. It is also necessary to know the stress value for which the failure probability does not exceed 1 in a million. It is shown that, at such a low-failure probability, the nacre-like structures exhibit additional advantages. The strength increases by about 10%, while at fixed, correspondingly low, stress, the failure probability decreases by 1 to 2 orders of magnitude, compared with the standard (Weibullian) extrapolation from the deterministic prediction and coefficient of variation. These are advantages important for biomimetic engineering applications.
Glycosyltransferase MDR1 assembles a dividing ring for mitochondrial proliferation comprising polyglucan nanofilaments
Authors: Yoshida Yamato , Kuroiwa Haruko , Shimada Takashi , Yoshida Masaki , Ohnuma Mio , Fujiwara Takayuki , Imoto Yuuta , Yagisawa Fumi , Nishida Keiji , Hirooka Shunsuke , Misumi Osami , Mogi Yuko , Akakabe Yoshihiko , Matsushita Kazunobu , Kuroiwa Tsuneyoshi
Published: November 2017

Significance

The mitochondrion-dividing (MD) ring mediates binary division of mitochondria. However, the molecular identity of the MD ring is currently unknown. We show that the glycosyltransferase MITOCHONDRION-DIVIDING RING1 (MDR1) regulates the synthesis of the polyglucan nanofilament bundle that assembles the MD ring. MDR1 is essential for mitochondrial division and forms a single ring at the mitochondrial division site in the unicellular red alga
Cyanidioschyzon merolae
. Nanoscale imaging and componential analysis demonstrated that MDR1 is involved in MD ring formation and that the MD ring filaments are composed of polymeric-glucose nanofilaments. An MDR1 homologue performs a similar function in chloroplast division, suggesting that the establishment of the MDR1 family was crucial for the emergence of endosymbiotic organelles.
The compliment response strategies of Egyptian Arabic-English bilinguals
Authors: Salam El-Dakhs Dina Abdel
Published: November 2017

The present study examined the compliment response behaviour of Egyptian Arabic-English bilinguals in both spoken Egyptian Arabic and English. A total of 433 undergraduates completed the Arabic and English versions of a Discourse Completion Task comprising 12 imaginary situations that varied in topic and in the relation between the interlocutors. The results revealed the participants’ preference for agreement and additional response types in both Arabic and English to varying extents while non-agreement responses were rarely used. Significant differences were noted for language type, gender, social distance, social dominance and topic while exposure to the foreign language resulted in minimal differences. Results are interpreted within a pragmatic and sociolinguistic framework and implications are proposed.
The language of Akan herbal drug sellers and advertisers
Authors: Agyekum Kofi
Published: November 2017

This paper addresses the language and pragmatic strategies used by Akan herbal drug sellers to persuade would-be-buyers. It adopts the theoretical framework of Weigand’s Mixed Game Model (MGM) and defines persuasion as a variable of competence-in-performance, and language use as the basis of dialogic interaction. It investigates how sellers employ politeness, honorifics, humour, digression, personification, proverbs, metaphors and hyperbole in dialogic action games. The herbal drug sellers are grouped into three: (a) those normally plying on Ghana’s major roads and at bus stations, (b) those who are on radio and TV and (c) those who advertise on radio and TV. We will discuss excerpts of five recordings in the Akan language and translated into English.
Biodegradation of high concentrations of formaldehyde using Escherichia coli expressing the formaldehyde dismutase gene of Methylobacterium sp. FD1
Authors: Yonemitsu Hiroshi , Kikuchi Yuta
Published: November 2017

In the present study, formaldehyde dismutase from Methylobacterium sp. FD1 was partially purified and analyzed by nanoLC–MS/MS; it was then cloned from the genomic DNA of FD1 by PCR. The open reading frame of the formaldehyde dismutase gene of FD1 was estimated to be 1203 bp in length. The molecular weight and pI of formaldehyde dismutase (401 aa), as deduced from the FD1 gene, were calculated at 42,877.32 and 6.56, respectively. NAD(H)-binding residues and zinc-binding residues were found in the amino acid sequence of the deduced formaldehyde dismutase of FD1 by BLAST search. The resting Escherichia coli cells that were transformed with the FD1 formaldehyde dismutase gene degraded high concentrations of formaldehyde and produced formic acid and methanol that were molar equivalents of one-half of the degraded formaldehyde. The lyophilized cells of the recombinant E. coli also degraded high concentrations of formaldehyde.
Lessons from three cases of biological control of native freshwater macrophytes isolated from their natural enemies
Authors: Cabrera Walsh Guillermo , Hernández M. Cristina , McKay Fernando , Oleiro Marina , Guala Mariel , Sosa Alejandro
Published: November 2017

Classical biological control–or biocontrol–is a form of pest management comprising the release of specialized natural enemies (biocontrol agents) of an exotic pest. Classical biocontrol agents are scientifically selected from among the natural enemies the pest has in its native region. However, biological control is firmly resisted in many countries because of the belief that it is more risky than not doing anything, or using the more familiar chemical and mechanical control methods. In this review, three classical biocontrol projects from Argentina are described. These projects had the peculiarity that native insects were used to control two native aquatic plants–Water Hyacinth and Water Lettuce–in isolated water bodies where their natural enemies were absent. In two of these projects complete control of the weeds were achieved, and preliminary results are quite promising for the most recent project, as well. This article stresses that classical biocontrol can be applied in a weed's native range under special circumstances, and describes why such cases can be used to promote biological control of native invaders while circumventing the more resisted aspect of classical biocontrol: introducing exotic species.
Upgrade of Tile Calorimeter of the ATLAS Detector for the High Luminosity LHC.
Authors: Santurio Eduardo Valdes
Published: November 2017

The Tile Calorimeter (TileCal) is the hadronic calorimeter of ATLAS covering the central region of the ATLAS experiment. TileCal is a sampling calorimeter with steel as absorber and scintillators as active medium. The scintillators are read out by wavelength shifting fibers coupled to photomultiplier tubes (PMT). The analogue signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The High Luminosity Large Hadron Collider (HL-LHC) will have a peak luminosity of 5 × 1034
cm
−2
s
−1, five times higher than the design luminosity of the LHC. TileCal will undergo a major replacement of its on- and off-detector electronics for the high luminosity programme of the LHC in 2026. The calorimeter signals will be digitized and sent directly to the off-detector electronics, where the signals are reconstructed and shipped to the first level of trigger at a rate of 40 MHz. This will provide a better precision of the calorimeter signals used by the trigger system and will allow the development of more complex trigger algorithms. Three different options are presently being investigated for the front-end electronic upgrade. Extensive test beam studies will determine which option will be selected. Field Programmable Gate Arrays (FPGAs) are extensively used for the logic functions of the off- and on-detector electronics. One hybrid demonstrator prototype module with the new calorimeter module electronics, but still compatible with the present system, may be inserted in ATLAS at the end of 2016.
ℤ₂-orbifold construction associated with (-1)-isometry and uniqueness of holomorphic vertex operator algebras of central charge 24
Authors: Kawasetsu Kazuya , Lam Ching Hung , Lin Xingjun
Published: November 2017

The vertex operator algebra structure of a strongly regular holomorphic vertex operator algebra

V
V

of central charge

24
24

is proved to be uniquely determined by the Lie algebra structure of its weight one space

V
1

V_1

if

V
1

V_1

is a Lie algebra of the type

A

1
,
4

12

A_{1,4}^{12}

,

B

2
,
2

6

B_{2,2}^6

,

B

3
,
2

4

B_{3,2}^4

,

B

4
,
2

3

B_{4,2}^3

,

B

6
,
2

2

B_{6,2}^2

,

B

12
,
2

B_{12,2}

,

D

4
,
2

2

B

2
,
1

4

D_{4,2}^2B_{2,1}^4

,

D

8
,
2

B

4
,
1

2

D_{8,2}B_{4,1}^2

,

A

3
,
2

4

A

1
,
1

4

A_{3,2}^4A_{1,1}^4

,

D

5
,
2

2

A

3
,
1

2

D_{5,2}^2A_{3,1}^2

,

D

9
,
2

A

7
,
1

D_{9,2}A_{7,1}

,

C

4
,
1

4

C_{4,1}^4

, or

D

6
,
2

B

3
,
1

2

C

4
,
1

D_{6,2}B_{3,1}^2C_{4,1}

.
Möbius orthogonality for the Zeckendorf sum-of-digits function
Authors: Drmota Michael , Müllner Clemens , Spiegelhofer Lukas
Published: November 2017

We show that the (morphic) sequence

(
−
1

)

s
φ

(
n
)

(-1)^{s_\varphi (n)}

is asymptotically orthogonal to all bounded multiplicative functions, where

s
φ

s_\varphi

denotes the Zeckendorf sum-of-digits function. In particular we have
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="sigma-summation Underscript n greater-than upper N Endscripts left-parenthesis negative 1 right-parenthesis Superscript s Super Subscript phi Superscript left-parenthesis n right-parenthesis Baseline mu left-parenthesis n right-parenthesis equals o left-parenthesis upper N right-parenthesis">

∑

n
>
N

(
−
1

)

s
φ

(
n
)

μ
(
n
)
=
o
(
N
)

\sum _{n>N} (-1)^{s_\varphi (n)} \mu (n) = o(N)

, that is, this sequence satisfies the Sarnak conjecture.
Ideals of Steinberg algebras of strongly effective groupoids, with applications to Leavitt path algebras
Authors: Clark Lisa , Edie-Michell Cain , an Huef Astrid , Sims Aidan
Published: November 2017

We consider the ideal structure of Steinberg algebras over a commutative ring with identity. We focus on Hausdorff groupoids that are strongly effective in the sense that their reductions to closed subspaces of their unit spaces are all effective. For such a groupoid, we completely describe the ideal lattice of the associated Steinberg algebra over any commutative ring with identity. Our results are new even for the special case of Leavitt path algebras; so we describe explicitly what they say in this context, and give two concrete examples.
Multi-omics integration—a comparison of unsupervised clustering methodologies
Authors: Tini Giulia , Marchetti Luca , Priami Corrado , Scott-Boyer Marie-Pier
Published: November 2017

With the recent developments in the field of multi-omics integration, the interest in factors such as data preprocessing, choice of the integration method and the number of different omics considered had increased. In this work, the impact of these factors is explored when solving the problem of sample classification, by comparing the performances of five unsupervised algorithms: Multiple Canonical Correlation Analysis, Multiple Co-Inertia Analysis, Multiple Factor Analysis, Joint and Individual Variation Explained and Similarity Network Fusion. These methods were applied to three real data sets taken from literature and several ad hoc simulated scenarios to discuss classification performance in different conditions of noise and signal strength across the data types. The impact of experimental design, feature selection and parameter training has been also evaluated to unravel important conditions that can affect the accuracy of the result.
Process for Consensus Statements on Lumbar Total Disc Replacement
Authors: Ferko Nicole , Hollmann Sarah
Published: November 2017

Consensus statements regarding the evidence-base for lumbar total disc replacement, as it pertains to payer decision-making, were developed through a modified-Delphi technique involving 17 spine surgeons and a former payer medical director. The Delphi process involved one round of anonymous survey and one round with a face-to-face meeting. The survey was a 51-item, electronically administered questionnaire to determine level of agreement with proposed statements on the evidence for lumbar total disc replacement and to provide additional diagnosis and management practice information for further deliberations. A subset of the proposed statements was discussed at the face-to-face meeting to identify reasons for disagreement, revise wording, and obtain consensus. The meeting involved presentation of the current evidence base for lumbar total disc replacement, as well as three themed sessions that were moderated by surgeons on the panel. The voting processes during meeting deliberations remained anonymous. Consensus was defined as ≥ 90% agreement. Consensus was reached on 11 statements, divided into themes that focused on patient eligibility and diagnosis, evidence criteria for coverage decisions, clinical evidence, and budgetary implications.
X-ray physico-chemical imaging during activation of cobalt-based Fischer–Tropsch synthesis catalysts
Authors: Beale Andrew M. , Jacques Simon D. M. , Di Michiel Marco , Mosselmans J. Frederick W. , Price Stephen W. T. , Senecal Pierre , Vamvakeros Antonios , Paterson James
Published: November 2017

The imaging of catalysts and other functional materials under reaction conditions has advanced significantly in recent years. The combination of the computed tomography (CT) approach with methods such as X-ray diffraction (XRD), X-ray fluorescence (XRF) and X-ray absorption near-edge spectroscopy (XANES) now enables local chemical and physical state information to be extracted from within the interiors of intact materials which are, by accident or design, inhomogeneous. In this work, we follow the phase evolution during the initial reduction step(s) to form Co metal, for Co-containing particles employed as Fischer–Tropsch synthesis (FTS) catalysts; firstly, working at small length scales (approx. micrometre spatial resolution), a combination of sample size and density allows for transmission of comparatively low energy signals enabling the recording of ‘multimodal’ tomography, i.e. simultaneous XRF–CT, XANES–CT and XRD–CT. Subsequently, we show high-energy XRD–CT can be employed to reveal extent of reduction and uniformity of crystallite size on millimetre-sized TiO
2
trilobes. In both studies, the CoO phase is seen to persist or else evolve under particular operating conditions and we speculate as to why this is observed.

This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.
Integrating protein engineering with process design for biocatalysis
Authors: Woodley John M.
Published: November 2017

Biocatalysis uses enzymes for chemical synthesis and production, offering selective, safe and sustainable catalysis. While today the majority of applications are in the pharmaceutical sector, new opportunities are arising every day in other industry sectors, where production costs become a more important driver. In the early applications of the technology, it was necessary to design processes to match the properties of the biocatalyst. With the advent of protein engineering, organic chemists started to develop and improve enzymes to suit their needs. Likewise in industry, although not widespread, a new paradigm was already implemented several years ago to engineer enzymes to suit process needs. Today, a new era is entered, where the effectiveness with which such integrated protein and process engineering is achieved becomes critical to implementation. In this paper, the development of a tool to improve the effectiveness of this approach is discussed, namely the use of target-setting based on process requirements, to guide the necessary protein engineering.

This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.
Efficient utilization of renewable feedstocks: the role of catalysis and process design
Authors: Palkovits Regina , Delidovich Irina
Published: November 2017

Renewable carbon feedstocks such as biomass and CO
2
present an important element of future circular economy. Especially biomass as highly functionalized feedstock provides manifold opportunities for the transformation into attractive platform chemicals. However, this change of the resources requires a paradigm shift in refinery design. Fossil feedstocks are processed in gas phase at elevated temperature. In contrast, biorefineries are based on processes in polar solvents at moderate conditions to selectively deoxygenate the polar, often thermally instable and high-boiling molecules. Here, challenges of catalytic deoxygenation, novel strategies for separation and opportunities provided at the interface to biotechnology are discussed in form of showcases.

This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.
Is the LAN effect in morphosyntactic processing an ERP artifact?
Authors: Caffarra Sendy , Mendoza Martha , Davidson Doug
Published: November 2017

The left anterior negativity (LAN) is an ERP component that has been often associated with morphosyntactic processing, but recent reports have questioned whether the LAN effect, in fact, exists. The present project examined whether the LAN effect, observed in the grand average response to local agreement violations, is the result of the overlap between two different ERP effects (N400, P600) at the level of subjects (n=80), items (n=120), or trials (n=6160). By-subject, by-item, and by-trial analyses of the ERP effect between 300 and 500 ms showed a LAN for 55% of the participants, 46% of the items, and 49% of the trials. Many examples of the biphasic LAN-P600 response were observed. Mixed-linear models showed that the LAN effect size was not reduced after accounting for subject variability. The present results suggest that there are cases where the grand average LAN effect represents the brain responses of individual participants, items, and trials.
Experimental evidence that female rhesus macaques (Macaca mulatta) perceive variation in male facial masculinity
Authors: Rosenfield Kevin A. , Semple Stuart , Georgiev Alexander V. , Maestripieri Dario , Higham James P. , Dubuc Constance
Published: November 2017

Among many primate species, face shape is sexually dimorphic, and male facial masculinity has been proposed to influence female mate choice and male-male competition by signalling competitive ability. However, whether conspecifics pay attention to facial masculinity has only been assessed in humans. In a study of free-ranging rhesus macaques, Macaca mulatta, we used a two-alternative look-time experiment to test whether females perceive male facial masculinity. We presented 107 females with pairs of images of male faces – one with a more masculine shape and one more feminine – and recorded their looking behaviour. Females looked at the masculine face longer than at the feminine face in more trials than predicted by chance. Although there was no overall difference in average look-time between masculine and feminine faces across all trials, females looked significantly longer at masculine faces in a subset of trials for which the within-pair difference in masculinity was most pronounced. Additionally, the proportion of time subjects looked toward the masculine face increased as the within-pair difference in masculinity increased. This study provides evidence that female macaques perceive variation in male facial shape, a necessary condition for intersexual selection to operate on such a trait. It also highlights the potential impact of perceptual thresholds on look-time experiments.
The feasibility and stability of large complex biological networks: a random matrix approach
Authors: Stone Lewi
Published: November 2017

In his theoretical work of the 70’s, Robert May introduced a Random Matrix Theory (RMT) approach for studying the stability of large complex biological systems. Unlike the established paradigm, May demonstrated that complexity leads to instability in generic models of biological networks. The RMT approach has since similarly been applied in many disciplines. Central to the approach is the famous “circular law” that describes the eigenvalue distribution of an important class of random matrices. However the “circular law” generally does not apply for ecological and biological systems in which density-dependence (DD) operates. Here we directly determine the far more complicated eigenvalue distributions of complex DD systems. A simple mathematical solution falls out, that allows us to explore the connection between feasible systems (i.e., having all equilibrium populations positive) and stability. In particular, for these RMT systems, almost all feasible systems are stable. The degree of stability, or resilience, is shown to depend on the minimum equilibrium population, and not directly on factors such as network topology.
5-Formylcytosine controls nucleosome positioning through covalent histone-DNA interaction
Authors: Raiber Eun-Ang , Portella Guillem , Cuesta Sergio Martínez , Hardisty Robyn , Murat Pierre , Li Zhe , Iurlaro Mario , Dean Wendy , Spindel Julia , Beraldi Dario , Dawson Mark A. , Reik Wolf , Balasubramanian Shankar
Published: November 2017

Nucleosomes are the basic unit of chromatin that ensure genome integrity and control access to the genetic information. The organization of nucleosomes is influenced by the underlying DNA sequence itself, transcription factors or other transcriptional machinery associated proteins and chromatin remodeling complexes (1–4). Herein, we show that the naturally occurring DNA modification, 5-formylcytosine (5fC) contributes to the positioning of nucleosomes. We show that the ability of 5fC to position nucleosomesin vitrois associated with the formation of covalent interactions between histone residues and 5fC in the form of Schiff bases. We demonstrate that similar interactions can occur in a cellular environment and define their specific genomic loci in mouse embryonic stem cells. Collectively, our findings identify 5fC as a determinant of nucleosomal organization in which 5fC plays a role in establishing distinct regulatory regions that are linked to gene expression Our study provides a previously unknown molecular mechanism, involving the formation of reversible-covalent bonds between chromatin and DNA that supports a molecular linkage between DNA sequence, DNA base modification and chromatin structure.
Brain-Computer Interfaces for Post-Stroke Motor Rehabilitation: A Meta-Analysis
Authors: Cervera Maria A. , Soekadar Surjo R. , Ushiba Junichi , Millán José del R. , Liu Meigen , Birbaumer Niels , Garipelli Gangadhar
Published: November 2017

Objective

Brain-computer interfaces (BCIs) can provide sensory feedback of ongoing brain oscillations enabling stroke survivors to modulate their sensorimotor rhythms purposefully. A number of recent clinical studies indicate that repeated use of such BCIs might trigger neurological recovery and hence improvement in motor function. Here we provide a first meta-analysis evaluating the clinical effectiveness of BCI-based post-stroke motor rehabilitation.

Methods

Trials were identified using MEDLINE, CENTRAL, PEDro and by inspection of references in several review articles. We selected randomized controlled trials that used BCIs for post-stroke motor rehabilitation and provided motor impairment scores before and after the intervention. A random-effects inverse variance method was used to calculate the summary effect size.

Results

We initially identified 524 articles and, after removing duplicates, we screened titles and abstracts of 473 articles. We found 26 articles corresponding to BCI clinical trials, of these, there were nine studies that involved a total of 235 post-stroke survivors fulfilling the inclusion criterion (randomized controlled trials that examined motor performance as an outcome measure) for the meta-analysis. Motor improvements, mostly quantified by the upper limb Fugl-Meyer Assessment (FMA-UE), exceeded the minimal clinical important difference (MCID=5.25) in six BCI studies, while such improvement was reached only in three control groups. Overall, the BCI training was associated with a standardized mean difference (SMD) of 0.79 (95% CI: 0.37 to 1.20) in FMA-UE compared to control conditions, which is in the range of medium to large summary effect size. In addition, several studies indicated BCI-induced functional and structural neuroplasticity at a sub-clinical level.

Interpretation

We found a medium to large effect size of BCI therapy compared to controls. This suggests that BCI technology might be an effective intervention for post-stroke upper limb rehabilitation. However, more studies with larger sample size are required to increase the reliability of these results.
Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria
Authors: Frénoy Antoine , Bonhoeffer Sebastian
Published: November 2017

The stress-induced mutagenesis paradigm postulates that in response to stress, bacteria increase their genome-wide mutation rate, in turn increasing the chances that a descendant is able to withstand the stress. This has implications for antibiotic treatment: exposure to sub-inhibitory doses of antibiotics has been reported to increase bacterial mutation rates, and thus probably the rate at which resistance mutations appear and lead to treatment failure.

Measuring mutation rates under stress, however, is problematic, because existing methods assume there is no death. Yet sub-inhibitory stress levels may induce a substantial death rate. Death events need to be compensated by extra replication to reach a given population size, thus giving more opportunities to acquire mutations. We show that ignoring death leads to a systematic overestimation of mutation rates under stress.

We developed a system using plasmid segregation to measure death and growth rates simultaneously in bacterial populations. We use it to replicate classical experiments reporting antibiotic-induced mutagenesis. We found that a substantial death rate occurs at the tested sub-inhibitory concentrations, and taking this death into account lowers and sometimes removes the signal for stress-induced mutagenesis. Moreover even when antibiotics increase mutation rate, sub-inhibitory treatments do not increase genetic diversity and evolvability, again because of effects of the antibiotics on population dynamics.

Beside showing that population dynamic is a crucial but neglected parameter affecting evolvability, we provide better experimental and computational tools to study evolvability under stress, leading to a re-assessment of the magnitude and significance of the stress-induced mutagenesis paradigm.
Antigen B from Echinococcus granulosus enters mammalian cells by endocytic pathways
Authors: da Silva Edileuza Danieli , Cancela Martin , Monteiro Karina Mariante , Ferreira Henrique Bunselmeyer , Zaha Arnaldo
Published: November 2017

Cystic hydatid disease is a zoonosis caused by the larval stage (hydatid cyst) of Echinococcus granulosus (Cestoda, Taeniidae). The hydatid cyst develops in the viscera of intermediate host as a unilocular structure filled by the hydatid fluid, which contains parasitic excretory/secretory products. Antigen B (AgB) is the major component of E. granulosus metacestode hydatid fluid. Functionally, AgB has been implicated in immunomodulation and lipid transport. However, the mechanisms underlying AgB functions are not completely known. In this study, we investigated AgB interactions with different mammalian cell types and the pathways involved in its internalization. AgB uptake was observed in four different cell lines, NIH-3T3, A549, J774 and RH. Inhibition of raft-mediated endocytosis causes about 50 and 69% decrease in AgB internalization by RH and A549 cells, respectively. Interestingly, AgB colocalized with the raft endocytic marker, but also showed a partial colocalization with the clathrin endocytic marker. The results indicate that raft-mediated endocytosis is the main route to AgB internalization, and that a clathrin-mediated entry may also occur at a lower frequency. Cellular internalization could be a requirement for AgB functions as a lipid carrier and/or immunomodulatory molecule, contributing to create a more permissive microenvironment to metacestode development and survival.

Author summary

Antigen B (AgB) is an oligomeric lipoprotein highly abundant in Echinococcus granulosus hydatid fluid. AgB has already been characterized as an immunomodulatory protein, capable of inducing a permissive immune response to parasite development. Also, an important role in lipid acquisition is attributed to AgB, because it has been found associated to different classes of host lipids. However, the mechanisms of interaction employed by AgB to perform its functions remain undetermined. In this study, we demonstrate that mammalian cells are able to internalize E. granulosus AgB in culture and found that specific mechanisms of endocytosis are involved. Our results extend the understanding of AgB biological role indicating cellular internalization as a mechanism of interaction, which in turn, may represent a target to intervention.
Functional Plasticity of the gut and the Malpighian tubules underlies cold acclimation and mitigates cold-induced hyperkalemia inDrosophila melanogaster
Authors: Yerushalmi Gil Y. , Misyura Lidiya , MacMillan Heath A. , Donini Andrew
Published: November 2017

At low temperatures,Drosophila, like most insects, lose the ability to regulate ion and water balance across the gut epithelia, which can lead to a lethal increase of [K+] in the hemolymph (hyperkalemia). Cold-acclimation, the physiological response to low temperature exposure, can mitigate or entirely prevent these ion imbalances, but the physiological mechanisms that facilitate this process are not well understood. Here, we test whether plasticity in the ionoregulatory physiology of the gut and Malpighian tubules ofDrosophilamay aid in preserving ion homeostasis in the cold. Upon adult emergence,D. melanogasterfemales were subjected to seven days at warm (25°C) or cold (10°C) acclimation conditions. The cold acclimated flies had a lower critical thermal minimum (CTmin), recovered from chill coma more quickly, and better maintained hemolymph K+ balance in the cold. The improvements in chill tolerance coincided with increased Malpighian tubule fluid secretion and better maintenance of K+secretion rates in the cold, as well as reduced rectal K+reabsorption in cold-acclimated flies. To test whether modulation of ion-motive ATPases, the main drivers of epithelial transport in the alimentary canal, mediate these changes, we measured the activities of Na+-K+-ATPase and V-type H+-ATPase at the Malpighian tubules, midgut, and hindgut. Na+/K+-ATPase and V-type H+-ATPase activities were lower in the midgut and the Malpighian tubules of cold-acclimated flies, but unchanged in the hindgut of cold acclimated flies, and were not predictive of the observed alterations in K+transport. Our results suggest that modification of Malpighian tubule and gut ion and water transport likely prevents cold-induced hyperkalemia in cold-acclimated flies and that this process is not directly related to the activities of the main drivers of ion transport in these organs, Na+/K+- and V-type H+-ATPases.

Summary Statement

At low temperatures,insectslose the ability to regulate ion and water balance and can experience a lethal increase in hemolymph [K+]. Previous exposure to low temperatures can mitigate this effect and improve chill tolerance. Here, we show that plasticity of ion and fluid transport across the Malpighian tubule and rectal epithelia likely drive this response.
DECENT: Differential Expression with Capture Efficiency adjustmeNT for single-cell RNA-seq data
Authors: Ye Chengzhong , Speed Terence P , Salim Agus
Published: November 2017

Dropout is a common phenomenon in single-cell RNA-seq (scRNA-seq) data, and when left unaddressed affects the validity of the statistical analyses. Despite this, few current methods for differential expression (DE) analysis of scRNA-seq data explicitly model the dropout process. We develop DECENT, a DE method for scRNA-seq data that explicitly models the dropout process and performs statistical analyses on the inferred pre-dropout counts. We demonstrate using simulated and real datasets the superior performance of DECENT compared to existing methods. DECENT does not require spike-in data, but spike-ins can be used to improve performance when available. The method is implemented in a publicly-available R package.