bluuebunny/crossref_metadata_2025_split huggingface dataset:
Healthy dietary indices and risk of depressive outcomes: a
systematic review and meta-analysis of observational studies
Authors: Lassale Camille , Batty G. David , Baghdadli Amaria , Jacka Felice , Sánchez-Villegas Almudena , Kivimäki Mika , Akbaraly Tasnime 
Published: September 2018

AbstractWith depression being the psychiatric disorder incurring the largest
societal costs in developed countries, there is a need to gather evidence on the
role of nutrition in depression, to help develop recommendations and guide future
psychiatric health care. The aim of this systematic review was to synthesize the
link between diet quality, measured using a range of predefined indices, and
depressive outcomes. Medline, Embase and PsychInfo were searched up to
31st May 2018 for studies that examined adherence to a
healthy diet in relation to depressive symptoms or clinical depression. Where
possible, estimates were pooled using random effect meta-analysis with
stratification by observational study design and dietary score. A total of 20
longitudinal and 21 cross-sectional studies were included. These studies utilized an
array of dietary measures, including: different measures of adherence to the
Mediterranean diet, the Healthy Eating Index (HEI) and Alternative HEI (AHEI), the
Dietary Approaches to Stop Hypertension, and the Dietary Inflammatory Index. The
most compelling evidence was found for the Mediterranean diet and incident
depression, with a combined relative risk estimate of highest vs. lowest adherence
category from four longitudinal studies of 0.67 (95% CI 0.55–0.82). A lower Dietary
Inflammatory Index was also associated with lower depression incidence in four
longitudinal studies (relative risk 0.76; 95% CI: 0.63–0.92). There were fewer
longitudinal studies using other indices, but they and cross-sectional evidence also
suggest an inverse association between healthy diet and depression (e.g., relative
risk 0.65; 95% CI 0.50–0.84 for HEI/AHEI). To conclude, adhering to a healthy diet,
in particular a traditional Mediterranean diet, or avoiding a pro-inflammatory diet
appears to confer some protection against depression in observational studies. This
provides a reasonable evidence base to assess the role of dietary interventions to
prevent depression. This systematic review was registered in the PROSPERO
International Prospective Register of Systematic Reviews under the number
CRD42017080579.
Increased inflammation and brain glutamate define a subtype of depression with decreased regional homogeneity, impaired network integrity, and anhedonia
Authors: Haroon Ebrahim , Chen Xiangchuan , Li Zhihao , Patel Thrusharth , Woolwine Bobbi J. , Hu Xiaoping P. , Felger Jennifer C. , Miller Andrew H. 
Published: September 2018

AbstractCombined increases in peripheral inflammation and brain glutamate may identify a subtype of depression with distinct neuroimaging signatures. Two contrasting subgroups of depressed subjects—with and without combined elevations in plasma C-reactive protein (CRP) and basal ganglia glutamate (high and low CRP-Glu, respectively) were identified by hierarchical clustering using plasma CRP (indexing peripheral inflammation) and magnetic resonance spectroscopy (MRS)-based measurement of left basal ganglia glutamate. High CRP-Glu group status was associated with greater severity of anhedonia and cognitive and motor slowing. Local- and network-level measures of functional integrity were determined using brain oxygen level-dependent (BOLD)-oscillatory activity and graph theory. Greater decreases in concordance of oscillatory activity between neighboring voxels (Regional Homogeneity ‘ReHo’,p < 0.01) within the MRS volume-of-interest was associated with the High CRP-Glu subgroup. Using brain-wide, CRP-Glu ReHo contrast maps, a covariance network of 41 regions-of-interest (ROIs) with similar ReHo decreases was identified in the High CRP-Glu group and was located to brain structures previously implicated in depression. The 41-ROI network was further decomposed into four subnetworks. ReHo decreases within Subnetwork4—comprised of reward processing regions —was associated with anhedonia. Subnetwork4 ReHo also predicted decreased network integrity, which mediated the link between local ReHo and anhedonia in the Low but not High CRP-Glu group. These findings suggest that decreased ReHo and related disruptions in network integrity may reflect toxic effects of inflammation-induced increases in extrasynaptic glutamate signaling. Moreover, local BOLD oscillatory activity as reflected in ReHo might be a useful measure of target-engagement in the brain for treatment of inflammation-induced behaviors.
Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation
Authors: Luijk René , Wu Haoyu , Ward-Caviness Cavin K , Hannon Eilis , Carnero-Montoro Elena , Min Josine L. , Mandaviya Pooja , Müller-Nurasyid Martina , Mei Hailiang , van der Maarel Silvere M. ,   BIOS Consortium, Beekman Marian , der Breggen Ruud van , Deelen Joris , Lakenberg Nico , Moed Matthijs , Suchiman H. Eka D. , Arindrarto Wibowo , van’t Hof Peter , Jan Bonder Marc , Deelen Patrick , Tigchelaar Ettje F. , Zhernakova Alexandra , Zhernakova Dasha V. , van Dongen Jenny , Hottenga Jouke J. , Pool René , Isaacs Aaron , Hofman Bert A. , Jhamai Mila , van der Kallen Carla J. H. , Schalkwijk Casper G. , Stehouwer Coen D. A. , van den Berg Leonard H. , van Galen Michiel , Vermaat Martijn , van Rooij Jeroen , Uitterlinden André G. , Verbiest Michael , Verkerk Marijn , Kielbasa P. Szymon M. , Bot Jan , Nooren Irene , van Dijk Freerk , Swertz Morris A. , van Heemst Diana , Relton Caroline , Mill Jonathan , Waldenberger Melanie , Bell Jordana T. , Jansen Rick , Zhernakova Alexandra , Franke Lude , ‘t Hoen Peter A. C. , Boomsma Dorret I. , van Duijn Cornelia M. , van Greevenbroek Marleen M. J. , Veldink Jan H. , Wijmenga Cisca , van Meurs Joyce , Daxinger Lucia , Slagboom P. Eline , van Zwet Erik W. , Heijmans Bastiaan T. 
Published: September 2018

AbstractX-chromosome inactivation (XCI), i.e., the inactivation of one of the female X chromosomes, restores equal expression of X-chromosomal genes between females and males. However, ~10% of genes show variable degrees of escape from XCI between females, although little is known about the causes of variable XCI. Using a discovery data-set of 1867 females and 1398 males and a replication sample of 3351 females, we show that genetic variation at three autosomal loci is associated with female-specific changes in X-chromosome methylation. Through cis-eQTL expression analysis, we map these loci to the genes SMCHD1/METTL4, TRIM6/HBG2, and ZSCAN9. Low-expression alleles of the loci are predominantly associated with mild hypomethylation of CpG islands near genes known to variably escape XCI, implicating the autosomal genes in variable XCI. Together, these results suggest a genetic basis for variable escape from XCI and highlight the potential of a population genomics approach to identify genes involved in XCI.
Implementation and benchmarking of a novel analytical framework to clinically evaluate tumor-specific fluorescent tracers
Authors: Koller Marjory , Qiu Si-Qi , Linssen Matthijs D. , Jansen Liesbeth , Kelder Wendy , de Vries Jakob , Kruithof Inge , Zhang Guo-Jun , Robinson Dominic J. , Nagengast Wouter B. , Jorritsma-Smit Annelies , van der Vegt Bert , van Dam Gooitzen M. 
Published: September 2018

AbstractDuring the last decade, the emerging field of molecular fluorescence imaging has led to the development of tumor-specific fluorescent tracers and an increase in early-phase clinical trials without having consensus on a standard methodology for evaluating an optical tracer. By combining multiple complementary state-of-the-art clinical optical imaging techniques, we propose a novel analytical framework for the clinical translation and evaluation of tumor-targeted fluorescent tracers for molecular fluorescence imaging which can be used for a range of tumor types and with different optical tracers. Here we report the implementation of this analytical framework and demonstrate the tumor-specific targeting of escalating doses of the near-infrared fluorescent tracer bevacizumab-800CW on a macroscopic and microscopic level. We subsequently demonstrate an 88% increase in the intraoperative detection rate of tumor-involved margins in primary breast cancer patients, indicating the clinical feasibility and support of future studies to evaluate the definitive clinical impact of fluorescence-guided surgery.
Nonreciprocal responses from non-centrosymmetric quantum materials
Authors: Tokura Yoshinori , Nagaosa Naoto 
Published: September 2018

AbstractDirectional transport and propagation of quantum particle and current, such as electron, photon, spin, and phonon, are known to occur in the materials system with broken inversion symmetry, as exemplified by the diode in semiconductor p–n junction and the natural optical activity in chiral materials. Such a nonreciprocal response in the quantum materials of noncentrosymmetry occurs ubiquitously when the time-reversal symmetry is further broken by applying a magnetic field or with spontaneous magnetization, such as the magnetochiral effect and the nonreciprocal magnon transport or spin current in chiral magnets. In the nonlinear regime responding to the square of current and electric field, even a more variety of nonreciprocal phenomena can show up, including the photocurrent of topological origin and the unidirectional magnetoresistance in polar/chiral semiconductors. Microscopically, these nonreciprocal responses in the quantum materials are frequently encoded by the quantum Berry phase, the toroidal moment, and the magnetoelectric monopole, thus cultivating the fertile ground of the functional topological materials. Here, we review the basic mechanisms and emergent phenomena and functions of the nonreciprocal responses in the noncentrosymmetric quantum materials.
The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice
Authors: Kindt Alida , Liebisch Gerhard , Clavel Thomas , Haller Dirk , Hörmannsperger Gabriele , Yoon Hongsup , Kolmeder Daniela , Sigruener Alexander , Krautbauer Sabrina , Seeliger Claudine , Ganzha Alexandra , Schweizer Sabine , Morisset Rosalie , Strowig Till , Daniel Hannelore , Helm Dominic , Küster Bernhard , Krumsiek Jan , Ecker Josef 
Published: September 2018

AbstractInteractions between the gut microbial ecosystem and host lipid homeostasis are highly relevant to host physiology and metabolic diseases. We present a comprehensive multi-omics view of the effect of intestinal microbial colonization on hepatic lipid metabolism, integrating transcriptomic, proteomic, phosphoproteomic, and lipidomic analyses of liver and plasma samples from germfree and specific pathogen-free mice. Microbes induce monounsaturated fatty acid generation by stearoyl-CoA desaturase 1 and polyunsaturated fatty acid elongation by fatty acid elongase 5, leading to significant alterations in glycerophospholipid acyl-chain profiles. A composite classification score calculated from the observed alterations in fatty acid profiles in germfree mice clearly differentiates antibiotic-treated mice from untreated controls with high sensitivity. Mechanistic investigations reveal that acetate originating from gut microbial degradation of dietary fiber serves as precursor for hepatic synthesis of C16 and C18 fatty acids and their related glycerophospholipid species that are also released into the circulation.
Extremely rare variants reveal patterns of germline mutation rate heterogeneity in humans
Authors: Carlson Jedidiah , Locke Adam E. , Flickinger Matthew , Zawistowski Matthew , Levy Shawn , Myers Richard M. , Boehnke Michael , Kang Hyun Min , Scott Laura J. , Li Jun Z. , Zöllner Sebastian ,   The BRIDGES Consortium, Absher Devin , Akil Huda , Breen Gerome , Burmeister Margit , Cohen-Woods Sarah , Iacono William G. , Knowles James A. , Legrand Lisa , Lu Qing , McGue Matthew , McInnis Melvin G. , Pato Carlos N. , Pato Michele T. , Rivera Margarita , Sobell Janet L. , Vincent John B. , Watson Stanley J. 
Published: September 2018

AbstractA detailed understanding of the genome-wide variability of single-nucleotide germline mutation rates is essential to studying human genome evolution. Here, we use ~36 million singleton variants from 3560 whole-genome sequences to infer fine-scale patterns of mutation rate heterogeneity. Mutability is jointly affected by adjacent nucleotide context and diverse genomic features of the surrounding region, including histone modifications, replication timing, and recombination rate, sometimes suggesting specific mutagenic mechanisms. Remarkably, GC content, DNase hypersensitivity, CpG islands, and H3K36 trimethylation are associated with both increased and decreased mutation rates depending on nucleotide context. We validate these estimated effects in an independent dataset of ~46,000 de novo mutations, and confirm our estimates are more accurate than previously published results based on ancestrally older variants without considering genomic features. Our results thus provide the most refined portrait to date of the factors contributing to genome-wide variability of the human germline mutation rate.
Aerosol-induced intensification of cooling effect of clouds during Indian summer monsoon
Authors: Sarangi Chandan , Kanawade Vijay P. , Tripathi Sachchida N. , Thomas Abin , Ganguly Dilip 
Published: September 2018

AbstractMeasurements and models show that enhanced aerosol concentrations can modify macro- and micro-physical properties of clouds. Here, we examine the effect of aerosols on continental mesoscale convective cloud systems during the Indian summer monsoon and find that these aerosol–cloud interactions have a net cooling effect at the surface and the top-of-atmosphere. Long-term (2002–2016) satellite data provide evidence of aerosol-induced cloud invigoration effect (AIvE) during the Indian summer monsoon. The AIvE leads to enhanced formation of thicker stratiform anvil clouds at higher altitudes. These AIvE-induced stratiform anvil clouds are also relatively brighter because of the presence of smaller sized ice particles. As a result, AIvE-induced increase in shortwave cloud radiative forcing is much larger than longwave cloud radiative forcing leading to the intensified net cooling effect of clouds over the Indian summer monsoon region. Such aerosol-induced cooling could subsequently decrease the surface diurnal temperature range and have significant feedbacks on lower tropospheric turbulence in a warmer and polluted future scenario.
Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
Authors: Seif Yara , Kavvas Erol , Lachance Jean-Christophe , Yurkovich James T. , Nuccio Sean-Paul , Fang Xin , Catoiu Edward , Raffatellu Manuela , Palsson Bernhard O. , Monk Jonathan M. 
Published: September 2018

AbstractSalmonellastrains are traditionally classified into serovars based on their surface antigens. While increasing availability of whole-genome sequences has allowed for more detailed subtyping of strains, links between genotype, serovar, and host remain elusive. Here we reconstruct genome-scale metabolic models for 410Salmonellastrains spanning 64 serovars. Model-predicted growth capabilities in over 530 different environments demonstrate that: (1) theSalmonellaaccessory metabolic network includes alternative carbon metabolism, and cell wall biosynthesis; (2) metabolic capabilities correspond to each strain’s serovar and isolation host; (3) growth predictions agree with 83.1% of experimental outcomes for 12 strains (690 out of 858); (4) 27 strains are auxotrophic for at least one compound, includingl-tryptophan, niacin,l-histidine,l-cysteine, and p-aminobenzoate; and (5) the catabolic pathways that are important for fitness in the gastrointestinal environment are lost amongst extraintestinal serovars. Our results reveal growth differences that may reflect adaptation to particular colonization sites.
Microglial dopamine receptor elimination defines sex-specific nucleus accumbens development and social behavior in adolescent rats
Authors: Kopec Ashley M. , Smith Caroline J. , Ayre Nathan R. , Sweat Sean C. , Bilbo Staci D. 
Published: September 2018

AbstractAdolescence is a developmental period in which the mesolimbic dopaminergic “reward” circuitry of the brain, including the nucleus accumbens (NAc), undergoes significant plasticity. Dopamine D1 receptors (D1rs) in the NAc are critical for social behavior, but how these receptors are regulated during adolescence is not well understood. In this report, we demonstrate that microglia and complement-mediated phagocytic activity shapes NAc development by eliminating D1rs in male, but not female rats, during adolescence. Moreover, immune-mediated elimination of D1rs is required for natural developmental changes in male social play behavior. These data demonstrate for the first time that microglia and complement-mediated immune signaling (i) participate in adolescent brain development in a sex-specific manner, and (ii) are causally implicated in developmental changes in behavior. These data have broad implications for understanding the adolescent critical period of development, the molecular mechanisms underlying social behavior, and sex differences in brain structure and function.
rec-YnH enables simultaneous many-by-many detection of direct protein–protein and protein–RNA interactions
Authors: Yang Jae-Seong , Garriga-Canut Mireia , Link Nele , Carolis Carlo , Broadbent Katrina , Beltran-Sastre Violeta , Serrano Luis , Maurer Sebastian P. 
Published: September 2018

AbstractKnowing which proteins and RNAs directly interact is essential for understanding cellular mechanisms. Unfortunately, discovering such interactions is costly and often unreliable. To overcome these limitations, we developed rec-YnH, a new yeast two and three-hybrid-based screening pipeline capable of detecting interactions within protein libraries or between protein libraries and RNA fragment pools. rec-YnH combines batch cloning and transformation with intracellular homologous recombination to generate bait–prey fusion libraries. By developing interaction selection in liquid–gels and using an ORF sequence-based readout of interactions via next-generation sequencing, we eliminate laborious plating and barcoding steps required by existing methods. We use rec-Y2H to simultaneously map interactions of protein domains and reveal novel putative interactors of PAR proteins. We further employ rec-Y2H to predict the architecture of published coprecipitated complexes. Finally, we use rec-Y3H to map interactions between multiple RNA-binding proteins and RNAs—the first time interactions between protein and RNA pools are simultaneously detected.
A conserved glycine harboring disease-associated mutations permits NMDA receptor slow deactivation and high Ca2+ permeability
Authors: Amin Johansen B. , Leng Xiaoling , Gochman Aaron , Zhou Huan-Xiang , Wollmuth Lonnie P. 
Published: September 2018

AbstractA variety of de novo and inherited missense mutations associated with neurological disorders are found in the NMDA receptor M4 transmembrane helices, which are peripheral to the pore domain in eukaryotic ionotropic glutamate receptors. Subsets of these mutations affect receptor gating with dramatic effects, including in one instance halting it, occurring at a conserved glycine near the extracellular end of M4. Functional experiments and molecular dynamic simulations of constructs with and without substitutions at this glycine indicate that it acts as a hinge, permitting the intracellular portion of the ion channel to laterally expand. This expansion stabilizes long-lived open states leading to slow deactivation and high Ca2+ permeability. Our studies provide a functional and structural framework for the effect of missense mutations on NMDARs at central synapses and highlight how the M4 segment may represent a pathway for intracellular modulation of NMDA receptor function.
Proteomics reveals signal peptide features determining the client specificity in human TRAP-dependent ER protein import
Authors: Nguyen Duy , Stutz Regine , Schorr Stefan , Lang Sven , Pfeffer Stefan , Freeze Hudson H. , Förster Friedrich , Helms Volkhard , Dudek Johanna , Zimmermann Richard 
Published: September 2018

AbstractIn mammalian cells, one-third of all polypeptides are transported into or across the ER membrane via the Sec61 channel. While the Sec61 complex facilitates translocation of all polypeptides with amino-terminal signal peptides (SP) or transmembrane helices, the Sec61-auxiliary translocon-associated protein (TRAP) complex supports translocation of only a subset of precursors. To characterize determinants of TRAP substrate specificity, we here systematically identify TRAP-dependent precursors by analyzing cellular protein abundance changes upon TRAP depletion using quantitative label-free proteomics. The results are validated in independent experiments by western blotting, quantitative RT-PCR, and complementation analysis. The SPs of TRAP clients exhibit above-average glycine-plus-proline content and below-average hydrophobicity as distinguishing features. Thus, TRAP may act as SP receptor on the ER membrane’s cytosolic face, recognizing precursor polypeptides with SPs of high glycine-plus-proline content and/or low hydrophobicity, and triggering substrate-specific opening of the Sec61 channel through interactions with the ER-lumenal hinge of Sec61α.
Complex strain evolution of polar and magnetic order in multiferroic BiFeO3 thin films
Authors: Chen Zuhuang , Chen Zhanghui , Kuo Chang-Yang , Tang Yunlong , Dedon Liv R. , Li Qian , Zhang Lei , Klewe Christoph , Huang Yen-Lin , Prasad Bhagwati , Farhan Alan , Yang Mengmeng , Clarkson James D. , Das Sujit , Manipatruni Sasikanth , Tanaka A. , Shafer Padraic , Arenholz Elke , Scholl Andreas , Chu Ying-Hao , Qiu Z. Q. , Hu Zhiwei , Tjeng Liu-Hao , Ramesh Ramamoorthy , Wang Lin-Wang , Martin Lane W. 
Published: September 2018

AbstractElectric-field control of magnetism requires deterministic control of the magnetic order and understanding of the magnetoelectric coupling in multiferroics like BiFeO3 and EuTiO3. Despite this critical need, there are few studies on the strain evolution of magnetic order in BiFeO3 films. Here, in (110)-oriented BiFeO3 films, we reveal that while the polarization structure remains relatively unaffected, strain can continuously tune the orientation of the antiferromagnetic-spin axis across a wide angular space, resulting in an unexpected deviation of the classical perpendicular relationship between the antiferromagnetic axis and the polarization. Calculations suggest that this evolution arises from a competition between the Dzyaloshinskii–Moriya interaction and single-ion anisotropy wherein the former dominates at small strains and the two are comparable at large strains. Finally, strong coupling between the BiFeO3 and the ferromagnet Co0.9Fe0.1 exists such that the magnetic anisotropy of the ferromagnet can be effectively controlled by engineering the orientation of the antiferromagnetic-spin axis.