bluuebunny/crossref_metadata_2025 huggingface dataset:
Romantic functioning mediates prospective associations between childhood abuse and neglect and parenting outcomes in adulthood
Authors: Labella Madelyn H. , Raby K. Lee , Martin Jodi , Roisman Glenn I.
Published: February 2019

Research suggests intergenerational links between childhood abuse and neglect and subsequent parenting quality, but little is known about the potential mechanisms underlying intergenerational continuities in parenting. Adult romantic functioning may be one plausible mechanism, given its documented associations with both adverse caregiving in childhood and parenting quality in adulthood. The present study used data from the Minnesota Longitudinal Study of Risk and Adaptation to (a) investigate prospective associations between childhood experiences of abuse and neglect and multiple parenting outcomes in adulthood, and (b) evaluate the degree to which adult romantic functioning mediates those associations. Information regarding childhood abuse and neglect was gathered prospectively from birth through age 17.5 years. Multimethod assessments of romantic functioning were collected repeatedly through early adulthood (ages 20 to 32 years), and parenting quality was assessed as participants assumed a parenting role (ages 21 to 38 years). As expected, childhood abuse and neglect experiences predicted less supportive parenting (observed and interview rated) and higher likelihood of self-reported Child Protective Services involvement. The association with interview-rated supportive parenting was partially mediated by lower romantic competence, whereas the association with Child Protective Services involvement was partially mediated by more relational violence in adult romantic relationships. Implications of these novel prospective findings for research and clinical intervention are discussed.
Barriers to Breastfeeding in Disasters in the Context of Iran
Authors: MirMohamadaliIe Mandana , Khani Jazani Reza , Sohrabizadeh Sanaz , Nikbakht Nasrabadi Alireza
Published: February 2019

Introduction

Natural disasters have many effects on vulnerable groups, especially infants and children. Protecting breastfeeding in disasters is important, because artificial feeding puts a lot of risk to the child. In disasters, artificial nutrition is dangerous to children and its supplementation requires special equipment. There is little information on the nutritional status of infants after disasters in Iran.

Problem

The purpose of this study was to explore the barriers to appropriate lactation after disasters in Iran.

Method

This was a qualitative study using a content analysis method. A total of 19 midwives with disaster-relief experiences were approached for interview. Data were collected using semi-structured interviews. Data analysis was performed using the Graneheim’s approach.

Results

The categories of maternal factors, neonatal factors, management factors, and context-base factors were extracted from the data.

Conclusion

The challenges of social support, mothers’ self-efficacy, educated staff for disasters, and privacy for breastfeeding can be considered as important barriers to breastfeeding in disasters. Training programs, as well as health system support, can help overcome the breastfeeding barriers in disasters.

MirMohamadaliIeM, Khani JazaniR, SohrabizadehS, Nikbakht NasrabadiA. Barriers to breastfeeding in disasters in the context of Iran. Prehosp Disaster Med. 2019;34(1):20–24.
Spatial and Compositional Biases Introduced by Position Sensitive Detection Systems in APT: A Simulation Approach
Authors: Bacchi C. , Da Costa G. , Vurpillot F.
Published: February 2019

Due to the low capacity of contemporary position-sensitive detectors in atom probe tomography (APT) to detect multiple events, material analyses that exhibit high numbers of multiple events are the most subject to compositional biases. To solve this limitation, some researchers have developed statistical correction algorithms. However, those algorithms are only efficient when one is confronted with homogeneous materials having nearly the same evaporation field between elements. Therefore, dealing with more complex materials must be accompanied by a better understanding of the signal loss mechanism during APT experiments. By modeling the evaporation mechanism and the whole APT detection system, it may be possible to predict compositional and spatial biases induced by the detection system. This paper introduces a systematic study of the impact of the APT detection system on material analysis through the development of a simulation tool.
Beyond the Field: Ethics after Fieldwork in Politically Dynamic Contexts
Authors: Knott Eleanor
Published: February 2019

As researchers, when do our ethical obligations end? How should our ethical obligations respond to dynamic and unstable political contexts? Political scientists frequently work in dynamic political situations that can pose new ethical questions beyond those existing at the point of fieldwork. Yet, research ethics are often conceived in terms of a static, if not hermetically sealed, field site that remains frozen in time at the point we conduct fieldwork and collect data. I argue, first, that we need to consider more systematically how a dynamic field intersects with ethical obligations. Second, I argue that new and unexpected ethical questions can emerge after exiting the field, including responsibilities to research participants, dissemination, and publication, and returning to the field, which should be a part of how we conceive of ethical obligations.
Performing Authoritarian Citizenship: Public Transcripts in China
Authors: Distelhorst Greg , Fu Diana
Published: February 2019

How should we study citizenship in authoritarian regimes? We propose studying how citizenship is performed using the “public transcript”—communication between ordinary citizens and political authorities. The stakes of these strategic communications allow us to observe the roles citizens play to elicit assistance from authoritarian elites. We use this technique to study citizenship in contemporary China, analyzing evidence from an original database of over eight thousand appeals to local officials. These public transcripts reveal three ideal-type scripts of citizenship. First, we observe individuals performing subjecthood, positioning themselves as subalterns before benevolent rulers. We also identify an authoritarian legal citizenship that appeals to the formal legal commitments of the state. Finally, we find evidence for a socialist citizenship which appeals to the moral duties of officials to provide collective welfare. This approach eschews a classification scheme based on regime types, instead acknowledging that diverse performances of citizenship can coexist within a single state.
Location of Seismic “Hum” Sources Following Storms in the North Pacific Ocean
Authors: Maurya Satish , Taira Taka'aki , Romanowicz Barbara
Published: February 2019

We investigate the spatially and temporally varying distributions of sources of the Earth's low‐frequency seismic hum at high space‐time resolution during a seismically quiet 7‐day period in December 2015, when two large storms with different reaches propagate across the North Pacific Ocean. We integrate information from a variety of data from ocean wave height, infragravity wave prediction model, and broadband seismic data. We analyze seismic data to understand the seismic hum better: power spectral density at stations for detection and location of sources using array beamforming and backprojection methods, with a ~3‐hr temporal and ~5° spatial resolution. For storms propagating west to east across the northern Pacific hitting the west coast of North America broadscale, we show that the distribution of hum sources is consistent with a model of seismic energy generated via infragravity waves, produced near the impact location of the storm, and propagating along the coast as well as toward the open ocean. The generation of seismic hum depends strongly on the reach of the storm and is very weak for a storm with more northerly propagation toward Alaska. At shorter periods (e.g., ~70 s), the seismic hum is generated in a narrow band that follows the coast, reaching progressively further to the north, while at longer periods (e.g. 150 s), it covers a broader area reaching far into the deep ocean. It may thus be possible to predict the distribution of the strongest “hum” sources, to first order, from the knowledge of the direction of propagation and strength of northern Pacific storms.
Exospheric Neutral Hydrogen Density at the Nominal 10 RE Subsolar Point Deduced From XMM‐Newton X‐Ray Observations
Authors: Connor Hyunju K. , Carter Jennifer A.
Published: February 2019

We investigate the exospheric neutral density near the subsolar magnetopause, assuming Xgse = 10 RE as its typical location, to support the upcoming Solar wind‐Magnetosphere‐Ionosphere Link Explorer that will visualize the Earth's magnetosheath and cusps in soft X‐rays. Neutral hydrogen density is a key parameter that controls soft X‐ray emission and can be inversely extracted from the soft X‐ray observations. We introduce a unique method to estimate the dayside neutral density by using X‐ray Multi‐Mirror Mission (XMM)‐Newton astrophysics X‐ray observations and Open Geospace Global Circulation Model (OpenGGCM) global magnetosphere‐ionosphere magnetohydrodynamics (MHD) model. On 4 May 2003 and 16 October 2001, the XMM‐Newton line of sight traversed the dayside of the Earth's magnetosheath and observed strong near‐Earth soft X‐ray emission. We simulate these two events using the OpenGGCM model. Although the model tends to produce a spatially thicker magnetosheath than measured, modeled magnetosheath plasma fluxes match well with the in situ observations of Cluster and Geotail. We calculate the neutral densities every thousand seconds by comparing the modeled count rates with the XMM‐Newton rates. The densities are averaged at 39.9 ± 8.0 and 57.6 ± 8.0 cm−3 for the 4 May 2003 and 16 October 2001 events, respectively. Since our MHD tends to underestimate neutral densities due to its thicker magnetosheath, the true neutral density is likely to lie within the upper half of these error bars.
Observations of Rising Methane Bubbles in Trondheimsfjord and Its Implications to Gas Dissolution
Authors: Olsen J. E. , Krause D. F. , Davies E. J. , Skjetne P.
Published: February 2019

Gas dissolution reduces the release of methane to the atmosphere from subsea sources. Being able to predict and assess the methane flux to the atmosphere requires knowledge on gas dissolution and mass transfer. This can be obtained by studying the size evolution of bubbles rising in water. New data of bubble size evolution have been obtained by releasing, tracking, and filming methane bubbles with an ROV in the Trondheimsfjord from depths varying between 100 and 300 m. Released bubbles had an initial diameter between 5 and 7 mm and were tracked until they reached a diameter of roughly 2 mm. The new data were compared against theory, applying established correlations for the mass transfer coefficient. There was an inconsistency between experiment and theory. Thus, new correlations for the mass transfer are proposed. The new correlations are consistent with both the new experiments and previously published experiments. They indicate that the conditions in the ocean can be labeled as partly contaminated with respect to mass transfer.
Dam Operations and Subsurface Hydrogeology Control Dynamics of Hydrologic Exchange Flows in a Regulated River Reach
Authors: Shuai Pin , Chen Xingyuan , Song Xuehang , Hammond Glenn E. , Zachara John , Royer Patrick , Ren Huiying , Perkins William A. , Richmond Marshall C. , Huang Maoyi
Published: February 2019

Hydrologic exchange flows (HEFs) across the river‐aquifer interface have important implications for biogeochemical processes and contaminant plume migration in the river corridor, yet little is known about the hydrogeomorphic factors that control HEFs dynamics under dynamic flow conditions. Here, we developed a 3‐D numerical model for a large regulated river corridor along the Columbia River to study how HEFs are controlled by the interplays between dam‐regulated flow conditions and hydrogeomorphic features of such river corridor system. Our results revealed highly variable intra‐annual spatiotemporal patterns in HEFs along the 75‐km river reach, as well as strong interannual variability with larger exchange volumes in wet years than dry years. In general, the river was losing during late spring to early summer when the river stage was high, and river was gaining in fall and winter when river stage was low. The magnitude and timing of river stage fluctuations controlled the timing of high exchange rates. Both river channel geomorphology and the thickness of a highly permeable river bank geologic layer controlled the locations of exchange hot spots, while the latter played a dominant role. Dam‐induced, subdaily to daily river stage fluctuations drove high‐frequency variations in HEFs across the river‐aquifer interfaces, resulting in greater overall exchange volumes as compared to the case without high‐frequency flows. Our results demonstrated that upstream dam operations enhanced the exchange between river water and groundwater with strong potential influence on the associated biogeochemical processes and on the fate and transport of groundwater contaminant plumes in such river corridors.
Subverted regulation of Nox1 NADPH oxidase-dependent oxidant generation by protein disulfide isomerase A1 in colon carcinoma cells with overactivated KRas
Authors: De Bessa Tiphany Coralie , Pagano Alessandra , Moretti Ana Iochabel Soares , Oliveira Percillia Victoria Santos , Mendonça Samir Andrade , Kovacic Herve , Laurindo Francisco Rafael Martins
Published: February 2019

Protein disulfide isomerases including PDIA1 are implicated in cancer progression, but underlying mechanisms are unclear. PDIA1 is known to support vascular Nox1 NADPH oxidase expression/activation. Since deregulated reactive oxygen species (ROS) production underlies tumor growth, we proposed that PDIA1 is an upstream regulator of tumor-associated ROS. We focused on colorectal cancer (CRC) with distinct KRas activation levels. Analysis of RNAseq databanks and direct validation indicated enhanced PDIA1 expression in CRC with constitutive high (HCT116) vs. moderate (HKE3) and basal (Caco2) Ras activity. PDIA1 supported Nox1-dependent superoxide production in CRC; however, we first reported a dual effect correlated with Ras-level activity: in Caco2 and HKE3 cells, loss-of-function experiments indicate that PDIA1 sustains Nox1-dependent superoxide production, while in HCT116 cells PDIA1 restricted superoxide production, a behavior associated with increased Rac1 expression/activity. Transfection of Rac1G12V active mutant into HKE3 cells induced PDIA1 to become restrictive of Nox1-dependent superoxide, while in HCT116 cells treated with Rac1 inhibitor, PDIA1 became supportive of superoxide. PDIA1 silencing promoted diminished cell proliferation and migration in HKE3, not detectable in HCT116 cells. Screening of cell signaling routes affected by PDIA1 silencing highlighted GSK3β and Stat3. Also, E-cadherin expression after PDIA1 silencing was decreased in HCT116, consistent with PDIA1 support of epithelial–mesenchymal transition. Thus, Ras overactivation switches the pattern of PDIA1-dependent Rac1/Nox1 regulation, so that Ras-induced PDIA1 bypass can directly activate Rac1. PDIA1 may be a crucial regulator of redox-dependent adaptive processes related to cancer progression.
Dyke intrusion between neighbouring arc volcanoes responsible for 2017 pre-eruptive seismic swarm at Agung
Authors: Albino Fabien , Biggs Juliet , Syahbana Devy Kamil
Published: February 2019

Forecasting explosive eruptions relies on using monitoring data to interpret the patterns and timescales of magma transport and mixing. In September 2017, a distal seismic swarm triggered the evacuation of around 140,000 people from Agung volcano, Bali. From satellite imagery and 3D numerical models, we show that seismicity was associated with a deep, sub-vertical magma intrusion between Agung and its neighbour Batur. This, combined with observations of the 1963 eruption which caused more than thousand fatalities, suggests a vertically and laterally interconnected system experiencing recurring magma mixing. The geometry of the 2017 dyke is consistent with transport from a deep mafic source to a shallow andesitic reservoir controlled by stresses induced by the topographic load, but not the regional tectonics. The ongoing interactions between Agung and Batur have important implications for interpretation of distal seismicity, the links between closely spaced arc volcanoes, and the potential for cascading hazards.
Enhanced photoelectrical response of thermodynamically epitaxial organic crystals at the two-dimensional limit
Authors: Cao Min , Zhang Cong , Cai Zhi , Xiao Chengcheng , Chen Xiaosong , Yi Kongyang , Yang Yingguo , Lu Yunhao , Wei Dacheng
Published: February 2019

Owing to strong light-matter interaction, two-dimensional (2D) organic crystal is regarded as promising materials for ultrasensitive photodetectors, however it still received limited success due to degraded photoelectrical response and problems in controllable growth. Here, we find the growth of 2D organic crystal obeys Gibbs-Curie-Wulff law, and develop a seed-epitaxial drop-casting method to grow millimeter-sized 1,4-bis(4-methylstyryl)benzene 2D crystals on SiO2/Si in a thermodynamically controlled process. On SiO2/Si, a distinct 2D limit effect is observed, which remarkably enhances internal photoresponsivity compared with bulk crystals. Experiment and calculation show the molecules stack more compactly at the 2D limit, thus better molecular orbital overlap and corresponding changes in the band structure lead to efficient separation and transfer of photo-generated carriers as well as enhanced photo-gating modulation. This work provides a general insight into the growth and the dimension effect of the 2D organic crystal, which is valuable for the application in high-performance photoelectrical devices.
Diversity within the adenovirus fiber knob hypervariable loops influences primary receptor interactions
Authors: Baker Alexander T. , Greenshields-Watson Alexander , Coughlan Lynda , Davies James A. , Uusi-Kerttula Hanni , Cole David K. , Rizkallah Pierre J. , Parker Alan L.
Published: February 2019

Adenovirus based vectors are of increasing importance for wide ranging therapeutic applications. As vaccines, vectors derived from human adenovirus species D serotypes 26 and 48 (HAdV-D26/48) are demonstrating promising efficacy as protective platforms against infectious diseases. Significant clinical progress has been made, yet definitive studies underpinning mechanisms of entry, infection, and receptor usage are currently lacking. Here, we perform structural and biological analysis of the receptor binding fiber-knob protein of HAdV-D26/48, reporting crystal structures, and modelling putative interactions with two previously suggested attachment receptors, CD46 and Coxsackie and Adenovirus Receptor (CAR). We provide evidence of a low affinity interaction with CAR, with modelling suggesting affinity is attenuated through extended, semi-flexible loop structures, providing steric hindrance. Conversely, in silico and in vitro experiments are unable to provide evidence of interaction between HAdV-D26/48 fiber-knob with CD46, or with Desmoglein 2. Our findings provide insight into the cell-virus interactions of HAdV-D26/48, with important implications for the design and engineering of optimised Ad-based therapeutics.
Tree-ring isotopes capture interannual vegetation productivity dynamics at the biome scale
Authors: Levesque Mathieu , Andreu-Hayles Laia , Smith William Kolby , Williams A. Park , Hobi Martina L. , Allred Brady W. , Pederson Neil
Published: February 2019

Historical and future trends in net primary productivity (NPP) and its sensitivity to global change are largely unknown because of the lack of long-term, high-resolution data. Here we test whether annually resolved tree-ring stable carbon (δ13C) and oxygen (δ18O) isotopes can be used as proxies for reconstructing past NPP. Stable isotope chronologies from four sites within three distinct hydroclimatic environments in the eastern United States (US) were compared in time and space against satellite-derived NPP products, including the long-term Global Inventory Modeling and Mapping Studies (GIMMS3g) NPP (1982–2011), the newest high-resolution Landsat NPP (1986–2015), and the Moderate Resolution Imaging Spectroradiometer (MODIS, 2001–2015) NPP. We show that tree-ring isotopes, in particular δ18O, correlate strongly with satellite NPP estimates at both local and large geographical scales in the eastern US. These findings represent an important breakthrough for estimating interannual variability and long-term changes in terrestrial productivity at the biome scale.
X-ray nanotomography of coccolithophores reveals that coccolith mass and segment number correlate with grid size
Authors: Beuvier T. , Probert I. , Beaufort L. , Suchéras-Marx B. , Chushkin Y. , Zontone F. , Gibaud A.
Published: February 2019

Coccolithophores of the Noëlaerhabdaceae family are covered by imbricated coccoliths, each composed of multiple calcite crystals radially distributed around the periphery of a grid. The factors that determine coccolith size remain obscure. Here, we used synchrotron-based three-dimensional Coherent X-ray Diffraction Imaging to study coccoliths of 7 species of Gephyrocapsa, Emiliania and Reticulofenestra with a resolution close to 30 nm. Segmentation of 45 coccoliths revealed remarkable size, mass and segment number variations, even within single coccospheres. In particular, we observed that coccolith mass correlates with grid perimeter which scales linearly with crystal number. Our results indirectly support the idea that coccolith mass is determined in the coccolith vesicle by the size of the organic base plate scale (OBPS) around which R-unit nucleation occurs every 110–120 nm. The curvation of coccoliths allows inference of a positive correlation between cell nucleus, OBPS and coccolith sizes.
Numerous cultivated and uncultivated viruses encode ribosomal proteins
Authors: Mizuno Carolina M. , Guyomar Charlotte , Roux Simon , Lavigne Régis , Rodriguez-Valera Francisco , Sullivan Matthew B. , Gillet Reynald , Forterre Patrick , Krupovic Mart
Published: February 2019

Viruses modulate ecosystems by directly altering host metabolisms through auxiliary metabolic genes. However, viral genomes are not known to encode the core components of translation machinery, such as ribosomal proteins (RPs). Here, using reference genomes and global-scale viral metagenomic datasets, we identify 14 different RPs across viral genomes arising from cultivated viral isolates and metagenome-assembled viruses. Viruses tend to encode dynamic RPs, easily exchangeable between ribosomes, suggesting these proteins can replace cellular versions in host ribosomes. Functional assays confirm that the two most common virus-encoded RPs, bS21 and bL12, are incorporated into 70S ribosomes when expressed inEscherichia coli. Ecological distribution of virus-encoded RPs suggests some level of ecosystem adaptations as aquatic viruses and viruses of animal-associated bacteria are enriched for different subsets of RPs. Finally, RP genes are under purifying selection and thus likely retained an important function after being horizontally transferred into virus genomes.
Electron-nuclear correlated multiphoton-route to Rydberg fragments of molecules
Authors: Zhang Wenbin , Gong Xiaochun , Li Hui , Lu Peifen , Sun Fenghao , Ji Qinying , Lin Kang , Ma Junyang , Li Hanxiao , Qiang Junjie , He Feng , Wu Jian
Published: February 2019

Atoms and molecules exposed to strong laser fields can be excited to the Rydberg states with very high principal quantum numbers and large orbitals. It allows acceleration of neutral particles, generate near-threshold harmonics, and reveal multiphoton Rabi oscillations and rich photoelectron spectra. However, the physical mechanism of Rydberg state excitation in strong laser fields is yet a puzzle. Here, we identify the electron-nuclear correlated multiphoton excitation as the general mechanism by coincidently measuring all charged and neutral fragments ejected from a H2 molecule. Ruled by the ac-Stark effect, the internuclear separation for resonant multiphoton excitation varies with the laser intensity. It alters the photon energy partition between the ejected electrons and nuclei and thus leads to distinct kinetic energy spectra of the nuclear fragments. The electron-nuclear correlation offers an alternative visual angle to capture rich ultrafast processes of complex molecules.
Subcortical electrophysiological activity is detectable with high-density EEG source imaging
Authors: Seeber Martin , Cantonas Lucia-Manuela , Hoevels Mauritius , Sesia Thibaut , Visser-Vandewalle Veerle , Michel Christoph M.
Published: February 2019

Subcortical neuronal activity is highly relevant for mediating communication in large-scale brain networks. While electroencephalographic (EEG) recordings provide appropriate temporal resolution and coverage to study whole brain dynamics, the feasibility to detect subcortical signals is a matter of debate. Here, we investigate if scalp EEG can detect and correctly localize signals recorded with intracranial electrodes placed in the centromedial thalamus, and in the nucleus accumbens. Externalization of deep brain stimulation (DBS) electrodes, placed in these regions, provides the unique opportunity to record subcortical activity simultaneously with high-density (256 channel) scalp EEG. In three patients during rest with eyes closed, we found significant correlation between alpha envelopes derived from intracranial and EEG source reconstructed signals. Highest correlation was found for source signals in close proximity to the actual recording sites, given by the DBS electrode locations. Therefore, we present direct evidence that scalp EEG indeed can sense subcortical signals.
Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen
Authors: Depledge Daniel P. , Srinivas Kalanghad Puthankalam , Sadaoka Tomohiko , Bready Devin , Mori Yasuko , Placantonakis Dimitris G. , Mohr Ian , Wilson Angus C.
Published: February 2019

Characterizing complex viral transcriptomes by conventional RNA sequencing approaches is complicated by high gene density, overlapping reading frames, and complex splicing patterns. Direct RNA sequencing (direct RNA-seq) using nanopore arrays offers an exciting alternative whereby individual polyadenylated RNAs are sequenced directly, without the recoding and amplification biases inherent to other sequencing methodologies. Here we use direct RNA-seq to profile the herpes simplex virus type 1 (HSV-1) transcriptome during productive infection of primary cells. We show how direct RNA-seq data can be used to define transcription initiation and RNA cleavage sites associated with all polyadenylated viral RNAs and demonstrate that low level read-through transcription produces a novel class of chimeric HSV-1 transcripts, including a functional mRNA encoding a fusion of the viral E3 ubiquitin ligase ICP0 and viral membrane glycoprotein L. Thus, direct RNA-seq offers a powerful method to characterize the changing transcriptional landscape of viruses with complex genomes.
Nanometric axial resolution of fibronectin assembly units achieved with an efficient reconstruction approach for multi-angle-TIRF microscopy
Authors: Soubies Emmanuel , Radwanska Agata , Grall Dominique , Blanc-Féraud Laure , Van Obberghen-Schilling Ellen , Schaub Sébastien
Published: February 2019

High resolution imaging of molecules at the cell-substrate interface is required for understanding key biological processes. Here we propose a complete pipeline for multi-angle total internal reflection fluorescence microscopy (MA-TIRF) going from instrument design and calibration procedures to numerical reconstruction. Our custom setup is endowed with a homogeneous field illumination and precise excitation beam angle. Given a set of MA-TIRF acquisitions, we deploy an efficient joint deconvolution/reconstruction algorithm based on a variational formulation of the inverse problem. This algorithm offers the possibility of using various regularizations and can run on graphics processing unit (GPU) for rapid reconstruction. Moreover, it can be easily used with other MA-TIRF devices and we provide it as an open-source software. This ensemble has enabled us to visualize and measure with unprecedented nanometric resolution, the depth of molecular components of the fibronectin assembly machinery at the basal surface of endothelial cells.
Antibody-mediated biorecognition of myelin oligodendrocyte glycoprotein: computational evidence of demyelination-related epitopes
Authors: Ierich Jéssica Cristiane Magalhães , Brum Doralina Guimarães , Moraes Ariana de Souza , Higa Akemi Martins , Garcia Pâmela Soto , Miyazaki Celina Massumi , Ferreira Marystela , Peroni Luís Antonio , Oliveira Guedmiller Souza de , Franca Eduardo de Faria , Freitas Luiz Carlos Gomide , Leite Fabio Lima
Published: February 2019

Antigen-antibody interaction is crucial in autoimmune disease pathogenesis, as multiple sclerosis and neuromyelitis optica. Given that, autoantibodies are essential biomolecules, of which the myelin oligodendrocyte glycoprotein (MOG) can figure as a target. Here we combined Molecular Dynamics (MD), Steered Molecular Dynamics (SMD), and Atomic Force Microscope (AFM) to detail MOG recognition by its specific antibody. The complex model consisted of the MOG external domain interacting with an experimental anti-MOG antibody from the Protein Data Bank (1PKQ). Computational data demonstrated thirteen MOG residues with a robust contribution to the antigen-antibody interaction. Comprising five of the thirteen anchor residues (ASP102, HIS103, SER104, TYR105, and GLN106), the well-known MOG92–106peptide in complex with the anti-MOG was analysed by AFM and SMD. These analyses evidenced similar force values of 780 pN and 765 pN for computational and experimental MOG92–106and anti-MOG detachment, respectively. MOG92–106was responsible for 75% of the total force measured between MOG external domain and anti-MOG, holding the interaction with the antibody. The antigen-antibody binding was confirmed by Surface Plasmon Resonance (SPR) measurements. Combined approaches presented here can conveniently be adjusted to detail novel molecules in diseases research. This can optimize pre-clinical steps, guiding experiments, reducing costs, and animal model usage.
Development and validation of whole genome-wide and genic microsatellite markers in oil palm (Elaeis guineensis Jacq.): First microsatellite database (OpSatdb)
Authors: B. Kalyana Babu , K. L. Mary Rani , Sahu Sarika , Mathur R. K. , P. Naveen Kumar , G. Ravichandran , P. Anitha , H. P. Bhagya
Published: February 2019

The availability of large expressed sequence tag (EST) and whole genome databases of oil palm enabled the development of a data base of microsatellite markers. For this purpose, an EST database consisting of 40,979 EST sequences spanning 27 Mb and a chromosome-wise whole genome databases were downloaded. A total of 3,950 primer pairs were identified and developed from EST sequences. The tri and tetra nucleotide repeat motifs were most prevalent (each 24.75%) followed by di-nucleotide repeat motifs. Whole genome-wide analysis found a total of 245,654 SSR repeats across the 16 chromosomes of oil palm, of which 38,717 were compound microsatellite repeats. A web application, OpSatdb, the first microsatellite database of oil palm, was developed using the PHP and MySQL database (https://ssr.icar.gov.in/index.php). It is a simple and systematic web-based search engine for searching SSRs based on repeat motif type, repeat type, and primer details. High synteny was observed between oil palm and rice genomes. The mapping of ESTs having SSRs by Blast2GO resulted in the identification of 19.2% sequences with gene ontology (GO) annotations. Randomly, a set of ten genic SSRs and five genomic SSRs were used for validation and genetic diversity on 100 genotypes belonging to the world oil palm genetic resources. The grouping pattern was observed to be broadly in accordance with the geographical origin of the genotypes. The identified genic and genome-wide SSRs can be effectively useful for various genomic applications of oil palm, such as genetic diversity, linkage map construction, mapping of QTLs, marker-assisted selection, and comparative population studies.
How context influences the interpretation of facial expressions: a source localization high-density EEG study on the “Kuleshov effect”
Authors: Calbi Marta , Siri Francesca , Heimann Katrin , Barratt Daniel , Gallese Vittorio , Kolesnikov Anna , Umiltà Maria Alessandra
Published: February 2019

Few studies have explored the specificities of contextual modulations of the processing of facial expressions at a neuronal level. This study fills this gap by employing an original paradigm, based on a version of the filmic “Kuleshov effect”. High-density EEG was recorded while participants watched film sequences consisting of three shots: the close-up of a target person’s neutral face (Face_1), the scene that the target person was looking at (happy, fearful, or neutral), and another close-up of the same target person’s neutral face (Face_2). The participants’ task was to rate both valence and arousal, and subsequently to categorize the target person’s emotional state. The results indicate that despite a significant behavioural ‘context’ effect, the electrophysiological indexes still indicate that the face is evaluated as neutral. Specifically, Face_2 elicited a high amplitude N170 when preceded by neutral contexts, and a high amplitude Late Positive Potential (LPP) when preceded by emotional contexts, thus showing sensitivity to the evaluative congruence (N170) and incongruence (LPP) between context and Face_2. The LPP activity was mainly underpinned by brain regions involved in facial expressions and emotion recognition processing. Our results shed new light on temporal and neural correlates of context-sensitivity in the interpretation of facial expressions.
Triggering The Birth of New Cycle’s Sunspots by Solar Tsunami
Authors: Dikpati Mausumi , McIntosh Scott W. , Chatterjee Subhamoy , Banerjee Dipankar , Yellin-Bergovoy Ron , Srivastava Abhishek
Published: February 2019

When will a new cycle’s sunspots appear? We demonstrate a novel physical mechanism, namely, that a “solar tsunami” occurring in the Sun’s interior shear-fluid layer can trigger new cycle’s magnetic flux emergence at high latitudes, a few weeks after the cessation of old cycle’s flux emergence near the equator. This tsunami is excited at the equator when magnetic dams, created by the oppositely-directed old cycle’s toroidal field in North and South hemispheres, break due to mutual annihilation of toroidal flux there. The fluid supported by these dams rushes to the equator; the surplus of fluid cannot be contained there, so it reflects back towards high latitudes, causing a tsunami. This tsunami propagates poleward at a speed of ~300 m/s until it encounters the new cycle’s spot-producing toroidal fields in mid-latitudes, where it perturbs the fields, triggering their surface-eruption in the form of new cycle spots. A new sunspot cycle is preceded for several years by other forms of high-latitude magnetic activity, such as coronal bright points and ephemeral regions, until the tsunami causes the birth of new cycle’s spots. The next tsunami is due by 2020, portending the start of intense ‘space weather’ that can adversely impact the Earth.
Expression, activity and localization of lysosomal sulfatases in Chronic Obstructive Pulmonary Disease
Authors: Weidner Julie , Jogdand Prajakta , Jarenbäck Linnea , Åberg Ida , Helihel Dalja , Ankerst Jaro , Westergren-Thorsson Gunilla , Bjermer Leif , Erjefält Jonas S. , Tufvesson Ellen
Published: February 2019

Chronic obstructive pulmonary disease (COPD) is a leading cause of death world-wide. Recently, we showed that COPD is associated with gene polymorphisms in SUMF1, a master regulator of sulfatases. Sulfatases are involved in extracellular matrix remodeling and activated by SUMF1, but their role in the lung is poorly described. We aimed to examine how sulfatases are affected in the airways of patients with COPD compared to ever smokers and never smokers. We observed that mRNA expression of the sulfatases GALNS, GNS and IDS was increased, while protein expression of many sulfatases was decreased in COPD fibroblasts. Several sulfatases, including GALNS, IDS, and SGSH, showed increased activity in COPD fibroblasts. Examination of different sulfatases by immunofluorescence showed that IDS, ARSB, GNS and SGSH in fibroblasts were localized to sites other than their reported destination. Using a master panel from different organs, RNA expression of all sulfatases could be observed in lung tissue. Additionally, immunohistochemistry on lung biopsies indicated differing expression of sulfatases in COPD patients. In conclusion, mRNA, protein expression, sulfatase activity levels, and localization of sulfatases are altered in lung fibroblasts and lung tissue from COPD patients and may be mechanistically important in COPD pathogenesis. This could contribute to the understanding of the disease mechanism in COPD and in the long run, to lead to more individualized therapies.
Corpora amylacea in human hippocampal brain tissue are intracellular bodies that exhibit a homogeneous distribution of neo-epitopes
Authors: Augé Elisabet , Bechmann Ingo , Llor Núria , Vilaplana Jordi , Krueger Martin , Pelegrí Carme
Published: February 2019

Corpora amylacea are spherical bodies of unknown origin and function, which accumulate in the human brain during the aging process and neurodegenerative disorders. In recent work, we reported that they contain some neo-epitopes that are recognized by natural IgMs, revealing a possible link between them and the natural immune system. Here, we performed an ultrastructural study complemented with confocal microscopy in order to shed light on the formation of corpora amylacea and to precisely localize the neo-epitopes. We show that immature corpora amylacea are intracellular astrocytic structures formed by profuse cellular debris and membranous blebs entrapped in a scattered mass of randomly oriented short linear fibers. In mature corpora amylacea, the structure becomes compacted and fibrillary material constitutes the principal component. We also determined that the neo-epitopes were uniformly localized throughout the whole structure. All these observations reinforce the idea that corpora amylacea of human brain are equivalent to another type of polyglucosan bodies named PAS granules, present in mouse brain and originated from degenerative processes. All those findings support the hypothesis that corpora amylacea are involved in the entrapment of damaged materials and non-degradable products and have a role in protective or cleaning mechanisms.
Integrative taxonomy of a new Redudasys species (Gastrotricha: Macrodasyida) sheds light on the invasion of fresh water habitats by macrodasyids
Authors: Garraffoni André R. S. , Araújo Thiago Q. , Lourenço Anete P. , Guidi Loretta , Balsamo Maria
Published: February 2019

The order Macrodasyida (Gastrotricha) includes over 350 marine species, and only 3 freshwater species (Marinellina flagellata, Redudasys fornerise, R. neotemperatus). Herein we describe a new freshwater species of Macrodasyida, Redudasys brasiliensis sp. nov., from Brazil through an integrative taxonomic approach. The external morphology and internal anatomy were investigated using differential interference contrast microscopy, confocal microscopy, scanning and transmission electron microscopy. The systematization of the new taxon was inferred by nuclear (18S and 28S) and mitochondrial (COI) genes, and its intra-order relationships were assessed using data from most of available macrodasyids. Phylogenetic analyses yielded congruent trees, in which the new taxon is nested within the family Redudasyidae, but it was genetically distinct from the other species of the genus Redudasys. The new species shares the gross morphology and reproductive traits with other Redudasyidae and the presence of only 1 anterior adhesive tube per side with Redudasys neotemperatus, but it has a specific pattern of ventral ciliation and muscle organization. Results support the hypothesis that dispersion into fresh water habitats by Macrodasyida and Chaetonotida taxa occurred independently and that within Macrodasyida a single lineage invaded the freshwater environment only once. Furthermore, the Neotropical region seems to be peculiar for the evolution of the freshwater macrodasyid clade.
Thermodynamic Signatures of Weyl Fermions in NbP
Authors: Modic K. A. , Meng Tobias , Ronning Filip , Bauer Eric D. , Moll Philip J. W. , Ramshaw B. J.
Published: February 2019

We present a high magnetic field study of NbP—a member of the monopnictide Weyl semimetal (WSM) family. While the monoarsenides (NbAs and TaAs) have topologically distinct left and right-handed Weyl fermi surfaces, NbP is argued to be “topologically trivial” due to the fact that all pairs of Weyl nodes are encompassed by a single Fermi surface. We use torque magnetometry to measure the magnetic response of NbP up to 60 tesla and uncover a Berry paramagnetic response, characteristic of the topological Weyl nodes, across the entire field range. At the quantum limit B* (≈32 T), τ/B experiences a change in slope when the chemical potential enters the last Landau level. Our calculations confirm that this magnetic response arises from band topology of the Weyl pocket, even though the Fermi surface encompasses both Weyl nodes at zero magnetic field. We also find that the magnetic field pulls the chemical potential to the chiral n = 0 Landau level in the quantum limit, providing a disorder-free way of accessing chiral Weyl fermions in systems that are “not quite” WSMs in zero magnetic field.
Quantifying dynamic mechanisms of auto-regulation in Escherichia coli with synthetic promoter in response to varying external phosphate levels
Authors: Uluşeker Cansu , Torres-Bacete Jesús , García José L. , Hanczyc Martin M. , Nogales Juan , Kahramanoğulları Ozan
Published: February 2019

Escherichia coli have developed one of the most efficient regulatory response mechanisms to phosphate starvation. The machinery involves a cascade with a two-component system (TCS) that relays the external signal to the genetic circuit, resulting in a feedback response. Achieving a quantitative understanding of this system has implications in synthetic biology and biotechnology, for example, in applications for wastewater treatment. To this aim, we present a computational model and experimental results with a detailed description of the TCS, consisting of PhoR and PhoB, together with the mechanisms of gene expression. The model is parameterised within the feasible range, and fitted to the dynamic response of our experimental data on PhoB as well as PhoA, the product of this network that is used in alkaline phosphatase production. Deterministic and stochastic simulations with our model predict the regulation dynamics in higher external phosphate concentrations while reproducing the experimental observations. In a cycle of simulations and experimental verification, our model predicts and explores phenotypes with various synthetic promoter designs that can optimise the inorganic phosphate intake in E. coli. Sensitivity analysis demonstrates that the Pho-controlled genes have a significant influence over the phosphate response. Together with experimental findings, our model should thus provide insights for the investigations on engineering new sensors and regulators for living technologies.
Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems
Authors: Ravindran Vandana , Nacher Jose C. , Akutsu Tatsuya , Ishitsuka Masayuki , Osadcenco Adrian , Sunitha V. , Bagler Ganesh , Schwartz Jean-Marc , Robertson David L.
Published: February 2019

In recent years control theory has been applied to biological systems with the aim of identifying the minimum set of molecular interactions that can drive the network to a required state. However, in an intra-cellular network it is unclear how control can be achieved in practice. To address this limitation we use viral infection, specifically human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV), as a paradigm to model control of an infected cell. Using a large human signalling network comprised of over 6000 human proteins and more than 34000 directed interactions, we compared two states: normal/uninfected and infected. Our network controllability analysis demonstrates how a virus efficiently brings the dynamically organised host system into its control by mostly targeting existing critical control nodes, requiring fewer nodes than in the uninfected network. The lower number of control nodes is presumably to optimise exploitation of specific sub-systems needed for virus replication and/or involved in the host response to infection. Viral infection of the human system also permits discrimination between available network-control models, which demonstrates that the minimum dominating set (MDS) method better accounts for how the biological information and signals are organised during infection by identifying most viral proteins as critical driver nodes compared to the maximum matching (MM) method. Furthermore, the host driver nodes identified by MDS are distributed throughout the pathways enabling effective control of the cell via the high ‘control centrality’ of the viral and targeted host nodes. Our results demonstrate that control theory gives a more complete and dynamic understanding of virus exploitation of the host system when compared with previous analyses limited to static single-state networks.
In vivo characterization of doxycycline-mediated protection of aortic function and structure in a mouse model of Marfan syndrome-associated aortic aneurysm
Authors: Cui Jason Z. , Lee Ling , Sheng Xiaoye , Chu Fanny , Gibson Christine P. , Aydinian Taline , Walker David C. , Sandor George G. S. , Bernatchez Pascal , Tibbits Glen F. , van Breemen Cornelis , Esfandiarei Mitra
Published: February 2019

Aortic aneurysm is the most life-threatening complication in Marfan syndrome (MFS) patients. Doxycycline, a nonselective matrix metalloproteinases inhibitor, was reported to improve the contractile function and elastic fiber structure and organization in a Marfan mouse aorta usingex vivosmall chamber myography. In this study, we assessed the hypothesis that a long-term treatment with doxycycline would reduce aortic root growth, improve aortic wall elasticity as measured by pulse wave velocity, and improve the ultrastructure of elastic fiber in the mouse model of MFS. In our study, longitudinal measurements of aortic root diameters using high-resolution ultrasound imaging display significantly decreased aortic root diameters and lower pulse wave velocity in doxycycline-treated Marfan mice starting at 6 months as compared to their non-treated MFS counterparts. In addition, at the ultrastructural level, our data show that long-term doxycycline treatment corrects the irregularities of elastic fibers within the aortic wall of Marfan mice to the levels similar to those observed in control subjects. Our findings underscore the key role of matrix metalloproteinases during the progression of aortic aneurysm, and provide new insights into the potential therapeutic value of doxycycline in blocking MFS-associated aortic aneurysm.