bluuebunny/crossref_metadata_2025 huggingface dataset:
Frequency of eating alone is associated with adolescent dietary intake, perceived food-related parenting practices and weight status: cross-sectional Family Life, Activity, Sun, Health, and Eating (FLASHE) Study results
Authors: Reicks Marla , Davey Cynthia , Anderson Alex Kojo , Banna Jinan , Cluskey Mary , Gunther Carolyn , Jones Blake , Richards Rickelle , Topham Glade , Wong Siew Sun
Published: February 2019

Objective

To examine relationships between frequency of adolescents eating alone (dependent variable) and diet, weight status and perceived food-related parenting practices (independent variables).

Design

Analyses of publicly available, cross-sectional, web-based survey data from adolescents.

Setting

Online consumer opinion panel.

Subjects

A US nationwide sample of adolescents (12–17 years) completed Family Life, Activity, Sun, Health, and Eating (FLASHE) Study surveys to report demographic and family meal characteristics, weight, dietary intake, home food availability and perceptions of parenting practices. Parents provided information about demographic characteristics. Logistic regression analyses were used to test for associations between variables.

Results

About 20 % of adolescents reported often eating alone (n 343) v. not often eating alone (n 1309). Adjusted odds of adolescents often eating alone were significantly higher for non-Hispanic Black compared with non-Hispanic White adolescents (OR=1·7) and for overweight or obese compared with normal- or underweight adolescents (OR=1·6). Adjusted odds of adolescents eating alone were significantly lower for those who reported that fruits and vegetables were often/always available in the home (OR=0·65), for those who perceived that parents had expectations about fruit and vegetable intake (OR=0·71) and for those who agreed with parental authority to make rules about intake of junk food/sugary drinks (OR=0·71). Junk food and sugary drink daily intake frequency was positively associated with often eating alone.

Conclusions

Often eating alone was related to being overweight/obese, having less healthy dietary intake and perceptions of less supportive food-related parenting practices.
Optimizing Answer Set Computation via Heuristic-Based Decomposition
Authors: CALIMERI FRANCESCO , PERRI SIMONA , ZANGARI JESSICA
Published: February 2019

Answer Set Programming (ASP) is a purely declarative formalism developed in the field of logic programming and non-monotonic reasoning: computational problems are encoded by logic programs whose answer sets, corresponding to solutions, are computed by an ASP system. Different, semantically equivalent, programs can be defined for the same problem; however, performance of systems evaluating them might significantly vary. We propose an approach for automatically transforming an input logic program into an equivalent one that can be evaluated more efficiently. One can make use of existing tree-decomposition techniques for rewriting selected rules into a set of multiple ones; the idea is to guide and adaptively apply them on the basis of proper new heuristics, to obtain a smart rewriting algorithm to be integrated into an ASP system. The method is rather general: it can be adapted to any system and implement different preference policies. Furthermore, we define a set of new heuristics tailored at optimizing grounding, one of the main phases of the ASP computation; we use them in order to implement the approach into the ASP systemDLV, in particular into its grounding subsystemℐ-DLV, and carry out an extensive experimental activity for assessing the impact of the proposal.
The role of regulation in constituting markets: a co-evolutionary perspective on the UK television production sector
Authors: Lourenço Ana , Turner Simon
Published: February 2019

This article builds on a legal institutionalist approach to assess market-based regulatory change in British television production over the last three decades. It explores how formal rules governing television production constitute market relations, and whether these rules are likely to be evaded by television producers and commissioners in a context where contracting depends heavily on social norms of cooperation, reciprocity and flexibility. Using qualitative data, this article suggests that changes in law and terms of trade intended to promote a market in television production have not had a straightforward or linear effect: compulsory independent production quotas and licensing models of terms of trade have redrawn organizational boundaries in unexpected ways, disturbed the public service remit and engendered new financial flows. Formal rules were nonetheless central to the trajectory of the television production industry, as they were a constitutive element of changes in the power structure of the sector towards producers’ interests.
Unemployment, Self-esteem, and Depression: Differences between Men and Women
Authors: Álvaro José Luis , Garrido Alicia , Pereira Cícero Roberto , Torres Ana Raquel , Barros Sabrina Cavalcanti
Published: February 2019

Although there is a vast bibliography on the negative consequences of unemployment for mental health, there are no studies that analyze the differences between men and women in relation to the consequences that unemployment could have simultaneously on self-esteem and depression. The main objective of this study was to analyze whether, unemployment is differentially associated with the self-esteem of men and women, and to test whether this circumstance can be considered a psychological mechanism by which we could explain differences in depression for men and women. Results show that self-esteem is a mediating variable (indirect effect = .11; 90% CI [.04, .19]), considering its differential impact on depression, but this mediation is moderated by the gender of the respondents (b = .21, 90% IC [.01, .40]. In summary, unemployment is associated with lower self-esteem, which in turn is related to greater depressive symptoms. This relationship is only observed for men and not for women.
Improvement of cytoprotective and antioxidant activity of Rosa canina L. and Salix alba L. by controlled differential sieving process against H2O2-induced oxidative stress in mouse primary splenocytes
Authors: Soualeh Nidhal , Stiévenard Aliçia , Baudelaire Elie , Soulimani Rachid , Bouayed Jaouad
Published: February 2019

Abstract. In this study, cytoprotective and antioxidant activities of Rosa canina (RC) and Salix alba (SA), medicinal plants, were studied on mouse primary splenocytes by comparing Controlled Differential Sieving process (CDSp), which is a novel green solvent-free process, versus a conventional technique, employing hydroethanolic extraction (HEE). Thus, preventive antioxidant activity of three plant powders of homogeneous particle sizes, 50–100 µm, 100–180 µm and 180–315 µm, dissolved directly in the cellular buffer, were compared to those of hydroethanolic (HE) extract, at 2 concentrations (250 and 500 µg/mL) in H2O2-treated spleen cells. Overall, compared to HE extract, the superfine powders, i. e., fractions < 180 µm, at the lowest concentration, resulted in greater reactive oxygen species (ROS) elimination, increased glutathione peroxidase (GPx) activity and lower malondialdehyde (MDA) production. Better antioxidant and preventive effects in pre-treated cells were found with the superfine powders for SA (i. e., 50–100 µm and 100–180 µm, both p < 0.001), and with the intermediate powder for RC (i. e., 100–180 µm, p < 0.05) versus HE extract. The activity levels of catalase (CAT) and superoxide dismutase (SOD) in pretreated splenocytes exposed to H2O2, albeit reduced, were near to those in unexposed cells, suggesting that pretreatment with the fine powders has relatively restored the normal levels of antioxidant-related enzymes. These findings supported that CDSp improved the biological activities of plants, avoiding the use of organic solvents and thus it could be a good alternative to conventional extraction techniques.
Proverb Comprehension Deficits in Patients with Schizophrenia
Authors: Mohnke Margaux , Bach Claudia , Roesch-Ely Daniela
Published: February 2019

Abstract. Patients suffering from schizophrenia typically show difficulty comprehending proverbs. This deficit has been linked to social and neurocognitive domains, such as theory of mind (TOM) and, more recently, working memory (WM). It is still unclear which cognitive deficits underlie proverb comprehension. We analyzed possible associations of proverb comprehension to neurocognitive and social cognitive dysfunctions in 64 patients with schizophrenia spectrum disorders, by combining tests measuring executive functions (inhibition, cognitive flexibility, planning), WM (verbal and visuo-spatial), and social cognition (TOM). A hierarchical regression demonstrated that WM and executive dysfunction best predicted proverb comprehension, which in turn supports the conceptual integration model. Social cognition showed no additional predictive value. The ability to comprehend figurative language might depend more on neurocognitive than on social cognitive abilities.
Differences in Suicide Risk Severity Among Suicidal Youth With Anxiety Disorders
Authors: Herres Joanna , Shearer Annie , Kodish Tamar , Kim Barunie , Wang Shirley B. , Diamond Guy S.
Published: February 2019

Abstract. Background: Adolescent suicidality is a growing public health concern. Although evidence supports a link between anxiety and suicidality, little is known about risk associated with specific anxiety disorders. Aims: This study examined the prevalence of anxiety disorders in a sample of adolescents with depression and suicidal ideation and the associations between specific anxiety disorders and suicide ideation severity and attempt history. Method: The sample consisted of 115 adolescents ( Mage = 14.96 years; 55.8% African American) entering a clinical trial for suicidal ideation and depressive symptoms. Prior to treatment, adolescents completed self-report and interview measures. Results: In all, 48% of the sample met criteria for an anxiety disorder, 22% met criteria for social anxiety disorder (SAD), and 40% met criteria for major depressive disorder (MDD). SAD was uniquely associated with more severe suicidal ideation. Limitations: Findings may not generalize to all suicidal adolescents, and non-measured variables may account for the observed relationships. Conclusion: Future research should examine whether targeting social anxiety would improve treatment response for suicidal adolescents.
Investigation on the Multiparameter of Hydrate‐Bearing Sands Using Nano‐Focus X‐Ray Computed Tomography
Authors: Li Chengfeng , Liu Changling , Hu Gaowei , Sun Jianye , Hao Xiluo , Liu Lele , Meng Qingguo
Published: February 2019

In this study, a nano‐focus X‐ray computed tomography (X‐CT) is used to observe the formation of methane hydrate in sands on pore scale and to quantify hydrate saturation, pore structure parameters, and permeability of hydrate‐bearing sands. A new analytical technique is developed to improve the identification of water‐hydrate boundary. Three hydrate accumulation habits (i.e., floating, contacting, and cementing) in pore spaces are observed. When there is no methane bubble, hydrate distribution evolves from floating to contacting and then to cementing as hydrate saturation increases. In contrast, only contacting and cementing distribution patterns appear in the pores with methane bubbles. Based on the surface extraction and defect detection from 3‐D images, both the gas/water/hydrate distributions and the pore structure characteristics are investigated. The results show that the porosity, the maximal pore volume, and maximal diameter decrease as hydrates accumulate in the pores. However, the maximal pore surface, the total pore number, and the large pores (>100 voxels) number increase gradually until the hydrate saturation reaches 35%, when they turn to decrease rapidly. The pore structure parameters show detailed changes of hydrate and water on pore scale. The incompressible Navier‐Stokes equations are used to calculate absolute permeability of hydrate‐bearing sands based on X‐ray computed tomography digital images. It indicates that the microdistribution of the hydrate has a significant effect on the permeability calculation. The fluid streamlines obtained through simulation are used to track the water transport paths.
Tomographic Pn Velocity and Anisotropy Structure in Mongolia and the Adjacent Regions
Authors: He Jing , Li Yonghua , Sandvol Eric , Wu Qingju , Du Guangbao , Zhang Ruiqing , Yu Daxin , Liu Hanlin , Lei Jianshe , Huang Jianping
Published: February 2019

We present new high‐resolution Pn velocity and anisotropy models beneath Mongolia and the adjacent regions by inverting 169,406 Pn arrivals. The data are selected from 786 permanent stations and 106 portable seismographs recently deployed in Mongolia and China's Inner Mongolia. The availability of new data acquired has allowed us to explore the uppermost mantle structures in great detail in this region, and the 2° × 2° model resolution is capable of distinguishing small‐scale geological features. Pn average velocity is 8.18 km/s, substantially faster than the global average. Distinct contrast in the velocity of the uppermost mantle is observed between the central part and two ends of the Baikal Rift, with the presence of higher velocities under the Central Baikal Rift, indicating strong variation of lithospheric thinning across the entire Baikal Rift. Low velocity beneath the Hangay Dome implies partial melting of mantle reflected by asthenospheric upwelling. Azimuthal anisotropy in the upper and lower mantle lid is measured by grouping the travel time data into two phases by epicenter distance. The obvious depth dependence of Pn anisotropy beneath the Hentey Mountains suggests different origins of fabrics. The lower anisotropy may origin from asthenospheric flow, while the shallower fabric may exhibit the preserved lattice preferred orientation anisotropy in the uppermost mantle. Meanwhile, depth‐dependent anisotropic structures and significantly low velocity are found beneath Tien Shan, most possibly suggesting that the lithospheric mantle thinning is experienced by either delamination or local asthenospheric upwelling.
A Hybrid Correlation Model for the Spaced‐Receiver Technique
Authors: Wang Jun , Morton Y. Jade
Published: February 2019

A Global Navigation Satellite System (GNSS) spaced‐receiver technique estimates ionospheric irregularity drift velocity by correlating the received GNSS signals across a closely spaced receiver array during ionospheric scintillations. This paper focuses on the correlation models accounting for the topology of the received diffraction pattern. Space‐time correlation schematics are developed to analyze and compare several prevalent models, including the classic isotropy model, the front velocity model, and the anisotropy model. Based on the merits and drawbacks of each model, a hybrid correlation model is proposed, integrating the front velocity model and the anisotropy model. To validate the hybrid model, the corresponding drift velocity estimates are cross compared with the measurements from a colocated all‐sky imager and incoherent scatter radar. A case study was conducted for a geomagnetic storm event on 20 December 2015. Favorable agreement was found in terms of direction and magnitude of the drift motion, orientation of the irregularity, temporal and spatial features of the irregularity, and the statistical behavior of the drift velocity estimates. In addition, the root‐mean‐square velocity magnitude and orientation against the incoherent scatter radar measurements demonstrate the superior performance of the hybrid model.
A Preliminary Impact Study of CYGNSS Ocean Surface Wind Speeds on Numerical Simulations of Hurricanes
Authors: Cui Zhiqiang , Pu Zhaoxia , Tallapragada Vijay , Atlas Robert , Ruf Christopher S.
Published: February 2019

The NASA Cyclone Global Navigation Satellite System (CYGNSS) was launched in December 2016, providing an unprecedented opportunity to obtain ocean surface wind speeds including wind estimates over the hurricane inner‐core region. This study demonstrates the influence of assimilating an early version of CYGNSS observations of ocean surface wind speeds on numerical simulations of two notable landfalling hurricanes, Harvey and Irma (2017). A research version of the National Centers for Environmental Prediction operational Hurricane Weather Research and Forecasting model and the Gridpoint Statistical Interpolation‐based hybrid ensemble three‐dimensional variational data assimilation system are used. It is found that the assimilation of CYGNSS data results in improved track, intensity, and structure forecasts for both hurricane cases, especially for the weak phase of a hurricane, implying potential benefits of using such data for future research and operational applications.
Correction: Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence
Authors: Smet Annemieke , Yahara Koji , Rossi Mirko , Tay Alfred , Backert Steffen , Ensser Armin , Fox James G , Flahou Bram , Ducatelle Richard , Haesebrouck Freddy , Corander Jukka
Published: February 2019

The original version of this Article contained an error in the presentation of the author Armin Ensser, which was incorrectly given as Ensser Armin. The correct author list is as follows:
Correction: High expression of HMGA2 independently predicts poor clinical outcomes in acute myeloid leukemia
Authors: Marquis Miriam , Beaubois Cyrielle , Lavallée Vincent-Philippe , Abrahamowicz Michal , Danieli Coraline , Lemieux Sébastien , Ahmad Imran , Wei Andrew , Ting Stephen B. , Fleming Shaun , Schwarer Anthony , Grimwade David , Grey William , Hills Robert K. , Vyas Paresh , Russell Nigel , Sauvageau Guy , Hébert Josée
Published: February 2019

Since the publication of the original article the authors noticed the the affiliation details for Paresh Vyas are incorrect. The correct affiliation details for this author are given below:
Maturation-associated gene expression profiles during normal human bone marrow erythropoiesis
Authors: Mello Fabiana V. , Land Marcelo G. P. , Costa Elaine. S. , Teodósio Cristina , Sanchez María-Luz , Bárcena Paloma , Peres Rodrigo T. , Pedreira Carlos E. , Alves Liliane R. , Orfao Alberto
Published: February 2019

Erythropoiesis has been extensively studied using in vitro and in vivo animal models. Despite this, there is still limited data about the gene expression profiles (GEP) of primary (ex vivo) normal human bone marrow (BM) erythroid maturation. We investigated the GEP of nucleated red blood cell (NRBC) precursors during normal human BM erythropoiesis. Three maturation-associated populations of NRBC were identified and purified from (fresh) normal human BM by flow cytometry and the GEP of each purified cell population directly analyzed using DNA-oligonucleotide microarrays. Overall, 6569 genes (19% of the genes investigated) were expressed in ≥1 stage of BM erythropoiesis at stable (e.g., genes involved in DNA process, cell signaling, protein organization and hemoglobin production) or variable amounts (e.g., genes related to cell differentiation, apoptosis, metabolism), the latter showing a tendency to either decrease from stage 1 to 3 (genes associated with regulation of erythroid differentiation and survival, e.g., SPI1, STAT5A) or increase from stage 2 to stage 3 (genes associated with autophagy, erythroid functions such as heme production, e.g., ALAS1, ALAS2), iron metabolism (e.g., ISCA1, SLC11A2), protection from oxidative stress (e.g., UCP2, PARK7), and NRBC enucleation (e.g., ID2, RB1). Interestingly, genes involved in apoptosis (e.g., CASP8, P2RX1) and immune response (e.g., FOXO3, TRAF6) were also upregulated in the last stage (stage 3) of maturation of NRBC precursors. Our results confirm and extend on previous observations and providing a frame of reference for better understanding the critical steps of human erythroid maturation and its potential alteration in patients with different clonal and non-clonal erythropoietic disorders.
Gamma oscillations in somatosensory cortex recruit prefrontal and descending serotonergic pathways in aversion and nociception
Authors: Tan Linette Liqi , Oswald Manfred Josef , Heinl Céline , Retana Romero Oscar Andrés , Kaushalya Sanjeev Kumar , Monyer Hannah , Kuner Rohini
Published: February 2019

In humans, gamma-band oscillations in the primary somatosensory cortex (S1) correlate with subjective pain perception. However, functional contributions to pain and the nature of underlying circuits are unclear. Here we report that gamma oscillations, but not other rhythms, are specifically strengthened independently of any motor component in the S1 cortex of mice during nociception. Moreover, mice with inflammatory pain show elevated resting gamma and alpha activity and increased gamma power in response to sub-threshold stimuli, in association with behavioral nociceptive hypersensitivity. Inducing gamma oscillations via optogenetic activation of parvalbumin-expressing inhibitory interneurons in the S1 cortex enhances nociceptive sensitivity and induces aversive avoidance behavior. Activity mapping identified a network of prefrontal cortical and subcortical centers whilst morphological tracing and pharmacological studies demonstrate the requirement of descending serotonergic facilitatory pathways in these pain-related behaviors. This study thus describes a mechanistic framework for modulation of pain by specific activity patterns in the S1 cortex.
Atomically engineering activation sites onto metallic 1T-MoS2 catalysts for enhanced electrochemical hydrogen evolution
Authors: Huang Yichao , Sun Yuanhui , Zheng Xueli , Aoki Toshihiro , Pattengale Brian , Huang Jier , He Xin , Bian Wei , Younan Sabrina , Williams Nicholas , Hu Jun , Ge Jingxuan , Pu Ning , Yan Xingxu , Pan Xiaoqing , Zhang Lijun , Wei Yongge , Gu Jing
Published: February 2019

Engineering catalytic sites at the atomic level provides an opportunity to understand the catalyst’s active sites, which is vital to the development of improved catalysts. Here we show a reliable and tunable polyoxometalate template-based synthetic strategy to atomically engineer metal doping sites onto metallic 1T-MoS2, using Anderson-type polyoxometalates as precursors. Benefiting from engineering nickel and oxygen atoms, the optimized electrocatalyst shows great enhancement in the hydrogen evolution reaction with a positive onset potential of ~ 0 V and a low overpotential of −46 mV in alkaline electrolyte, comparable to platinum-based catalysts. First-principles calculations reveal co-doping nickel and oxygen into 1T-MoS2 assists the process of water dissociation and hydrogen generation from their intermediate states. This research will expand on the ability to improve the activities of various catalysts by precisely engineering atomic activation sites to achieve significant electronic modulations and improve atomic utilization efficiencies.
Ion mobility conformational lipid atlas for high confidence lipidomics
Authors: Leaptrot Katrina L. , May Jody C. , Dodds James N. , McLean John A.
Published: February 2019

Lipids are highly structurally diverse molecules involved in a wide variety of biological processes. Here, we use high precision ion mobility-mass spectrometry to compile a structural database of 456 mass-resolved collision cross sections (CCS) of sphingolipid and glycerophospholipid species. Our CCS database comprises sphingomyelin, cerebroside, ceramide, phosphatidylethanolamine, phosphatidylcholine, phosphatidylserine, and phosphatidic acid classes. Primary differences observed are between lipid categories, with sphingolipids exhibiting 2–6% larger CCSs than glycerophospholipids of similar mass, likely a result of the sphingosine backbone’s restriction of the sn1 tail length, limiting gas-phase packing efficiency. Acyl tail length and degree of unsaturation are found to be the primary structural descriptors determining CCS magnitude, with degree of unsaturation being four times as influential per mass unit. The empirical CCS values and previously unmapped quantitative structural trends detailed in this work are expected to facilitate prediction of CCS in broadscale lipidomics research.
Chromosomal markers in the genus Karenia: Towards an understanding of the evolution of the chromosomes, life cycle patterns and phylogenetic relationships in dinoflagellates
Authors: Cuadrado Ángeles , De Bustos Alfredo , Figueroa Rosa I.
Published: February 2019

Dinoflagellates are a group of protists whose genome is unique among eukaryotes in terms of base composition, chromosomal structure and gene expression. Even after decades of research, the structure and behavior of their amazing chromosomes—which without nucleosomes exist in a liquid crystalline state—are still poorly understood. We used flow cytometry and fluorescence in situ hybridization (FISH) to analyze the genome size of three species of the toxic dinoflagellate genus Karenia as well the organization and behavior of the chromosomes in different cell-cycle stages. FISH was also used to study the distribution patterns of ribosomal DNA (45S rDNA), telomeric and microsatellites repeats in order to develop chromosomal markers. The results revealed several novel and important features regarding dinoflagellate chromosomes during mitosis, including their telocentric behavior and radial arrangement along the nuclear envelope. Additionally, using the (AG)10 probe we identified an unusual chromosome in K. selliformis and especially in K. mikimotoi that is characterized by AG repeats along its entire length. This feature was employed to easily differentiate morphologically indistinguishable life-cycle stages. The evolutionary relationship between Karenia species is discussed with respect to differences in both DNA content and the chromosomal distribution patterns of the DNA sequences analyzed.
Migrated T lymphocytes into malignant pleural effusions: an indicator of good prognosis in lung adenocarcinoma patients
Authors: Nieto Juan C. , Zamora Carlos , Porcel José M. , Mulet Maria , Pajares Virginia , Muñoz-Fernandez Ana M. , Calvo Nuria , Espinosa Iñigo , Pascual-García Mónica , Bielsa Silvia , Vidal Silvia
Published: February 2019

The presence of leukocyte subpopulations in malignant pleural effusions (MPEs) can have a different impact on tumor cell proliferation and vascular leakiness, their analysis can help to understand the metastatic microenvironment. We analyzed the relationship between the leukocyte subpopulation counts per ml of pleural fluid and the tumor cell count, molecular phenotype of lung adenocarcinoma (LAC), time from cancer diagnosis and previous oncologic therapy. We also evaluated the leukocyte composition of MPEs as a biomarker of prognosis. We determined CD4+ T, CD8+ T and CD20+ B cells, monocytes and neutrophils per ml in pleural effusions of 22 LAC and 10 heart failure (HF) patients by flow cytometry. Tumor cells were identified by morphology and CD326 expression. IFNγ, IL-10 and IL-17, and chemokines were determined by ELISAs and migratory response to pleural fluids by transwell assays. MPEs from LAC patients had more CD8+ T lymphocytes and a tendency to more CD4+ T and CD20+ B lymphocytes than HF-related fluids. However, no correlation was found between lymphocytes and tumor cells. In those MPEs which were detected >1 month from LAC diagnosis, there was a negative correlation between pleural tumor cells and CD8+ T lymphocytes. CXCL10 was responsible for the attraction of CD20+ B, CD4+ T and CD8+ T lymphocytes in malignant fluids. Concentrations of IL-17 were higher in MPEs than in HF-related effusions. Survival after MPE diagnosis correlated positively with CD4+ T and CD8+ T lymphocytes, but negatively with neutrophils and IL-17 levels. In conclusion, lymphocyte enrichment in MPEs from LAC patients is mostly due to local migration and increases patient survival.
Brain-stiffness-mimicking tilapia collagen gel promotes the induction of dorsal cortical neurons from human pluripotent stem cells
Authors: Iwashita Misato , Ohta Hatsumi , Fujisawa Takahiro , Cho Minyoung , Ikeya Makoto , Kidoaki Satoru , Kosodo Yoichi
Published: February 2019

The mechanical properties of the extracellular microenvironment, including its stiffness, play a crucial role in stem cell fate determination. Although previous studies have demonstrated that the developing brain exhibits spatiotemporal diversity in stiffness, it remains unclear how stiffness regulates stem cell fate towards specific neural lineages. Here, we established a culture substrate that reproduces the stiffness of brain tissue using tilapia collagen for in vitro reconstitution assays. By adding crosslinkers, we obtained gels that are similar in stiffness to living brain tissue (150–1500 Pa). We further examined the capability of the gels serving as a substrate for stem cell culture and the effect of stiffness on neural lineage differentiation using human iPS cells. Surprisingly, exposure to gels with a stiffness of approximately 1500 Pa during the early period of neural induction promoted the production of dorsal cortical neurons. These findings suggest that brain-stiffness-mimicking gel has the potential to determine the terminal neural subtype. Taken together, the crosslinked tilapia collagen gel is expected to be useful in various reconstitution assays that can be used to explore the role of stiffness in neurogenesis and neural functions. The enhanced production of dorsal cortical neurons may also provide considerable advantages for neural regenerative applications.
Digestion dynamics in broilers fed rapeseed meal
Authors: Recoules E. , Lessire M. , Labas V. , Duclos M. J. , Combes-Soia L. , Lardic L. , Peyronnet C. , Quinsac A. , Narcy A. , Réhault-Godbert S.
Published: February 2019

Rapeseed proteins are described to be poorly digestible in chickens. To further identify some molecular locks that may limit their use in poultry nutrition, we conducted a proteomic study on the various chicken digestive contents and proposed an integrative view of the proteins recruited in the crop, proventriculus/gizzard, duodenum, jejunum, and ileum for digestion of rapeseed by-products. Twenty-seven distinct rapeseed proteins were identified in the hydrosoluble fraction of the feed prior ingestion. The number of rapeseed proteins identified in digestive contents decreases throughout the digestion process while some are progressively solubilized in the most distal digestive segment, likely due to a combined effect of pH and activity of specific hydrolytic enzymes. Fifteen chicken proteins were identified in the hydrosoluble proventriculus/gizzard content, including chymotrypsin-like elastase and pepsin. Interestingly, on the 69 distinct proteins identified in duodenum, only 9 were proteolytic enzymes, whereas the others were associated with homeostasis, and carbohydrate, lipid, vitamin and hormone metabolisms. In contrast, chicken proteins identified in jejunal and ileal contents were mostly proteases and peptidases. The present work highlights the relevance of using integrative proteomics applied to the entire digestive tract to better appreciate the protein profile and functions of each digestive segment.
Comprehensive sequencing of the myocilin gene in a selected cohort of severe primary open-angle glaucoma patients
Authors: O’Gorman Luke , Cree Angela J. , Ward Daniel , Griffiths Helen L. , Sood Roshan , Denniston Alastair K. , Self Jay E. , Ennis Sarah , Lotery Andrew J. , Gibson Jane
Published: February 2019

Primary open-angle glaucoma (POAG) is the most common form of glaucoma, prevalent in approximately 1–2% of Caucasians in the UK over the age of 40. It is characterised by an open anterior chamber angle, raised intraocular pressure (IOP) and optic nerve damage leading to loss of sight. The myocilin gene (MYOC) is the most common glaucoma-causing gene, accounting for ~2% of British POAG cases. 358 patients were selected for next generation sequencing (NGS) with the following selection criteria: Caucasian ethnicity, intraocular pressure (IOP) 21–40 mm Hg, cup:disc ratio ≥0.6 and visual field mean deviation ≤−3. The entire MYOC gene (17,321 bp) was captured including the promoter, introns, UTRs and coding exons. We identify 12 exonic variants (one stop-gain, five missense and six synonymous variants), two promoter variants, 133 intronic variants, two 3′ UTR variants and 23 intergenic variants. Four known or predicted pathogenic exonic variants (p.R126W, p.K216K, p.Q368* and p.T419A) were identified across 11 patients, which accounts for 3.07% of this POAG cohort. This is the first time that the entire region of MYOC has been sequenced and variants reported for a cohort of POAG patients.
Reward cues readily direct monkeys’ auditory performance resulting in broad auditory cortex modulation and interaction with sites along cholinergic and dopaminergic pathways
Authors: Wikman Patrik , Rinne Teemu , Petkov Christopher I.
Published: February 2019

In natural settings, the prospect of reward often influences the focus of our attention, but how cognitive and motivational systems influence sensory cortex is not well understood. Also, challenges in training nonhuman animals on cognitive tasks complicate cross-species comparisons and interpreting results on the neurobiological bases of cognition. Incentivized attention tasks could expedite training and evaluate the impact of attention on sensory cortex. Here we develop an Incentivized Attention Paradigm (IAP) and use it to show that macaque monkeys readily learn to use auditory or visual reward cues, drastically influencing their performance within a simple auditory task. Next, this paradigm was used with functional neuroimaging to measure activation modulation in the monkey auditory cortex. The results show modulation of extensive auditory cortical regions throughout primary and non-primary regions, which although a hallmark of attentional modulation in human auditory cortex, has not been studied or observed as broadly in prior data from nonhuman animals. Psycho-physiological interactions were identified between the observed auditory cortex effects and regions including basal forebrain sites along acetylcholinergic and dopaminergic pathways. The findings reveal the impact and regional interactions in the primate brain during an incentivized attention engaging auditory task.
Gold-Nanocluster-Assisted Nanotransfer Printing Method for Metasurface Hologram Fabrication
Authors: Hwang Soon Hyoung , Cho Jaebum , Jeon Sohee , Kang Hyeok-Jung , Zhao Zhi-Jun , Park Sungjae , Lee Yohan , Lee Jonghyun , Kim Mugeon , Hahn Joonku , Lee Byoungho , Jeong Jun Ho , Kim Hwi , Youn Jae Ryoun
Published: February 2019

Given the development of nano/microscale patterning techniques, efforts are being made to use them for fabricating metasurfaces. In particular, by using abrupt phase discontinuities, it is possible to generate holographic images from two-dimensional nanoscale-patterned metasurfaces. However, the fabrication of metasurface holograms is hindered by the high costs and long fabrication time involved, because the process requires expensive equipment such as that for electron-beam lithography. Therefore, it is difficult to realize metasurface holograms in a fast and repetitive manner. In this study, we propose a method for fabricating metasurface holograms based on the nanotransfer printing of the desired nanoscale patterns, which is assisted by Au nanoclusters, while controlling the bonding energy based on the shape of the deposited Au layer. Robust covalent bonds are formed between the Si of the adhesive used and the O of the SiO2 layer in order to transfer the deposited Au onto the transparent substrate quickly. It was found that the fabricated metasurface hologram coincides with the one designed by computer-generated holography. The proposed method should lead to a significant breakthrough in the fabrication of holograms based on different types of metasurfaces at a low cost in a fast, repetitive manner with various metals.
Inferring Temporal Information from a Snapshot of a Dynamic Network
Authors: Sreedharan Jithin K. , Magner Abram , Grama Ananth , Szpankowski Wojciech
Published: February 2019

The problem of reverse-engineering the evolution of a dynamic network, known broadly as network archaeology, is one of profound importance in diverse application domains. In analysis of infection spread, it reveals the spatial and temporal processes underlying infection. In analysis of biomolecular interaction networks (e.g., protein interaction networks), it reveals early molecules that are known to be differentially implicated in diseases. In economic networks, it reveals flow of capital and associated actors. Beyond these recognized applications, it provides analytical substrates for novel studies – for instance, on the structural and functional evolution of the human brain connectome. In this paper, we model, formulate, and rigorously analyze the problem of inferring the arrival order of nodes in a dynamic network from a single snapshot. We derive limits on solutions to the problem, present methods that approach this limit, and demonstrate the methods on a range of applications, from inferring the evolution of the human brain connectome to conventional citation and social networks, where ground truth is known.
Comparison Between Performances of In2O3 and In2TiO5-Based EIS Biosensors Using Post Plasma CF4 Treatment Applied in Glucose and Urea Sensing
Authors: Lin Chun Fu , Kao Chyuan Haur , Lin Chan Yu , Liu Chia Shao , Liu Yi Wen
Published: February 2019

In this study, the effect of post-deposition tetrafluoromethane (CF4) plasma treatment on the physical and electrical characteristics of an In2TiO5 based electrolyte-insulator-semiconductor (EIS) sensor was investigated. Post-deposition CF4 plasma treatment typically improved the crystalline structure and repaired dangling bonds at the grain boundaries. We used the newly fabricated device to detect several ions, such as sodium and potassium, which are essential for many biological processes. The as-deposited and CF4 plasma treated In2TiO5 sensing window with an EIS structure was also able to detect the pH of a solution, different alkali ions (Na+ and K+), glucose, and urea. The sensing membrane after a 60-sec CF4 plasma treatment displayed improved biosensing characteristics, such as higher sensitivity (59.64 mV/pH), better drift rate, and a smaller hysteresis voltage of approximately 0.424 mV/h. The In2TiO5 sensing membrane treated with CF4 plasma is a promising material for use in EIS biosensing applications.
Insights into the karyotype and genome evolution of haplogyne spiders indicate a polyploid origin of lineage with holokinetic chromosomes
Authors: Král Jiří , Forman Martin , Kořínková Tereza , Lerma Azucena C. Reyes , Haddad Charles R. , Musilová Jana , Řezáč Milan , Herrera Ivalú M. Ávila , Thakur Shefali , Dippenaar-Schoeman Ansie S. , Marec František , Horová Lucie , Bureš Petr
Published: February 2019

Spiders are an ancient and extremely diverse animal order. They show a considerable diversity of genome sizes, karyotypes and sex chromosomes, which makes them promising models to analyse the evolution of these traits. Our study is focused on the evolution of the genome and chromosomes in haplogyne spiders with holokinetic chromosomes. Although holokinetic chromosomes in spiders were discovered a long time ago, information on their distribution and evolution in these arthropods is very limited. Here we show that holokinetic chromosomes are an autapomorphy of the superfamily Dysderoidea. According to our hypothesis, the karyotype of ancestral Dysderoidea comprised three autosome pairs and a single X chromosome. The subsequent evolution has frequently included inverted meiosis of the sex chromosome and an increase of 2n. We demonstrate that caponiids, a sister clade to Dysderoidea, have enormous genomes and high diploid and sex chromosome numbers. This pattern suggests a polyploid event in the ancestors of caponiids. Holokinetic chromosomes could have arisen by subsequent multiple chromosome fusions and a considerable reduction of the genome size. We propose that spider sex chromosomes probably do not pose a major barrier to polyploidy due to specific mechanisms that promote the integration of sex chromosome copies into the genome.
Evaluating a scale of excessive mind wandering among males and females with and without attention-deficit/hyperactivity disorder from a population sample
Authors: Mowlem Florence D. , Agnew-Blais Jessica , Pingault Jean-Baptiste , Asherson Philip
Published: February 2019

Recent studies highlight the role of excessive mind wandering in attention-deficit/hyperactivity disorder (ADHD) and its association with impairment. We believe assessing mind wandering could be especially relevant to individuals, including many females, who present with less externalising manifestations of ADHD. Using a new measure based on ADHD patient reports, the Mind Excessively Wandering Scale (MEWS), we previously found adults with ADHD had elevated levels of mind wandering that contributed to impairment independently of core ADHD symptoms. Using data from an online general population survey, the current study assessed the factor-structure, reliability, validity and measurement invariance of the MEWS. We also investigated sex differences in mind wandering, as well as ADHD symptoms, impairment and wellbeing in those with and without ADHD. The MEWS had a unidimensional structure, was invariant across sex, age and ADHD status, and accounted for unique variance in impairment and wellbeing beyond core ADHD symptoms. Among those with ADHD, we found no evidence for sex differences in mind wandering and among those without ADHD males had higher scores. We also found similar levels of hyperactivity/impulsivity, emotional lability, and impairment in males and females with ADHD, but males reported greater inattention and lower wellbeing. Results suggest the MEWS is a reliable and valid instrument measuring the same construct across sex, age and ADHD status, which could aid diagnosis and monitoring of outcomes.
Genotoxic stress increases cytoplasmic mitochondrial DNA editing by human APOBEC3 mutator enzymes at a single cell level
Authors: Mussil Bianka , Suspène Rodolphe , Caval Vincent , Durandy Anne , Wain-Hobson Simon , Vartanian Jean-Pierre
Published: February 2019

Human cells are stressed by numerous mechanisms that can lead to leakage of mitochondrial DNA (mtDNA) to the cytoplasm and ultimately apoptosis. This agonist DNA constitutes a danger to the cell and is counteracted by cytoplasmic DNases and APOBEC3 cytidine deamination of DNA. To investigate APOBEC3 editing of leaked mtDNA to the cytoplasm, we performed a PCR analysis of APOBEC3 edited cytoplasmic mtDNA (cymtDNA) at the single cell level for primary CD4+ T cells and the established P2 EBV blast cell line. Up to 17% of primary CD4+ T cells showed signs of APOBEC3 edited cymtDNA with ~50% of all mtDNA sequences showing signs of APOBEC3 editing – between 1500–5000 molecules. Although the P2 cell line showed a much lower frequency of stressed cells, the number of edited mtDNA molecules in such cells was of the same order. Addition of the genotoxic molecules, etoposide or actinomycin D increased the number of cells showing APOBEC3 edited cymtDNA to around 40%. These findings reveal a very dynamic image of the mitochondrial network, which changes considerably under stress. APOBEC3 deaminases are involved in the catabolism of mitochondrial DNA to circumvent chronic immune stimulation triggered by released mitochondrial DNA from damaged cells.
Insights from distribution dynamics inform strategies to conserve a dhole Cuon alpinus metapopulation in India
Authors: Srivathsa Arjun , Karanth K. Ullas , Kumar N. Samba , Oli Madan K.
Published: February 2019

Most large carnivore populations currently occur in heterogeneous landscapes, with source populations embedded in a matrix of human-dominated habitats. Understanding changes in distribution of endangered carnivores is critical for prioritizing and implementing conservation strategies. We examined distribution and dynamics of a dhole Cuon alpinus metapopulation, first in 2007 and subsequently in 2015, based on indirect sign surveys across 37, 000sq. km of India’s Western Ghats. Predicted dhole occupancy declined from 0.62 (95% CI: 0.58–0.66) in 2007 to 0.54 (95% CI: 0.50–0.58) in 2015. Occupancy was associated with abundance of primary prey species and anthropogenic disturbance. Local extinction appeared to be influenced by forest cover loss, and offset by protected reserves; colonization was influenced by occupancy in neighbouring sites. Perturbation analysis indicated that occupancy was more sensitive to local extinction within reserves and to colonization in sites abutting reserves. The Western Ghats could serve as a stronghold for the endangered dhole, provided future colonizations are facilitated through habitat consolidation beyond reserve boundaries, and local extinctions are prevented by increasing protection efforts within select reserves. We advocate for wildlife managers to adopt a landscape-based approach and periodic monitoring to ensure persistence of the dhole metapopulation in Western Ghats, and in other critical conservation regions across the species’ geographic range.
Optimal estimation of entanglement and discord in two-qubit states
Authors: Virzì Salvatore , Rebufello Enrico , Avella Alessio , Piacentini Fabrizio , Gramegna Marco , Ruo Berchera Ivano , Degiovanni Ivo Pietro , Genovese Marco
Published: February 2019

Recently, the fast development of quantum technologies led to the need for tools allowing the characterization of quantum resources. In particular, the ability to estimate non-classical aspects, e.g. entanglement and quantum discord, in two-qubit systems, is relevant to optimise the performance of quantum information processes. Here we present an experiment in which the amount of entanglement and discord are measured exploiting different estimators. Among them, some will prove to be optimal, i.e., able to reach the ultimate precision bound allowed by quantum mechanics. These estimation techniques have been tested with a specific family of states ranging from nearly pure Bell states to completely mixed states. This work represents a significant step towards the development of reliable metrological tools for quantum technologies.
An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria
Authors: Wei Yulong , Silke Jordan R. , Xia Xuhua
Published: February 2019

The degree to which codon usage can be explained by tRNA abundance in bacterial species is often inadequate, partly because differential tRNA abundance is often approximated by tRNA copy numbers. To better understand the coevolution between tRNA abundance and codon usage, we provide a better estimate of tRNA abundance by profiling tRNA mapped reads (tRNA tpm) using publicly available RNA Sequencing data. To emphasize the feasibility of our approach, we demonstrate that tRNA tpm is consistent with tRNA abundances derived from RNA fingerprinting experiments in Escherichia coli, Bacillus subtilis, and Salmonella enterica. Furthermore, we do not observe an appreciable reduction in tRNA sequencing efficiency due to post-transcriptional methylations in the seven bacteria studied. To determine optimal codons, we calculate codon usage in highly and lowly expressed genes determined by protein per transcript. We found that tRNA tpm is sensitive to identify more translationally optimal codons than gene copy number and early tRNA fingerprinting abundances. Additionally, tRNA tpm improves the predictive power of tRNA adaptation index over codon preference. Our results suggest that dependence of codon usage on tRNA availability is not always associated with species growth-rate. Conversely, tRNA availability is better optimized to codon usage in fast-growing than slow-growing species.