bluuebunny/crossref_metadata_2025 huggingface dataset:
Perinatal Malnutrition Leads to Sexually Dimorphic Behavioral Responses with Associated Epigenetic Changes in the Mouse Brain
Authors: Nätt Daniel , Barchiesi Riccardo , Murad Josef , Feng Jian , Nestler Eric J. , Champagne Frances A. , Thorsell Annika
Published: September 2017

Childhood malnutrition is a risk factor for mental disorders, such as major depression and anxiety. Evidence shows that similar early life adversities induce sex-dependent epigenetic reprogramming. However, little is known about how genes are specifically affected by early malnutrition and the implications for males and females respectively. One relevant target is neuropeptide Y (NPY), which regulates both stress and food-intake. We studied maternal low protein diet (LPD) during pregnancy/lactation in mice. Male, but not female, offspring of LPD mothers consistently displayed anxiety- and depression-like behaviors under acute stress. Transcriptome-wide analysis of the effects of acute stress in the amygdala, revealed a list of transcription factors affected by either sex or perinatal LPD. Among these immediate early genes (IEG), members of theEarly growth responsefamily (Egr1/2/4) were consistently upregulated by perinatal LPD in both sexes. EGR1 also bound theNPY receptor Y1gene (Npy1r), which co-occurred with sex-specific effects of perinatal LPD on bothNpy1rDNA-methylation and gene transcription. Our proposed pathway connecting early malnutrition, sex-independent regulatory changes inEgr1, and sex-specific epigenetic reprogramming of its effector gene,Npy1r, represents the first molecular evidence of how early life risk factors may generate sex-specific epigenetic effects relevant for mental disorders.
Generative Models for Global Collaboration Relationships
Authors: Ciftcioglu Ertugrul Necdet , Ramanathan Ram , Basu Prithwish
Published: September 2017

When individuals interact with each other and meaningfully contribute toward a common goal, it results in a collaboration. The artifacts resulting from collaborations are best captured using a hypergraph model, whereas the relation of who has collaborated with whom is best captured via an abstract simplicial complex (SC). We propose a generative algorithm GENESCs for SCs modeling fundamental collaboration relations. The proposed network growth process favors attachment that is preferential not to an individual’s degree, i.e., how many people has he/she collaborated with, but to his/her facet degree, i.e., how many maximal groups or facets has he/she collaborated within. Based on our observation that several real-world facet size distributions have significant deviation from power law–mainly since larger facets tend to subsume smaller ones–we adopt a data-driven approach. We prove that the facet degree distribution yielded by GENESCs is power law distributed for large SCs and show that it is in agreement with real world co-authorship data. Finally, based on our intuition of collaboration formation in domains such as collaborative scientific experiments and movie production, we propose two variants of GENESCs based on clamped and hybrid preferential attachment schemes, and show that they perform well in these domains.
A Chinese Pane-Like 2D Metal-Organic Framework Showing Magnetic Relaxation and Luminescence Dual-Functions
Authors: Liu Cai-Ming , Zhang De-Qing , Hao Xiang , Zhu Dao-Ben
Published: September 2017

The discovery of graphene kicked off the curtain of atom-type two-dimensional (2D) materials. Layered metal-organic frameworks (MOFs) as parallel molecule-based 2D materials are more designable and more diverse, and magnetism may be induced by their metal ion nodes. However, the multifunctional 2D plane-like MOFs are very difficult to obtain. Here we describe a Chinese pane-like 2D MOF constructed from the Ln3+ cation and the nanoscale luminescent tritopic ligand tris(4′-carboxybiphenyl)-amine, responding to the slow magnetic relaxation and luminescence properties, respectively. Notably, the Dy-Dy distances separated by the tritopic ligand are up to 2 nm. Such a 2D molecular material is expected to have potential applications in optoelectronics and multimodal sensing.
Emerging negative Atlantic Multidecadal Oscillation index in spite of warm subtropics
Authors: Frajka-Williams Eleanor , Beaulieu Claudie , Duchez Aurelie
Published: September 2017

Sea surface temperatures in the northern North Atlantic have shown a marked decrease over the past several years. The sea surface in the subpolar gyre is now as cold as it was during the last cold phase of the Atlantic Multidecadal Oscillation index in the 1990s. This climate index is associated with shifts in hurricane activity, rainfall patterns and intensity, and changes in fish populations. However, unlike the last cold period in the Atlantic, the spatial pattern of sea surface temperature anomalies in the Atlantic is not uniformly cool, but instead has anomalously cold temperatures in the subpolar gyre, warm temperatures in the subtropics and cool anomalies over the tropics. The tripole pattern of anomalies has increased the subpolar to subtropical meridional gradient in SSTs, which are not represented by the AMO index value, but which may lead to increased atmospheric baroclinicity and storminess. Here we show that the recent Atlantic cooling is likely to persist, as predicted by a statistical forecast of subsurface ocean temperatures and consistent with the irreversible nature of watermass changes involved in the recent cooling of the subpolar gyre.
Formation of ferromagnetic Co–H–Co complex and spin-polarized conduction band in Co-doped ZnO
Authors: Lee Seunghun , Park Ji Hun , Kim Bum-Su , Cho Deok-Yong , Choi Yong Nam , Lee Tae-Woo , Kim Won-Kyung , Kim Doukyun , Cho Chae Ryong , Moriyoshi Chikako , Park Chul Hong , Kuroiwa Yoshihiro , Jeong Se-Young
Published: September 2017

Magnetic oxide semiconductors with wide band gaps have promising spintronic applications, especially in the case of magneto-optic devices. Co-doped ZnO (ZnCoO) has been considered for these applications, but the origin of its ferromagnetism has been controversial for several decades and no substantial progress for a practical application has been made to date. In this paper, we present direct evidence of hydrogen-mediated ferromagnetism and spin polarization in the conduction band of ZnCoO. Electron density mapping reveals the formation of Co–H–Co, in agreement with theoretical predictions. Electron spin resonance measurement elucidates the ferromagnetic nature of ZnCoO by the formation of Co–H–Co. We provide evidence from magnetic circular dichroism measurements supporting the hypothesis that Co–H–Co contributes to the spin polarization of the conduction band of hydrogen-doped ZnCoO.
Functional modulation of LHCSR1 protein from Physcomitrella patens by zeaxanthin binding and low pH
Authors: Pinnola Alberta , Ballottari Matteo , Bargigia Ilaria , Alcocer Marcelo , D’Andrea Cosimo , Cerullo Giulio , Bassi Roberto
Published: September 2017

Light harvesting for oxygenic photosynthesis is regulated to prevent the formation of harmful photoproducts by activation of photoprotective mechanisms safely dissipating the energy absorbed in excess. Lumen acidification is the trigger for the formation of quenching states in pigment binding complexes. With the aim to uncover the photoprotective functional states responsible for excess energy dissipation in green algae and mosses, we compared the fluorescence dynamic properties of the light-harvesting complex stress-related (LHCSR1) protein, which is essential for fast and reversible regulation of light use efficiency in lower plants, as compared to the major LHCII antenna protein, which mainly fulfills light harvesting function. Both LHCII and LHCSR1 had a chlorophyll fluorescence yield and lifetime strongly dependent on detergent concentration but the transition from long- to short-living states was far more complete and fast in the latter. Low pH and zeaxanthin binding enhanced the relative amplitude of quenched states in LHCSR1, which were characterized by the presence of 80 ps fluorescence decay components with a red-shifted emission spectrum. We suggest that energy dissipation occurs in the chloroplast by the activation of 80 ps quenching sites in LHCSR1 which spill over excitons from the photosystem II antenna system.
Principal contribution of HLA-DQ alleles, DQB1*06:04 and DQB1*03:01, to disease resistance against primary biliary cholangitis in a Japanese population
Authors: Yasunami Michio , Nakamura Hitomi , Tokunaga Katsushi , Kawashima Minae , Nishida Nao , Hitomi Yuki , Nakamura Minoru
Published: September 2017

Identification of the primary allele(s) inHLA class IIassociated diseases remains challenging because of a tight linkage between alleles ofHLA-DRand-DQloci. In the present study, we determined the genotypes of sevenHLAloci (HLA-A,-B,-DRB1,-DQA1,-DQB1,-DPA1and-DPB1) for 1200 Japanese patients with primary biliary cholangitis and 1196 controls. Observation of recombination derivatives facilitated an evaluation of the effects of individualHLAalleles consisting of disease-prone/disease-resistantHLAhaplotypes. Consequently, a primary contribution ofDQB1*06:04(odds ratio: 0.19, p = 1.91 × 10−22),DQB1*03:01(odds ratio: 0.50, p = 6.76 × 10−10),DRB1*08:03(odds ratio: 1.75, p = 1.01 × 10−7) andDQB1*04:01(odds ratio: 1.50, p = 9.20 × 10−6) was suggested. Epistasis of the protectiveDQB1*06:04to risk conferred byDRB1*08:03was demonstrated by subpopulation analysis, implicating the presence of an active immunological mechanism that alleviates pathogenic autoimmune reactions. Further, the contribution of the aforementionedHLAalleles as well as anHLA-DPallele,DPB1*02:01to the association signals of 304 loci among 4103 SNPs in theHLAregion at the genome-wide level of significance (p values less than 5 × 10−8) was demonstrated by the stepwise exclusion of the individuals possessing theseHLAalleles from the comparison.
Melatonin enhances the developmental competence of porcine somatic cell nuclear transfer embryos by preventing DNA damage induced by oxidative stress
Authors: Liang Shuang , Jin Yong-Xun , Yuan Bao , Zhang Jia-Bao , Kim Nam-Hyung
Published: September 2017

Melatonin has antioxidant and scavenger effects in the cellular antioxidant system. This research investigated the protective effects and underlying mechanisms of melatonin action in porcine somatic cell nuclear transfer (SCNT) embryos. The results suggested that the developmental competence of porcine SCNT embryos was considerably enhanced after melatonin treatment. In addition, melatonin attenuated the increase in reactive oxygen species levels induced by oxidative stress, the decrease in glutathione levels, and the mitochondrial dysfunction. Importantly, melatonin inhibited phospho-histone H2A.X (γH2A.X) expression and comet tail formation, suggesting that γH2A.X prevents oxidative stress-induced DNA damage. The expression of genes involved in homologous recombination and non-homologous end-joining pathways for the repair of double-stranded breaks (DSB) was reduced upon melatonin treatment in porcine SCNT embryos at day 5 of development under oxidative stress condition. These results indicated that melatonin promoted porcine SCNT embryo development by preventing oxidative stress-induced DNA damage via quenching of free radical formation. Our results revealed a previously unrecognized regulatory effect of melatonin in response to oxidative stress and DNA damage. This evidence provides a novel mechanism for the improvement in SCNT embryo development associated with exposure to melatonin.
Novel detection of post-translational modifications in human monocyte-derived dendritic cells after chronic alcohol exposure: Role of inflammation regulator H4K12ac
Authors: Parira Tiyash , Figueroa Gloria , Laverde Alejandra , Casteleiro Gianna , Gomez Hernandez Mario E. , Fernandez-Lima Francisco , Agudelo Marisela
Published: September 2017

Previous reports on epigenetic mechanisms involved in alcohol abuse have focus on hepatic and neuronal regions, leaving the immune system and specifically monocyte-derived dendritic cells (MDDCs) understudied. Our lab has previously shown histone deacetylases are modulated in cells derived from alcohol users and after in vitro acute alcohol treatment of human MDDCs. In the current study, we developed a novel screening tool using matrix assisted laser desorption ionization-fourier transform-ion cyclotron resonance mass spectrometry (MALDI-FT-ICR MS) and single cell imaging flow cytometry to detect post-translational modifications (PTMs) in human MDDCs due to chronic alcohol exposure. Our results demonstrate, for the first time, in vitro chronic alcohol exposure of MDDCs modulates H3 and H4 and induces a significant increase in acetylation at H4K12 (H4K12ac). Moreover, the Tip60/HAT inhibitor, NU9056, was able to block EtOH-induced H4K12ac, enhancing the effect of EtOH on IL-15, RANTES, TGF-β1, and TNF-α cytokines while restoring MCP-2 levels, suggesting that H4K12ac may be playing a major role during inflammation and may serve as an inflammation regulator or a cellular stress response mechanism under chronic alcohol conditions.
Characterization of Volume-Based Changes in Cortical Auditory Evoked Potentials and Prepulse Inhibition
Authors: Potter Thomas , Li Sheng , Nguyen Thinh , Nguyen Trac , Ince Nuri , Zhang Yingchun
Published: September 2017

The auditory evoked startle reflex is a conserved response resulting in neurological and motor activity. The presence of a mild prepulse immediately before the main pulse inhibits startle responses, though the mechanism for this remains unknown. In this study, the electroencephalography (EEG) data recorded from 15 subjects was analyzed to study the N1 and P2 components of cortical auditory evoked potentials (CAEPs) evoked by 70, 80, 90, 100, and 110 dB stimuli both in the presence and absence of 70 dB prepulses. Results without a prepulse showed an evolution of N1 amplitudes, increasing with stimulus intensity and showing largely significant differences. Results from prepulse trials only showed noteworthy changes in peak-to-peak amplitude in the 100 dB condition. Prepulse and non-prepulse conditions were then compared using peak amplitudes and theta power. Prepulse conditions significantly decreased the amplitude for both components in the 110 dB condition, i.e., pre-pulse inhibition, but significantly increased the N1 amplitude in the 70 dB condition, i.e., pre-pulse facilitation. Similarly theta band power significantly increased in the 70 dB prepulse condition and significantly decreased in the 110 dB prepulse condition. These results expand the basis of knowledge regarding how CAEPs change and elaborate on their neural function and representation.
Biophysical characterisation of the novel zinc binding property in Suppressor of Fused
Authors: Jabrani Amira , Makamte Staëlle , Moreau Emilie , Gharbi Yasmine , Plessis Anne , Bruzzone Lucia , Sanial Matthieu , Biou Valérie
Published: September 2017

Suppressor of Fused (SUFU) is a highly conserved protein that acts as a negative regulator of the Hedgehog (HH) signalling pathway, a major determinant of cell differentiation and proliferation. Therefore, SUFU deletion in mammals has devastating effects on embryo development. SUFU is part of a multi-protein cytoplasmic signal-transducing complex. Its partners include the Gli family of transcription factors that function either as repressors, or as transcription activators according to the HH activation state. The crystal structure of SUFU revealed a two-domain arrangement, which undergoes a closing movement upon binding a peptide from Gli1. There remains however, much to be discovered about SUFU’s behaviour. To this end, we expressed recombinant, full-length SUFU from Drosophila, Zebrafish and Human. Guided by a sequence analysis that revealed a conserved potential metal binding site, we discovered that SUFU binds zinc. This binding was found to occur with a nanomolar affinity to SUFU from all three species. Mutation of one histidine from the conserved motif induces a moderate decrease in affinity for zinc, while circular dichroism indicates that the mutant remains structured. Our results reveal new metal binding affinity characteristics about SUFU that could be of importance for its regulatory function in HH.
Small RNAs in vancomycin-resistant Enterococcus faecium involved in daptomycin response and resistance
Authors: Sinel Clara , Augagneur Yoann , Sassi Mohamed , Bronsard Julie , Cacaci Margherita , Guérin François , Sanguinetti Maurizio , Meignen Pierrick , Cattoir Vincent , Felden Brice
Published: September 2017

Vancomycin-resistant Enterococcus faecium is a leading cause of hospital-acquired infections and outbreaks. Regulatory RNAs (sRNAs) are major players in adaptive responses, including antibiotic resistance. They were extensively studied in gram-negative bacteria, but less information is available for gram-positive pathogens. No sRNAs are described in E. faecium. We sought to identify a set of sRNAs expressed in vancomycin-resistant E. faecium Aus0004 strain to assess their roles in daptomycin response and resistance. Genomic and transcriptomic analyses revealed a set of 61 sRNA candidates, including 10 that were further tested and validated by Northern and qPCR. RNA-seq was performed with and without subinhibitory concentrations (SICs) of daptomycin, an antibiotic used to treat enterococcal infections. After daptomycin SIC exposure, the expression of 260 coding and srna genes was altered, with 80 upregulated and 180 downregulated, including 51% involved in carbohydrate and transport metabolisms. Daptomycin SIC exposure significantly affected the expression of seven sRNAs, including one experimentally confirmed, sRNA_0160. We studied sRNA expression in isogenic mutants with increasing levels of daptomycin resistance and observed that expression of several sRNAs, including sRNA_0160, was modified in the stepwise mutants. This first genome-wide sRNA identification in E. faecium suggests that some sRNAs are linked to antibiotic stress response and resistance.
N-terminomics identifies widespread endoproteolysis and novel methionine excision in a genome-reduced bacterial pathogen
Authors: Berry Iain J. , Jarocki Veronica M. , Tacchi Jessica L. , Raymond Benjamin B. A. , Widjaja Michael , Padula Matthew P. , Djordjevic Steven P.
Published: September 2017

Proteolytic processing alters protein function. Here we present the first systems-wide analysis of endoproteolysis in the genome-reduced pathogen Mycoplasma hyopneumoniae. 669 N-terminal peptides from 164 proteins were identified, demonstrating that functionally diverse proteins are processed, more than half of which 75 (53%) were accessible on the cell surface. Multiple cleavage sites were characterised, but cleavage with arginine in P1 predominated. Putative functions for a subset of cleaved fragments were assigned by affinity chromatography using heparin, actin, plasminogen and fibronectin as bait. Binding affinity was correlated with the number of cleavages in a protein, indicating that novel binding motifs are exposed, and protein disorder increases, after a cleavage event. Glyceraldehyde 3-phosphate dehydrogenase was used as a model protein to demonstrate this. We define the rules governing methionine excision, show that several aminopeptidases are involved, and propose that through processing, genome-reduced organisms can expand protein function.
Effect of prenatal DINCH plasticizer exposure on rat offspring testicular function and metabolism
Authors: Campioli Enrico , Lee Sunghoon , Lau Matthew , Marques Lucas , Papadopoulos Vassilios
Published: September 2017

In 2002, the plasticizer 1,2-cyclohexane dicarboxylic acid diisononyl ester (DINCH) was introduced in the European market as a substitute for endocrine-disrupting phthalates. We found that in utero exposure of rats to DINCH from gestational day 14 until parturition affected reproductive organ physiology and reduced circulating testosterone levels at post-natal day 60, indicating a long-term effect on Leydig cells of the testis. Metabolically, animals exhibited randomly increased serum glucose concentrations not associated with impaired glucose utilization. Analysis of liver markers in the serum showed a hepatic effect; e.g. reduced bilirubin levels and albumin/globulin ratio. At post-natal day 200, random appearance of testicular atrophy was noted in exposed offspring, and limited changes in other reproductive parameters were observed. In conclusion, DINCH exposure appears to directly affect Leydig cell function, likely causing premature aging of the testes and impaired liver metabolic capacity. These effects might be attenuated with physiologic aging.
Ambient air pollution, smog episodes and mortality in Jinan, China
Authors: Zhang Jun , Liu Yao , Cui Liang-liang , Liu Shou-qin , Yin Xi-xiang , Li Huai-chen
Published: September 2017

We aimed to assess the acute effects of ambient air pollution and weather conditions on mortality in the context of Chinese smog episodes. A total of 209,321 deaths were recorded in Jinan, a large city in eastern China, during 2011–15. The mean concentrations of daily particulate matter ≤10 μm (PM10), fine particulate matter (PM2.5), sulfur dioxide (SO2) and nitrogen dioxide (NO2) were 169 μg/m3, 100 μg/m3, 77 μg/m3, and 54 μg/m3, respectively. Increases of 10 μg/m3 in PM10, PM2.5, SO2 and NO2 were associated with 1.11% (95% CI 0.96–1.26%), 0.71% (95% CI 0.60–0.82%), 1.69% (95% CI 1.56–1.83%), and 3.12% (95% CI 2.72–3.53%) increases in daily non-accidental mortality rates, respectively. Moreover, the risk estimates for these 4 pollutants were higher in association with respiratory and cardiovascular mortality. The effects of all the evaluated pollutants on mortality were greater in winter than in summer. Smog episodes were associated with a 5.87% (95% CI 0.16–11.58%) increase in the rate of overall mortality. This study highlights the effect of exposure to air pollution on the rate of mortality in China.
A regime shift in the Sun-Climate connection with the end of the Medieval Climate Anomaly
Authors: Smirnov D. A. , Breitenbach S. F. M. , Feulner G. , Lechleitner F. A. , Prufer K. M. , Baldini J. U. L. , Marwan N. , Kurths J.
Published: September 2017

Understanding the influence of changes in solar activity on Earth’s climate and distinguishing it from other forcings, such as volcanic activity, remains a major challenge for palaeoclimatology. This problem is best approached by investigating how these variables influenced past climate conditions as recorded in high precision paleoclimate archives. In particular, determining if the climate system response to these forcings changes through time is critical. Here we use the Wiener-Granger causality approach along with well-established cross-correlation analysis to investigate the causal relationship between solar activity, volcanic forcing, and climate as reflected in well-established Intertropical Convergence Zone (ITCZ) rainfall proxy records from Yok Balum Cave, southern Belize. Our analysis reveals a consistent influence of volcanic activity on regional Central American climate over the last two millennia. However, the coupling between solar variability and local climate varied with time, with a regime shift around 1000–1300 CE after which the solar-climate coupling weakened considerably.
Multiple Streptomyces species with distinct secondary metabolomes have identical 16S rRNA gene sequences
Authors: Antony-Babu Sanjay , Stien Didier , Eparvier Véronique , Parrot Delphine , Tomasi Sophie , Suzuki Marcelino T.
Published: September 2017

Microbial diversity studies using small subunit (SSU) rRNA gene sequences continue to advance our understanding of biological and ecological systems. Although a good predictor of overall diversity, using this gene to infer the presence of a species in a sample is more controversial. Here, we present a detailed polyphasic analysis of 10 bacterial strains isolated from three coastal lichens Lichina confinis, Lichina pygmaea and Roccella fuciformis with SSU rRNA gene sequences identical to the type strain of Streptomyces cyaneofuscatus. This analysis included phenotypic, microscopic, genetic and genomic comparisons and showed that despite their identical SSU rRNA sequences the strains had markedly different properties, and could be distinguished as 5 different species. Significantly, secondary metabolites profiles from these strains were also found to be different. It is thus clear that SSU rRNA based operational taxonomy units, even at the most stringent cut-off can represent multiple bacterial species, and that at least for the case of Streptomyces, strain de-replication based on SSU gene sequences prior to screening for bioactive molecules can miss potentially interesting novel molecules produced by this group that is notorious for the production of drug-leads.
Prevalence and causes of low vision and blindness in a Chinese population with type 2 diabetes: the Dongguan Eye Study
Authors: Cui Ying , Zhang Liang , Zhang Min , Yang Xiaohong , Zhang Lixin , Kuang Jian , Zhang Guanrong , Liu Qingyang , Guo Haike , Meng Qianli
Published: September 2017

To assess the prevalence and causes of low vision and blindness in type 2 diabetes patients, a population-based cross-sectional study including 8952 rural-dwelling residents aged 40 years or older from Hengli Town in Southern China was conducted. Participants underwent standard interviews, physical measurements, laboratory tests, and comprehensive eye examinations. Low vision and blindness were defined based on WHO criteria. Visual acuity data were available for 1348 (89.9%) of the 1500 subjects with type 2 diabetes. Age-standardized prevalence of bilateral low vision and blindness assessed in the better-seeing eye was 2.9% (95% confidence interval [CI]: 2.0–3.8) and 0.7% (95% CI: 0.2–1.1) based on best-corrected visual acuity (BCVA). Cataracts were the primary cause of low vision and blindness. Visual impairment was associated with age (odds ratio [OR]: 3.73, 95% CI: 2.39–5.83), education level (OR: 3.21, 95% CI: 1.63–6.29), duration of diabetes (OR: 1.14, 95% CI: 1.04–1.25) and body mass index (OR: 0.86, 95% CI: 0.77–0.95). Our data suggest that approximately 70% of visual impairment in this diabetic population could be eliminated with appropriate cataract surgery or spectacle correction. Greater consideration should be given to older type 2 diabetes patients with a level of lower education.
Light guiding and switching using eccentric core-shell geometries
Authors: Barreda Ángela I. , Gutiérrez Yael , Sanz Juan M. , González Francisco , Moreno Fernando
Published: September 2017

High Refractive Index (HRI) dielectric nanoparticles have been proposed as an alternative to metallic ones due to their low absorption and magnetodielectric response in the VIS and NIR ranges. For the latter, important scattering directionality effects can be obtained. Also, systems constituted by dimers of HRI dielectric nanoparticles have shown to produce switching effects by playing with the polarization, frequency or intensity of the incident radiation. Here, we show that scattering directionality effects can be achieved with a single eccentric metallo-HRI dielectric core-shell nanoparticle. As an example, the effect of the metallic core displacements for a single Ag-Si core-shell nanoparticle has been analyzed. We report rotation of the main scattering lobe either clockwise or counterclockwise depending on the polarization of the incident radiation leading to new scattering configurations for switching purposes. Also, the efficiency of the scattering directionality can be enhanced. Finally, chains of these scattering units have shown good radiation guiding effects, and for 1D periodic arrays, redirection of diffracted intensity can be observed as a consequence of blazing effects. The proposed scattering units constitute new blocks for building systems for optical communications, solar energy harvesting devices and light guiding at the nanoscale level.
Sexual congruency in the connectome and translatome of VTA dopamine neurons
Authors: Chung Amanda S. , Miller Samara M. , Sun Yanjun , Xu Xiangmin , Zweifel Larry S.
Published: September 2017

The ventral tegmental area (VTA) dopamine system is important for reward, motivation, emotion, learning, and memory. Dysfunctions in the dopamine system are linked to multiple neurological and neuropsychiatric disorders, many of which present with sex differences. Little is known about the extent of heterogeneity in the basic organization of VTA dopamine neurons with regard to sex. Here, we characterized the cell-specific connectivity of VTA dopamine neurons, their mRNA translational profile, and basic electrophysiological characteristics in a common strain of mice. We found no major differences in these metrics, except for differential expression of a Y-chromosome associated mRNA transcript, Eif2s3y, and the X-linked, X-inactivation transcript Xist. Of note, Xist transcript was significantly enriched in dopamine neurons, suggesting tight regulation of X-linked gene expression to ensure sexual congruency. These data indicate that the features that make dopamine neurons unique are highly concordant and not a principal source of sexual dimorphism.
Angstrom-Resolved Metal-Organic Framework-Liquid Interfaces
Authors: Chiodini Stefano , Reinares-Fisac Daniel , Espinosa Francisco M. , Gutiérrez-Puebla Enrique , Monge Angeles , Gándara Felipe , Garcia Ricardo
Published: September 2017

Metal-organic frameworks (MOFs) are a class of crystalline materials with a variety of applications in gas storage, catalysis, drug delivery or light harvesting. The optimization of those applications requires the characterization of MOF structure in the relevant environment. Dynamic force microscopy has been applied to follow dynamic processes of metal-organic-framework material. We provide images with spatial and time resolutions, respectively, of angstrom and seconds that show that Ce-RPF-8 surfaces immersed in water and glycerol experience a surface reconstruction process that is characterized by the diffusion of the molecular species along the step edges of the open terraces. The rate of the surface reconstruction process depends on the liquid. In water it happens spontaneously while in glycerol is triggered by applying an external force.
Lactate-utilizing community is associated with gut microbiota dysbiosis in colicky infants
Authors: Pham Van T. , Lacroix Christophe , Braegger Christian P. , Chassard Christophe
Published: September 2017

The aetiology of colic, a functional gastrointestinal disorder in infants, is not yet resolved. Different mechanisms have been suggested involving the gut microbiota and intermediate metabolites such as lactate. Lactate can be metabolized by lactate-utilizing bacteria (LUB) to form different end-products. Using a functional approach, we hypothesized that H2 production and accumulation by LUB is associated with the development of colic. The LUB communities in the feces of forty infants, including eight colicky infants, were characterized using a combination of culture- and molecular-based methods, and metabolite concentrations were measured by HPLC. Interactions among LUB strains isolated from feces were investigated with pure and mixed cultures using anaerobic techniques. We emphasized high prevalence of crying, flatulence, colic and positive correlations thereof in the first 3 months of life. Crying infants showed significantly higher ratio of LUB non-sulfate-reducing bacteria (LUB non-SRB) (H2-producer), to LUB SRB (H2-utilizer) at 3 months. Colicky infants had significantly higher number of H2-producing Eubacterium hallii at 2 weeks compared to non-colicky infants. We revealed the function of Desulfovibrio piger and Eubacterium limosum to reduce H2 accumulation in co-cultures with H2-producing Veillonella ratti. Our data suggest that the balance between H2-producing and H2-utilizing LUB might contribute to colic symptoms.
Consumption of crustaceans by megaherbivorous dinosaurs: dietary flexibility and dinosaur life history strategies
Authors: Chin Karen , Feldmann Rodney M. , Tashman Jessica N.
Published: September 2017

Large plant-eating dinosaurs are usually presumed to have been strictly herbivorous, because their derived teeth and jaws were capable of processing fibrous plant foods. This inferred feeding behavior offers a generalized view of dinosaur food habits, but rare direct fossil evidence of diet provides more nuanced insights into feeding behavior. Here we describe fossilized feces (coprolites) that demonstrate recurring consumption of crustaceans and rotted wood by large Late Cretaceous dinosaurs. These multi-liter coprolites from the Kaiparowits Formation are primarily composed of comminuted conifer wood tissues that were fungally degraded before ingestion. Thick fragments of laminar crustacean cuticle are scattered within the coprolite contents and suggest that the dinosaurian defecators consumed sizeable crustaceans that sheltered in rotting logs. The diet of decayed wood and crustaceans offered a substantial supply of plant polysaccharides, with added dividends of animal protein and calcium. Nevertheless, it is unlikely that the fossilized fecal residues depict year-round feeding habits. It is more reasonable to infer that these coprolites reflected seasonal dietary shifts—possibly related to the dinosaurs’ oviparous breeding activities. This surprising fossil evidence challenges conventional notions of herbivorous dinosaur diets and reveals a degree of dietary flexibility that is consistent with that of extant herbivorous birds.
Nuisance Flooding and Relative Sea-Level Rise: the Importance of Present-Day Land Motion
Authors: Karegar Makan A. , Dixon Timothy H. , Malservisi Rocco , Kusche Jürgen , Engelhart Simon E.
Published: September 2017

Sea-level rise is beginning to cause increased inundation of many low-lying coastal areas. While most of Earth’s coastal areas are at risk, areas that will be affected first are characterized by several additional factors. These include regional oceanographic and meteorological effects and/or land subsidence that cause relative sea level to rise faster than the global average. For catastrophic coastal flooding, when wind-driven storm surge inundates large areas, the relative contribution of sea-level rise to the frequency of these events is difficult to evaluate. For small scale “nuisance flooding,” often associated with high tides, recent increases in frequency are more clearly linked to sea-level rise and global warming. While both types of flooding are likely to increase in the future, only nuisance flooding is an early indicator of areas that will eventually experience increased catastrophic flooding and land loss. Here we assess the frequency and location of nuisance flooding along the eastern seaboard of North America. We show that vertical land motion induced by recent anthropogenic activity and glacial isostatic adjustment are contributing factors for increased nuisance flooding. Our results have implications for flood susceptibility, forecasting and mitigation, including management of groundwater extraction from coastal aquifers.
Improving the Accuracy of the Hyperspectral Model for Apple Canopy Water Content Prediction using the Equidistant Sampling Method
Authors: Zhao Huan-San , Zhu Xi-Cun , Li Cheng , Wei Yu , Zhao Geng-Xing , Jiang Yuan-Mao
Published: September 2017

The influence of the equidistant sampling method was explored in a hyperspectral model for the accurate prediction of the water content of apple tree canopy. The relationship between spectral reflectance and water content was explored using the sample partition methods of equidistant sampling and random sampling, and a stepwise regression model of the apple canopy water content was established. The results showed that the random sampling model was Y = 0.4797 − 721787.3883 × Z3 − 766567.1103 × Z5 − 771392.9030 × Z6; the equidistant sampling model was Y = 0.4613 − 480610.4213 × Z2 − 552189.0450 × Z5 − 1006181.8358 × Z6. After verification, the equidistant sampling method was verified to offer a superior prediction ability. The calibration set coefficient of determination of 0.6599 and validation set coefficient of determination of 0.8221 were higher than that of the random sampling model by 9.20% and 10.90%, respectively. The root mean square error (RMSE) of 0.0365 and relative error (RE) of 0.0626 were lower than that of the random sampling model by 17.23% and 17.09%, respectively. Dividing the calibration set and validation set by the equidistant sampling method can improve the prediction accuracy of the hyperspectral model of apple canopy water content.
Long-term Administration of Nuclear Bile Acid Receptor FXR Agonist Prevents Spontaneous Hepatocarcinogenesis in Abcb4−/− Mice
Authors: Cariello Marica , Peres Claudia , Zerlotin Roberta , Porru Emanuele , Sabbà Carlo , Roda Aldo , Moschetta Antonio
Published: September 2017

Altered bile acid (BA) signaling is associated with hepatotoxicity. The farnesoid X receptor (FXR) is a nuclear receptor that transcriptionally regulates BA homeostasis. Mice with FXR ablation present hepatocarcinoma (HCC) due to high toxic BA levels. Mice with Abcb4 ablation accumulate toxic BA within the bile ducts and present HCC. We have previously shown that intestinal specific activation of FXR by transgenic VP16-FXR chimera is able to reduce BA pool size and prevent HCC. Here we tested chemical FXR activation by administering for 15 months the dual FXR/ membrane G protein-coupled receptor (TGR5) agonist INT-767 (6α-ethyl-3α,7α,23-trihydroxy-24-nor-5β-cholan-23-sulphate) to Fxr−/− and Abcb4−/− mice. HCC number and size were significantly reduced by INT-767 administration. In contrast, no changes in HCC tumor number and size were observed in Fxr−/− mice fed with or without INT-767. Notably, INT-767 preserved the hepatic parenchyma, improved hepatic function and down-regulated pro-inflammatory cytokines. Moreover, in Abcb4−/− mice INT-767 prevented fibrosis by reducing collagen expression and deposition. Thus, long term activation of FXR is able to reduce BA pool, reprogram BA metabolism and prevent HCC. These data provide the impetus to address the bona fide therapeutic potential of FXR activation in disease with BA-associated development of HCC.
A Multi-Institutional Comparison of Dynamic Contrast-Enhanced Magnetic Resonance Imaging Parameter Calculations
Authors:   Joint Head and Neck Radiotherapy-MRI Development Cooperative, Ger Rachel B. , Mohamed Abdallah S. R. , Awan Musaddiq J. , Ding Yao , Li Kimberly , Fave Xenia J. , Beers Andrew L. , Driscoll Brandon , Elhalawani Hesham , Hormuth David A. , Houdt Petra J. van , He Renjie , Zhou Shouhao , Mathieu Kelsey B. , Li Heng , Coolens Catherine , Chung Caroline , Bankson James A. , Huang Wei , Wang Jihong , Sandulache Vlad C. , Lai Stephen Y. , Howell Rebecca M. , Stafford R. Jason , Yankeelov Thomas E. , Heide Uulke A. van der , Frank Steven J. , Barboriak Daniel P. , Hazle John D. , Court Laurence E. , Kalpathy-Cramer Jayashree , Fuller Clifton D.
Published: September 2017

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) provides quantitative metrics (e.g. Ktrans, ve) via pharmacokinetic models. We tested inter-algorithm variability in these quantitative metrics with 11 published DCE-MRI algorithms, all implementing Tofts-Kermode or extended Tofts pharmacokinetic models. Digital reference objects (DROs) with known Ktrans and ve values were used to assess performance at varying noise levels. Additionally, DCE-MRI data from 15 head and neck squamous cell carcinoma patients over 3 time-points during chemoradiotherapy were used to ascertain Ktrans and ve kinetic trends across algorithms. Algorithms performed well (less than 3% average error) when no noise was present in the DRO. With noise, 87% of Ktrans and 84% of ve algorithm-DRO combinations were generally in the correct order. Low Krippendorff’s alpha values showed that algorithms could not consistently classify patients as above or below the median for a given algorithm at each time point or for differences in values between time points. A majority of the algorithms produced a significant Spearman correlation in ve of the primary gross tumor volume with time. Algorithmic differences in Ktrans and ve values over time indicate limitations in combining/comparing data from distinct DCE-MRI model implementations. Careful cross-algorithm quality-assurance must be utilized as DCE-MRI results may not be interpretable using differing software.
Non-cell-autonomous effects yield lower clonal diversity in expanding tumors
Authors: Tissot Tazzio , Thomas Frédéric , Roche Benjamin
Published: September 2017

Recent cancer research has investigated the possibility that non-cell-autonomous (NCA) driving tumor growth can support clonal diversity (CD). Indeed, mutations can affect the phenotypes not only of their carriers (“cell-autonomous”, CA effects), but also sometimes of other cells (NCA effects). However, models that have investigated this phenomenon have only considered a restricted number of clones. Here, we designed an individual-based model of tumor evolution, where clones grow and mutate to yield new clones, among which a given frequency have NCA effects on other clones’ growth. Unlike previously observed for smaller assemblages, most of our simulations yield lower CD with high frequency of mutations with NCA effects. Owing to NCA effects increasing competition in the tumor, clones being already dominant are more likely to stay dominant, and emergent clones not to thrive. These results may help personalized medicine to predict intratumor heterogeneity across different cancer types for which frequency of NCA effects could be quantified.
The Novel Compound Sul-121 Preserves Endothelial Function and Inhibits Progression of Kidney Damage in Type 2 Diabetes Mellitus in Mice
Authors: Lambooy S. P. H. , Bidadkosh A. , Nakladal D. , van Buiten A. , Girgis R. A. T. , van der Graaf A. C. , Wiedenmann T. J. , Koster R. A. , Vogelaar P. , Buikema H. , Henning R. H. , Deelman L. E.
Published: September 2017

Diabetic nephropathy is still a common complication of type 2 diabetes mellitus (T2DM) and improvement of endothelial dysfunction (ED) and inhibition of reactive oxygen species (ROS) are considered important targets for new therapies. Recently, we developed a new class of compounds (Sul compounds) which inhibit mitochondrial ROS production. Here, we tested the therapeutic effects of Sul-121 on ED and kidney damage in experimental T2DM. Diabetic db/db and lean mice were implanted with osmotic pumps delivering Sul-121 (2.2 mg/kg/day) or vehicle from age 10 to 18 weeks. Albuminuria, blood pressure, endothelial mediated relaxation, renal histology, plasma creatinine, and H2O2 levels were assessed. Sul-121 prevented progression of albuminuria and attenuated kidney damage in db/db, as evidenced by lower glomerular fibronectin expression (~50%), decreased focal glomerular sclerosis score (~40%) and normalization of glomerular size and kidney weight. Further, Sul-121 restored endothelium mediated vasorelaxation through increased production of Nitric Oxide production and normalized plasma H2O2 levels. Sul-121 treatment in lean mice demonstrated no observable major side-effects, indicating that Sul-121 is well tolerated. Our data show that Sul-121 inhibits progression of diabetic kidney damage via a mechanism that involves restoration of endothelial function and attenuation of oxidative stress.
Correlative Evaluation of Mental and Physical Workload of Laparoscopic Surgeons Based on Surface Electromyography and Eye-tracking Signals
Authors: Zhang Jian-Yang , Liu Sheng-Lin , Feng Qing-Min , Gao Jia-Qi , Zhang Qiang
Published: September 2017

Surgeons’ mental and physical workloads are major focuses of operating room (OR) ergonomics, and studies on this topic have generally focused on either mental workload or physical workload, ignoring the interaction between them. Previous studies have shown that physically demanding work may affect mental performance and may be accompanied by impaired mental processing and decreased performance. In this study, 14 participants were recruited to perform laparoscopic cholecystectomy (LC) procedures in a virtual simulator. Surface electromyography (sEMG) signals of the bilateral trapezius, bicipital, brachioradialis and flexor carpi ulnaris (FCU) muscles and eye-tracking signals were acquired during the experiment. The results showed that the least square means of muscle activity during the LC phases of surgery in an all-participants mixed effects model were 0.79, 0.81, and 0.98, respectively. The observed muscle activities in the different phases exhibited some similarity, while marked differences were found between the forearm bilateral muscles. Regarding mental workload, significant differences were observed in pupil dilation between the three phases of laparoscopic surgery. The mental and physical workloads of laparoscopic surgeons do not appear to be generally correlated, although a few significant negative correlations were found. This result further indicates that mental fatigue does markedly interfere with surgeons’ operating movements.
Reversible naftifine-induced carotenoid depigmentation in Rhodotorula mucilaginosa (A. Jörg.) F.C. Harrison causing onychomycosis
Authors: Moț Augustin C. , Pârvu Marcel , Pârvu Alina E. , Roşca-Casian Oana , Dina Nicoleta E. , Leopold Nicolae , Silaghi-Dumitrescu Radu , Mircea Cristina
Published: September 2017

Rhodotorula mucilaginosa was isolated from a patient with onychomycosis, and identification was confirmed by morphological and cultural characteristics as well as by DNA molecular analysis. Antifungal agents naftifine (10 mg/mL, active substance in Exoderil) and bifonazole (10 mg/mL, active substance in Canespor) were tested in different concentrations to assess in vitro effects on fungal growth and carotenoid synthesis. The antifungal mechanisms of action of naftifine and bifonazole against R. mucilaginosa isolates were similar and affected the biosynthetic pathway of ergosterol. For the first time, this research demonstrates that naftifine affects the carotenoid biosynthetic pathway, producing depigmentation of R. mucilaginosa in solid and liquid media. Furthermore, depigmentation was a reversible process; naftifine-treated yeast cells that were depigmented resumed carotenoid production upon transfer to fresh media. Raman and UV-vis spectrophotometry in conjunction with chromatographic analysis detected changes in carotenoids in yeast cells, with torulene decreasing and B-carotene increasing after repigmentation. Transmission electron micrographs revealed critical ultrastructural modifications in the depigmented cells after naftifine treatment, i.e., a low-electron-density cell wall without visible mucilage or lamellate structure.
Sub-picosecond temporal resolution of anomalous Hall currents in GaAs
Authors: Schmidt Christian B. , Priyadarshi Shekhar , Bieler Mark
Published: September 2017

The anomalous Hall (AH) and spin Hall effects are important tools for the generation, control, and detection of spin and spin-polarized currents in solids and, thus, hold promises for future spintronic applications. Despite tremendous work on these effects, their ultrafast dynamic response is still not well explored. Here, we induce ultrafast AH currents in a magnetically-biased semiconductor by optical femtosecond excitation at room temperature. The currents’ dynamics are studied by detecting the simultaneously emitted THz radiation. We show that the temporal shape of the AH currents can be extracted by comparing its THz radiation to the THz radiation emitted from optically induced currents whose temporal shape is well known. We observe a complex temporal shape of the AH currents suggesting that different microscopic origins contribute to the current dynamics. This is further confirmed by photon energy dependent measurements revealing a current inversion at low optical excitation intensities. Our work is a first step towards full time resolution of AH and spin Hall currents and helps to better understand the underlying microscopic origins, being a prerequisite for ultrafast spintronic applications using such currents.