bluuebunny/crossref_metadata_2025 huggingface dataset:
Elevated moisture stimulates carbon loss from mineral soils by releasing protected organic matter
Authors: Huang Wenjuan , Hall Steven J.
Published: November 2017

Moisture response functions for soil microbial carbon (C) mineralization remain a critical uncertainty for predicting ecosystem-climate feedbacks. Theory and models posit that C mineralization declines under elevated moisture and associated anaerobic conditions, leading to soil C accumulation. Yet, iron (Fe) reduction potentially releases protected C, providing an under-appreciated mechanism for C destabilization under elevated moisture. Here we incubate Mollisols from ecosystems under C3/C4plant rotations at moisture levels at and above field capacity over 5 months. Increased moisture and anaerobiosis initially suppress soil C mineralization, consistent with theory. However, after 25 days, elevated moisture stimulates cumulative gaseous C-loss as CO2and CH4to >150% of the control. Stable C isotopes show that mineralization of older C3-derived C released following Fe reduction dominates C losses. Counter to theory, elevated moisture may significantly accelerate C losses from mineral soils over weeks to months—a critical mechanistic deficiency of current Earth system models.
Oncogenic PIK3CA induces centrosome amplification and tolerance to genome doubling
Authors: Berenjeno Inma M. , Piñeiro Roberto , Castillo Sandra D. , Pearce Wayne , McGranahan Nicholas , Dewhurst Sally M. , Meniel Valerie , Birkbak Nicolai J. , Lau Evelyn , Sansregret Laurent , Morelli Daniele , Kanu Nnennaya , Srinivas Shankar , Graupera Mariona , Parker Victoria E. R. , Montgomery Karen G. , Moniz Larissa S. , Scudamore Cheryl L. , Phillips Wayne A. , Semple Robert K. , Clarke Alan , Swanton Charles , Vanhaesebroeck Bart
Published: November 2017

Mutations in PIK3CA are very frequent in cancer and lead to sustained PI3K pathway activation. The impact of acute expression of mutant PIK3CA during early stages of malignancy is unknown. Using a mouse model to activate the Pik3caH1047R hotspot mutation in the heterozygous state from its endogenous locus, we here report that mutant Pik3ca induces centrosome amplification in cultured cells (through a pathway involving AKT, ROCK and CDK2/Cyclin E-nucleophosmin) and in mouse tissues, and increased in vitro cellular tolerance to spontaneous genome doubling. We also present evidence that the majority of PIK3CAH1047R mutations in the TCGA breast cancer cohort precede genome doubling. These previously unappreciated roles of PIK3CA mutation show that PI3K signalling can contribute to the generation of irreversible genomic changes in cancer. While this can limit the impact of PI3K-targeted therapies, these findings also open the opportunity for therapeutic approaches aimed at limiting tumour heterogeneity and evolution.
International roadmap for artificial gravity research
Authors: Clément Gilles
Published: November 2017

In this paper, we summarize the current and future research activities that will determine the requirements for implementing artificial gravity (AG) to mitigate the effects of long duration exposure to microgravity on board exploration class space vehicles. NASA and its international partners have developed an AG roadmap that contains a common set of goals, objectives, and milestones. This roadmap includes both ground-based and space-based projects, and involves human subjects as well as animal and cell models. It provides a framework that facilitates opportunities for collaboration using the full range of AG facilities that are available worldwide, and a forum for space physiologists, crew surgeons, astronauts, vehicle designers, and mission planners to review, evaluate, and discuss the issues of incorporating AG technologies into the vehicle design.
Vertebrate food products as a potential source of prion-like α-synuclein
Authors: Killinger Bryan Andrew , Labrie Viviane
Published: November 2017

The aberrant aggregation of the protein α-synuclein is thought to be involved in Parkinson’s disease (PD). However, the factors that lead to initiation and propagation of α-synuclein aggregation are not clearly understood. Recently, the hypothesis that α-synuclein aggregation spreads via a prion-like mechanism originating in the gut has gained much scientific attention. If α-synuclein spreads via a prion-like mechanism, then an important question becomes, what are the origins of this prion-like species? Here we review the possibility that α-synuclein aggregation could be seeded via the ingestion of a prion-like α-synuclein species contained within food products originating from vertebrates. To do this, we highlight current evidence for the gut-to-brain hypothesis of PD, and put this in context of available routes of α-synuclein prion infectivity via the gastrointestinal (GI) tract. We then discuss meat as a ready exogenous source of α-synuclein and how certain risk factors, including inflammation, may allow for dietary α-synuclein to pass from the GI lumen into the host to induce pathology. Lastly, we review epidemiological evidence that dietary factors may be involved in PD. Overall, research to date has yet to directly test the contribution of dietary α-synuclein to the mechanism of initiation and progression of the disease. However, numerous experimental findings, including the potent seeding and spreading behavior of α-synuclein fibrils, seem to support, at least in part, the feasibility of an infection with a prion α-synuclein particle via the GI tract. Further studies are required to determine whether dietary α-synuclein contributes to seeding pathology in the gut.
Disulfide loop cleavage of Legionella pneumophila PlaA boosts lysophospholipase A activity
Authors: Lang Christina , Hiller Miriam , Flieger Antje
Published: November 2017

L. pneumophila, an important facultative intracellular bacterium, infects the human lung and environmental protozoa. At least fifteen phospholipases A (PLA) are encoded in its genome. Three of which, namely PlaA, PlaC, and PlaD, belong to the GDSL lipase family abundant in bacteria and higher plants. PlaA is a lysophospholipase A (LPLA) that destabilizes the phagosomal membrane in absence of a protective factor. PlaC shows PLA and glycerophospholipid: cholesterol acyltransferase (GCAT) activities which are activated by zinc metalloproteinase ProA via cleavage of a disulphide loop. In this work, we compared GDSL enzyme activities, their secretion, and activation of PlaA. We found that PlaA majorly contributed to LPLA, PlaC to PLA, and both substrate-dependently to GCAT activity. Western blotting revealed that PlaA and PlaC are type II-secreted and both processed by ProA. Interestingly, ProA steeply increased LPLA but diminished GCAT activity of PlaA. Deletion of 20 amino acids within a predicted disulfide loop of PlaA had the same effect. In summary, we propose a model by which ProA processes PlaA via disulfide loop cleavage leading to a steep increase in LPLA activity. Our results help to further characterize the L. pneumophila GDSL hydrolases, particularly PlaA, an enzyme acting in the Legionella-containing phagosome.
Phosphoproteomics of cAMP signaling of Bordetella adenylate cyclase toxin in mouse dendritic cells
Authors: Novák Jakub , Fabrik Ivo , Linhartová Irena , Link Marek , Černý Ondřej , Stulík Jiří , Šebo Peter
Published: November 2017

The adenylate cyclase toxin (CyaA) of the whooping cough agent Bordetella pertussis subverts immune functions of host myeloid cells expressing the αMβ2 integrin (CD11b/CD18, CR3 or Mac-1). CyaA delivers into cytosol of cells an extremely catalytically active adenylyl cyclase enzyme, which disrupts the innate and adaptive immune functions of phagocytes through unregulated production of the key signaling molecule cAMP. We have used phosphoproteomics to analyze cAMP signaling of CyaA in murine bone marrow-derived dendritic cells. CyaA action resulted in alterations of phosphorylation state of a number of proteins that regulate actin cytoskeleton homeostasis, including Mena, Talin-1 and VASP. CyaA action repressed mTOR signaling through activation of mTORC1 inhibitors TSC2 and PRAS40 and altered phosphorylation of multiple chromatin remodelers, including the class II histone deacetylase HDAC5. CyaA toxin action further elicited inhibitory phosphorylation of SIK family kinases involved in modulation of immune response and provoked dephosphorylation of the transcriptional coactivator CRTC3, indicating that CyaA-promoted nuclear translocation of CRTC3 may account for CyaA-induced IL-10 production. These findings document the complexity of subversive physiological manipulation of myeloid phagocytes by the CyaA toxin, serving in immune evasion of the pertussis agent.
Understanding heat patterns produced by vehicular flows in urban areas
Authors: Zhu Rui , Wong Man Sing , Guilbert Éric , Chan Pak-Wai
Published: November 2017

Vehicular traffic has strong implication in the severity and degree of Urban Heat Island (UHI) effect in a city. It is crucial to map and monitor the spatio-temporal heat patterns from vehicular traffic in a city. Data observed from traffic counting stations are readily available for mapping the traffic-related heat across the stations. However, macroscopic models utilizing traffic counting data to estimate dynamic directional vehicular flows are rarely established. Our work proposes a simple and robust cell-transmission-model to simulate all the possible cell-based origin-destination trajectories of vehicular flows over time, based on the traffic counting stations. Result shows that the heat patterns have notable daily and weekly periodical circulation/pattern, and volumes of heat vary significantly in different grid cells. The findings suggest that vehicular flows in some places are the dominating influential factor that make the UHI phenomenon more remarkable.
In vivo evidence that RBM5 is a tumour suppressor in the lung
Authors: Jamsai Duangporn , Watkins D. Neil , O’Connor Anne E. , Merriner D. Jo , Gursoy Selen , Bird Anthony D. , Kumar Beena , Miller Alistair , Cole Timothy J. , Jenkins Brendan J. , O’Bryan Moira K.
Published: November 2017

Cigarette smoking is undoubtedly a risk factor for lung cancer. Moreover, smokers with genetic mutations on chromosome 3p21.3, a region frequently deleted in cancer and notably in lung cancer, have a dramatically higher risk of aggressive lung cancer. The RNA binding motif 5 (RBM5) is one of the component genes in the 3p21.3 tumour suppressor region. Studies using human cancer specimens and cell lines suggest a role for RBM5 as a tumour suppressor. Here we demonstrate, for the first time, an in vivo role for RBM5 as a tumour suppressor in the mouse lung. We generated Rbm5 loss-of-function mice and exposed them to a tobacco carcinogen NNK. Upon exposure to NNK, Rbm5 loss-of-function mice developed lung cancer at similar rates to wild type mice. As tumourigenesis progressed, however, reduced Rbm5 expression lead to significantly more aggressive lung cancer i.e. increased adenocarcinoma nodule numbers and tumour size. Our data provide in vivo evidence that reduced RBM5 function, as occurs in a large number of patients, coupled with exposure to tobacco carcinogens is a risk factor for an aggressive lung cancer phenotype. These data suggest that RBM5 loss-of-function likely underpins at least part of the pro-tumourigenic consequences of 3p21.3 deletion in humans.
Population-scale organization of cerebellar granule neuron signaling during a visuomotor behavior
Authors: Sylvester Sherika J. G. , Lee Melanie M. , Ramirez Alexandro D. , Lim Sukbin , Goldman Mark S. , Aksay Emre R. F.
Published: November 2017

Granule cells at the input layer of the cerebellum comprise over half the neurons in the human brain and are thought to be critical for learning. However, little is known about granule neuron signaling at the population scale during behavior. We used calcium imaging in awake zebrafish during optokinetic behavior to record transgenically identified granule neurons throughout a cerebellar population. A significant fraction of the population was responsive at any given time. In contrast to core precerebellar populations, granule neuron responses were relatively heterogeneous, with variation in the degree of rectification and the balance of positive versus negative changes in activity. Functional correlations were strongest for nearby cells, with weak spatial gradients in the degree of rectification and the average sign of response. These data open a new window upon cerebellar function and suggest granule layer signals represent elementary building blocks under-represented in core sensorimotor pathways, thereby enabling the construction of novel patterns of activity for learning.
MRI Simulation Study Investigating Effects of Vessel Topology, Diffusion, and Susceptibility on Transverse Relaxation Rates Using a Cylinder Fork Model
Authors: Shazeeb Mohammed Salman , Kalpathy-Cramer Jayashree , Issa Bashar
Published: November 2017

Brain vasculature is conventionally represented as straight cylinders when simulating blood oxygenation level dependent (BOLD) contrast effects in functional magnetic resonance imaging (fMRI). In reality, the vasculature is more complicated with branching and coiling especially in tumors. Diffusion and susceptibility changes can also introduce variations in the relaxation mechanisms within tumors. This study introduces a simple cylinder fork model (CFM) and investigates the effects of vessel topology, diffusion, and susceptibility on the transverse relaxation rates R2* and R2. Simulations using Monte Carlo methods were performed to quantify R2* and R2 by manipulating the CFM at different orientations, bifurcation angles, and rotation angles. Other parameters of the CFM were chosen based on physiologically relevant values: vessel diameters (~2‒10 µm), diffusion rates (1 × 10−11‒1 × 10−9 m2/s), and susceptibility values (3 × 10−8–4 × 10−7 cgs units). R2* and R2 measurements showed a significant dependence on the bifurcation and rotation angles in several scenarios using different vessel diameters, orientations, diffusion rates, and susceptibility values. The angular dependence of R2* and R2 using the CFM could potentially be exploited as a tool to differentiate between normal and tumor vessels. The CFM can also serve as the elementary building block to simulate a capillary network reflecting realistic topological features.
Modulation of individual auditory-motor coordination dynamics through interpersonal visual coupling
Authors: Miyata Kohei , Varlet Manuel , Miura Akito , Kudo Kazutoshi , Keller Peter E.
Published: November 2017

The current study investigated whether visual coupling between two people producing dance-related movements (requiring whole-body auditory-motor coordination) results in interpersonal entrainment and modulates individual auditory-motor coordination dynamics. Paired participants performed two kinds of coordination tasks – either knee flexion or extension repeatedly with metronome beats (Flexion-on-the-beat and Extension-on-the-beat conditions) while standing face-to-face or back-to-back to manipulate visual interaction. The results indicated that the relative phases between paired participants’ movements were closer to 0° and less variable when participants could see each other. In addition, visibility of the partner reduced individual differences in the dynamics of auditory-motor coordination by modulating coordination variability and the frequency of phase transitions from Extension-on-the-beat to Flexion-on-the-beat. Together, these results indicate that visual coupling takes place when paired participants can see each other and leads to interpersonal entrainment during rhythmic auditory-motor coordination, which compensates for individual differences via behavioural assimilation and thus enables individuals to achieve unified and cohesive performances.
PsiQuaSP–A library for efficient computation of symmetric open quantum systems
Authors: Gegg Michael , Richter Marten
Published: November 2017

In a recent publication we showed that permutation symmetry reduces the numerical complexity of Lindblad quantum master equations for identical multi-level systems from exponential to polynomial scaling. This is important for open system dynamics including realistic system bath interactions and dephasing in, for instance, the Dicke model, multi-Λ system setups etc. Here we present an object-oriented C++ library that allows to setup and solve arbitrary quantum optical Lindblad master equations, especially those that are permutationally symmetric in the multi-level systems. PsiQuaSP (Permutation symmetry for identical Quantum Systems Package) uses the PETSc package for sparse linear algebra methods and differential equations as basis. The aim of PsiQuaSP is to provide flexible, storage efficient and scalable code while being as user friendly as possible. It is easily applied to many quantum optical or quantum information systems with more than one multi-level system. We first review the basics of the permutation symmetry for multi-level systems in quantum master equations. The application of PsiQuaSP to quantum dynamical problems is illustrated with several typical, simple examples of open quantum optical systems.
Development of a quantitative NS1-capture enzyme-linked immunosorbent assay for early detection of yellow fever virus infection
Authors: Ricciardi-Jorge Taissa , Bordignon Juliano , Koishi Andrea , Zanluca Camila , Mosimann Ana Luiza , Duarte dos Santos Claudia Nunes
Published: November 2017

Yellow fever is an arboviral disease that causes thousands of deaths every year in Africa and the Americas. However, few commercial diagnostic kits are available. Non-structural protein 1 (NS1) is an early marker of several flavivirus infections and is widely used to diagnose dengue virus (DENV) infection. Nonetheless, little is known about the dynamics of Yellow fever virus (YFV) NS1 expression and secretion, to encourage its use in diagnosis. To tackle this issue, we developed a quantitative NS1-capture ELISA specific for YFV using a monoclonal antibody and recombinant NS1 protein. This test was used to quantify NS1 in mosquito and human cell line cultures infected with vaccine and wild YFV strains. Our results showed that NS1 was detectable in the culture supernatants of both cell lines; however, a higher concentration was maintained as cell-associated rather than secreted into the extracellular milieu. A panel of 73 human samples was used to demonstrate the suitability of YFV NS1 as a diagnostic tool, resulting in 80% sensitivity, 100% specificity, a 100% positive predictive value and a 95.5% negative predictive value compared with RT-PCR. Overall, the developed NS1-capture ELISA showed potential as a promising assay for the detection of early YF infection.
Regulation of mating type switching by the mating type genes and RME1 in Ogataea polymorpha
Authors: Yamamoto Katsuyoshi , Tran Thi N. M. , Takegawa Kaoru , Kaneko Yoshinobu , Maekawa Hiromi
Published: November 2017

Saccharomyces cerevisiae and its closely related yeasts undergo mating type switching by replacing DNA sequences at the active mating type locus (MAT) with one of two silent mating type cassettes. Recently, a novel mode of mating type switching was reported in methylotrophic yeast, including Ogataea polymorpha, which utilizes chromosomal recombination between inverted-repeat sequences flanking two MAT loci. The inversion is highly regulated and occurs only when two requirements are met: haploidy and nutritional starvation. However, links between this information and the mechanism associated with mating type switching are not understood. Here we investigated the roles of transcription factors involved in yeast sexual development, such as mating type genes and the conserved zinc finger protein Rme1. We found that co-presence of mating type a1 and α2 genes was sufficient to prevent mating type switching, suggesting that ploidy information resides solely in the mating type locus. Additionally, RME1 deletion resulted in a reduced rate of switching, and ectopic expression of O. polymorpha RME1 overrode the requirement for starvation to induce MAT inversion. These results suggested that mating type switching in O. polymorpha is likely regulated by two distinct transcriptional programs that are linked to the ploidy and transmission of the starvation signal.
Strategic inhibition of distractors with visual working memory contents after involuntary attention capture
Authors: Lu Jiachen , Tian Lili , Zhang Jiafeng , Wang Jing , Ye Chaoxiong , Liu Qiang
Published: November 2017

Previous research has suggested that visual working memory (VWM) contents had a guiding effect on selective attention, and once participants realized that the distractors shared the same information with VWM contents in the search task, they would strategically inhibit the potential distractors with VWM contents. However, previous behavioral studies could not reveal the way how distractors with VWM contents are inhibited strategically. By employing the eye-tracking technique and a dual-task paradigm, we manipulated the probability of memory items occurring as distractors to explore this issue. Consistent with previous behavioral studies, the results showed that the inhibitory effect occurred only in the high-probability condition, while the guiding effect emerged in the low-probability condition. More importantly, the eye-movement results indicated that in the high-probability condition, once few (even one) distractors with VWM contents were captured at first, all the remaining distractors with VWM contents would be rejected as a whole. However, in the low-probability condition, attention could be captured by the majority of distractors with VWM contents. These results suggested that the guiding effect of VWM contents on attention is involuntary in the early stage of visual search. After the completion of this involuntary stage, the guiding effect of task-irrelevant VWM contents on attention could be strategically controlled.
Tuning magnetic properties for domain wall pinning via localized metal diffusion
Authors: Jin T. L. , Ranjbar M. , He S. K. , Law W. C. , Zhou T. J. , Lew W. S. , Liu X. X. , Piramanayagam S. N.
Published: November 2017

Precise control of domain wall displacement in nanowires is essential for application in domain wall based memory and logic devices. Currently, domain walls are pinned by creating topographical notches fabricated by lithography. In this paper, we propose localized diffusion of non-magnetic metal into ferromagnetic nanowires by annealing induced mixing as a non-topographical approach to form pinning sites. As a first step to prove this new approach, magnetodynamic properties of permalloy (Ni80Fe20) films coated with different capping layers such as Ta, Cr, Cu and Ru were investigated. Ferromagnetic resonance (FMR), and anisotropy magnetoresistance (AMR) measurements were carried out after annealing the samples at different temperatures (T
an
). The saturation magnetization of Ni80Fe20 film decreased, and damping constant increased with T
an
. X-Ray photoelectron spectroscopy results confirmed increased diffusion of Cr into the middle of Ni80Fe20 layers with T
an
. The resistance vs magnetic field measurements on nanowires showed intriguing results.
Emergent wave phenomena in coupled elastic bars: from extreme attenuation to realization of elastodynamic switches
Authors: Chen Qianli , Elbanna Ahmed
Published: November 2017

Metamaterials with acoustic and elastic band gaps are of great interest to scientists and engineers. Here, we introduce a novel mechanism for emergence of multiple band gaps with extreme attenuation by coupling continuous one-dimensional elastic structures. We show that it is possible to develop extreme attenuation at several frequencies from coupling two homogenous bars of different elastodynamic properties even though each bar individually possesses no such gaps. Moreover, if each bar is a composite on its own, multiple resonant band gaps appear in the compound system which do not exist in either bar. We verify our results by conducting numerical simulations for the elastodynamic response and show that the resonant gaps are efficient in attenuating wave propagation. Furthermore, we show that by carefully tailoring the properties of the coupled bars we may construct elastodynamic signal choppers. These results open a new gate for designing Metamaterial with unique wave modulation properties.
Notoginsenoside R1 Alleviates Oxygen–Glucose Deprivation/Reoxygenation Injury by Suppressing Endoplasmic Reticulum Calcium Release via PLC
Authors: Wang Yan , Tu Liu , Li Yingbo , Chen Di , Liu Zhao , Hu Xuelian , Wang Shali
Published: November 2017

As documented in our previous study, notoginsenoside R1 (NGR1) can inhibit neuron apoptosis and the expression of endoplasmic reticulum (ER) stress-associated pro-apoptotic proteins in hypoxic–ischemic encephalopathy. Recent evidence indicates that the Phospholipase C (PLC)/inositol 1,4,5-trisphosphate receptor (IP3R) is important for the regulation of Ca2+ release in the ER. Ca2+ imbalance can stimulate ER stress, CAMKII, and cell apoptosis. The purpose of this study was to further investigate the neuroprotective effect of NGR1 and elucidate how NGR1 regulates ER stress and cell apoptosis in the oxygen–glucose deprivation/reoxygenation (OGD/R) model. Cells were exposed to NGR1 or the PLC activator m-3M3FBS. Then, IP3R- and IP3-induced Ca2+ release (IICR) and activation of the ER stress and CaMKII signal pathway were measured. The results showed that NGR1 inhibited IICR and strengthened the binding of GRP78 with PERK and IRE1. NGR1 also alleviated the activation of the CaMKII pathway. Pretreatment with m-3M3FBS attenuated the neuroprotective effect of NGR1; IICR was activated, activation of the ER stress and CaMKII pathway was increased, and more cells were injured. These results indicate that NGR1 may suppress activation of the PLC/IP3R pathway, subsequently inhibiting ER Ca2+ release, ER stress, and CaMKII and resulting in suppressed cell apoptosis.
Very high density EEG elucidates spatiotemporal aspects of early visual processing
Authors: Robinson Amanda K. , Venkatesh Praveen , Boring Matthew J. , Tarr Michael J. , Grover Pulkit , Behrmann Marlene
Published: November 2017

Standard human EEG systems based on spatial Nyquist estimates suggest that 20–30 mm electrode spacing suffices to capture neural signals on the scalp, but recent studies posit that increasing sensor density can provide higher resolution neural information. Here, we compared “super-Nyquist” density EEG (“SND”) with Nyquist density (“ND”) arrays for assessing the spatiotemporal aspects of early visual processing. EEG was measured from 128 electrodes arranged over occipitotemporal brain regions (14 mm spacing) while participants viewed flickering checkerboard stimuli. Analyses compared SND with ND-equivalent subsets of the same electrodes. Frequency-tagged stimuli were classified more accurately with SND than ND arrays in both the time and the frequency domains. Representational similarity analysis revealed that a computational model of V1 correlated more highly with the SND than the ND array. Overall, SND EEG captured more neural information from visual cortex, arguing for increased development of this approach in basic and translational neuroscience.
Potassium Regulation in Medaka (Oryzias latipes) Larvae Acclimated to Fresh Water: Passive Uptake and Active Secretion by the Skin Cells
Authors: Horng Jiun-Lin , Yu Li-Lu , Liu Sian-Tai , Chen Po-Yen , Lin Li-Yih
Published: November 2017

Molecular mechanisms of Na+, Cl−, and Ca2+ regulation in ionocytes of fish have been well investigated. However, the regulatory mechanism of K+ in fishes has been largely unknown. In this study, we investigated the mechanism of K+ regulation in medaka larvae acclimated to fresh water. Using a scanning ion-selective electrode technique (SIET) to measure the K+ fluxes at skin cells, significant K+ effluxes were found at ionocytes; in contrast, significant K+ influxes were found at the boundaries between keratinocytes. High K+ water (HK) acclimation induced the K+ effluxes at ionocytes and suppressed the K+ influxes at keratinocytes. The K+ effluxes of ionocytes were suppressed by VU591, bumetanide and ouabain. The K+ influxes of keratinocytes were suppressed by TAP. In situ hybridization analysis showed that mRNA of ROMKa was expressed by ionocytes in the skin and gills of medaka larvae. Quantitative PCR showed that mRNA levels of ROMKa and NKCC1a in gills of adult medaka were upregulated after HK acclimation. This study suggests that medaka obtain K+ through a paracellular pathway between keratinocytes and extrude K+ through ionocytes; apical ROMKa and basolateral NKCC1a are involved in the K+ secretion by ionocytes.
Social adversity and epigenetic aging: a multi-cohort study on socioeconomic differences in peripheral blood DNA methylation
Authors: Fiorito Giovanni , Polidoro Silvia , Dugué Pierre-Antoine , Kivimaki Mika , Ponzi Erica , Matullo Giuseppe , Guarrera Simonetta , Assumma Manuela B. , Georgiadis Panagiotis , Kyrtopoulos Soterios A. , Krogh Vittorio , Palli Domenico , Panico Salvatore , Sacerdote Carlotta , Tumino Rosario , Chadeau-Hyam Marc , Stringhini Silvia , Severi Gianluca , Hodge Allison M. , Giles Graham G. , Marioni Riccardo , Karlsson Linnér Richard , O’Halloran Aisling M. , Kenny Rose A. , Layte Richard , Baglietto Laura , Robinson Oliver , McCrory Cathal , Milne Roger L. , Vineis Paolo
Published: November 2017

Low socioeconomic status (SES) is associated with earlier onset of age-related chronic conditions and reduced life-expectancy, but the underlying biomolecular mechanisms remain unclear. Evidence of DNA-methylation differences by SES suggests a possible association of SES with epigenetic age acceleration (AA). We investigated the association of SES with AA in more than 5,000 individuals belonging to three independent prospective cohorts from Italy, Australia, and Ireland. Low SES was associated with greater AA (β = 0.99 years; 95% CI 0.39,1.59; p = 0.002; comparing extreme categories). The results were consistent across different SES indicators. The associations were only partially modulated by the unhealthy lifestyle habits of individuals with lower SES. Individuals who experienced life-course SES improvement had intermediate AA compared to extreme SES categories, suggesting reversibility of the effect and supporting the relative importance of the early childhood social environment. Socioeconomic adversity is associated with accelerated epigenetic aging, implicating biomolecular mechanisms that may link SES to age-related diseases and longevity.
Nanoscale investigation of enhanced electron field emission for silver ion implanted/post-annealed ultrananocrystalline diamond films
Authors: Panda Kalpataru , Hyeok Jeong Jin , Park Jeong Young , Sankaran Kamatchi Jothiramalingam , Balakrishnan Sundaravel , Lin I.-Nan
Published: November 2017

Silver (Ag) ions are implanted in ultrananocrystalline diamond (UNCD) films to enhance the electron field emission (EFE) properties, resulting in low turn-on field of 8.5 V/μm with high EFE current density of 6.2 mA/cm2(at an applied field of 20.5 V/μm). Detailed nanoscale investigation by atomic force microscopy based peak force-controlled tunneling atomic force microscopy (PF-TUNA) and ultra-high vacuum scanning tunneling microscopy (STM) based current imaging tunneling spectroscopy (CITS) reveal that the UNCD grain boundaries are the preferred electron emission sites. The two scanning probe microscopic results supplement each other well. However, the PF-TUNA measurement is found to be better for explaining the local electron emission behavior than the STM-based CITS technique. The formation of Ag nanoparticles induced abundant sp2nanographitic phases along the grain boundaries facilitate the easy transport of electrons and is believed to be a prime factor in enhancing the conductivity/EFE properties of UNCD films. The nanoscale understanding on the origin of electron emission sites in Ag-ion implanted/annealed UNCD films using the scanning probe microscopic techniques will certainly help in developing high-brightness electron sources for flat-panel displays applications.
Rapid resetting of human peripheral clocks by phototherapy during simulated night shift work
Authors: Cuesta Marc , Boudreau Philippe , Cermakian Nicolas , Boivin Diane B.
Published: November 2017

A majority of night shift workers have their circadian rhythms misaligned to their atypical schedule. While bright light exposure at night is known to reset the human central circadian clock, the behavior of peripheral clocks under conditions of shift work is more elusive. The aim of the present study was to quantify the resetting effects of bright light exposure on both central (plasma cortisol and melatonin) and peripheral clocks markers (clock gene expression in peripheral blood mononuclear cells, PBMCs) in subjects living at night. Eighteen healthy subjects were enrolled to either a control (dim light) or a bright light group. Blood was sampled at baseline and on the 4th day of simulated night shift. In response to a night-oriented schedule, the phase of PER1 and BMAL1 rhythms in PBMCs was delayed by ~2.5–3 h (P < 0.05), while no shift was observed for the other clock genes and the central markers. Three cycles of 8-h bright light induced significant phase delays (P < 0.05) of ~7–9 h for central and peripheral markers, except BMAL1 (advanced by +5h29; P < 0.05). Here, we demonstrate in humans a lack of peripheral clock adaptation under a night-oriented schedule and a rapid resetting effect of nocturnal bright light exposure on peripheral clocks.
Genomic data reveal a loss of diversity in two species of tuco-tucos (genus Ctenomys) following a volcanic eruption
Authors: Hsu Jeremy L. , Crawford Jeremy Chase , Tammone Mauro N. , Ramakrishnan Uma , Lacey Eileen A. , Hadly Elizabeth A.
Published: November 2017

Marked reductions in population size can trigger corresponding declines in genetic variation. Understanding the precise genetic consequences of such reductions, however, is often challenging due to the absence of robust pre- and post-reduction datasets. Here, we use heterochronous genomic data from samples obtained before and immediately after the 2011 eruption of the Puyehue-Cordón Caulle volcanic complex in Patagonia to explore the genetic impacts of this event on two parapatric species of rodents, the colonial tuco-tuco (Ctenomys sociabilis) and the Patagonian tuco-tuco (C. haigi). Previous analyses using microsatellites revealed no post-eruption changes in genetic variation in C. haigi, but an unexpected increase in variation in C. sociabilis. To explore this outcome further, we used targeted gene capture to sequence over 2,000 putatively neutral regions for both species. Our data revealed that, contrary to the microsatellite analyses, the eruption was associated with a small but significant decrease in genetic variation in both species. We suggest that genome-level analyses provide greater power than traditional molecular markers to detect the genetic consequences of population size changes, particularly changes that are recent, short-term, or modest in size. Consequently, genomic analyses promise to generate important new insights into the effects of specific environmental events on demography and genetic variation.
Distinct neural substrates of visuospatial and verbal-analytic reasoning as assessed by Raven’s Advanced Progressive Matrices
Authors: Chen Zhencai , De Beuckelaer Alain , Wang Xu , Liu Jia
Published: November 2017

Recent studies revealed spontaneous neural activity to be associated with fluid intelligence (gF) which is commonly assessed by Raven’s Advanced Progressive Matrices, and embeds two types of reasoning: visuospatial and verbal-analytic reasoning. With resting-state fMRI data, using global brain connectivity (GBC) analysis which averages functional connectivity of a voxel in relation to all other voxels in the brain, distinct neural correlates of these two reasoning types were found. For visuospatial reasoning, negative correlations were observed in both the primary visual cortex (PVC) and the precuneus, and positive correlations were observed in the temporal lobe. For verbal-analytic reasoning, negative correlations were observed in the right inferior frontal gyrus (rIFG), dorsal anterior cingulate cortex and temporoparietal junction, and positive correlations were observed in the angular gyrus. Furthermore, an interaction between GBC value and type of reasoning was found in the PVC, rIFG and the temporal lobe. These findings suggest that visuospatial reasoning benefits more from elaborate perception to stimulus features, whereas verbal-analytic reasoning benefits more from feature integration and hypothesis testing. In sum, the present study offers, for different types of reasoning in gF, first empirical evidence of separate neural substrates in the resting brain.
Atomistic simulation of the measurement of mechanical properties of gold nanorods by AFM
Authors: Reischl Bernhard , Rohl Andrew L. , Kuronen Antti , Nordlund Kai
Published: November 2017

Mechanical properties of nanoscale objects can be measured with an atomic force microscope (AFM) tip. However, the continuum models typically used to relate the force measured at a certain indentation depth to quantities such as the elastic modulus, may not be valid at such small scales, where the details of atomistic processes need to be taken into account. On the other hand, molecular dynamics (MD) simulations of nanoindentation, which can offer understanding at an atomistic level, are often performed on systems much smaller than the ones studied experimentally. Here, we present large scale MD simulations of the nanoindentation of single crystal and penta-twinned gold nanorod samples on a silicon substrate, with a spherical diamond AFM tip apex. Both the sample and tip sizes and geometries match commercially available products, potentially linking simulation and experiment. Different deformation mechanisms, involving the creation, migration and annihilation of dislocations are observed depending on the nanorod crystallographic structure and orientation. Using the Oliver-Pharr method, the Young’s moduli of the (100) terminated and (110) terminated single crystal nanorods, and the penta-twinned nanorod, have been determined to be 103 ± 2, 140 ± 4 and 108 ± 2 GPa, respectively, which is in good agreement with bending experiments performed on nanowires.
Non-destructive evaluation of UV pulse laser-induced damage performance of fused silica optics
Authors: Huang Jin , Wang Fengrui , Liu Hongjie , Geng Feng , Jiang Xiaodong , Sun Laixi , Ye Xin , Li Qingzhi , Wu Weidong , Zheng Wanguo , Sun Dunlu
Published: November 2017

The surface laser damage performance of fused silica optics is related to the distribution of surface defects. In this study, we used chemical etching assisted by ultrasound and magnetorheological finishing to modify defect distribution in a fused silica surface, resulting in fused silica samples with different laser damage performance. Non-destructive test methods such as UV laser-induced fluorescence imaging and photo-thermal deflection were used to characterize the surface defects that contribute to the absorption of UV laser radiation. Our results indicate that the two methods can quantitatively distinguish differences in the distribution of absorptive defects in fused silica samples subjected to different post-processing steps. The percentage of fluorescence defects and the weak absorption coefficient were strongly related to the damage threshold and damage density of fused silica optics, as confirmed by the correlation curves built from statistical analysis of experimental data. The results show that non-destructive evaluation methods such as laser-induced fluorescence and photo-thermal absorption can be effectively applied to estimate the damage performance of fused silica optics at 351 nm pulse laser radiation. This indirect evaluation method is effective for laser damage performance assessment of fused silica optics prior to utilization.
Cleavage of poly(A)-binding protein by duck hepatitis A virus 3C protease
Authors: Sun Di , Wang Mingshu , Wen Xingjian , Cheng Anchun , Jia Renyong , Sun Kunfeng , Yang Qiao , Wu Ying , Zhu Dekang , Chen Shun , Liu Mafeng , Zhao Xinxin , Chen Xiaoyue
Published: November 2017

During viral infections, some viruses subvert the host proteins to promote the translation or RNA replication with their protease-mediated cleavage. Poly (A)-binding protein (PABP) is a target for several RNA viruses; however, the impact of duck hepatitis A virus (DHAV) on PABP remains unknown. In this study, we demonstrated for the first time that DHAV infection stimulates a decrease in endogenous PABP and generates two cleavage fragments. On the basis of in vitro cleavage assays, an accumulation of PABP cleavage fragments was detected in duck embryo fibroblast (DEF) cell extracts incubated with functional DHAV 3C protease. In addition, DHAV 3C protease was sufficient for the cleavage of recombinant PABP without the assistance of other eukaryotic cellular cofactors. Furthermore, using site-directed mutagenesis, our data demonstrated a 3C protease cleavage site located between Q367 and G368 in duck PABP. Moreover, the knockdown of PABP inhibited the production of viral RNA, and the C-terminal domain of PABP caused a reduction in viral replication compared to the N-terminal domain. Taken together, these findings suggested that DHAV 3C protease mediates the cleavage of PABP, which may be a strategy to manipulate viral replication.
Association of rs6983267 at 8q24, HULC rs7763881 polymorphisms and serum lncRNAs CCAT2 and HULC with colorectal cancer in Egyptian patients
Authors: Shaker Olfat G. , Senousy Mahmoud A. , Elbaz Eman M.
Published: November 2017

The impact of HULC rs7763881 on colorectal cancer (CRC) susceptibility is not yet known. Also, the biological function of the cancer-related rs6983267 remains unclear. We investigated the association of these SNPs with the risk of CRC and adenomatous polyps (AP), their correlation with CCAT2 and HULC expression, and the potential of serum CCAT2 and HULC as biomarkers for CRC. 120 CRC patients, 30 AP patients, and 96 healthy controls were included. Genotyping and serum lncRNAs were assayed by qPCR. Studied SNPs were not associated with AP susceptibility. rs6983267 GG was associated with increased CRC risk, whereas rs7763881 AC was protective. rs7763881 and rs6983267 CT haplotype was protective. Serum CCAT2 and HULC were upregulated in CRC and AP patients versus controls and discriminated these groups by ROC analysis. rs6983267 GG and rs7763881 AA patients demonstrated higher serum CCAT2 and HULC compared with GT/TT and AC, respectively. rs6983267 and serum HULC predicted CRC diagnosis among non-CRC groups (AP + controls) by multivariate analysis. Studied SNPs or serum long noncoding RNAs weren’t correlated with nodal or distant metastasis. In conclusion, rs6983267 and rs7763881 are potential genetic markers of CRC predisposition and correlate with serum CCAT2 and HULC, two novel potential non-invasive diagnostic biomarkers for CRC.
Recognition of a likely two phased extinction at the K-Pg boundary in Antarctica
Authors: Tobin Thomas S.
Published: November 2017

The southernmost Cretaceous – Paleogene (K-Pg) outcrop exposure is the well-studied exposure on Seymour Island, Antarctica. Deposition across the K-Pg boundary there is uninterrupted, and as a consequence the ammonite fossil record is commonly used to test statistical methods of evaluating mass extinctions to account for the incompleteness of the fossil record. Numerous detailed fossil data sets from Seymour Island, comprised dominantly of mollusks, have been published over the last 30 years, but in most cases have not received statistical treatment. Here a previously published statistical technique is modified, automated, and applied to all published macrofossil data sets available from Seymour Island. All data sets reveal likely evidence of two separate multi-species extinctions, one synchronous with bolide impact evidence at the K-Pg boundary, and another 45 ± 15 meters (~140–290 ky) below the boundary. The apparent earlier extinction primarily affects benthic mollusks, while the boundary extinction primarily affects ammonites. While there is no unique sedimentological change over the interval where the earlier extinction is identified, it is impossible to exclude the possibility that this pattern is stratigraphically controlled. The automation of this technique allows it to be applied easily to other large fossil data sets.
Identification of the pheromone biosynthesis genes from the sex pheromone gland transcriptome of the diamondback moth, Plutella xylostella
Authors: Chen Da-Song , Dai Jian-Qing , Han Shi-Chou
Published: November 2017

The diamondback moth was estimated to increase costs to the global agricultural economy as the global area increase of Brassica vegetable crops and oilseed rape. Sex pheromones traps are outstanding tools available in Integrated Pest Management for many years and provides an effective approach for DBM population monitoring and control. The ratio of two major sex pheromone compounds shows geographical variations. However, the limitation of our information in the DBM pheromone biosynthesis dampens our understanding of the ratio diversity of pheromone compounds. Here, we constructed a transcriptomic library from the DBM pheromone gland and identified genes putatively involved in the fatty acid biosynthesis, pheromones functional group transfer, and β-oxidation enzymes. In addition, odorant binding protein, chemosensory protein and pheromone binding protein genes encoded in the pheromone gland transcriptome, suggest that female DBM moths may receive odors or pheromone compounds via their pheromone gland and ovipositor system. Tissue expression profiles further revealed that two ALR, three DES and one FAR5 genes were pheromone gland tissue biased, while some chemoreception genes expressed extensively in PG, pupa, antenna and legs tissues. Finally, the candidate genes from large-scale transcriptome information may be useful for characterizing a presumed biosynthetic pathway of the DBM sex pheromone.
Enhancement of Power Output by using Alginate Immobilized Algae in Biophotovoltaic Devices
Authors: Ng Fong-Lee , Phang Siew-Moi , Periasamy Vengadesh , Yunus Kamran , Fisher Adrian C.
Published: November 2017

We report for the first time a photosynthetically active algae immobilized in alginate gel within a fuel cell design for generation of bioelectricity. The algal-alginate biofilm was utilized within a biophotovoltaics (BPV) device developed for direct bioelectricity generation from photosynthesis. A peak power output of 0.289 mWm−2 with an increase of 18% in power output compared to conventional suspension culture BPV device was observed. The increase in maximum power density was correlated to the maximum relative electron transport rate (rETRm). The semi-dry type of photosynthetically active biofilm proposed in this work may offer significantly improved performances in terms of fuel cell design, bioelectricity generation, oxygen production and CO2 reduction.
An Open Software Platform for the Automated Design of Paper-Based Microfluidic Devices
Authors: DeChiara Nicholas S. , Wilson Daniel J. , Mace Charles R.
Published: November 2017

Paper-based microfluidic devices have many applications in biomedical and environmental analysis. However, the process of prototyping device designs can be tedious, error-prone, and time-consuming. Here, we present a cross-platform, open-source software tool—AutoPAD—developed to quickly create and modify device designs and provide a free alternative to commercial design software. The capabilities that we designed to be inherent to AutoPAD (e.g., automatic zone alignment and design refactoring) highlight its potential use in nearly any paper-based microfluidic device application and for creating nearly any desired design, which we demonstrate through the recreation of numerous device designs from the literature.