bluuebunny/crossref_metadata_2025 huggingface dataset:
Removing instabilities in the hierarchical equations of motion: Exact and approximate projection approaches
Authors: Dunn Ian S. , Tempelaar Roel , Reichman David R.
Published: May 2019

The hierarchical equations of motion (HEOM) provide a numerically exact approach for computing the reduced dynamics of a quantum system linearly coupled to a bath. We have found that HEOM contains temperature-dependent instabilities that grow exponentially in time. In the case of continuous-bath models, these instabilities may be delayed to later times by increasing the hierarchy dimension; however, for systems coupled to discrete, nondispersive modes, increasing the hierarchy dimension does little to alleviate the problem. We show that these instabilities can also be removed completely at a potentially much lower cost via projection onto the space of stable eigenmodes; furthermore, we find that for discrete-bath models at zero temperature, the remaining projected dynamics computed with few hierarchy levels are essentially identical to the exact dynamics that otherwise might require an intractably large number of hierarchy levels for convergence. Recognizing that computation of the eigenmodes might be prohibitive, e.g., for large or strongly coupled models, we present a Prony filtration algorithm that may be useful as an alternative for accomplishing this projection when diagonalization is too costly. We present results demonstrating the efficacy of HEOM projected via diagonalization and Prony filtration. We also discuss issues associated with the non-normality of HEOM.
Origin of structural stability of ScH3 molecular nanowires and their chemical-bonding behavior: Correlation effects of the Sc 3d electrons
Authors: Lou Ping , Lee Jin Yong
Published: May 2019

A new stable transition-metal trihydride (ScH3) molecular nanowire was recently reported by Li et al. [J. Am. Chem. Soc. 139, 6290–6293 (2017)]. Of the two typical structures (T–ScH3 and O–ScH3), T–ScH3 is more stable than O–ScH3. However, the reason why O–ScH3 is less stable than T–ScH3 was not known. Using Perdew–Burke–Ernzerhof (PBE), PBE+U, SCAN, and HSE06, as well as crystal orbital Hamilton populations (COHPs), we investigate the orbital-projected band structures and chemical bonding of T–ScH3 and O–ScH3. It is found that the energies calculated by PBE, SCAN, and HSE06 indeed reveal that T–ScH3 is more stable than O–ScH3, and there is no occupied antibonding state at the Fermi level of the COHP curves of T–ScH3, supporting the stable Sc–H bonding of T–ScH3. To the contrary, the Sc–H bonding of O–ScH3 is unstable because there exist occupied antibonding states at the Fermi level of the COHP curves of O–ScH3. We found that the results of PBE+U are consistent with those of PBE, SCAN, and HSE06 in the case of U < Uc. However, when U > Uc, the results of PBE+U are opposite to those of PBE, SCAN, and HSE06.
Epitaxial Co50Fe50(110)/Pt(111) films on MgAl2O4(001) and its enhancement of perpendicular magnetic anisotropy
Authors: Lee Aidan J. , Ahmed Adam S. , Guo Side , Esser Bryan D. , McComb David W. , Yang Fengyuan
Published: May 2019

Perpendicular magnetic anisotropy (PMA) in magnetic thin films with low coercivity is desirable for magnetic memory devices. It has been found that a (111)-oriented or textured Pt seed layer can enhance PMA and is, therefore, commonly utilized in spintronic structures. We grow (111)-oriented Pt epitaxial films via off-axis sputtering on various substrates and investigate the optimal substrate and orientation for high quality, epitaxial growth. Our results show that Pt(111) epitaxial films grow remarkably well on MgAl2O4(001) with an exceptionally narrow X-ray diffraction rocking curve. This high-quality seed layer is found to promote epitaxial growth of Pt/Co50Fe50/Pt trilayers with strong PMA comparable to many repeats of the magnetic multilayers reported previously. In addition, the Pt seed layer enhances the maximum thicknesses of Co50Fe50 that can still maintain PMA up to 1.07 nm.
Inelastic H and D atom scattering from Au(111) as benchmark for theory
Authors: Jiang Hongyan , Dorenkamp Yvonne , Krüger Kerstin , Bünermann Oliver
Published: May 2019

Efficient transfer of translational energy to electron-hole pair excitation involving multiple collisions dominates H atom collisions with metal surfaces. For this reason, H atom interaction with metal surfaces cannot be modeled within the commonly used Born-Oppenheimer approximation (BOA). This fact makes H atom scattering from metal surfaces an ideal model system for dynamics that go beyond the BOA. We chose the H/Au(111) system as a model system to obtain a detailed dataset that can serve as a benchmark for theoretical models developed for describing electronically nonadiabatic processes at metal surfaces. Therefore, we investigate the influence of various experimental parameters on the energy loss in detail including isotopic variant, incidence translational energy, incidence polar and azimuthal angles, and outgoing scattering angles.
Linking the two-field dynamics of plasma edge turbulence with the one-field balanced model through systematic unstable forcing at low resistivity
Authors: Qi Di , Majda Andrew J.
Published: May 2019

After the original contributions of Hasegawa and Wakatani (HW), basic two-field models such as the modified and balanced Hasegawa-Wakatani (BHW) models improve the understanding of plasma edge turbulence. The recent two-field flux-BHW model provides an improved treatment for the balanced electron dynamics on magnetic flux surfaces. The Hasegawa-Mima (HM) model offers another simplified one-field characterization of the zonal flow–drift wave interaction mechanism. A major restriction in the original HM model is the lack of intrinsic instability which is essential to maintain drift wave turbulence and plasma transport. We overcome this limitation by linking this model with the two-field HW equations with drift instability while keeping the simplicity in the one-field balanced formulation. A systematically derived unstable forcing is introduced to the modified HM model mimicking the role of the inherent instability near the low resistivity limit, where the unstable branch of the HW solution gradually becomes aligned with the HM potential vorticity. Detailed numerical experiments are performed to test the skill in the one-field model with unstable forcing. It is shown with qualitative and quantitative agreement that the one-field modified HM model is able to replicate the typical drift wave and zonal flow interacting procedure under a more analytically tractable framework. The insight gained from the simple model analysis can also offer guidelines for the development of model reduction methods for more complicated systems.
Dissipative dynamics in a tunable Rabi dimer with periodic harmonic driving
Authors: Huang Zhongkai , Zheng Fulu , Zhang Yuyu , Wei Yadong , Zhao Yang
Published: May 2019

Recent progress on qubit manipulation allows application of periodic driving signals on qubits. In this study, a harmonic driving field is added to a Rabi dimer to engineer photon and qubit dynamics in a circuit quantum electrodynamics device. To model environmental effects, qubits in the Rabi dimer are coupled to a phonon bath with a sub-Ohmic spectral density. A nonperturbative treatment, the Dirac-Frenkel time-dependent variational principle together with the multiple Davydov D2 ansatz, is employed to explore the dynamical behavior of the tunable Rabi dimer. In the absence of the phonon bath, the amplitude damping of the photon number oscillation is greatly suppressed by the driving field, and photons can be created, thanks to the resonance between the periodic driving field and the photon frequency. In the presence of the phonon bath, one can still change the photon numbers in two resonators and indirectly alter the photon imbalance in the Rabi dimer by directly varying the driving signal in one qubit. It is shown that qubit states can be manipulated directly by the harmonic driving. The environment is found to strengthen the interqubit asymmetry induced by the external driving, opening up a new venue to engineer the qubit states.
Excitation of low-frequency dust density waves in flowing complex plasmas
Authors: Yaroshenko V. V. , Khrapak S. A. , Pustylnik M. Y. , Thomas H. M. , Jaiswal S. , Lipaev A. M. , Usachev A. D. , Petrov O. F. , Fortov V. E.
Published: May 2019

We study low frequency dust density waves excited in the microparticle streams of the Plasmakristall-4 chamber under microgravity conditions on board the International Space Station. Dispersion relations and instability conditions are analyzed for the dust density modes propagating along the axial electric field and in the reversed direction, revealing some important implications for the dust diagnostics. The results clearly point out to the Havnes parameter as a key factor for the excitation of the dust density modes.
Frequency-dependent current density tensors as density functions of dynamic polarizabilities
Authors: Lazzeretti Paolo
Published: May 2019

Relationships accounting for contributions to the first-order charge density ρ(1) and current density J(1), induced in the electrons of a molecule by a monochromatic plane wave, have been obtained via time-dependent quantum mechanical perturbation theory. Their gauge invariance and invariance in passive translations of the coordinate system have been demonstrated (i) within the (long wavelengths) electric dipole approximation, in which only the electric field contributions to these densities are required, and (ii) within the electric quadrupole approximation, in which nonseparable terms provided by the magnetic field and by the electric field gradient, assumed uniform over the molecular domain, are needed. It is shown that the physical meaning of current density tensors depending on the frequency ω of the monochromatic wave shone on the molecule, and corresponding to derivatives of the current density J(1)(r, ω) with respect to components of the perturbing fields, is that of property density. Therefore, frequency-dependent current density tensors can be interpreted as the integrand function in 3d-space integrals defining dynamic molecular response tensors, e.g., electric dipole, mixed electric dipole-magnetic dipole, and electric dipole-quadrupole polarizabilites. Plots of current density tensors are expected to provide important information on the molecular domains giving dominant contributions to these properties.
Numerical treatment for fluidic system of activation energy with non-linear mixed convective and radiative flow of magneto nanomaterials with Navier’s velocity slip
Authors: Uddin Iftikhar , Akhtar Rizwan , Khan Muhammd Abdul Rehman , Zhiyu Zhu , Islam Saeed , Shoaib Muhammad , Raja Muhammad Asif Zahoor
Published: May 2019

A novel application of Lobatto IIIA computing solver is presented for the solution of nanofluidic Buongiorno model in the porous space. Incompressible electrically conducting fluid mixed with nanomaterial is considered. Flow expression is modelled via nonlinear mixed convection and Navier’s slip condition. Activation energy, Joule heating and non-liner thermal radiation characterise the heat/mass transport. The governing PDEs of the considered problem are transformed into an equivalent system of ODEs using similarity variables. The resulting system is solved numerically by exploiting the strength of Lobatto IIIA computing solver. Numerical and graphical illustrations are utilized to interpret the behaviour of sundry physical parameters on velocity, concentration and temperature profiles. Skin friction, temperature and concentration gradients for different scenarios of embedding variables are tabulated and analysed. Furthermore, numerical data for mesh points, error analysis, ODEs and boundary conditions evaluation are also displayed. Our computed analysis indicates that velocity of nanofluid increases for large value of slip parameter while it decreases with the increase of porosity parameter. In addition, concentration distribution is decaying and increasing functions of chemical reaction and activation energy parameters respectively.
Anomalous photovoltaic effect originates from shift current under interband excitation in ferroelectrics
Authors: Frank Jodi Ackerman
Published: May 2019

Researchers focus on waveform and spectrum using THz spectroscopy to determine the shift-current origin of the anomalous photovoltaic effect in ferroelectrics.
Quantifying the interactions between koalas in a high-density population during the breeding period
Authors: Watchorn Darcy J. , Whisson Desley A.
Published: May 2019

A species’ social structure influences its patterns of gene flow and disease transmission. Knowledge of social structure therefore is critical for understanding conservation challenges and informing management strategies. We examined the social structure of 33 free-ranging koalas (Phascolarctos cinereus) in a high-density population (6.7 koalas per hectare) during the early and peak phase of the breeding period (August–December) at Cape Otway, Victoria. We used GPS and proximity loggers to quantify koala space use and interactions, and direct observations to determine behaviours associated with interactions. Our proximity loggers recorded 661 interactions (64% male–female, 28% male–male and 8% female–female). A peak in male–male interactions at the onset of the breeding period suggested that males may physically compete for mates at this time. Male–female interactions increased from the onset of the breeding period, and were mostly of short duration (median duration 5.5 min). From field observations of interactions, and the absence of pouch young in December, many of these interactions may have been unsuccessful copulation attempts. Space use and social network analyses revealed that most males had strong links (total interaction duration >30 min) with only one or two females, despite their spatial overlap and interactions with multiple females. Body mass did not influence a male’s mating success in terms of number of female mates. Our results contrast with those of a lower-density population in central eastern Queensland, suggesting that some aspects of koala social structure may be plastic relative to population density.
Activation of PASK by mTORC1 is required for the onset of the terminal differentiation program
Authors: Kikani Chintan K. , Wu Xiaoying , Fogarty Sarah , Kang Seong Anthony Woo , Dephoure Noah , Gygi Steven P. , Sabatini David M. , Rutter Jared
Published: May 2019

Significance

Skeletal muscle harbors a robust, yet quiescent stem cell population. These stem cells are activated upon myofiber injury to repair damaged myotome. This regenerative myogenesis is guided by external signaling cues that allow stem cells to acquire various stem cell fates. Here, we describe a growth factor and nutrient-stimulated pathway, whereby mammalian target of rapamycin (mTOR) activates Per–Arnt–Sim domain kinase (PASK) protein kinase in muscle stem cells. This mTOR-dependent activation of PASK is required for the transcriptional induction of the
myogenin
gene and subsequent terminal differentiation program. Finally, our results suggest that mTOR-PASK and mTOR-S6 Kinase signaling are required for distinct stages of myogenesis program, and link nutrient environment to early stages of the myogenesis program.
Leptin in hippocampus mediates benefits of mild exercise by an antioxidant on neurogenesis and memory
Authors: Yook Jang Soo , Rakwal Randeep , Shibato Junko , Takahashi Kanako , Koizumi Hikaru , Shima Takeru , Ikemoto Mitsushi J. , Oharomari Leandro K. , McEwen Bruce S. , Soya Hideaki
Published: May 2019

Significance

Leptin (LEP), produced and acting in the hippocampus, mediates enhancement by mild exercise (ME) of hippocampus-related memory and neurogenesis, which are further increased by an antioxidant carotenoid, astaxanthin (AX). Both are facilitated by the administration of ME or AX alone. The up-regulation of the
LEP
gene and LEP protein expression in the hippocampus by ME is further elevated when combined with AX. Consistently, the combined interventions increased hippocampal LEP protein. In LEP-deficient
ob/ob
mice, LEP replacement in the brain restored the ability of ME+AX to enhance hippocampal function. Thus, a combined lifestyle intervention based on ME, including yoga and tai chi, and specific dietary supplements that include antioxidants may together improve cognition and possibly retard cognitive decline in humans.
Clonal Vγ6
+
Vδ4
+
T cells promote IL-17–mediated immunity against
Staphylococcus aureus
skin infection
Authors: Marchitto Mark C. , Dillen Carly A. , Liu Haiyun , Miller Robert J. , Archer Nathan K. , Ortines Roger V. , Alphonse Martin P. , Marusina Alina I. , Merleev Alexander A. , Wang Yu , Pinsker Bret L. , Byrd Angel S. , Brown Isabelle D. , Ravipati Advaitaa , Zhang Emily , Cai Shuting S. , Limjunyawong Nathachit , Dong Xinzhong , Yeaman Michael R. , Simon Scott I. , Shen Wei , Durum Scott K. , O’Brien Rebecca L. , Maverakis Emanual , Miller Lloyd S.
Published: May 2019

T cell cytokines contribute to immunity against
Staphylococcus aureus
, but the predominant T cell subsets involved are unclear. In an
S. aureus
skin infection mouse model, we found that the IL-17 response was mediated by γδ T cells, which trafficked from lymph nodes to the infected skin to induce neutrophil recruitment, proinflammatory cytokines IL-1α, IL-1β, and TNF, and host defense peptides. RNA-seq for
TRG
and
TRD
sequences in lymph nodes and skin revealed a single clonotypic expansion of the encoded complementarity-determining region 3 amino acid sequence, which could be generated by canonical nucleotide sequences of
TRGV5
or
TRGV6
and
TRDV4
. However, only
TRGV6
and
TRDV4
but not
TRGV5
sequences expanded. Finally, Vγ6
+
T cells were a predominant γδ T cell subset that produced IL-17A as well as IL-22, TNF, and IFNγ, indicating a broad and substantial role for clonal Vγ6
+
Vδ4
+
T cells in immunity against
S. aureus
skin infections.
Spatial patterning among savanna trees in high-resolution, spatially extensive data
Authors: Staver A. Carla , Asner Gregory P. , Rodriguez-Iturbe Ignacio , Levin Simon A. , Smit Izak P.J.
Published: May 2019

Significance

Understanding how environmental variation shapes vegetation distributions is crucial for predicting biosphere responses to global change. Savannas represent a major challenge, and repeated efforts have failed to constrain variation in savanna vegetation structure to a useful degree. Here, we find that trees cluster in savannas and that their clustering is governed by power laws, with parameters and geometries that are invariant to environment. This explains why savannas have resisted mechanistic characterization and offers a possible tool for constraining variability in vegetation structure.
Hidden interactions in financial markets
Authors: Stavroglou Stavros K. , Pantelous Athanasios A. , Stanley H. Eugene , Zuev Konstantin M.
Published: May 2019

Significance

The importance of understanding the structure of financial markets has been progressively coming to a head in public discourse. With the rise and prevalence of big datasets, it is a crucial time for academics to study the interdependency outside conventional analysis. Thus, the methodology proposed in this paper does not only allow distinction between positive and negative interdependence, but additionally identifies a yet unexplored form of interaction we coin as “dark causality.” We benchmark this method on asset pairs and on a network of sovereign credit default swaps, where the dominant form of interaction is that of dark causality. Our results are relevant to finance practitioners who, by virtue of their profession, tend to engage on a regular basis with retail investors.
Inhibition of β-catenin/B cell lymphoma 9 protein−protein interaction using α-helix–mimicking sulfono-γ-AApeptide inhibitors
Authors: Sang Peng , Zhang Min , Shi Yan , Li Chunpu , Abdulkadir Sami , Li Qi , Ji Haitao , Cai Jianfeng
Published: May 2019

Significance

The design of cell-penetrating long peptidomimetic scaffolds for interacting with large protein binding interfaces is challenging because they involve various necessary functional groups. Here we report the first series of helical sulfono-γ-AApeptides that disrupt protein–protein interactions. Specifically, we discovered that these helical mimetics can structurally and functionally mimic the B Cell Lymphoma 9 (BCL9) helix and disrupt cancer-related β-catenin/BCL9 protein–protein interaction in cells with excellent potency and specificity. Enzymatic stability studies demonstrate the remarkable stability of the helical sulfono-γ-AApeptides, augmenting their biological potential. This strategy could be adapted to target a myriad of other disease-related protein–protein interactions.
Unsupervised determination of protein crystal structures
Authors: Ufimtsev Ivan S. , Levitt Michael
Published: May 2019

Significance

Solving crystal structures of large biological macromolecules in the absence of experimental phase information, especially at low resolution, is a tedious problem prone to mistakes and overfitting. Due to errors stemming from poorly interpretable parts of the electron density map, human experience and intuition are imperative for building a correct atomistic model. For this reason, tools for automatic structure determination used nowadays require constant human supervision. Here we present a method that can overcome the difficulties; it greatly reduces or even eliminates human involvement in the solution process by working with ensembles of possible solutions. This approach can find solution of a higher quality than can humans and can solve difficult cases not amenable to other methods.
Structural insights into the aPKC regulatory switch mechanism of the human cell polarity protein lethal giant larvae 2
Authors: Almagor Lior , Ufimtsev Ivan S. , Ayer Aruna , Li Jingzhi , Weis William I.
Published: May 2019

Metazoan cell polarity is controlled by a set of highly conserved proteins. Lethal giant larvae (Lgl) functions in apical-basal polarity through phosphorylation-dependent interactions with several other proteins as well as the plasma membrane. Phosphorylation of Lgl by atypical protein kinase C (aPKC), a component of the partitioning-defective (Par) complex in epithelial cells, excludes Lgl from the apical membrane, a crucial step in the establishment of epithelial cell polarity. We present the crystal structures of human Lgl2 in both its unphosphorylated and aPKC-phosphorylated states. Lgl2 adopts a double β-propeller structure that is unchanged by aPKC phosphorylation of an unstructured loop in its second β-propeller, ruling out models of phosphorylation-dependent conformational change. We demonstrate that phosphorylation controls the direct binding of purified Lgl2 to negative phospholipids in vitro. We also show that a coil–helix transition of this region that is promoted by phosphatidylinositol 4,5-bisphosphate (PIP
2
) is also phosphorylation-dependent, implying a highly effective phosphorylative switch for membrane association.
Aneuploidy drives lethal progression in prostate cancer
Authors: Stopsack Konrad H. , Whittaker Charles A. , Gerke Travis A. , Loda Massimo , Kantoff Philip W. , Mucci Lorelei A. , Amon Angelika
Published: May 2019

Significance

Aneuploidy is usually quantified by measuring intracellular DNA content or chromosome structure and number. We show that the number of altered chromosome arms can be estimated from transcriptome profiling, which allows for assessing aneuploidy within repositories of archival, formalin-fixed, paraffin-embedded tumors. While aneuploidy impedes proliferation in primary cells, we show that it is a feature of aggressiveness in primary prostate cancers that are more likely to become lethal. Our data suggest that losses or gains of entire chromosome arms confers aggressiveness beyond affecting copy numbers of tumor suppressors or oncogenes on those arms. Beyond helping understand the etiology of aggressive prostate cancer, we propose that extent of aneuploidy could also be employed clinically to inform risk stratification and treatment.
Microbial production of methyl anthranilate, a grape flavor compound
Authors: Luo Zi Wei , Cho Jae Sung , Lee Sang Yup
Published: May 2019

Significance

Methyl anthranilate (MANT) is widely used in the flavoring and cosmetics industry to give grape scent and flavor. In an effort to replace the conventional petroleum-based synthesis of MANT, we report the direct fermentative production of MANT from glucose in metabolically engineered
Escherichia coli
and
Corynebacterium glutamicum
strains. A synthetic plant-derived metabolic pathway was introduced and extensive metabolic engineering was performed including fine-tuning key enzyme levels and increasing the availability of precursor and cofactor metabolites. A two-phase extractive cultivation was developed using an extractant solvent to recover MANT in situ, which led to high levels of MANT production. This work demonstrates a promising sustainable alternative to MANT production and presents strategies applicable toward production of other valuable natural compounds.
Effects of the relationships between forms within and across paradigms on lexical processing and
representation
Authors: Parker Jeff
Published: May 2019

The frequency and distribution of forms within a lexeme’s paradigm affect how quickly forms are accessed (e.g.,
Kostić, 1991; Milin, Filipović Đurđević, &
Moscoso del Prado Martín, 2009; Moscoso del Prado Martı́n, Kostić, & Baayen,
2004). The distribution of forms across paradigms, in contrast, has received little experimental attention. Theoretical
studies investigate the distribution of forms across paradigms because forms vary in how predictive they are of other (unknown)
forms. Such investigations have uncovered typological tendencies (e.g., Ackerman & Malouf,
2013; Stump & Finkel, 2013) and contribute to explanations of
language-specific phenomena (e.g., Sims, 2015; Parker & Sims, To appear). The intersection of these research approaches raises questions about how the
distribution of forms within and across paradigms affects lexical access and representation. Based on forms of
Russian nouns representing two morphosyntactic property sets and lexemes from three inflection classes, it is shown that speakers
are sensitive to differences in form and morphosyntactic property set in a visual lexical decision task. In a priming task,
nominative forms prime locative forms better than vice versa regardless of suffix, despite differences between the same forms in
the lexical decision task. These results suggest that speakers make generalizations about forms across classes, including at the
level of word forms and morphosyntactic property sets.
Spring‐mass characteristics during human locomotion: Running experience and physiological considerations of blood lactate accumulation
Authors: Bitchell C. L. , McCarthy‐Ryan M. , Goom T. , Moore I. S.
Published: May 2019

The aim of this study was to examine how running experience affects leg stiffness (Kleg) and spring‐mass characteristics during running stages associated with the onset of blood lactate accumulation (OBLA). Seven trained (66.9 ± 4.8 kg; 182 ± 4.0 cm; 23.1 ± 3.1 years) and 13 untrained (78.5 ± 7.6 kg; 182 ± 3.0 cm; 20.3 ± 1.5 years) runners completed an incremental treadmill run. Running velocity was increased by 1 km.h−1 every four minutes and blood lactate samples were taken at every stage, in addition to a 10 s video recording using ‘Runmatic’. Once 4 mmol L−1 (OBLA; the second lactate turn point) had been reached one more stage was completed. Spring‐mass characteristics across groups and at pre‐OBLA, OBLA and post‐OBLA were compared. The velocity at OBLA was higher for the trained runners compared to the untrained runners (18 ± 0.7 vs 11 ± 1.3 km.h−1, p < 0.001). Kleg was similar between untrained and trained runners across each stage (15.8 ± 0.3 vs 14.3 ± 0.3 kN.m) and did not change between stages, yet spring‐mass characteristics differed between groups. Vertical stiffness increased in the trained runners from pre‐OBLA to post‐OBLA (45.5 ± 3.35–51.9 ± 3.61 kN−1), but not in untrained runners (35.0 ± 5.2–39.6 ± 5.7 kN−1). Kleg was strongly related to Fpeak for trained runners only (r = 0.79; untrained runners, r = 0.34). Kleg was unaffected by physiological training status and was maintained across all OBLA stages. Trained runners appear to have optimised their spring‐mass system in a homogenous manner, whilst less consistent spring‐mass characteristics were observed in untrained runners.
Junctional tumor suppressors interact with 14-3-3 proteins to control planar spindle alignment
Authors: Nakajima Yu-ichiro , Lee Zachary T. , McKinney Sean A. , Swanson Selene K. , Florens Laurence , Gibson Matthew C.
Published: May 2019

Proper orientation of the mitotic spindle is essential for cell fate determination, tissue morphogenesis, and homeostasis. During epithelial proliferation, planar spindle alignment ensures the maintenance of polarized tissue architecture, and aberrant spindle orientation can disrupt epithelial integrity. Nevertheless, in vivo mechanisms that restrict the mitotic spindle to the plane of the epithelium remain poorly understood. Here we show that the junction-localized tumor suppressors Scribbled (Scrib) and Discs large (Dlg) control planar spindle orientation via Mud and 14-3-3 proteins in the Drosophila wing disc epithelium. During mitosis, Scrib is required for the junctional localization of Dlg, and both affect mitotic spindle movements. Using coimmunoprecipitation and mass spectrometry, we identify 14-3-3 proteins as Dlg-interacting partners and further report that loss of 14-3-3s causes both abnormal spindle orientation and disruption of epithelial architecture as a consequence of basal cell delamination and apoptosis. Combined, these biochemical and genetic analyses indicate that 14-3-3s function together with Scrib, Dlg, and Mud during planar cell division.
The COMMD3/8 complex determines GRK6 specificity for chemoattractant receptors
Authors: Nakai Akiko , Fujimoto Jun , Miyata Haruhiko , Stumm Ralf , Narazaki Masashi , Schulz Stefan , Baba Yoshihiro , Kumanogoh Atsushi , Suzuki Kazuhiro
Published: May 2019

Lymphocyte migration is mediated by G protein–coupled receptors (GPCRs) that respond to chemoattractive molecules. After their activation, GPCRs are phosphorylated by different GPCR kinases (GRKs), which produces distinct functional outcomes through β-arrestins. However, the molecular machinery that targets individual GRKs to activated GPCRs remains elusive. Here, we identified a protein complex consisting of copper metabolism MURR1 domain–containing (COMMD) 3 and COMMD8 (COMMD3/8 complex) as an adaptor that selectively recruits a specific GRK to chemoattractant receptors and promotes lymphocyte chemotaxis. COMMD8, whose stability depended on COMMD3, was recruited to multiple chemoattractant receptors. Deficiency of COMMD8 or COMMD3 impaired B cell migration and humoral immune responses. Using CXC-chemokine receptor 4 (CXCR4) as a model, we demonstrated that the COMMD3/8 complex selectively recruited GRK6 and induced GRK6-mediated phosphorylation of the receptor and activation of β-arrestin–mediated signaling. Thus, the COMMD3/8 complex is a specificity determinant of GRK targeting to GPCRs and represents a point of regulation for immune responses.
Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities
Authors: Trabelsi Ameni , Chaabane Mohamed , Ben-Hur Asa
Published: May 2019

Motivation

Deep learning architectures have recently demonstrated their power in predicting DNA- and RNA-binding specificity. Existing methods fall into three classes: Some are based on convolutional neural networks (CNNs), others use recurrent neural networks (RNNs) and others rely on hybrid architectures combining CNNs and RNNs. However, based on existing studies the relative merit of the various architectures remains unclear.

Results

In this study we present a systematic exploration of deep learning architectures for predicting DNA- and RNA-binding specificity. For this purpose, we present deepRAM, an end-to-end deep learning tool that provides an implementation of a wide selection of architectures; its fully automatic model selection procedure allows us to perform a fair and unbiased comparison of deep learning architectures. We find that deeper more complex architectures provide a clear advantage with sufficient training data, and that hybrid CNN/RNN architectures outperform other methods in terms of accuracy. Our work provides guidelines that can assist the practitioner in choosing an appropriate network architecture, and provides insight on the difference between the models learned by convolutional and recurrent networks. In particular, we find that although recurrent networks improve model accuracy, this comes at the expense of a loss in the interpretability of the features learned by the model.

Availability and implementation

The source code for deepRAM is available at https://github.com/MedChaabane/deepRAM.

Supplementary information

Supplementary data are available at Bioinformatics online.
Reconstructing signaling pathways using regular language constrained paths
Authors: Wagner Mitchell J , Pratapa Aditya , Murali T M
Published: May 2019

Motivation

High-quality curation of the proteins and interactions in signaling pathways is slow and painstaking. As a result, many experimentally detected interactions are not annotated to any pathways. A natural question that arises is whether or not it is possible to automatically leverage existing pathway annotations to identify new interactions for inclusion in a given pathway.

Results

We present RegLinker, an algorithm that achieves this purpose by computing multiple short paths from pathway receptors to transcription factors within a background interaction network. The key idea underlying RegLinker is the use of regular language constraints to control the number of non-pathway interactions that are present in the computed paths. We systematically evaluate RegLinker and five alternative approaches against a comprehensive set of 15 signaling pathways and demonstrate that RegLinker recovers withheld pathway proteins and interactions with the best precision and recall. We used RegLinker to propose new extensions to the pathways. We discuss the literature that supports the inclusion of these proteins in the pathways. These results show the broad potential of automated analysis to attenuate difficulties of traditional manual inquiry.

Availability and implementation

https://github.com/Murali-group/RegLinker.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Role of Radical Economic Restructuring in Truancy from School and Engagement in Crime
Authors: Farrall Stephen , Gray Emily , Mike Jones Philip
Published: May 2019

Of late, criminologists have become acutely aware of the relationship between school outcomes and engagement in crime as an adult. This phenomenon—which has come to be known as the ‘school-to-prison-pipeline’—has been studied in North America and the United Kingdom, and requires longitudinal data sets. Typically, these studies approach the phenomenon from an individualist perspective and examine truancy in terms of the truants’ attitudes, academic achievement or their home life. What remains unclear, however, is a consideration of (1) how macro-level social and economic processes may influence the incidence of truancy, and (2) how structural processes fluctuate over time, and in so doing produce variations in truancy rates or the causal processes associated with truancy. Using longitudinal data from two birth cohort studies, we empirically address these blind spots and test the role of social-structural processes in truancy, and how these may change over time.
Social Work With Unaccompanied Asylum-Seeking Young People: Reframing Social Care Professionals As ‘Co-Navigators’
Authors: Devenney Kelly
Published: May 2019

This article explores the relationships between unaccompanied asylum-seeking young people and the social care professionals who work with them. Based on the interviews with both young people and professionals, analysed using a thematic narrative approach, the findings seek to reframe practitioners in this field as ‘co-navigators’. Such co-navigators assist asylum-seeking young people to plot a course through complex and uncertain social terrain, including the shifting and inhospitable terrain of immigration regimes. Viewing practice in this way brings into focus the interplay of agency and control in these relationships. In contrast to some previous conceptualisations, the agency of the young people here is expressed through relationships with professionals as many of the young people relied on social care to help them manifest their goals and aspirations; both through pragmatic assistance in navigating the complexity of institutional bureaucracy and through developing emotional, therapeutic bonds. Understanding social care professionals as ‘co-navigators’ allows us to understand the emotional value of practical forms of assistance as well as explore how agency might operate as such relationships evolve.
Improved Meet-in-the-Middle Attacks on Reduced-Round Kiasu-BC and Joltik-BC
Authors: Liu Ya , Shi Yifan , Gu Dawu , Zeng Zhiqiang , Zhao Fengyu , Li Wei , Liu Zhiqiang , Bao Yang
Published: May 2019

Kiasu-BC and Joltik-BC are internal tweakable block ciphers of authenticated encryption algorithms Kiasu and Joltik submitted to the CAESAR competition. Kiasu-BC is a 128-bit block cipher, of which tweak and key sizes are 64 and 128 bits, respectively. Joltik-BC-128 is a 64-bit lightweight block cipher supporting 128 bits tweakey. Its designers recommended the key and tweak sizes are both 64 bits. In this paper, we propose improved meet-in-the-middle attacks on 8-round Kiasu-BC, 9-round and 10-round Joltik-BC-128 by exploiting properties of their structures and using precomputation tables and the differential enumeration. For Kiasu-BC, we build a 5-round distinguisher to attack 8-round Kiasu-BC with $2^{109}$ plaintext–tweaks, $2^{112.8}$ encrytions and $2^{92.91}$ blocks. Compared with previously best known cryptanalytic results on 8-round Kiasu-BC under chosen plaintext attacks, the data and time complexities are reduced by $2^{7}$ and $2^{3.2}$ times, respectively. For the recommended version of Joltik-BC-128, we construct a 6-round distinguisher to attack 9-round Joltik-BC-128 with $2^{53}$ plaintext–tweaks, $2^{56.6}$ encryptions and $2^{52.91}$ blocks, respectively. Compared with previously best known results, the data and time complexities are reduced by $2^7$ and $2^{5.1}$ times, respectively. In addition, we present a 6.5-round distinguisher to attack 10-round Joltik-BC-128 with $2^{53}$ plaintext–tweaks, $2^{101.4}$ encryptions and $2^{76.91}$ blocks.
Mechanotransduction, immunoregulation, and metabolic functions of CD31 in cardiovascular pathophysiology
Authors: Caligiuri Giuseppina
Published: May 2019

Biomechanical changes in the heart and vessels drive rapid and dynamic regulation of blood flow, a vital process for meeting the changing metabolic needs of the peripheral tissues at any given point in time. The fluid movement of the blood exerts haemodynamic stress upon the solid elements of the cardiovascular system: the heart, vessels, and cellular components of the blood. Cardiovascular diseases can lead to prolonged mechanical stress, such as cardiac remodelling during heart failure or vascular stiffening in atherosclerosis. This can lead to a significantly reduced or increasingly turbulent blood supply, inducing a shift in cellular metabolism that, amongst other effects, can trigger the release of reactive oxygen species and initiate a self-perpetuating cycle of inflammation and oxidative stress. CD31 is the most abundant constitutive co-signalling receptor glycoprotein on endothelial cells, which line the cardiovascular system and form the first-line of cellular contact with the blood. By associating with most endothelial receptors involved in mechanosensing, CD31 regulates the response to biomechanical stimuli. In addition, by relocating in the lipid rafts of endothelial cells as well as of cells stably interacting with the endothelium, including leucocytes and platelets, CD31–CD31 trans-homophilic engagement guides and restrains platelet and immune cell accumulation and activation and at sites of damage. In this way, CD31 is at the centre of mediating mechanical, metabolic, and immunological changes within the circulation and provides a single target that may have pleiotropic beneficial effects.
Effects of Site Thermal Variation and Physiography on Flight Synchrony and Phenology of the North American Spruce Beetle (Coleoptera: Curculionidae, Scolytinae) and Associated Species in Colorado
Authors: Dell Isaac Hans , Davis Thomas Seth
Published: May 2019

Spruce beetle, Dendroctonus rufipennis Kirby, is associated with forest mortality in Colorado and across western North America, yet it is not well understood how thermal variability affects basic population processes such as flight phenology. However, phenology–temperature relationships are important for understanding patterns of ecosystem disturbance, especially under projected climate warming. Here, we use a multiyear trapping study to test the hypothesis that spruce beetle flight synchrony, timing, and fitness traits (body size) are affected by variation in regional temperature and physiography. Large quantities of co-colonizing scolytines (Polygraphus convexifrons) (Coleoptera: Curculionidae, Scolytinae) and predatory beetles (Thanasimus undulatus) (Coleoptera: Cleridae) that may affect D. rufipennis populations also responded to spruce beetle synthetic pheromone lures. Relationships between flight patterns and environmental conditions were also analyzed for these species. The winter of 2018 was warmer and drier than winter 2017 and was associated with earlier flight for both scolytine species across most sites. The most important environmental factor driving D. rufipennis flight phenology was accumulated growing degree-days, with delayed flight cessation under warmer conditions and larger beetles following a warm winter. Flight was consistently more synchronous under colder growing season conditions for all species, but synchrony was not associated with winter temperatures. Warmer-than-average years promoted earlier flight of D. rufipennis and associated species, and less synchronous, prolonged flight across the region. Consequently, climate warming may be associated with earlier and potentially extended biotic pressure for spruce trees in the Rocky Mountain region, and flight phenology of multiple scolytines is plastic in response to thermal conditions.
Extra-anatomical ascending-thoraco-abdominal bypass for aortic fistula after thoracic endovascular aortic repair
Authors: Al Rstum Zain , Tanaka Akiko , Safi Hazim J , Estrera Anthony L
Published: May 2019

Aortobronchial and aorto-oesophageal fistulae after thoracic endovascular aortic repair (TEVAR) for traumatic aortic injuries are rare but serious. Potentially fatal complications may occur years after the stent graft deployment. Surgical management is challenging. We report on a 33-year-old male with aorto-oesophageal fistula and a 25-year-old male with aortobronchial fistula—both of whom received TEVAR for traumatic aortic injury. Each underwent successful staged open surgical repair with extra-anatomical bypass from the ascending aorta to the thoraco-abdominal aorta, along with arch vessel reconstructions and debridement of infected lesions. They remained alive after 18 months.
The impact of labial fixed appliance orthodontic treatment on patient expectation, experience, and satisfaction: an overview of systematic reviews
Authors: Yassir Yassir A , McIntyre Grant T , Bearn David R
Published: May 2019

Background

Patient perception with fixed appliance orthodontic treatment is important to improve oral health-related quality of life.

Objective

The main objective of this study was to evaluate the impact of labial fixed appliance orthodontic care on patient perception before, during, and after the treatment.

Search methods

Relevant systematic reviews investigating patient perception with fixed appliance orthodontic treatment were identified by searching electronic databases: MEDLINE via OVID (1946 to 31 December 2018), EMBASE (1974 to 31 December 2018), AMED (Allied and Complementary Medicine Database; 1985 to November 2018), PubMed (inception to 31 December 2018), Web of Science (1900 to 2018), and PsychINFO (1806 to 31 December 2018). Ongoing systematic reviews were searched using Prospero and a grey literature search was undertaken using Google Scholar and OpenGrey (www.opengrey.eu/). No language restriction was applied.

Selection criteria

Only studies investigating patient perception of fixed appliance orthodontic treatment were included.

Data collection and analysis

Screening, quality assessment [using the AMSTAR 2 tool (A Measurement Tool to Assess Systematic Reviews)], and data extraction were performed by two authors independently. Information was categorized and narratively synthesized for the key findings.

Results

A total of 163 articles investigating patient expectation, experience, and satisfaction with conventional ligation labial fixed orthodontic appliances were obtained. Of these, 152 observational or interventional studies were excluded, resulting in 11 eligible systematic reviews. Two were excluded as earlier reports of a Cochrane review. The quality of the reviews was variable (critically low, low, and moderate). The findings were as follows: aesthetics represents a primary motive for orthodontic treatment; a temporary deterioration in the quality of life occurs during the initial phases of treatment; gender and ethnicity factors do not have an impact on patient perception of treatment; and a positive relationship between orthodontist–patient–parent is important to achieve patient compliance and satisfaction.

Conclusions

There is a lack of high-quality studies in terms of systematic reviews and meta-analyses for assessing patient perception with fixed appliance orthodontic treatment. The aesthetic impact of malocclusion is the main motive for seeking orthodontic treatment. Quality of life reduces during the initial stages of orthodontic treatment but improves in the later stages of treatment. Assessment before, during, and after orthodontic treatment is necessary to comprehensively assess patient perception at all stages of care.

Trial registration

CRD42019122653.

Conflict of Interest

None to declare.
Prosocial Behaviour in Interethnic Encounters: Evidence from a Field Experiment with High- and Low-Status Immigrants
Authors: Zhang Nan , Aidenberger Amelie , Rauhut Heiko , Winter Fabian
Published: May 2019

Recent waves of immigration have changed the demographic face of European societies and fueled considerable debate over the consequences of ethnic diversity for social cohesion. One prominent argument in this debate holds that individuals are less willing to extend trust and solidarity across ethnic lines, leading to lower social capital in multiethnic communities. We present a direct test of this proposition in a field experiment involving native-immigrant interactions in Zurich's Central Train Station. Our intervention consists of approaching commuters with a small request for assistance (borrowing a mobile phone), which we take as a measure of prosociality. We further differentiate between reactions towards natives as well as both high- and low-status immigrant groups. Compared to native-native interactions, we find lower solidarity in native-immigrant encounters, especially in cases involving stereotypically low-status immigrants. In exploratory analyses, we further show that discrimination only obtains in 'low cost' situations where commuters could easily justify not helping (e.g. by claiming not to carry a phone). Overall our results shed light on key theoretical mechanisms underlying patterns of solidarity in contemporary multiethnic societies.