bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of correlation between open-circuit voltage deficit and carrier recombination rates in Cu(In,Ga)(S,Se)2-based thin-film solar cells
Authors: Chantana Jakapan , Kato Takuya , Sugimoto Hiroki , Minemoto Takashi
Published: April 2018

The temperature-illumination-dependent open-circuit voltage (VOC) method is utilized to separately and quantitatively estimate carrier recombination rates at the buffer/absorber interface, in the space-charge region (SCR), and in the quasi-neutral region (QNR) of Cu(In,Ga)(S,Se)2 (CIGSSe)-based thin-film solar cells with various device structures. The correlation between open-circuit voltage deficits (VOC,def) among the carrier recombination rates of the CIGSSe solar cells with a conversion efficiency (η) above 17% is examined. It is revealed that VOC,def is decreased to 0.373 V with the reduced carrier recombination rate at the buffer/absorber interface through the development of device structures. To further decrease VOC,def (for the improved η), the carrier recombination rates in SCR and QNR are essential to be reduced by the further improvement of CIGSSe quality. Consequently, understanding the quantitative carrier recombination rates across the device, estimated from the temperature-illumination-dependent VOC method, is practical to know which part of the solar cell needs to be developed for high η above 20%.
Yield degradation in inertial-confinement-fusion implosions due to shock-driven kinetic fuel-species stratification and viscous heating
Authors: Taitano W. T. , Simakov A. N. , Chacón L. , Keenan B.
Published: April 2018

Anomalous thermonuclear yield degradation (i.e., that not describable by single-fluid radiation hydrodynamics) in Inertial Confinement Fusion (ICF) implosions is ubiquitously observed in both Omega and National Ignition experiments. Multiple experimental and theoretical studies have been carried out to investigate the origin of such a degradation. Relative concentration changes of fuel-ion species, as well as kinetically enhanced viscous heating, have been among possible explanations proposed for certain classes of ICF experiments. In this study, we investigate the role of such kinetic plasma effects in detail. To this end, we use the iFP code to perform multi-species ion Vlasov-Fokker-Planck simulations of ICF capsule implosions with the fuel comprising various hydrodynamically equivalent mixtures of deuterium (D) and helium-3 (3He), as in the original Rygg experiments [J. R. Rygg et al., Phys. Plasmas 13, 052702 (2006)]. We employ the same computational setup as in O. Larroche [Phys. Plasmas 19, 122706 (2012)], which was the first to simulate the experiments kinetically. However, unlike the Larroche study, and in partial agreement with experimental data, we find a systematic yield degradation in multi-species simulations versus averaged-ion simulations when the D-fuel fraction is decreased. This yield degradation originates in the fuel-ion species stratification induced by plasma shocks, which imprints the imploding system and results in the relocation of the D ions from the core of the capsule to its periphery, thereby reducing the yield relative to a non-separable averaged-ion case. By comparing yields from the averaged-ion kinetic simulations and from the hydrodynamic scaling, we also observe yield variations associated with ion kinetic effects other than fuel-ion stratification, such as ion viscous heating, which is typically neglected in hydrodynamic implosions' simulations. Since our kinetic simulations are driven by hydrodynamic boundary conditions at the fuel-ablator interface, they cannot capture the effects of ion viscosity on the capsule compression, or effects associated with the interface, which are expected to be important. Studies of such effects are left for future work.
Observation of phonon-polaritons in thin flakes of hexagonal boron nitride on gold
Authors: Ciano C. , Giliberti V. , Ortolani M. , Baldassarre L.
Published: April 2018

Hexagonal Boron Nitride (hBN) is a layered van der Waals material able to sustain hyperbolic phonon-polaritons within its mid-infrared reststrahlen bands. We study the effect of a metallic substrate adjacent to hBN flakes on the polariton dispersion and on the standing wave patterns in nanostructures by means of mid-infrared nanospectroscopy and nanoimaging. We exploit the gold-coated tip apex for atomic force microscopy to launch polaritons in thin hBN flakes. The photo-thermal induced mechanical resonance is used to detect the amplitude profile of polariton standing waves with a lateral resolution of 30 nm. We observe the polariton excitation spectra on hBN flakes as thin as 4 nm, thanks to the infrared field enhancement in the nanogap between the gold-coated tip apex and an ultraflat gold substrate. The data indicate no major effect of remote screening of the free electrons in gold on the phonon-polariton excitation that appears robust also against geometrical imperfections.
Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions
Authors: Nguyen Thuong T. , Székely Eszter , Imbalzano Giulio , Behler Jörg , Csányi Gábor , Ceriotti Michele , Götz Andreas W. , Paesani Francesco
Published: April 2018

The accurate representation of multidimensional potential energy surfaces is a necessary requirement for realistic computer simulations of molecular systems. The continued increase in computer power accompanied by advances in correlated electronic structure methods nowadays enables routine calculations of accurate interaction energies for small systems, which can then be used as references for the development of analytical potential energy functions (PEFs) rigorously derived from many-body (MB) expansions. Building on the accuracy of the MB-pol many-body PEF, we investigate here the performance of permutationally invariant polynomials (PIPs), neural networks, and Gaussian approximation potentials (GAPs) in representing water two-body and three-body interaction energies, denoting the resulting potentials PIP-MB-pol, Behler-Parrinello neural network-MB-pol, and GAP-MB-pol, respectively. Our analysis shows that all three analytical representations exhibit similar levels of accuracy in reproducing both two-body and three-body reference data as well as interaction energies of small water clusters obtained from calculations carried out at the coupled cluster level of theory, the current gold standard for chemical accuracy. These results demonstrate the synergy between interatomic potentials formulated in terms of a many-body expansion, such as MB-pol, that are physically sound and transferable, and machine-learning techniques that provide a flexible framework to approximate the short-range interaction energy terms.
The effect of the condensed-phase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates
Authors: Powers Anna , Scribano Yohann , Lauvergnat David , Mebe Elsy , Benoit David M. , Bačić Zlatko
Published: April 2018

We report a theoretical study of the frequency shift (redshift) of the stretching fundamental transition of an H2 molecule confined inside the small dodecahedral cage of the structure II clathrate hydrate and its dependence on the condensed-phase environment. In order to determine how much the hydrate water molecules beyond the confining small cage contribute to the vibrational frequency shift, quantum five-dimensional (5D) calculations of the coupled translation-rotation eigenstates are performed for H2 in the v=0 and v=1 vibrational states inside spherical clathrate hydrate domains of increasing radius and a growing number of water molecules, ranging from 20 for the isolated small cage to over 1900. In these calculations, both H2 and the water domains are treated as rigid. The 5D intermolecular potential energy surface (PES) of H2 inside a hydrate domain is assumed to be pairwise additive. The H2–H2O pair interaction, represented by the 5D (rigid monomer) PES that depends on the vibrational state of H2, v=0 or v=1, is derived from the high-quality ab initio full-dimensional (9D) PES of the H2–H2O complex [P. Valiron et al., J. Chem. Phys. 129, 134306 (2008)]. The H2 vibrational frequency shift calculated for the largest clathrate domain considered, which mimics the condensed-phase environment, is about 10% larger in magnitude than that obtained by taking into account only the small cage. The calculated splittings of the translational fundamental of H2 change very little with the domain size, unlike the H2 j = 1 rotational splittings that decrease significantly as the domain size increases. The changes in both the vibrational frequency shift and the j = 1 rotational splitting due to the condensed-phase effects arise predominantly from the H2O molecules in the first three complete hydration shells around H2.
The structure of PbCl2 on the {100} surface of NaCl and its consequences for crystal growth
Authors: Townsend Eleanor R. , Brugman Sander J. T. , Blijlevens Melian A. R. , Smets Mireille M. H. , de Poel Wester , van Enckevort Willem J. P. , Meijer Jan A. M. , Vlieg Elias
Published: April 2018

The role that additives play in the growth of sodium chloride is a topic which has been widely researched but not always fully understood at an atomic level. Lead chloride (PbCl2) is one such additive which has been reported to have growth inhibition effects on NaCl {100} and {111}; however, no definitive evidence has been reported which details the mechanism of this interaction. In this investigation, we used the technique of surface x-ray diffraction to determine the interaction between PbCl2 and NaCl {100} and the structure at the surface. We find that Pb2+ replaces a surface Na+ ion, while a Cl− ion is located on top of the Pb2+. This leads to a charge mismatch in the bulk crystal, which, as energetically unfavourable, leads to a growth blocking effect. While this is a similar mechanism as in the anticaking agent ferrocyanide, the effect of PbCl2 is much weaker, most likely due to the fact that the Pb2+ ion can more easily desorb. Moreover, PbCl2 has an even stronger effect on NaCl {111}.
Communication: Biological applications of coupled-cluster frozen-density embedding
Authors: Heuser Johannes , Höfener Sebastian
Published: April 2018

We report the implementation of the Laplace-transform scaled opposite-spin (LT-SOS) resolution-of-the-identity second-order approximate coupled-cluster singles and doubles (RICC2) combined with frozen-density embedding for excitation energies and molecular properties. In the present work, we furthermore employ the Hartree-Fock density for the interaction energy leading to a simplified Lagrangian which is linear in the Lagrangian multipliers. This approximation has the key advantage of a decoupling of the coupled-cluster amplitude and multipliers, leading also to a significant reduction in computation time. Using the new simplified Lagrangian in combination with efficient wavefunction models such as RICC2 or LT-SOS-RICC2 and density-functional theory (DFT) for the environment molecules (CC2–in–DFT) enables the efficient study of biological applications such as the rhodopsin and visual cone pigments using ab initio methods as routine applications.
Rugged spin-polarized electron sources based on negative electron affinity GaAs photocathode with robust Cs2Te coating
Authors: Bae Jai Kwan , Cultrera Luca , DiGiacomo Philip , Bazarov Ivan
Published: April 2018

Photocathodes capable of providing high intensity and highly spin-polarized electron beams with long operational lifetimes are of great interest for the next generation nuclear physics facilities like Electron Ion Colliders. We report on GaAs photocathodes activated by Cs2Te, a material well known for its robustness. GaAs activated by Cs2Te forms Negative Electron Affinity, and the lifetime for extracted charge is improved by a factor of 5 compared to that of GaAs activated by Cs and O2. The spin polarization of photoelectrons was measured using a Mott polarimeter and found to be independent from the activation method, thereby shifting the paradigm on spin-polarized electron sources employing photocathodes with robust coatings.
Calcium oxalate degradation is involved in aerenchyma formation in Typha angustifolia leaves
Authors: Du Xiaomin , Ren Xiaolong , Wang Lingli , Yang Ke , Xin Guiliang , Jia Guolun , Ni Xilu , Liu Wenzhe
Published: April 2018

Typha angustifolia L. (Typhaceae) is an emergent aquatic plant, and aerenchyma is formed through cell lysis in its leaves. The developing aerenchyma of T. angustifolia contains many CaOx crystals (raphides). Oxalate oxidase (OXO) (oxalate : oxygen oxidoreductase, EC1.2.3.4) can degrades calcium oxalate to carbon dioxide and hydrogen peroxide (H2O2). High level of H2O2 acts as a key inducer for different types of developmentally and environmentally programmed cell death (PCD) and can promote the formation of aerenchyma. Therefore, the objective of this study was to describe the relationship between aerenchyma formation and the degradation of CaOx crystals. Light and transmission electron microscopy (TEM) results showed that CaOx crystals occurred between PCD-susceptible cells in the early phase of aerenchyma formation, and those cells and CaOx crystals were degraded at aerenchyma maturation. Cytochemical localisation was used to detect H2O2, and H2O2 was found in crystal idioblasts. In addition, the oxalate content, H2O2 content and OXO activity were determined. The results showed that the concentration of oxalate was the highest in the third cavity formation stage and the H2O2 concentration was also highest at this stage. Meanwhile, the activity of OXO was also high in the third cavity formation stage. TpOXO was highly expressed during the CaOx crystal degradation period by quantitative real-time PCR analysis. These results show that the degradation of CaOx crystals is involved in the regulation of the PCD process of aerenchyma. This study will contribute to understanding the changes in CaOx crystals during the formation of aerenchyma in T. angustifolia.
How does marker choice affect your diet analysis: comparing genetic markers and digestion levels for diet metabarcoding of tropical-reef piscivores
Authors: Devloo-Delva Floriaan , Huerlimann Roger , Chua Gladys , Matley Jordan K. , Heupel Michelle R. , Simpfendorfer Colin A. , Maes Gregory E.
Published: April 2018

Tropical reefs are highly diverse ecosystems, and reliable biomonitoring, through diet metabarcoding, is needed to understand present and future trophic relationships in this changing habitat. Several studies have assessed the reliability and effectiveness of single molecular markers; however, a cross-marker validation has rarely been performed. This study identified crucial properties for 12S rDNA, 16S rDNA and COI metabarcoding in tropical-reef piscivores (Plectropomus spp.). In addition, three new versatile primer sets for 16S were designed in silico for metabarcoding of reef fish. Results showed that COI was overall better at recovering true diversity because of a well-supported database. Second, optimal 16S amplicon sizes ranged between 160 and 440 base pairs for full diversity recovery, with increased species detection for the 270-base pairs region. Finally, blocking of predator-specific COI sequences was not equally effective in all host species, potentially introducing bias when diet compositions are directly compared. In conclusion, this novel study showed that marker success for prey identification is highly dependent on the reference database, taxonomic scope, DNA quality, amplicon length and sequencing platform. Results suggest that COI, complemented with 16S, yields the best outcome for diet metabarcoding in reef piscivores. Findings in this paper are relevant to other piscivores and other metabarcoding applications.
Sharing solutions for a reasoned and evidence-based response: chemsex/party and play among gay and bisexual men
Authors: Bourne Adam , Ong Jason , Pakianathan Mark
Published: April 2018

This Special Issue of Sexual Health examines research and healthcare practice relating to sexualised drug use among gay, bisexual and other men who have sex with men (GBMSM), colloquially known as ‘chemsex’ or ‘party and play’ (PnP). It draws together evidence relating to the epidemiology, sociology and psychology of chemsex, as well as the policy, community and clinical interventions that are required to ensure men have access to high-quality health care that meets their needs and reduces harm. Findings and discussions within the Issue emphasise the need to sensitively, non-judgementally and meaningfully engage with gay men about their engagement in chemsex in order to help improve their sexual health and wider wellbeing.
KELCH F-BOX protein positively influences Arabidopsis seed germination by targeting PHYTOCHROME-INTERACTING FACTOR1
Authors: Majee Manoj , Kumar Santosh , Kathare Praveen Kumar , Wu Shuiqin , Gingerich Derek , Nayak Nihar R. , Salaita Louai , Dinkins Randy , Martin Kathleen , Goodin Michael , Dirk Lynnette M. A. , Lloyd Taylor D. , Zhu Ling , Chappell Joseph , Hunt Arthur G. , Vierstra Richard , Huq Enamul , Downie A. Bruce
Published: April 2018

Significance

The completion of seed germination is an irrevocable event for plants, determining, for most plants, the site of the remainder of their life cycle. One environmental cue important to the completion of seed germination is light, which, in
Arabidopsis thaliana
, can influence a host of transcription factors, including PHYTOCHROME-INTERACTING FACTOR1 (PIF1), a negative regulator of the completion of germination and seedling de-etiolation. The KELCH F-BOX protein COLD TEMPERATURE GERMINATING10 (CTG10) can recognize and bind to PIF1, negatively influencing PIF1 stability, stimulating the completion of germination, and promoting a de-etiolated seedling morphology. PIF1, in turn, can downregulate
CTG10
expression, revealing a complex coregulation orchestrated by light presence and quality that dictates whether the seed completes germination.
Spontaneous oscillation and fluid–structure interaction of cilia
Authors: Han Jihun , Peskin Charles S.
Published: April 2018

Significance

Motile cilia are hair-like structures that extend from the surfaces of eukaryotic cells and pump fluid. The motor protein dynein drives the motion of cilia, but it is unclear how the organized beat of a cilium emerges from the combined action of hundreds of dynein molecules. Here, we describe how the molecular architecture of a cilium constrains its possible motion, and we postulate a dynamical law that governs the dynein tensions. Based on this constraint and dynamical law, we construct a model cilium that beats spontaneously. Simulation of multiple copies of this model in fluid reveals that an array of cilia spontaneously breaks synchrony and adopts multiple phases and that such symmetry breaking is helpful in producing net fluid transport.
PARP-1 protects against colorectal tumor induction, but promotes inflammation-driven colorectal tumor progression
Authors: Dörsam Bastian , Seiwert Nina , Foersch Sebastian , Stroh Svenja , Nagel Georg , Begaliew Diana , Diehl Erika , Kraus Alexander , McKeague Maureen , Minneker Vera , Roukos Vassilis , Reißig Sonja , Waisman Ari , Moehler Markus , Stier Anna , Mangerich Aswin , Dantzer Françoise , Kaina Bernd , Fahrer Jörg
Published: April 2018

Significance

Poly(ADP-ribose) polymerase-1 (PARP-1) is a DNA repair protein and part of the genome maintenance network. On the other hand, PARP-1 is involved in pathophysiological processes such as inflammation. Chronic inflammation has emerged as a key event in carcinogenesis, including the formation of colorectal cancer (CRC). Our data reveal that PARP-1 is abundantly expressed in human CRC, correlating with disease progression. Using transgenic mouse models, we show that PARP-1 fosters inflammation-driven colorectal tumor growth and stimulates the IL6-STAT3-cyclin D1 axis in tumors. In turn, PARP-1 protects against alkylation-triggered colorectal tumor induction dependent on the repair protein
O
6
-methylguanine-DNA methyltransferase (MGMT). These findings unveil the opposing functions of PARP-1 in CRC initiation and CRC progression and its link to MGMT.
Aspect controls the survival of ice cliffs on debris-covered glaciers
Authors: Buri Pascal , Pellicciotti Francesca
Published: April 2018

Significance

Glaciers in High Mountain Asia (HMA) are important water sources for millions of people downstream. Ice cliffs on debris-covered glaciers act as hot spots for melt and may explain anomalously high glacier mass losses in HMA, but their temporal evolution remains unknown, hindering sound parameterizations of these features in glacier models. We simulate the evolution of cliff systems with different aspects, show that south-facing ice cliffs disappear within a few weeks in the Northern Hemisphere, and explain the processes driving this. Cliffs that persist melt 10 times faster than the surrounding glacier surfaces. These findings provide a basis for understanding the surface evolution of debris-covered glaciers with implications for their dynamics, mass balance, and hydrology.
Cell-specific discrimination of desmosterol and desmosterol mimetics confers selective regulation of LXR and SREBP in macrophages
Authors: Muse Evan D. , Yu Shan , Edillor Chantle R. , Tao Jenhan , Spann Nathanael J. , Troutman Ty D. , Seidman Jason S. , Henke Adam , Roland Jason T. , Ozeki Katherine A. , Thompson Bonne M. , McDonald Jeffrey G. , Bahadorani John , Tsimikas Sotirios , Grossman Tamar R. , Tremblay Matthew S. , Glass Christopher K.
Published: April 2018

Significance

The beneficial effects of LXR-pathway activation have long been appreciated, but clinical application of synthetic LXR ligands has been limited by coactivation of SREBP1c and consequent hypertriglyceridemia. Natural LXR ligands such as desmosterol do not promote hypertriglyceridemia because of coordinate down-regulation of the SREBP pathway. Here we demonstrate that synthetic desmosterol mimetics activate LXR in macrophages both in vitro and in vivo while suppressing SREBP target genes. Unexpectedly, desmosterol and synthetic desmosterol mimetics have almost no effect on LXR activity in hepatocytes in comparison with conventional synthetic LXR ligands. These findings reveal cell-specific differences in LXR responses to natural and synthetic ligands in macrophages and liver cells that provide a conceptually new basis for future drug development.
Individually addressable and dynamic DNA gates for multiplexed cell sorting
Authors: Dahotre Shreyas N. , Chang Yun Min , Wieland Andreas , Stammen Samantha R. , Kwong Gabriel A.
Published: April 2018

Significance

Biological specimens, such as whole blood, contain many different types of cells that have important applications for monitoring health, including tracking vaccine efficacy and HIV progression, and for treating complex diseases, like cancer. However, current cell-sorting technologies require expensive and large pieces of equipment and can only isolate a few types of cells at one time. Here, we develop a cell-sorting platform by engineering dynamic DNA devices that can label, sort, and recover different cell populations at high purity en masse. This DNA-based nanotechnology can potentially be expanded to exceed the capacity of current methods for sorting multiple types of cells, improve biomedical diagnostics, and provide new insights into cell biology.
Conformational sampling of membranes by Akt controls its activation and inactivation
Authors: Lučić Iva , Rathinaswamy Manoj K. , Truebestein Linda , Hamelin David J. , Burke John E. , Leonard Thomas A.
Published: April 2018

Significance

Akt is a paradigmatic lipid-activated kinase, which is frequently hyperactivated in human cancer. In the absence of PI(3,4,5)P
3
or PI(3,4)P
2
, Akt is maintained in an inactive conformation by an inhibitory interaction between its membrane-binding PH domain and its kinase domain. Here, we describe the conformational changes associated with its binding to PI(3,4,5)P
3
, leading to disruption of the inhibitory PH−kinase interface, and its consequent activation by protein kinases. Intriguingly, we find that reversal of those conformational changes promotes its inactivation by protein phosphatases. The activation of Akt is thereby restricted to discrete membrane locations, and it is rapidly inactivated upon dissociation. We propose a model in which activation, substrate phosphorylation, and inactivation of Akt are tightly coupled to the membrane.
Long-wavelength (reddish) hues induce unusually large gamma oscillations in the primate primary visual cortex
Authors: Shirhatti Vinay , Ray Supratim
Published: April 2018

Significance

Electrophysiological signals recorded from the brain exhibit prominent gamma oscillations (∼30–80 Hz) under sensory stimulation. These oscillations are modulated by stimulus properties and behavioral state, and implicated to play a role in cognitive functions, such as attention and object-binding. In visual areas, gamma oscillations have mainly been studied using achromatic gratings/gabors. Here we show that color stimuli generate unprecedented levels of gamma oscillations in the local field potentials recorded from primate area V1. The strongest oscillations are induced by long-wavelength (reddish) hues. Importantly, their strength depends on color saturation but not on luminance, and is strongly correlated with the L−M cone contrast produced by stimuli, suggesting that gamma oscillations may represent key components of the processing of visual chromatic information.
Live-cell analysis of endogenous GFP-RPB1 uncovers rapid turnover of initiating and promoter-paused RNA Polymerase II
Authors: Steurer Barbara , Janssens Roel C. , Geverts Bart , Geijer Marit E. , Wienholz Franziska , Theil Arjan F. , Chang Jiang , Dealy Shannon , Pothof Joris , van Cappellen Wiggert A. , Houtsmuller Adriaan B. , Marteijn Jurgen A.
Published: April 2018

Significance

Transcription by RNA Polymerase II (Pol II) is a highly dynamic process that is tightly regulated at each step of the transcription cycle. We generated GFP-RPB1 knockin cells and developed photobleaching of endogenous Pol II combined with computational modeling to study the in vivo dynamics of Pol II in real time. This approach allowed us to dissect promoter-paused Pol II from initiating and elongating Pol II and showed that initiation and promoter proximal pausing are surprisingly dynamic events, due to premature termination of Pol II. Our study provides new insights into Pol II dynamics and suggests that the iterative release and reinitiation of promoter-bound Pol II is an important component of transcriptional regulation.
Translation initiation in bacterial polysomes through ribosome loading on a standby site on a highly translated mRNA
Authors: Andreeva Irena , Belardinelli Riccardo , Rodnina Marina V.
Published: April 2018

Significance

Polysomes are ensembles of two or more consecutive ribosomes that translate mRNA into proteins. Adjacent ribosomes can affect the frequency with which a new ribosome is loaded into the polysome. Here we show that mRNA with a long 5′UTR can recruit the next ribosome when the genuine start site is still occupied by the leading ribosome. The second ribosome binds to the upstream standby site on the mRNA, helped by the ribosomal proteins S1/S2 of the preceding ribosome. When the translating ribosome has cleared the start codon, the consecutive ribosome can rapidly move to the translation start. Recruitment to the standby site is a mechanism to increase polysome density and to regulate the efficiency of translation in polysomes.
New class of transcription factors controls flagellar assembly by recruiting RNA polymerase II in
Chlamydomonas
Authors: Li Lili , Tian Guangmei , Peng Hai , Meng Dan , Wang Liang , Hu Xiao , Tian Cheng , He Miao , Zhou Junfei , Chen Lihong , Fu Cheng , Zhang Weixiong , Hu Zhangfeng
Published: April 2018

Significance

Transcriptional regulation of flagellar genes controls an initial step in flagellar assembly. In this study, we show that XAP5, a conserved protein of unknown function, defines a class of transcription factor for transcriptional regulation of genes involved in flagellar assembly. Phosphorylation of X chromosome-associated protein 5 (XAP5) during flagellar regeneration tracks flagellar length. Remarkably, recruitment of RNA polymerase II (Pol II) machinery for transcriptional activation depends on the activities of XAP5. Our data demonstrate that XAP5 functions as a transcription factor for transcriptional regulation of flagellar genes through recruitment of RNA Pol II. Our results enhance our understanding of the biochemical function of the XAP5 family and the transcriptional regulation of flagellar assembly.
Human hydroxymethylbilane synthase: Molecular dynamics of the pyrrole chain elongation identifies step-specific residues that cause AIP
Authors: Bung Navneet , Roy Arijit , Chen Brenden , Das Dibyajyoti , Pradhan Meenakshi , Yasuda Makiko , New Maria I. , Desnick Robert J. , Bulusu Gopalakrishnan
Published: April 2018

Significance

Human hydroxymethylbilane synthase (hHMBS) is a monomeric enzyme that catalyzes the stepwise head-to-tail condensation of four porphobilinogen (PBG) molecules to form the linear tetrapyrrole 1-hydroxymethylbilane (HMB). Mutations in thehHMBSgene cause autosomal-dominant acute intermittent porphyria (AIP). Although crystal structures of hHMBS have been reported, the specific active-site residues and the molecular mechanism of the stepwise PBG chain elongation are unknown. Here, by using molecular-dynamics simulations, the mechanisms and active-site residues for the HMB stepwise synthesis and HMB exit were determined. Mutagenesis of key active-site residues and in vitro expression studies identified the molecular basis of mutations causing AIP.
E3 ubiquitin ligase SOR1 regulates ethylene response in rice root by modulating stability of Aux/IAA protein
Authors: Chen Hui , Ma Biao , Zhou Yang , He Si-Jie , Tang San-Yuan , Lu Xiang , Xie Qi , Chen Shou-Yi , Zhang Jin-Song
Published: April 2018

Significance

Auxin signaling components participate in ethylene-mediated inhibition of root elongation. However, the interplay between TIR1/AFB2-auxin-Aux/indole acetic acid (IAA) signaling and ethylene response remains to be elucidated in detail. In this study, we report an E3 ubiquitin ligase soil-surface rooting 1 (SOR1), which targets a noncanonical Aux/IAA protein OsIAA26 for 26S proteasome-mediated degradation. The E3 ligase activity of SOR1 can be repressed by the canonical Aux/IAA protein OsIAA9, which is the target of OsTIR1/AFB2. Our study identifies a potential regulator that modulates auxin-mediated ethylene response at the auxin signaling level.
Stoichiometry and compositional plasticity of the yeast nuclear pore complex revealed by quantitative fluorescence microscopy
Authors: Rajoo Sasikumar , Vallotton Pascal , Onischenko Evgeny , Weis Karsten
Published: April 2018

Significance

The nuclear pore complex (NPC) is one of the largest protein assemblies in eukaryotes comprising over 500 nucleoporin subunits. The NPC is essential for the transport of biomolecules across the nuclear envelope; however, due to its enormous size, it has been a challenge to characterize its molecular architecture. Herein, we have developed a widely applicable imaging pipeline to determine the absolute nucleoporin abundances in native yeast NPCs. This reveals that the NPC composition dramatically differs between yeast and humans despite overall conservation of individual subunits. We also applied our imaging pipeline to examine yeast mutants revealing remarkable compositional plasticity of NPCs. Our stoichiometry analyses provide an important resource for the generation of high-resolution structure models of the NPC.
Alpha-v–containing integrins are host receptors for the
Plasmodium falciparum
sporozoite surface protein, TRAP
Authors: Dundas Kirsten , Shears Melanie J. , Sun Yi , Hopp Christine S. , Crosnier Cecile , Metcalf Tom , Girling Gareth , Sinnis Photini , Billker Oliver , Wright Gavin J.
Published: April 2018

Significance

Malaria is caused by a parasite that is deposited in the skin through the bite of an infected mosquito. From the skin, parasites navigate through host tissues where they must locate and invade liver cells. We know that a parasite surface protein called TRAP is important for this process, making it a leading vaccine candidate. TRAP is thought to work by specifically binding a defined host cell surface protein, but its identity has remained a long-standing mystery. Our research has identified an integrin—a class of host cell surface proteins—as a TRAP receptor. This finding provides an important piece of the puzzle relating to TRAP function and may help improve the development of an effective malaria vaccine.
A Mesoproterozoic iron formation
Authors: Canfield Donald E. , Zhang Shuichang , Wang Huajian , Wang Xiaomei , Zhao Wenzhi , Su Jin , Bjerrum Christian J. , Haxen Emma R. , Hammarlund Emma U.
Published: April 2018

Significance

Iron formations (IFs) are common before 1,800 million years ago (Ma) and again at ∼750 Ma, but are remarkably absent for the billion years in between. We report on a 1,400-Ma IF of ∼520 gigatons Fe from the Xiamaling Formation on the North China Craton. Biomarker analyses suggest that anoxygenic phototrophic bacteria were involved in Fe(II) oxidation, and further geochemical analysis shows that IF sediments supported active microbial Fe reduction that rivaled oxic respiration in its efficiency of organic matter oxidation. The Xiamaling Formation IF demonstrates that geochemical conditions occasionally conspired to produce world-class IFs during Earth’s “middle ages,” permitting critical insights into the biogeochemical processes of IF emplacement.
Correlating structural and photochemical heterogeneity in cyanobacteriochrome NpR6012g4
Authors: Lim Sunghyuk , Yu Qinhong , Gottlieb Sean M. , Chang Che-Wei , Rockwell Nathan C. , Martin Shelley S. , Madsen Dorte , Lagarias J. Clark , Larsen Delmar S. , Ames James B.
Published: April 2018

Significance

Photosynthetic organisms measure changing light conditions with photosensory proteins. In land plants, phytochromes use the ratio of red to far-red light to detect shading by neighboring plants. Cyanobacteria use distantly related cyanobacteriochromes (CBCRs) to detect a broad range of conditions so that they can optimize light harvesting, movement, and other photobiology. Both phytochromes and CBCRs naturally occur as heterogeneous mixtures of populations, but the links between structural and photochemical heterogeneity are unclear. We have solved the structure of a model CBCR in both photostates, allowing us to explicitly connect structural heterogeneity of conserved residues to populations having distinct spectral and photochemical properties.
Macrophages impede CD8 T cells from reaching tumor cells and limit the efficacy of anti–PD-1 treatment
Authors: Peranzoni Elisa , Lemoine Jean , Vimeux Lene , Feuillet Vincent , Barrin Sarah , Kantari-Mimoun Chahrazade , Bercovici Nadège , Guérin Marion , Biton Jérôme , Ouakrim Hanane , Régnier Fabienne , Lupo Audrey , Alifano Marco , Damotte Diane , Donnadieu Emmanuel
Published: April 2018

Significance

Cancer immunotherapy is a promising therapeutic intervention. However, complete and durable responses are seen in only a fraction of cancer patients. A key factor that limits therapeutic success is the lack of T cells in tumor cell regions, a profile termed “immune-excluded.” Here, we provide evidence that tumor-associated macrophages (TAMs) are an important determinant of the establishment of a T cell-excluded tumor phenotype. In human and murine tumors, we found that CD8 T cells poorly migrate and invade tumor nests due to long-lasting interactions with TAMs. The depletion of TAMs restores T cell migration and infiltration into tumor islets and improves the efficacy of anti–PD-1 immunotherapy. This study highlights the rationale of combining approaches targeting TAM and immune checkpoint proteins.
β-Amyloid accumulation in the human brain after one night of sleep deprivation
Authors: Shokri-Kojori Ehsan , Wang Gene-Jack , Wiers Corinde E. , Demiral Sukru B. , Guo Min , Kim Sung Won , Lindgren Elsa , Ramirez Veronica , Zehra Amna , Freeman Clara , Miller Gregg , Manza Peter , Srivastava Tansha , De Santi Susan , Tomasi Dardo , Benveniste Helene , Volkow Nora D.
Published: April 2018

Significance

There has been an emerging interest in sleep and its association with β-amyloid burden as a risk factor for Alzheimer’s disease. Despite the evidence that acute sleep deprivation elevates β-amyloid levels in mouse interstitial fluid and in human cerebrospinal fluid, not much is known about the impact of sleep deprivation on β-amyloid burden in the human brain. Using positron emission tomography, here we show that acute sleep deprivation impacts β-amyloid burden in brain regions that have been implicated in Alzheimer’s disease. Our observations provide preliminary evidence for the negative effect of sleep deprivation on β-amyloid burden in the human brain.
Unique organization of photosystem I–light-harvesting supercomplex revealed by cryo-EM from a red alga
Authors: Pi Xiong , Tian Lirong , Dai Huai-En , Qin Xiaochun , Cheng Lingpeng , Kuang Tingyun , Sui Sen-Fang , Shen Jian-Ren
Published: April 2018

Significance

Photosystem I (PSI) is one of the most efficient nanophotochemical machines in nature. To adapt to various environments, photosynthetic organisms developed different PSI structure during evolution from prokaryotic cyanobacteria to higher plants. Red algae are one of the most primitive eukaryotic algae, and their photosynthetic apparatus represents a transitional state between cyanobacteria and eukaryotes. We determined two forms of the PSI-LHCR structure from a red alga by cryo-EM. Our results revealed unique features and energy transfer pathways in the red algal PSI supercomplex with LHCI (light-harvesting complex I), as well as its remarkable differences with those of cyanobacterial PSI and higher plant PSI-LHCI. These results provide important information for delineating the function and evolution of PSI from prokaryotic to eukaryotic photosynthetic organisms.
Molecular spherical nucleic acids
Authors: Li Hui , Zhang Bohan , Lu Xueguang , Tan Xuyu , Jia Fei , Xiao Yue , Cheng Zehong , Li Yang , Silva Dagoberto O. , Schrekker Henri S. , Zhang Ke , Mirkin Chad A.
Published: April 2018

Significance

Spherical nucleic acids (SNAs) made thus far are inherently polydisperse due to variations in surface nucleic acid density, particle size, or both. In this article, we describe the synthesis and characterization of two types of molecular SNAs with precise numbers of surface DNA strands using T8polyoctahedral silsesquioxane and buckminsterfullerene C60scaffolds. The surface DNA densities for these molecular structures fall inside the range of typical SNAs, which allows them to exhibit SNA-related properties, including enhanced cellular uptake and the ability to function as a gene regulation agent. With a route to molecularly pure SNAs opened, it becomes possible to use them to unveil the molecular details of SNA interactions with complementary ligands and living systems.
Misha or Mihailik: A Sociolinguistic View on the Ukrainization of Russian Proper Names in Modern Ukraine
Authors: Knoblock Natalia
Published: April 2018

This article focuses on linguistic identity and ideology through analysis of the attitudes of Russian-speaking Ukrainians toward the Ukrainization of traditionally Russian proper names (personal names and toponyms). It summarizes the results of a survey conducted among Ukrainian refugees to Russia, which gauged whether this policy contributes to the alleged alienation of the Russian-speaking population of Ukraine from current political and social developments in the country. The results of the study appear to support the importance of preserving the Russian proper names. Their Ukrainization seems to cause some resentment, especially when it affects people’s own names and the names of their children.
A review of wire arc additive manufacturing and advances in wire arc additive manufacturing of aluminium
Authors: Derekar K. S.
Published: April 2018

Although wire arc additive manufacturing (WAAM) has proven its capability of fulfilling demands of production of medium-to-large-scale components for automotive and allied sectors made up of aluminium, at present, WAAM cannot be applied as a fully fledged manufacturing process because of practical challenges such as under-matched mechanical properties, the presence of large residual stresses and mandatory post-deposition operation for the formed component. This paper is a review of WAAM technology including a brief of WAAM history, status, advantages and constraints of the WAAM field. A focus is provided including the efforts directed towards the reduction of porosity, tensile properties, microstructural investigations and other valuable advancements in the field of WAAM of aluminium.

This review was submitted as part of the 2018 Materials Literature Review Prize of the Institute of Materials, Minerals and Mining run by the Editorial Board of MST. Sponsorship of the prize by TWI Ltd is gratefully acknowledged.
Residual stress generation in metal matrix composites after cooling
Authors: Wong Choo Siew , Pramanik A. , Basak A. K.
Published: April 2018

Effects of reinforcements’ shapes, sizes and contents on (a) von-Mises stress along a horizontal line in MMCs, (b) directions and distributions of principal stresses inside particles, matrix and interface, and (c) distribution of thermal residual stress in MMCs were analysed in this investigation. It was found that the matrix–particle interfaces experience a sudden change of von-Mises stress which depends on the reinforcement shape. The smoothest change of stress occurred in triangle particle-reinforced MMCs. However, the highest stress was concentrated at the corners of the triangular particles. The directions of stress vectors depend on the shape of the particles. The extent of the von-Mises stress increases with the increase in reinforcement content and a decrease in particles size at constant content.
Preparation and properties of nano-SiCp/A356 composites synthesised with a new process
Authors: Yuan Du , Hu Kun , Lü Shulin , Wu Shusen , Gao Qi
Published: April 2018

Nano-SiCp reinforced A356 aluminium alloy composites were prepared by solid–liquid mixed casting. Nano-SiC particles 40 nm in diameter were pre-oxidised at 850°C. Millimetre-sized composite granules were then fabricated by milling a mixture of nano-SiCp and Al powders, and then remelting to form an alloy melt, which was treated by mechanical stirring and ultrasonic vibration to prepare the composites. Results showed that nano-SiC particles were dispersed pretty well within the matrix and no serious agglomeration was observed. As the weight fraction of SiCp increased, the tensile strength, yield strength and elongation of the composites increased as well, by 22%, 62% and 24%, respectively, when compared to A356 alloy with 2wt-% nano-SiCp.
Optimum hot forming temperature of AZ61 magnesium alloy
Authors: Carsí Manuel , Alonso Manuel , Castellanos Jesús , Ruano Oscar A.
Published: April 2018

A new concept of stability of materials is introduced by defining the optimum hot forming temperature for any given strain rate. This temperature is obtained through forming maps that are based on Lyapunov concepts and the introduction of a Garofalo equation in the Lyapunov criterion. This new approach is applied to a magnesium alloy AZ61. Torsion tests were carried out in the temperature range 574–734 K and strain rate range 0.7–8.7 s−1 and the microstructures were determined using optical microscopy. Using the peak stress, optimum workability at 630 K is obtained at 12 s−1. The results and the maps are compared with data and maps of other authors for AZ61 alloys in various states.
Neuroprotective effect of polysaccharide separated from Perilla frutescens Britton var. acuta Kudo against H2O2-induced oxidative stress in HT22 hippocampus cells
Authors: Byun Eui-Baek , Cho Eun-Ji , Kim Yi-Eun , Kim Woo Sik , Byun Eui-Hong
Published: April 2018

This study was carried out to evaluate the neuroprotective activity of polysaccharide extracts isolated from Perilla frutescens (PEPF) in H2O2-treated HT22 hippocampus cells. The PEPF treatment was found to increase the anti-oxidant activities of HT22 hippocampus cells. PEPF treatment resulted in a significant protection of HT22 hippocampus cells against H2O2-induced neurotoxicity, this protection ultimately occurred through an inhibition of ROS-mediated intracellular Ca2+ levels leading to MAPKs and NF-κB, as well as the accumulation of PI3K/AKT and Nrf2-mediated HO-1/NQO1 pathways. Furthermore, PEPF not only decreased the expression of Bax, cytochrome c, and cleaved caspases-3, -8, and -9, but also increased the expression of PARP and Bcl-2 in the H2O2-treated HT22 hippocampus cells, which overall contributed to the neuroprotective action. PEPF retains its mitochondrial membrane potential and reduces the elevated levels of sub-G1 phase and apoptotic morphological features induced by H2O2. It also reduces the malondialdehyde levels and enhances the intracellular SOD activity.
Survival strategy of the salt-tolerant lactic acid bacterium, Tetragenococcus halophilus, to counteract koji mold, Aspergillus oryzae, in soy sauce brewing
Authors: Nishimura Ikuko , Shinohara Yasutomo , Oguma Tetsuya , Koyama Yasuji
Published: April 2018

In soy sauce brewing, the results of the fermentation of lactic acid greatly affect the quality of soy sauce. The soy sauce moromi produced with Aspergillus oryzae RIB40 allows the growth of Tetragenococcus halophilus NBRC 12172 but not T. halophilus D10. We isolated and identified heptelidic acid (HA), an inhibitor of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), produced by A. oryzae RIB40 as the growth inhibitor of the salt-tolerant lactic acid bacteria. The growth inhibition of T. halophilus D10 by HA was suggested to be associated with the direct inhibition of GAPDH activity under high salt environment. The difference in the susceptibility to HA among various strains of T. halophilus was caused by the mutations in the gene encoding GAPDH.
The importance of clinical history in suspected otosclerosis
Authors: Tulli Michele , Gatti Omar , Galli Andrea , Ferraro Milena , Di Santo Davide , Piccioni Lucia Oriella
Published: April 2018

Isolated malleus handle fracture (IMHF) is a lesser-known pathology. Its subtle and non-pathognomonic clinical characteristics mean its diagnosis is often overlooked. We describe a case of conductive hearing loss brought to our attention with a suspected diagnosis of otosclerosis. We describe the diagnostic workup and management of the patient. We underline the importance of performing a thorough and appropriate clinical exam, the value of computer tomography (CT) reconstruction and above all, an accurate anamnesis regarding the onset of the symptomatology in order to consider isolated fracture of the malleus amongst the possible differential diagnoses.