bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbial island biogeography: isolation shapes the life history characteristics but not diversity of root-symbiotic fungal communities
Authors: Davison John , Moora Mari , Öpik Maarja , Ainsaar Leho , Ducousso Marc , Hiiesalu Inga , Jairus Teele , Johnson Nancy , Jourand Philippe , Kalamees Rein , Koorem Kadri , Meyer Jean-Yves , Püssa Kersti , Reier Ülle , Pärtel Meelis , Semchenko Marina , Traveset Anna , Vasar Martti , Zobel Martin
Published: June 2018

Island biogeography theory is one of the most influential paradigms in ecology. That island characteristics, including remoteness, can profoundly modulate biological diversity has been borne out by studies of animals and plants. By contrast, the processes influencing microbial diversity in island systems remain largely undetermined. We sequenced arbuscular mycorrhizal (AM) fungal DNA from plant roots collected on 13 islands worldwide and compared AM fungal diversity on islands with existing data from mainland sites. AM fungal communities on islands (even those >6000 km from the closest mainland) comprised few endemic taxa and were as diverse as mainland communities. Thus, in contrast to patterns recorded among macro-organisms, efficient dispersal appears to outweigh the effects of taxogenesis and extinction in regulating AM fungal diversity on islands. Nonetheless, AM fungal communities on more distant islands comprised a higher proportion of previously cultured and large-spored taxa, indicating that dispersal may be human-mediated or require tolerance of significant environmental stress, such as exposure to sunlight or high salinity. The processes driving large-scale patterns of microbial diversity are a key consideration for attempts to conserve and restore functioning ecosystems in this era of rapid global change.
Blood–brain barrier opening in Alzheimer’s disease using MR-guided focused ultrasound
Authors: Lipsman Nir , Meng Ying , Bethune Allison J. , Huang Yuexi , Lam Benjamin , Masellis Mario , Herrmann Nathan , Heyn Chinthaka , Aubert Isabelle , Boutet Alexandre , Smith Gwenn S. , Hynynen Kullervo , Black Sandra E.
Published: June 2018

Magnetic resonance-guided focused ultrasound in combination with intravenously injected microbubbles has been shown to transiently open the blood–brain barrier, and reduce beta-amyloid and tau pathology in animal models of Alzheimer’s disease. Here, we used focused ultrasound to open the blood–brain barrier in five patients with early to moderate Alzheimer’s disease in a phase I safety trial. In all patients, the blood–brain barrier within the target volume was safely, reversibly, and repeatedly opened. Opening the blood–brain barrier did not result in serious clinical or radiographic adverse events, as well as no clinically significant worsening on cognitive scores at three months compared to baseline. Beta-amyloid levels were measured before treatment using [18F]-florbetaben PET to confirm amyloid deposition at the target site. Exploratory analysis suggested no group-wise changes in amyloid post-sonication. The results of this safety and feasibility study support the continued investigation of focused ultrasound as a potential novel treatment and delivery strategy for patients with Alzheimer’s disease.
Rice actin binding protein RMD controls crown root angle in response to external phosphate
Authors: Huang Guoqiang , Liang Wanqi , Sturrock Craig J. , Pandey Bipin K. , Giri Jitender , Mairhofer Stefan , Wang Daoyang , Muller Lukas , Tan Hexin , York Larry M. , Yang Jing , Song Yu , Kim Yu-Jin , Qiao Yang , Xu Jian , Kepinski Stefan , Bennett Malcolm J. , Zhang Dabing
Published: June 2018

Root angle has a major impact on acquisition of nutrients like phosphate that accumulate in topsoil and in many species; low phosphate induces shallower root growth as an adaptive response. Identifying genes and mechanisms controlling root angle is therefore of paramount importance to plant breeding. Here we show that the actin-binding protein Rice Morphology Determinant (RMD) controls root growth angle by linking actin filaments and gravity-sensing organelles termed statoliths. RMD is upregulated in response to low external phosphate and mutants lacking of RMD have steeper crown root growth angles that are unresponsive to phosphate levels. RMD protein localizes to the surface of statoliths, and rmd mutants exhibit faster gravitropic response owing to more rapid statoliths movement. We conclude that adaptive changes to root angle in response to external phosphate availability are RMD dependent, providing a potential target for breeders.
Efficient generation of mouse models of human diseases via ABE- and BE-mediated base editing
Authors: Liu Zhen , Lu Zongyang , Yang Guang , Huang Shisheng , Li Guanglei , Feng Songjie , Liu Yajing , Li Jianan , Yu Wenxia , Zhang Yu , Chen Jia , Sun Qiang , Huang Xingxu
Published: June 2018

A recently developed adenine base editor (ABE) efficiently converts A to G and is potentially useful for clinical applications. However, its precision and efficiency in vivo remains to be addressed. Here we achieve A-to-G conversion in vivo at frequencies up to 100% by microinjection of ABE mRNA together with sgRNAs. We then generate mouse models harboring clinically relevant mutations at Ar and Hoxd13, which recapitulates respective clinical defects. Furthermore, we achieve both C-to-T and A-to-G base editing by using a combination of ABE and SaBE3, thus creating mouse model harboring multiple mutations. We also demonstrate the specificity of ABE by deep sequencing and whole-genome sequencing (WGS). Taken together, ABE is highly efficient and precise in vivo, making it feasible to model and potentially cure relevant genetic diseases.
Anti-phage islands force their target phage to directly mediate island excision and spread
Authors: McKitterick Amelia C. , Seed Kimberley D.
Published: June 2018

Vibrio cholerae, the causative agent of the diarrheal disease cholera, is antagonized by the lytic phage ICP1 in the aquatic environment and in human hosts. Mobile genetic elements called PLEs (phage-inducible chromosomal island-like elements) protect V. cholerae from ICP1 infection and initiate their anti-phage response by excising from the chromosome. Here, we show that PLE 1 encodes a large serine recombinase, Int, that exploits an ICP1-specific protein as a recombination directionality factor (RDF) to excise PLE 1 in response to phage infection. We show that this phage-encoded protein is sufficient to direct Int-mediated recombination in vitro and that it is highly conserved in all sequenced ICP1 genomes. Our results uncover an aspect of the molecular specificity underlying the conflict between a single predatory phage and V. cholerae PLE and contribute to our understanding of long-term evolution between phage and their bacterial hosts.
A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits
Authors: Hibrand Saint-Oyant L. , Ruttink T. , Hamama L. , Kirov I. , Lakhwani D. , Zhou N. N. , Bourke P. M. , Daccord N. , Leus L. , Schulz D. , Van de Geest H. , Hesselink T. , Van Laere K. , Debray K. , Balzergue S. , Thouroude T. , Chastellier A. , Jeauffre J. , Voisine L. , Gaillard S. , Borm T. J. A. , Arens P. , Voorrips R. E. , Maliepaard C. , Neu E. , Linde M. , Le Paslier M. C. , Bérard A. , Bounon R. , Clotault J. , Choisne N. , Quesneville H. , Kawamura K. , Aubourg S. , Sakr S. , Smulders M. J. M. , Schijlen E. , Bucher E. , Debener T. , De Riek J. , Foucher F.
Published: June 2018

Rose is the world’s most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line (‘HapOB’) from Rosa chinensis ‘Old Blush’ and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1–96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
Exploring corrections to the Optomechanical Hamiltonian
Authors: Sala Kamila , Tufarelli Tommaso
Published: June 2018

We compare two approaches for deriving corrections to the “linear model” of cavity optomechanics, in order to describe effects that are beyond first order in the radiation pressure coupling. In the regime where the mechanical frequency is much lower than the cavity one, we compare: (I) a widely used phenomenological Hamiltonian conserving the photon number; (II) a two-mode truncation of C. K. Law’s microscopic model, which we take as the “true” system Hamiltonian. While these approaches agree at first order, the latter model does not conserve the photon number, resulting in challenging computations. We find that approach (I) allows for several analytical predictions, and significantly outperforms the linear model in our numerical examples. Yet, we also find that the phenomenological Hamiltonian cannot fully capture all high-order corrections arising from the C. K. Law model.
Influence of the ordering of impurities on the appearance of an energy gap and on the electrical conductance of graphene
Authors: Repetsky S. P. , Vyshyvana I. G. , Kruchinin S. P. , Bellucci Stefano
Published: June 2018

In the one-band model of strong coupling, the influence of substitutional impurity atoms on the energy spectrum and electrical conductance of graphene is studied. It is established that the ordering of substitutional impurity atoms on nodes of the crystal lattice causes the appearance of a gap in the energy spectrum of graphene with width η|δ| centered at the point yδ, where η is the parameter of ordering, δ is the difference of the scattering potentials of impurity atoms and carbon atoms, and y is the impurity concentration. The maximum value of the parameter of ordering is $${{\boldsymbol{\eta }}}_{{\boldsymbol{\max }}}{\boldsymbol{=}}{\bf{2}}{\boldsymbol{y}}{\boldsymbol{,}}\,{\boldsymbol{y}}{\boldsymbol{\le }}{\bf{1}}/{\bf{2}}$$

η

max

=
2
y
,

y
≤
1
/
2
. For the complete ordering of impurity atoms, the energy gap width equals $${\bf{2}}{\boldsymbol{y}}{\boldsymbol{|}}{\boldsymbol{\delta }}{\boldsymbol{|}}$$
2
y

|
δ
|

. If the Fermi level falls in the region of the mentioned gap, then the electrical conductance $${{\boldsymbol{\sigma }}}_{{\boldsymbol{\alpha }}{\boldsymbol{\alpha }}}{\boldsymbol{\to }}{\bf{0}}$$

σ

α
α

→
0
at the ordering of graphene, i.e., the metal–dielectric transition arises. If the Fermi level is located outside the gap, then the electrical conductance increases with the parameter of order η by the relation $${{\boldsymbol{\sigma }}}_{{\boldsymbol{\alpha }}{\boldsymbol{\alpha }}}{\boldsymbol{ \sim }}{{\boldsymbol{(}}{{\boldsymbol{y}}}^{{\bf{2}}}{\boldsymbol{-}}\frac{{\bf{1}}}{{\bf{4}}}{{\boldsymbol{\eta }}}^{{\bf{2}}}{\boldsymbol{)}}}^{{\boldsymbol{-}}{\bf{1}}}$$

σ

α
α

~

(

y

2

−

1
4

η

2

)

−
1

. At the concentration $${\boldsymbol{y}}{\boldsymbol{=}}{\bf{1}}{\boldsymbol{/}}{\bf{2}}$$
y
=
1
/
2
, as the ordering of impurity atoms η →1, the electrical conductance of graphene $${{\boldsymbol{\sigma }}}_{{\boldsymbol{\alpha }}{\boldsymbol{\alpha }}}{\boldsymbol{\to }}{\boldsymbol{\infty }}$$

σ

α
α

→
∞
, i.e., the transition of graphene in the state of ideal electrical conductance arises.
Large trees are surrounded by more heterospecific neighboring trees in Korean pine broad-leaved natural forests
Authors: Wang Hongxiang , Peng Hui , Hui Gangying , Hu Yanbo , Zhao Zhonghua
Published: June 2018

Negative conspecific density dependence is one of the principal mechanisms affecting plant performance and community spatial patterns. Although many studies identified the prevalence of density dependent effects in various vegetation types by analyzing conspecific spatial dispersal patterns (spatial patterning) of forest trees, interactions between individuals and heterospecific neighboring trees caused by density-dependent effects are often neglected. The effects of negative density dependence lead us to expect that neighbourhood species segregation would increase with increasing tree size and that larger trees would be surrounded by more heterospecific neighbours than would smaller trees. We studied four mapped 1-Ha plots on Changbaishan Mountain in North-eastern China and used marked point pattern analysis to explore whether trees of different sizes exhibited differences in neighbourhood species segregation; we also determined whether larger trees were more likely to have heterospecific neighbours than smaller trees were. Our results show that bigger trees generally have higher species mingling levels. Neighborhood species segregation ranged from lower than expected levels to random or nearly random patterns at small scales as tree size classes increased under heterogeneous Poisson null model tests. This study provides some evidence in support of negative density dependent effects in temperate forests.
Exposure to an anti-androgenic herbicide negatively impacts reproductive physiology and fertility in Xenopus tropicalis
Authors: Orton F. , Säfholm M. , Jansson E. , Carlsson Y. , Eriksson A. , Fick J. , Uren Webster T. , McMillan T. , Leishman M. , Verbruggen B. , Economou T. , Tyler C. R. , Berg C.
Published: June 2018

Amphibians are threatened on a global scale and pollutants may be contributing to population declines, but how chemicals impact on their reproduction is poorly understood. We conducted a life cycle analysis to investigate the impacts of early life exposure to two anti-androgens (exposure until completion of metamorphosis;stage 66): flutamide, (50 µg/L)/linuron (9 and 45 µg/L)) on sexual development and breeding competence in Xenopus tropicalis. Our analyses included: mRNA levels of dmrt1, cyp17, amh, cyp19, foxl2 and ar (tadpoles/metamorphs), gonadal histomorphology (metamorphs/adults), mRNA levels of ar/gr (adult male brain/gonad/forelimb), testosterone/corticosterone levels (adult males), secondary sexual characteristics (forelimb width/nuptial pad: adult males) and breeding competence (amplexus/fertility: adult males). Compared to controls, feminised sex ratios and increased number of spermatogonia (adults) were observed after exposure to flutamide and the lower linuron concentration. Exposure to the lower linuron concentration also resulted in demasculinisation of secondary sexual characteristics and reduced male fertility. Flutamide exposure resulted in masculinisation of the nuptial pad and elevated mRNA levels of dmrt1, cyp17, amh and foxl2 in brains (metamorphs). Testosterone levels were higher in all treatment groups, however, overall few effects were observed in response to the higher linuron concentration. Our findings advance understanding of reproductive biology of X. tropicalis and illustrate negative effects of linuron on reproductive processes at a concentration measured in freshwater environments.
Pathological modelling of pigmentation disorders associated with Hutchinson-Gilford Progeria Syndrome (HGPS) revealed an impaired melanogenesis pathway in iPS-derived melanocytes
Authors: Lo Cicero Alessandra , Saidani Manoubia , Allouche Jennifer , Egesipe Anne Laure , Hoch Lucile , Bruge Celine , Sigaudy Sabine , De Sandre-Giovannoli Annachiara , Levy Nicolas , Baldeschi Christine , Nissan Xavier
Published: June 2018

Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare genetic disorder that leads to premature aging. In this study, we used induced pluripotent stem cells to investigate the hypopigmentation phenotypes observed in patients with progeria. Accordingly, two iPS cell lines were derived from cells from HGPS patients and differentiated into melanocytes. Measurements of melanin content revealed a lower synthesis of melanin in HGPS melanocytes as compared to non-pathologic cells. Analysis of the melanosome maturation process by electron microscopy revealed a lower percentage of mature, fully pigmented melanosomes. Finally, a functional rescue experiment revealed the direct role of progerin in the regulation of melanogenesis. Overall, these results report a new dysregulated pathway in HGPS and open up novel perspectives in the study of pigmentation phenotypes that are associated with normal and pathological aging.
An Evolutionarily Conserved Structural Platform for PRC2 Inhibition by a Class of Ezh2 Inhibitors
Authors: Bratkowski Matthew , Yang Xin , Liu Xin
Published: June 2018

Polycomb repressive complex 2 (PRC2) mediates trimethylation of histone H3K27 (H3K27me3), an epigenetic hallmark for repressed chromatin. Overactive mutants of the histone lysine methyltransferase subunit of PRC2, Ezh2, are found in various types of cancers. Pyridone-containing inhibitors such as GSK126 compete with S-adenosylmethionine (SAM) for Ezh2 binding and effectively inhibit PRC2 activity. PRC2 from the thermophilic fungus Chaetomium thermophilum (ct) is functionally similar to the human version in several regards and has the added advantage of producing high-resolution crystal structures, although inhibitor-bound structures of human or human/chameleon PRC2 are also available at up to 2.6 Å resolution. We solved crystal structures of both human and ctPRC2 bound to GSK126 and the structurally similar inhibitor GSK343. While the two organisms feature a disparate degree of inhibitor potency, surprisingly, GSK126 binds in a similar manner in both structures. Structure-guided protein engineering of the drug binding pocket allowed us to introduce humanizing mutations into ctEzh2 to produce a ctPRC2 variant that is more susceptible to GSK126 inhibition. Additional analysis indicated that an evolutionarily conserved structural platform dictates a unique mode of GSK126 binding, suggesting a mechanism of drug selectivity. The existing drug scaffold may thus be used to probe the function and cellular regulation of PRC2 in a wide spectrum of organisms, ranging from fungi to humans.
Quantitative Study of Abdominal Blood Flow Patterns in Patients with Aortic Dissection by 4-Dimensional Flow MRI
Authors: Liu Dongting , Fan Zhanming , Li Yu , Zhang Nan , Sun Zhonghua , An Jing , Stalder Aurélien F. , Greiser Andreas , Liu Jiayi
Published: June 2018

The purpose of this study is to evaluate the hemodynamic characteristics of the true lumen (TL) and the false lumen (FL) in 16 patients with aortic dissection (AD) using 4D flow magnetic resonance imaging (MRI) and thoracic and abdominal computed tomography (CT) angiography. The quantitative parameters that were measured in the TL and FL included velocity and flow. The mean area and regurgitant fraction of the TL were significantly lesser at all four levels (p < 0.05); the average through-plane velocity, peak velocity magnitude, average net flow, peak flow, and net forward volume in the TL were considerably higher (p < 0.05). The intimal entry’s size was negatively correlated with the blood flow velocity and flow rate in the TL (p < 0.05) and positively correlated with the average through-plane velocity, average net flow, and peak flow in the FL (p < 0.05); the blood flow indices in the TL were enhanced with an increase in the intimal entry numbers (p < 0.05) and the peak flow in the FL was lowered (p = 0.025); if FL thrombosis existed, the average through-plane velocity and peak velocity magnitude in the TL were substantially higher (p < 0.05). 4D flow MRI facilitates qualitative and quantitative analysis of the alterations in the abdominal aortic blood flow patterns.
A deep learning framework to discern and count microscopic nematode eggs
Authors: Akintayo Adedotun , Tylka Gregory L. , Singh Asheesh K. , Ganapathysubramanian Baskar , Singh Arti , Sarkar Soumik
Published: June 2018

In order to identify and control the menace of destructive pests via microscopic image-based identification state-of-the art deep learning architecture is demonstrated on the parasitic worm, the soybean cyst nematode (SCN), Heterodera glycines. Soybean yield loss is negatively correlated with the density of SCN eggs that are present in the soil. While there has been progress in automating extraction of egg-filled cysts and eggs from soil samples counting SCN eggs obtained from soil samples using computer vision techniques has proven to be an extremely difficult challenge. Here we show that a deep learning architecture developed for rare object identification in clutter-filled images can identify and count the SCN eggs. The architecture is trained with expert-labeled data to effectively build a machine learning model for quantifying SCN eggs via microscopic image analysis. We show dramatic improvements in the quantification time of eggs while maintaining human-level accuracy and avoiding inter-rater and intra-rater variabilities. The nematode eggs are correctly identified even in complex, debris-filled images that are often difficult for experts to identify quickly. Our results illustrate the remarkable promise of applying deep learning approaches to phenotyping for pest assessment and management.
Temporal and spectral EEG dynamics can be indicators of stealth placement
Authors: Wang Regina W. Y. , Chen Yi-Chung , Liu I-Ning , Chuang Shang-Wen
Published: June 2018

Stealth placement marketing, where consumers are unaware that they are being marketed to, attempts to reduce the audiences’ resistance to traditional persuasive advertising. It is a form of advertising that involves targeted exposure of brands or products incorporated in other works, usually with or without explicit reference to the brands or products. Brand placement can be presented in different visual and auditory forms in video programs. The present study proposed that different ‘representations’ (i.e., representable or non-representable) and ‘sounds’ (i.e., speech or musical sound) of brand placement can affect the viewers’ perception of the brand. Event-related potential results indicated significant differences in P1, N1, P2, N270, and P3. Further, event-related spectral perturbation results indicated significant differences in theta, alpha, beta, and gamma (30–100 Hz), in the right parietal, right occipital area, and limbic lobe. ‘Non-representable’ or ‘speech sound’ brand placement induced significant temporal and spectral EEG dynamics in viewers.
Thermodynamics of CuPt nanoalloys
Authors: Rossi K. , Pártay L. B. , Csányi G. , Baletto F.
Published: June 2018

The control of structural and chemical transitions in bimetallic nanoalloys at finite temperatures is one of the challenges for their use in advanced applications. Comparing Nested Sampling and Molecular Dynamics simulations, we investigate the phase changes of CuPt nanoalloys with the aim to elucidate the role of kinetic effects during their solidification and melting processes. We find that the quasi-thermodynamic limit for the nucleation of (CuPt)309 is 965 ± 10 K, but its prediction is increasingly underestimated when the system is cooled faster than 109 K/s. The solidified nanoparticles, classified following a novel tool based on Steinhardt parameters and the relative orientation of characteristic atomic environments, are then heated back to their liquid phase. We demonstrate the kinetic origin of the hysteresis in the caloric curve as (i) it closes for rates slower than 108 K/s, with a phase change temperature of 970 K ± 25 K, in very good agreement with its quasi-thermodynamic limit; (ii) the process happens simultaneously in the inner and outer layers; (iii) an onion-shell chemical order - Cu-rich surface, Pt-rich sub-surface, and mixed core - is always preserved.
An ex vivo salivary lubrication system to mimic xerostomic conditions and to predict the lubricating properties of xerostomia relieving agents
Authors: Vinke Jeroen , Kaper Hans J. , Vissink Arjan , Sharma Prashant K.
Published: June 2018

Advances in medical research has resulted in successful treatment of many life-threatening infectious diseases as well as autoimmune and lifestyle-related diseases, increasing life-expectancy of both the developed and developing world. As a result of a growing ageing population, the focus has also turned on chronic diseases which seriously affect the quality of older patient life. Xerostomia (dry mouth) is one such condition, which leads to bad oral health and difficulty in consumption of dry foods and speech. Saliva substitutes are used to ease symptoms. However, they often don’t work properly and objective comparison of saliva substitutes to mimic natural salivary functions does not exist. The study thus aims to develop an ex vivo friction assay simulating dry mouth conditions and facilitating objective comparison of saliva substitutes. A reciprocating sliding tongue-enamel system was developed and compared to a PDMS (polydimethylsiloxane)-PDMS friction system. The tongue-enamel system, but not the PDMS-PDMS model, showed high mucin-containing saliva (unstimulated and submandibular/sublingual saliva) to give higher Relief than mucin-poor lubricants (water, parotid saliva, Dentaid Xeros) and correlated well (r = 0.97) with in vivo mouth feel. The tongue-enamel friction system mimicked dry mouth conditions and relief and seems suited to test agents meant to lubricate desiccated oral surfaces.
Oxidation of squalene by singlet oxygen and free radicals results in different compositions of squalene monohydroperoxide isomers
Authors: Shimizu Naoki , Ito Junya , Kato Shunji , Otoki Yurika , Goto Masashi , Eitsuka Takahiro , Miyazawa Teruo , Nakagawa Kiyotaka
Published: June 2018

Oxidation of squalene (SQ) causes a decline in the nutritional value of SQ in foods, as well as an accumulation of SQ oxidation products in skin lipids which lead to adverse skin conditions. However, mechanistic insights as to how SQ is oxidized by different oxidation mechanisms have been limited, and thus effective measures towards the prevention of SQ oxidation have not been identified. In this study, we oxidized SQ by either singlet oxygen oxidation or free radical oxidation, and monitored the formation of the six SQ monohydroperoxide (SQOOH) isomers, the primary oxidation products of SQ, at the isomeric level. While singlet oxygen oxidation of SQ resulted in the formation of similar amounts of the six SQOOH isomers, free radical oxidation of SQ mainly formed two types of isomers, 2-OOH-SQ and 3-OOH-SQ. The addition of β-carotene during singlet oxygen oxidation, and the addition of α-tocopherol during free radical oxidation lead to a dose-dependent decrease in the formation of SQOOH isomers. Such results suggest that the analysis of SQOOH at the isomeric level allows for the determination of the cause of SQ oxidation in various samples, and provides a foothold for future studies concerning the prevention of SQ oxidation.
Effect of testosterone treatment on bone remodelling markers and mineral density in obese dieting men in a randomized clinical trial
Authors: Ng Tang Fui Mark , Hoermann Rudolf , Nolan Brendan , Clarke Michelle , Zajac Jeffrey D. , Grossmann Mathis
Published: June 2018

To assess the effect of testosterone treatment on bone remodelling and density in dieting obese men, 100 obese men aged 53 years (interquartile range 47–60) with a total testosterone level <12 nmol/L receiving 10 weeks of a very low energy diet (VLED) followed by 46 weeks of weight maintenance were randomly assigned at baseline to 56 weeks of intramuscular testosterone undecanoate (n = 49, cases) or matching placebo (n = 51, controls). Pre-specified outcomes were between-group differences (mean adjusted difference, MAD) in serum c-telopeptide (CTx), N-terminal propeptide of type 1 procollagen (P1NP) and bone mineral density (BMD). At trial end, CTx was significantly reduced in men receiving testosterone compared to placebo, MAD −66 ng/L (95% CI −113, −18), p = 0.018, and this was apparent already after the 10 week VLED phase, MAD −63 ng/L (95% CI −108, −18), p = 0.018. P1NP was marginally increased after VLED, MAD +4.2 ug/L (95% CI −0.01, +8.4), p = 0.05 but lower at study end, MAD −5.6 ug/L (95% CI −10.1, −1.1), p = 0.03. No significant changes in sclerostin, lumbar spine BMD or femoral BMD were seen. We conclude that in obese men with low testosterone levels undergoing weight loss, bone remodelling markers are modulated in a way that may have favourable effects on bone mass.
Characterization and phylogenetic analysis of the complete mitochondrial genome of the medicinal fungus Laetiporus sulphureus
Authors: Li Qiang , Yang Mei , Chen Cheng , Xiong Chuan , Jin Xin , Pu Zhigang , Huang Wenli
Published: June 2018

The medicinal fungus Laetiporus sulphureus is widely distributed worldwide. To screen for molecular markers potentially useful for phylogenetic analyses of this species and related species, the mitochondrial genome of L. sulphureus was sequenced and assembled. The complete circular mitochondrial genome was 101,111 bp long, and contained 38 protein-coding genes (PCGs), 2 rRNA genes, and 25 tRNA genes. Our BLAST search aligned about 6.1 kb between the mitochondrial and nuclear genomes of L. sulphureus, indicative of possible gene transfer events. Both the GC and AT skews in the L. sulphureus mitogenome were negative, in contrast to the other seven Polyporales species tested. Of the 15 PCGs conserved across the seven species of Polyporales, the lengths of 11 were unique in the L. sulphureus mitogenome. The Ka/Ks of these 15 PCGs were all less than 1, indicating that PCGs were subject to purifying selection. Our phylogenetic analysis showed that three single genes (cox1, cob, and rnl) were potentially useful as molecular markers. This study is the first publication of a mitochondrial genome in the family Laetiporaceae, and will facilitate the study of population genetics and evolution in L. sulphureus and other species in this family.
Moringin Induces Neural Differentiation in the Stem Cell of the Human Periodontal Ligament
Authors: Romeo Letizia , Diomede Francesca , Gugliandolo Agnese , Scionti Domenico , Lo Giudice Fabrizio , Lanza Cariccio Veronica , Iori Renato , Bramanti Placido , Trubiani Oriana , Mazzon Emanuela
Published: June 2018

The therapeutic strategies for neurodegenerative diseases still represent a vast research field because of the lack of targeted, effective and resolutive treatment for neurodegenerative diseases. The use of stem cell-based therapy is an alternative approach that could lead to the replacement of damaged neuronal tissue. For this purpose, adult mesenchymal stem cells (MSC), including periodontal ligament stem cells (PDLSCs), could be very useful for their differentiation capacity, easy isolation and the ability to perform an autologous implant. The aim of this work was to test whether the Moringin [4-(α-L-rhamnosyloxy) benzyl isothiocyanate; GMG-ITC], an isothiocyanate extracted from Moringa oleifera seeds, was able to induce PDLSCs toward neural progenitor differentiation. Next-generation transcriptomics sequencing showed that moringin treatment increased the expression of genes involved in neuron cortical development and in particular in neuron belonging to upper and deep cortical layers. Moreover, moringin treatment upregulated genes involved in osteogenesis and adipogenesis although with a lower fold change compared to upregulated genes involved in neuronal differentiation. Finally, moringin did not induce the expression of oncogenes resulting in a safe treatment.
Griffiths phases in infinite-dimensional, non-hierarchical modular networks
Authors: Cota Wesley , Ódor Géza , Ferreira Silvio C.
Published: June 2018

Griffiths phases (GPs), generated by the heterogeneities on modular networks, have recently been suggested to provide a mechanism, rid of fine parameter tuning, to explain the critical behavior of complex systems. One conjectured requirement for systems with modular structures was that the network of modules must be hierarchically organized and possess finite dimension. We investigate the dynamical behavior of an activity spreading model, evolving on heterogeneous random networks with highly modular structure and organized non-hierarchically. We observe that loosely coupled modules act as effective rare-regions, slowing down the extinction of activation. As a consequence, we find extended control parameter regions with continuously changing dynamical exponents for single network realizations, preserved after finite size analyses, as in a real GP. The avalanche size distributions of spreading events exhibit robust power-law tails. Our findings relax the requirement of hierarchical organization of the modular structure, which can help to rationalize the criticality of modular systems in the framework of GPs.
Demonstration of large ionization coefficient ratio in AlAs0.56Sb0.44 lattice matched to InP
Authors: Yi Xin , Xie Shiyu , Liang Baolai , Lim Leh Woon , Zhou Xinxin , Debnath Mukul C. , Huffaker Diana L. , Tan Chee Hing , David John. P. R.
Published: June 2018

The electron and hole avalanche multiplication characteristics have been measured in bulk AlAs0.56Sb0.44 p-i-n and n-i-p homojunction diodes, lattice matched to InP, with nominal avalanche region thicknesses of ~0.6 μm, 1.0 μm and 1.5 μm. From these and data from two much thinner devices, the bulk electron and hole impact ionization coefficients (α and β respectively), have been determined over an electric-field range from 220–1250 kV/cm for α and from 360–1250 kV/cm for β for the first time. The α/β ratio is found to vary from 1000 to 2 over this field range, making it the first report of a wide band-gap III-V semiconductor with ionization coefficient ratios similar to or larger than that observed in silicon.
Evaluating novel synthetic compounds active against Bacillus subtilis and Bacillus cereus spores using Live imaging with SporeTrackerX
Authors: Omardien Soraya , Ter Beek Alexander , Vischer Norbert , Montijn Roy , Schuren Frank , Brul Stanley
Published: June 2018

An empirical approach was taken to screen a novel synthetic compound library designed to be active against Gram-positive bacteria. We obtained five compounds that were active against spores from the model organism Bacillus subtilis and the food-borne pathogen Bacillus cereus during our population based experiments. Using single cell live imaging we were able to observe effects of the compounds on spore germination and outgrowth. Difference in sensitivity to the compounds could be observed between B. subtilis and B. cereus using live imaging, with minor difference in the minimal inhibitory and bactericidal concentrations of the compounds against the spores. The compounds all delayed the bursting time of germinated spores and affected the generation time of vegetative cells at sub-inhibitory concentrations. At inhibitory concentrations spore outgrowth was prevented. One compound showed an unexpected potential for preventing spore germination at inhibitory concentrations, which merits further investigation. Our study shows the valuable role single cell live imaging can play in the final selection process of antimicrobial compounds.
Rectification and negative differential resistance via orbital level pinning
Authors: Thong Aaron Zhenghui , Shaffer Milo S. P. , Horsfield Andrew P.
Published: June 2018

A donor-acceptor system, 4-thiophenyl-azafulleroid (4TPA-C60), is investigated at the point of HOMO/LUMO resonance and beyond to understand how negative differential resistance (NDR) features may be observed in such systems. Our previous investigation showed that charge transfer between the occupied and unoccupied states at resonance hindered crossing of the HOMO and LUMO levels, thus preventing the formation of an NDR feature. In this work, it is shown that the negative differential resistance feature of 4TPA-C60 can be tailored based on the couplings at the metal/molecule interface. Ab initio calculations show that limited charge extraction from atomically sharp contacts results in a HOMO-LUMO pinning effect which delays the onset of the NDR feature. Subsequent unpinning of the states can only occur when additional charge extraction channels enter the bias window, highlighting an important role which non-frontier states play in charge transport. The proposed charge transfer mechanism is then exploited by introducing a fluorine atom into the C60 cage to tune the energies of the acceptor, and narrow the width of the current peak. These findings not only demonstrate the importance of the metal/molecule interface in the design of molecular electronic architectures but also serve to inform future design of molecular diodes and RTDs.
Element specific determination of the magnetic properties of two macrocyclic tetranuclear 3d–4f complexes with a Cu3Tb core by means of X-ray magnetic circular dichroism (XMCD)
Authors: Balinski K. , Schneider L. , Wöllermann J. , Buling A. , Joly L. , Piamonteze C. , Feltham H. L. C. , Brooker S. , Powell A. K. , Delley B. , Kuepper K.
Published: June 2018

We apply X-ray magnetic circular dichroism to study the internal magnetic structure of two very promising star shaped macrocyclic complexes with a CuII3TbIII core.
Comparative studies of the serum half-life extension of a protein via site-specific conjugation to a species-matched or -mismatched albumin
Authors: Yang Byungseop , Kim Jong Chul , Seong Jihyoun , Tae Giyoong , Kwon Inchan
Published: June 2018

Human serum albumin (HSA) has been investigated as a serum half-life extender of therapeutic proteins thanks to its unusually long serum half-life.
Light-mediated iodoperfluoroalkylation of alkenes/alkynes catalyzed by chloride ions: role of halogen bonding
Authors: Beniazza Redouane , Remisse Lionel , Jardel Damien , Lastécouères Dominique , Vincent Jean-Marc
Published: June 2018

A catalytic amount of chloride ions greatly facilitates the UVA-mediated iodoperfluoroalkylation of alkenes and alkynes.
Novel hemagglutinin-binding sulfated oligofucosides and their effect on influenza virus infection
Authors: Kosono Shuhei , Kasai Akihiro , Komaba Sumika , Matsubara Teruhiko , Sato Toshinori , Takahashi Daisuke , Toshima Kazunobu
Published: June 2018

A purpose-designed trimer10possessing three sulfated oligofucoside moieties of5effectively bound to hemagglutinins and inhibited influenza virus infection.
Conformational chiral polymorphism in cis-bis-triphenylphosphine complexes of transition metals
Authors: Tshabang Never , Makgatle Gaone P. , Bourne Susan A. , Kann Nina , Evans Jack D. , Coudert François-Xavier , Öhrström Lars
Published: June 2018

Analysis of conformation polymorphism in cis-bis-triphenylphosphine complexes points to the importance of coordination numbers and homochirality of PPh3 ligands.
Varying the regiochemistry of a [2 + 2] cycloaddition reaction within isostructural hydrogen bonded cocrystals containing 4-stilbazole
Authors: Grobelny Anna L. , Rath Nigam P. , Groeneman Ryan H.
Published: June 2018

Cocrystallization of 4-stilbazole with 4,6-diX resorcinol (X = Cl or Br) yields a pair of similar photoreactive solids that leads to different photoproducts.
Selective precipitation and in situ separation of rutile crystals from titanium bearing slag melt in a super-gravity field
Authors: Du Yu , Gao Jintao , Lan Xi , Guo Zhancheng
Published: June 2018

A method of selective precipitation, in situ separation and ex situ characterization of rutile crystals from slag melt under super-gravity is proposed.
Fermi resonance controlled product branching in the H + HOD reaction
Authors: Zhao Bin , Manthe Uwe , Guo Hua
Published: June 2018

Excitation of the first overtone of bending mode results in a significant enhancement in the HD + OH channel due to the 1 : 2 Fermi resonance between the fundamental OD stretch and the first overtone of the bend.
Developing effective electronic-only coupled-cluster and Møller–Plesset perturbation theories for the muonic molecules
Authors: Goli Mohammad , Shahbazian Shant
Published: June 2018

The coupled-cluster and the second order Møller–Plesset perturbation theories are extended within the context of the effective muon-specific electronic structure theory and applied computationally to the muoniated N-heterocyclic carbene/silylene/germylene and the muoniated triazolium cation.
Molecular quantum cellular automata cell design trade-offs: latching vs. power dissipation
Authors: Rahimi Ehsan , Reimers Jeffrey R.
Published: June 2018

A new way of using molecules to enact switches in quantum cellular automata (QCA) is proposed, utilizing monostable molecules that neither provide latching nor consume power; properties are compared to those for conventional bistable switches that both latch and consume power.
Incorporation of oxygen atoms as a mechanism for photoluminescence enhancement of chemically treated MoS2
Authors: Schwermann Christian , Stiehm Torsten , Tonndorf Philipp , Schneider Robert , Schmidt Robert , Kern Johannes , Michaelis de Vasconcellos Steffen , Bratschitsch Rudolf , Doltsinis Nikos L.
Published: June 2018

Ab initio calculations reveal a unified O transfer reaction from TFSI, H2O2, O2 and H2SO4 into an S vacancy in MoS2 significantly enhancing photoluminescence.
The dioxygen adducts of iron and manganese porphyrins: electronic structure and binding energy
Authors: Phung Quan Manh , Pierloot Kristine
Published: June 2018

The electronic structures of adducts of O2 and metal porphyrins were thoroughly investigated by highly accurate DMRG-CASPT2.
Mechanistic study of dry reforming of ethane by CO2 on a bimetallic PtNi(111) model surface
Authors: Kattel Shyam , Chen Jingguang G. , Liu Ping
Published: June 2018

A combined DFT and KMC study pinpoints the origin of high selectivity toward syngas during CO2 reduction by CH3CH3 on a PtNi model catalyst.
Designing a protonic ceramic fuel cell with novel electrochemically active oxygen electrodes based on doped Nd0.5Ba0.5FeO3−δ
Authors: Lyagaeva Julia , Danilov Nilolay , Tarutin Arthem , Vdovin Gennady , Medvedev Dmitry , Demin Anatoly , Tsiakaras Panagiotis
Published: June 2018

Slight co-doping of Nd0.5Ba0.5FeO3−δ results in enhancement of both ionic transport and electrochemical behavior, indicating that NBFCo is a promising electrode for proton-conducting electrolytes.
The use of poly-cation oxides to lower the temperature of two-step thermochemical water splitting
Authors: Zhai Shang , Rojas Jimmy , Ahlborg Nadia , Lim Kipil , Toney Michael F. , Jin Hyungyu , Chueh William C. , Majumdar Arun
Published: June 2018

We report the discovery of a new class of oxides – poly-cation oxides (PCOs) – that consist of multiple cations and can thermochemically split water in a two-step cycle to produce hydrogen (H2) and oxygen (O2).
Insights into polythiol-assisted AgNP dissolution induced by bio-relevant molecules
Authors: Marchioni Marianne , Gallon Thomas , Worms Isabelle , Jouneau Pierre-Henri , Lebrun Colette , Veronesi Giulia , Truffier-Boutry Delphine , Mintz Elisabeth , Delangle Pascale , Deniaud Aurélien , Michaud-Soret Isabelle
Published: June 2018

Polythiol molecules dissolve silver nanoparticles with kinetic rates that increase with the number of thiols per molecule and their pre-orientation.
Feasibility of using laser induced breakdown spectroscopy for quantitative measurement of calcium, magnesium, potassium and sodium in meat
Authors: Leme Flavio O. , Silvestre Daniel M. , Nascimento Angerson N. , Nomura Cassiana S.
Published: June 2018

The first report of quantitative measurement of calcium, magnesium, potassium and sodium in bovine and chicken meat by LIBS.
Optimization of the selectivity and rate of copper radioisotope complexation: formation and dissociation kinetic studies of 1,4,8-trimethylcyclam-based ligands with different coordinating pendant arms
Authors: Paúrová Monika , David Tomáš , Císařová Ivana , Lubal Přemysl , Hermann Petr , Kotek Jan
Published: June 2018

Influence of coordinating pendant arm character on selectivity and rate of copper(ii) complexation was investigated to optimize ligands for radiomedicinal use.
Surface modified mesoporous nanocast carbon as a catalyst for aqueous sulfide oxidation and adsorption of the produced polysulfides
Authors: Barrera Deicy , de Mendonça Fernanda Gomes , de Castro Arthur Henrique , de Mesquita João Paulo , Lago Rochel Montero , Sapag Karim
Published: June 2018

Surface modified mesoporous nanocast carbon can promote aqueous sulfide oxidation adsorbing the produced polysulfides.
Revisiting graphene–polymer nanocomposite for enhancing anticorrosion performance: a new insight into interface chemistry and diffusion model
Authors: Dutta Dipak , Ganda Andita Nataria Fitri , Chih Jui-Kung , Huang Cheng-Chun , Tseng Chung-Jen , Su Ching-Yuan
Published: June 2018

The interfacial chemistry and diffusion kinetics of a polymer–graphene nanocomposite anticorrosion coating were studied to minimize galvanic corrosion facilitated by the formation of an interconnected graphene percolation network.
Piezoelectricity in WSe2/MoS2 heterostructure atomic layers
Authors: Yu Sheng , Rice Quinton , Tabibi Bagher , Li Qiliang , Seo Felix Jaetae
Published: June 2018

A two-dimensional heterostructure of WSe2/MoS2 atomic layers has unique piezoelectric characteristics which depend on the number of atomic layers, stacking type and interlayer interaction size.
Catalytic alkylation reactions of weakly acidic carbonyl and related compounds using alkenes as electrophiles
Authors: Yamashita Yasuhiro , Igarashi Ryo , Suzuki Hirotsugu , Kobayashi Shū
Published: June 2018

Catalytic alkylation reactions of weakly acidic carbonyl and related pronucleophiles such as amides, esters, and sulfonamides with substituted alkenes have been reported.
Valdecoxib vs. borazavaldecoxib: isoxazole BN/CC isosterism as a case study in designing and stabilizing boron heterocycles
Authors: Boghi Michele , Hall Dennis G.
Published: June 2018

A comprehensive study on the preparation, hydrolytic stability, and the structural and spectrophotometric properties of 1,2,4,5-oxadiazaboroles is presented by way of a comparison between the NSAID drug valdecoxib (1) and its unprecedented B–N isostere, borazavaldecoxib (2).
Protected 2′-deoxyribonucleoside triphosphate building blocks for the photocaging of epigenetic 5-(hydroxymethyl)cytosine in DNA
Authors: Boháčová Soňa , Vaníková Zuzana , Poštová Slavětínská Lenka , Hocek Michal
Published: June 2018

2′-Deoxyribonucleoside triphosphates containing 5-(hydroxymethyl)cytosine protected with photocleavable groups were prepared and studied as substrates for the enzymatic synthesis of DNA containing a photocaged epigenetic 5hmC base.
Synthesis of substituted piperidines by enantioselective desymmetrizing intramolecular aza-Michael reactions
Authors: Guerola Marta , Escolano Marcos , Alzuet-Piña Gloria , Gómez-Bengoa Enrique , Ramírez de Arellano Carmen , Sánchez-Roselló María , del Pozo Carlos
Published: June 2018

An organocatalytic enantioselective intramolecular aza-Michael reaction has been described for the first time in a desymmetrization process employing substrates different from cyclohexadienones.