bluuebunny/crossref_metadata_2025 huggingface dataset:
Simultaneous inpainting and denoising by directional global three-part decomposition: connecting variational and Fourier domain-based image processing
Authors: Thai D. H. , Gottschlich C.
Published: July 2018

We consider the very challenging task of restoring images (i) that have a large number of missing pixels, (ii) whose existing pixels are corrupted by noise, and (iii) that ideally contain both cartoon and texture elements. The combination of these three properties makes this inverse problem a very difficult one. The solution proposed in this manuscript is based on directional global three-part decomposition (DG3PD) (Thai, Gottschlich. 2016
EURASIP. J. Image Video Process.
2016
, 1–20 (
doi:10.1186/s13640-015-0097-y
)) with a directional total variation norm, directional G-norm and ℓ
∞
-norm in the curvelet domain as key ingredients of the model. Image decomposition by DG3PD enables a decoupled inpainting and denoising of the cartoon and texture components. A comparison with existing approaches for inpainting and denoising shows the advantages of the proposed method. Moreover, we regard the image restoration problem from the viewpoint of a Bayesian framework and we discuss the connections between the proposed solution by function space and related image representation by harmonic analysis and pyramid decomposition.
BNPd single-atom catalysts for selective hydrogenation of acetylene to ethylene: a density functional theory study
Authors: Gong Wanqi , Kang Lihua
Published: July 2018

The mechanisms of selective hydrogenation of acetylene to ethylene on B
11
N
12
Pd single-atom catalyst were investigated through the density functional theory by using the 6-31++G** basis set. We studied the adsorption characteristics of H
2
and C
2
H
2
, and simulated the reaction mechanism. We discovered that H
2
underwent absolute dissociative chemisorption on single-atom Pd, forming the B
11
N
12
Pd(2H) dihydride complex, and then the hydrogenation reaction with C
2
H
2
proceeded. The hydrogenation reaction of acetylene on the B
11
N
12
Pd complex complies with the Horiuti–Polanyi mechanism, and the energy barrier was as low as 26.55 kcal mol
−1
. Meanwhile, it also has a higher selectivity than many bimetallic alloy single-atom catalysts.
Appetitive information seeking behaviour reveals robust daily rhythmicity for Internet-based food-related keyword searches
Authors: Scrutton Alvarado Nicolas , Stevenson Tyler J.
Published: July 2018

There has been an exponential growth of information seeking behaviour (ISB) via Internet-based programs over the past decade. The availability of software that record ISB temporal patterns has provided a valuable opportunity to examine biological rhythms in human behaviour. Internet search repositories, such as Google Trends, permit the analyses of large datasets that can be used to track ISB on a domestic and international scale. We examined daily and seasonal Google Trends search patterns for keywords related to food intake, using the most relevant search terms for the USA, UK, Canada, India and Australia. Daily and seasonal ISB rhythmicity were analysed using CircWave v. 1.4. Daily ISB data revealed a robust and significant sine waveform for general terms (e.g. ‘pizza delivery') and country-specific search terms (e.g. ‘just eat'). The pattern revealed clear evening double-peaks, occurring every day at 19.00 and 02.00. The patterns were consistent across search terms, days of the week and geographical locations, suggesting a common ISB rhythm that is not necessarily culture-dependent. Then, we conducted Cosinor v. 2.4 analyses to examine the daily amplitudes in ISB. The results indicated a non-significant linear increased from Monday to Sunday. Seasonal data did not show consistent significant ISB patterns. It is likely that two different human populations are responsible for the daily ‘early' and ‘late' evening ISB peaks. We propose that the major factor that contributes to the bimodal evening peak is age-dependent (e.g. adolescent, early adulthood versus midlife and mature adulthood) and a minor role for human chronotypes (e.g. late versus early). Overall, we present novel human appetitive behaviour for information seeking of food resources and propose that Internet-based search patterns reflect a biological rhythm of motivation for energy balance.
A long-forgotten ‘dinosaur’ bone from a museum cabinet, uncovered to be a Japan's iconic extinct mammal,Paleoparadoxia(Desmostylia, Mammalia)
Authors: Matsui Kumiko , Kimura Yuri , Nagata Mitsuhiro , Inose Hiroaki , Ikeda Kazuya , Beatty Brian Lee , Obayashi Hideyuki , Hirata Takafumi , Otoh Shigeru , Shinmura Tatsuya , Agematsu Sachiko , Sashida Katsuo
Published: July 2018

Here, we report a new ‘discovery’ of a desmostylian fossil in the geological collection at a national university in Japan. This fossil was unearthed over 60 years ago and donated to the university. Owing to the original hand-written note kept with the fossil in combination with interview investigation, we were able to reach two equally possible fossil sites in the town of Tsuchiyu Onsen, Fukushima. Through the interviews, we learned that the fossil was discovered during construction of a debris flow barrier and that it was recognized as a ‘dinosaur’ bone among the locals and displayed in the Village Hall before/until the town experienced a fire disaster in 1954. As scientific findings, the fossil was identified to be a right femur ofPaleoparadoxia(Desmostylia), which shows well-preserved muscle scars on the surface. The age was estimated to be 15.9 Ma or younger in zircon-dating. This study shows an excellent case that historical and scientific significances could be extracted from long-forgotten uncatalogued specimens as long as the original information is retained with the specimens.
Origin of the trochophora larva
Authors: Nielsen Claus
Published: July 2018

The trochophora larva, which is so well known from the marine plankton, is central to our understanding of the evolution of a large branch of the bilaterians. Two theories for this larval type have been prevalent, the trochaea theory and the theory proposed by Ivanova-Kazas. The embryology, or more precisely the cell-lineage, of these larvae seems to be central for our understanding of their origin, but important details have been missing. According to the trochaea theory, a circumblastoporal ring of blastomeres differentiates to follow the convoluted shape of the conspicuous ciliary bands of the larvae, with prototroch and metatroch around the mouth, forming a filtering system, and telotroch around the anus. According to the Ivanova-Kazas theory, the blastomeres with the ciliary bands develop through specialization of rings of cells of the general ciliation in a lecithotrophic larva. Now, a new cell-lineage study of the gastropod
Crepidula
has shown that the ring of cells at the edge of the blastopore develops into the band of cells carrying prototroch and metatroch, characteristic of the trochophora. This gives strong support to the trochaea theory.
Nanostructured carbon black for simultaneous electrochemical determination of trace lead and cadmium by differential pulse stripping voltammetry
Authors: Xie Ruigang , Zhou Lingli , Lan Cuiling , Fan Fangfang , Xie Ruifeng , Tan Hongyu , Xie Tiansheng , Zhao Lingmin
Published: July 2018

Nanostructured carbon black (CB) was first employed directly in this paper for the simultaneous electrochemical determination of trace Pb(II) and Cd(II) using differential pulse anodic stripping voltammetry. The morphology and surface properties of conductive CB were characterized by transmission electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, ultraviolet–visible spectroscopy and Raman spectroscopy. Special pore structures, as well as surface chemical functional groups, endow CB with excellent catalytic and adsorption properties. Some parameters affecting electrical analysis performance were investigated systematically including deposition time and potential, pH value of solution, volume of suspension, amount of Bi(III) and Nafion solution. CB–Nafion–glassy carbon electrode sensor linear response ranges from 6 to 1000 nM for selective and simultaneous determination. The detection limits were calculated to be 8 nM (0.9 µg l−1) for Cd(II) and 5 nM (1.0 µg l−1) for Pb(II) (S/N = 3) for the electrocatalytic determination under optimized conditions. The method was successfully used to the determination of actual samples and good recovery was achieved from different spiked samples. Low detection limits and good stability of the modified electrode demonstrated a promising perspective for the detection of trace metal ions in practical application.
Corrosion-resistant systems of formate packer fluid for G3/N80/TP110SS pipes at high temperature, high pressure and high H
2
S/CO
2
ratios
Authors: Xu Peng , Tao Zhengwu , Wang Zhihong
Published: July 2018

A series of corrosion problems caused by high-temperature, high-pressure and high-acid gas environments has been an issue in oil and gas production for a long time. During the development of a high-acid gas field, the petroleum pipe is subjected to many aspects of corrosion, and the corrosion mechanism is complicated by the condition of the coexistence of H
2
S/CO
2
. Based on the study of the corrosion problem associated with the formate packer fluid in Southwest China, three kinds of steels were studied for corrosion prevention in the alloy G3/N80 steel/TP110SS steel. The study shows that the corrosion rate of the formate packer fluid is low, but corrosion is severe in environments characterized by high temperatures, high pressures and high-acid gas contents. Based on the consideration of cost and the difficulty of realization, an anti-corrosion system was constructed based on the existing packer fluid, mainly through the introduction of a variety of anti-corrosion additives. Through the selection of various additives and corrosion experiments, a corrosion protection system of formate packer fluid was developed. Corrosion tests show that the corrosion rate of the system must be less than 0.076 mm yr
−1
to achieve the purpose of corrosion protection. The formate packer fluid with corrosion protection can meet the needs of the current application.
Unexpected formation of polymeric silver(I) complexes of azine-type ligand via self-assembly of Ag-salts with isatin oxamohydrazide
Authors: Soliman Saied M. , Albering Jörg H. , Barakat Assem
Published: July 2018

Isatin oxamohydrazide (L) reacted with the aqueous solution of silver nitrate at room temperature afforded the polymeric silver(I) nitrato complex, [Ag2L′(NO3)2]n,(1)of the azine ligand (L′). Similarly, the reaction ofLwith silver(I) perchlorate gave the [Ag2L′2(ClO4)2]n,(2)coordination polymer. Careful inspection of the crystals from the nitrato complex preparation showed the presence of another crystalline product which is found to be [Ag(Isatin-3-hydrazone)NO3],(3)suggesting that the reaction between silver(I) nitrate andLproceeds first by the hydrolysis ofLto the isatin hydrazone which attacks another molecule ofLto affordL′. Testing metal salts such as Ni2+, Co2+, Mn2+, Cu2+and Cd2+did not undergo any reaction withLeither under the same reaction conditions or with heating under reflux up to 24 h. Treatment of the warm alcoholic solution ofLwith few drops of 1 : 1 (v/v) hydrochloric acid gave the free ligand (L′) in good yield. The [Ag2L′(NO3)2]ncomplex forms a two-dimensional infinite coordination polymer, while the [Ag2L′2(ClO4)2]nforms one-dimensional infinite chains with an alternating silver-azine backbone. Quantitative analysis of the intermolecular interactions in their crystals is made using Hirshfeld surface analysis. Density functional theory studies were performed to investigate the coordination bonding in the studied complexes.
Has adaptation occurred in males and females since separate sexes evolved in the plantSilene latifolia?
Authors: Zemp Niklaus , Widmer Alex , Charlesworth Deborah
Published: July 2018

The evolution of separate sexes may involve changed expression of many genes, as each sex adapts to its new state. Evidence is accumulating for sex differences in expression even in organisms that have recently evolved separate sexes from hermaphrodite or monoecious (cosexual) ancestors, such as some dioecious flowering plants. We describe evidence that a dioecious plant species with recently evolved dioecy,Silene latifolia, has undergone adaptive changes that improve functioning in females, in addition to changes that are probably pleiotropic effects of male sterility. The results suggest pervasive adaptations as soon as males and females evolve from their cosexual ancestor.
Predator macroevolution drives trophic cascades and ecosystem functioning
Authors: Start Denon
Published: July 2018

Biologists now recognize that ecology can drive evolution, and that evolution in turn produces ecological patterns. I extend this thinking to include longer time scales, suggesting that macroevolutionary transitions can create phenotypic differences among species, which then have predictable impacts on species interactions, community assembly and ecosystem functioning. Repeated speciation can exacerbate these patterns by creating communities with similar phenotypes and hence ecological impacts. Here, I use several experiments to test these ideas in dragonfly larvae that occupy ponds with fish, ponds without fish, or both. I show that macroevolutionary transitions between habitats cause fishless pond species to be more active relative to fish pond specialists, reducing prey abundance, shifting prey community composition and creating stronger trophic cascades. These effects scale up to the community level with predictable consequences for ecosystem multi-functioning. I suggest that macroevolutionary history can have predictable impacts on phenotypic traits, with consequences for interacting species and ecosystems.
Low dose of neonicotinoid insecticide reduces foraging motivation of bumblebees
Authors: Lämsä Juho , Kuusela Erno , Tuomi Juha , Juntunen Sini , Watts Phillip C.
Published: July 2018

Widespread use of neonicotinoid insecticides, such as imidacloprid, is often associated with diminishing populations of bees; this loss of pollinators presents a concern for food security and may cause unpredictable changes in ecological networks. However, little is known about the potential behavioural mechanisms behind the neonicotinoid-associated pollinator decline. We quantified the effects of low-dose (1 ppb) imidacloprid exposure on the foraging behaviour of bumblebees (
Bombus terrestris
). Individual bumblebees were released into a flight arena containing three patches of robotic flowers whose colour (yellow, orange, blue) indicated whether the flower delivered a reward (sugar solution). Exposure to imidacloprid had no significant effect on measures of bumblebee physical performance (such as flight speed) or learning (identifying rewarding flowers). However, pesticide-treated bumblebees had reduced foraging motivation compared with the control bumblebees, as they visited fewer robotic flowers, were slower to start foraging and did not visit all three flower colours as often. Neonicotinoid concentrations of 1 ppb, often reported in plant nectar near agricultural lands, can thus affect the foraging behaviour of bumblebees. Even without a notable impact on flight performance and learning, a reduction in foraging motivation could explain the poor performance of colonies of bumblebees exposed to neonicotinoids.
A lipocalin protein, Neural Lazarillo, is key to social interactions that promote termite soldier differentiation
Authors: Yaguchi Hajime , Shigenobu Shuji , Hayashi Yoshinobu , Miyazaki Satoshi , Toga Kouhei , Masuoka Yudai , Maekawa Kiyoto
Published: July 2018

Social communication among castes is a crucial component of insect societies. However, the genes involved in soldier determination through the regulation of inter-individual interactions are largely unknown. In an incipient colony of the damp-wood termiteZootermopsis nevadensis, the first larva to develop into a third instar always differentiates into a soldier via frequent trophallactic feeding from the reproductives. Here, by performing RNA-seq analysis of third instar larvae, a homologue ofNeural Lazarillo(namedZnNLaz1) was found to be the most differentially expressed gene in these soldier-destined larvae, compared with worker-destined larvae. This gene encodes a lipocalin protein related to the transport of small hydrophobic molecules. RNAi-induced knockdown ofZnNLaz1significantly inhibited trophallactic interactions with the queen and decreased the soldier differentiation rates. This protein is localized in the gut, particularly in the internal wall, of soldier-destined larvae, suggesting that it is involved in the integration of social signals from the queen through frequent trophallactic behaviours. Based on molecular phylogenetic analysis, we suggest that a novel function of termite NLaz1 has contributed to social evolution from the cockroach ancestors of termites. These results indicated that a high larvalNLaz1expression is crucial for soldier determination through social communication in termites.
Risky business: linkingToxoplasma gondiiinfection and entrepreneurship behaviours across individuals and countries
Authors: Johnson Stefanie K. , Fitza Markus A. , Lerner Daniel A. , Calhoun Dana M. , Beldon Marissa A. , Chan Elsa T. , Johnson Pieter T. J.
Published: July 2018

Disciplines such as business and economics often rely on the assumption of rationality when explaining complex human behaviours. However, growing evidence suggests that behaviour may concurrently be influenced by infectious microorganisms. The protozoanToxoplasma gondiiinfects an estimated 2 billion people worldwide and has been linked to behavioural alterations in humans and other vertebrates. Here we integrate primary data from college students and business professionals with national-level information on cultural attitudes towards business to test the hypothesis thatT. gondiiinfection influences individual- as well as societal-scale entrepreneurship activities. Using a saliva-based assay, we found that students (n= 1495) who tested IgG positive forT. gondiiexposure were 1.4× more likely to major in business and 1.7× more likely to have an emphasis in ‘management and entrepreneurship' over other business-related emphases. Among professionals attending entrepreneurship events,T. gondii-positive individuals were 1.8× more likely to have started their own business compared with other attendees (n= 197). Finally, after synthesizing and combining country-level databases onT. gondiiinfection from the past 25 years with the Global Entrepreneurship Monitor of entrepreneurial activity, we found that infection prevalence was a consistent, positive predictor of entrepreneurial activity and intentions at the national scale, regardless of whether previously identified economic covariates were included. Nations with higher infection also had a lower fraction of respondents citing ‘fear of failure' in inhibiting new business ventures. While correlational, these results highlight the linkage between parasitic infection and complex human behaviours, including those relevant to business, entrepreneurship and economic productivity.
Bt
rice plants may protect neighbouring non-
Bt
rice plants against the striped stem borer,
Chilo suppressalis
Authors: Jiao Yaoyu , Hu Xiaoyun , Peng Yufa , Wu Kongming , Romeis Jörg , Li Yunhe
Published: July 2018

The area planted with insect-resistant genetically engineered crops expressing
Bacillus thuringiensis
(
Bt
) genes has greatly increased in many areas of the world. Given the nearby presence of non-
Bt
crops (including those planted as refuges) and non-crop habitats, pests targeted by the
Bt
trait have a choice between
Bt
and non-
Bt
crops or weeds, and their host preference may greatly affect insect management and management of pest resistance to
Bt
proteins. In this study, we examined the oviposition preference of the target pest of
Bt
rice,
Chilo suppressalis
, for
Bt
versus non-
Bt
rice plants as influenced by previous damage caused by
C. suppressalis
larvae. The results showed that
C. suppressalis
females had no oviposition preference for undamaged
Bt
or non-
Bt
plants but were repelled by conspecific-damaged plants whether
Bt
or non-
Bt
. Consequently,
C. suppressalis
egg masses were more numerous on
Bt
plants than on neighbouring non-
Bt
plants both in greenhouse and in field experiments due to the significantly greater caterpillar damage on non-
Bt
plants. We also found evidence of poorer performance of
C. suppressalis
larvae on conspecific-damaged rice plants when compared with undamaged plants. GC-MS analyses showed that larval damage induced the release of volatiles that repelled mated
C. suppressalis
females in wind tunnel experiments
.
These findings suggest that
Bt
rice could act as a dead-end trap crop for
C. suppressalis
and thereby protect adjacent non-
Bt
rice plants. The results also indicate that the oviposition behaviour of target pest females should be considered in the development of
Bt
resistance management strategies.
Modification of betanodavirus virulence by substitutions in the 3' terminal region of RNA2
Authors: Souto Sandra , Olveira José G. , Dopazo Carlos P. , Borrego Juan J. , Bandín Isabel
Published: July 2018

Betanodaviruses have bi-segmented positive-sense RNA genomes, consisting of RNAs 1 and 2. For some members of the related genus alphanodavirus, the 3′ terminal 50 nucleotides (nt) of RNA2, including a predicted stem-loop structure (3′SL), are essential for replication. We investigate the possible existence and role of a similar structure in a reassortant betanodavirus strain (RGNNV/SJNNV). In this study, we developed three recombinant strains containing nucleotide changes at positions 1408 and 1412. Predictive models showed stem-loop structures involving nt 1398–1421 of the natural reassortant whereas this structure is modified in the recombinant viruses harbouring point mutations r1408 and r1408–1412, but not in r1412. Results obtained from infectivity assays showed differences between the reference strains and the mutants in both RNA1 and RNA2 synthesis. Moreover, an imbalance between the synthesis of both segments was demonstrated, mainly with the double mutant. All these results suggest an interaction between RNA1 and the 3′ non-coding regions (3′NCR) of RNA2. In addition, the significant attenuation of the virulence for Senegalese sole and the delayed replication of r1408–1412 in brain tissues may point to an interaction of RNA2 with host cellular proteins.
Quantitative single-molecule three-color Förster resonance energy transfer by photon distribution analysis
Authors: Barth Anders , von Voithenberg Lena Voith , Lamb Don C.
Published: July 2018

Single-molecule Förster resonance energy transfer (FRET) is a powerful tool to study conformational dynamics of biomolecules. Using solution-based single-pair FRET by burst analysis, conformational heterogeneities and fluctuations of fluorescently labeled proteins or nucleic acids can be studied by monitoring a single distance at a time. Three-color FRET is sensitive to three distances simultaneously and can thus elucidate complex coordinated motions within single molecules. While three-color FRET has been applied on the single-molecule level before, a detailed quantitative description of the obtained FRET efficiency distributions is still missing. Direct interpretation of three-color FRET data is additionally complicated by an increased shot noise contribution when converting photon counts to FRET efficiencies. However, to address the question of coordinated motion, it is of special interest to extract information about the underlying distance heterogeneity, which is not easily extracted from the FRET efficiency histograms directly. Here, we present three-color photon distribution analysis (3C-PDA), a method to extract distributions of inter-dye distances from three-color FRET measurements. We present a model for diffusion-based three-color FRET experiments and apply Bayesian inference to extract information about the physically relevant distance heterogeneity in the sample. The approach is verified using simulated data sets and experimentally applied to triple-labeled DNA duplexes. Finally, 3C-FRET experiments on the Hsp70 chaperone BiP reveal conformational coordinated changes between individual domains. The possibility to address the co-occurrence of intramolecular distances makes 3C-PDA a powerful method to study the coordination of domain motions within biomolecules during conformational changes.

Significance

In solution-based single-molecule Förster resonance energy transfer (FRET) experiments, biomolecules are studied as they freely diffuse through the observation volume of a confocal microscope, resulting in bursts of fluorescence from single molecules. Using three fluorescent labels, one can concurrently measure three distances in a single molecule but the experimentally limited number of photons is not sufficient for a straight-forward analysis. Here, we present a probabilistic framework, called three-color photon distribution analysis (3C-PDA), to extract quantitative information from single-molecule three-color FRET experiments. By extracting distributions of interdye distances from the data, the method provides a three-dimensional description of the conformational space of biomolecules, enabling the detection of coordinated movements during conformational changes.
Convergent evolution of psilocybin biosynthesis by psychedelic mushrooms
Authors: Awan Ali R. , Winter Jaclyn M. , Turner Daniel , Shaw William M. , Suz Laura M. , Bradshaw Alexander J. , Ellis Tom , Dentinger Bryn T.M.
Published: July 2018

Psilocybin is a psychoactive compound with clinical applications produced by dozens of mushroom species1. There has been a longstanding interest in psilocybin research with regard to treatment for addiction2, depression3, and end-of-life suffering4. However, until recently very little was known about psilocybin biosynthesis and its ecological role. Here we confirm and refine recent findings5 about the genes underpinning psilocybin biosynthesis, discover that there is more than one psilocybin biosynthesis cluster in mushrooms, and we provide the first data directly addressing psilocybin’s ecological role. By analysing independent genome assemblies for the hallucinogenic mushrooms Psilocybe cyanescens and Pluteus salicinus we recapture the recently discovered psilocybin biosynthesis cluster5,6 and show that a transcription factor previously implicated in its regulation is actually not part of the cluster. Further, we show that the mushroom Inocybe corydalina produces psilocybin but does not contain the established biosynthetic cluster, and we present an alternative cluster. Finally, a meta-transcriptome analysis of wild-collected mushrooms provides evidence for intra-mushroom insect gene expression of flies whose larvae grow inside Psilocybe cyanescens. These larvae were successfully reared into adults. Our results show that psilocybin does not confer complete protection against insect mycophagy, and the hypothesis that it is produced as an adaptive defense compound may need to be reconsidered.
NAD consumption by PARP1 in response to DNA damage triggers metabolic shift critical for damaged cell survival
Authors: Murata Michael M. , Kong Xiangduo , Moncada Emmanuel , Chen Yumay , Wang Ping , Berns Michael W. , Yokomori Kyoko , Digman Michelle A.
Published: July 2018

DNA damage signaling is critical for the maintenance of genome integrity and cell fate decision. Poly(ADP-ribose) polymerase 1 (PARP1) is a DNA damage sensor rapidly activated in a damage dose and complexity-dependent manner playing a critical role in the initial chromatin organization and DNA repair pathway choice at damage sites. However, the cell-wide consequence of its activation in damaged cells is not well delineated. Using the phasor approach to fluorescence lifetime imaging microscopy (FLIM) and fluorescence-based biosensors in combination with laser microirradiation, we found a rapid cell-wide increase of the bound/free NADH ratio in response to nuclear DNA damage, which is triggered by NAD+ depletion by PARP activation. This change is linked to the metabolic balance shift to oxidative phosphorylation (oxphos) over glycolysis. Inhibition of the respiratory chain resulted in rapid PARP-dependent ATP reduction and intracellular acidification, and eventually, PARP-dependent, AIF-independent, apoptosis indicating that oxphos becomes critical for damaged cell survival. The results reveal the novel pro-survival effect of PARP activation through a change in cellular metabolism, and demonstrate how unique applications of advanced fluorescence imaging technologies in combination with laser microirradiation can be a powerful tool to interrogate damage-induced metabolic changes at high spatiotemporal resolution in a live cell.
Absence of GdX/UBL4A protects against inflammatory bowel diseases by regulating NF-κB signaling in DCs and macrophages
Authors: Liu Chunxiao , Zhou Yifan , Li Mengdi , Wang Ying , Yang Shigao , Feng Yarui , Wang Yinyin , Wang Yangmeng , Ren Fangli , Li Jun , Dong Zhongjun , Chin Y Eugene , Fu Xinyuan , Wu Li , Chang Zhijie
Published: July 2018

Nuclear factor-kappa B (NF-κB) activation is critical for innate immune responses. Here we report that the UBL4A (Ubiquitin-like protein 4A, also named GdX) enhances dendritic cells (DCs) and macrophages (Mφ)-mediated innate immune defenses by positively regulating NF-κB signaling. GdX-deficient mice were resistant to LPS-induced endotoxin shock and DSS-induced colitis. DC- or Mφ-specific GdX-deficient mice displayed alleviated mucosal inflammation, and the production of pro-inflammatory cytokines by GdX-deficient DCs and Mφ was reduced. Mechanistically, we found that PTPN2 (TC45) and PP2A form a complex with RelA (p65) to mediate its dephosphorylation whereas GdX interrupts the TC45/PP2A/p65 complex formation and restrict p65 dephosphorylation by trapping TC45. Our study provides a mechanism by which NF-κB signaling is positively regulated by an adaptor protein GdX in DC or Mφ to maintain the innate immune response. Targeting GdX could be a strategy to reduce over-activated immune response in inflammatory diseases.
Fast-backward replay of sequentially memorized items in humans
Authors: Huang Qiaoli , Jia Jianrong , Han Qiming , Luo Huan
Published: July 2018

Storing temporal sequences of events (i.e., sequence memory) is fundamental to many cognitive functions. However, how the sequence order information is maintained and represented in working memory and its behavioral significance, particularly in human subjects, remains unknown. Here, we recorded electroencephalography (EEG) in combination with a temporal response function (TRF) method to dissociate item-specific neuronal reactivations. We demonstrate that serially remembered items are successively reactivated during memory retention. The sequential replay displays two interesting properties compared to the actual sequence. First, the item-by-item reactivation is compressed within a 200-400 ms window, suggesting that external events are associated within a plasticity-relevant window to facilitate memory consolidation. Second, the replay is in a temporally reversed order and is strongly related to the recency effect in behavior. This fast-backward replay, previously revealed in rat hippocampus and demonstrated here in human cortical activities, might constitute a general neural mechanism for sequence memory and learning.
Fungal-bacterial interaction selects for quorum sensing mutants and a metabolic shift towards the production of natural antifungal compounds
Authors: Albarracín Orio Andrea G. , Petras Daniel , Tobares Romina A. , Aksenov Alexander A. , Wang Mingxun , Juncosa Florencia , Sayago Pamela , Moyano Alejandro J. , Dorrestein Pieter C. , Smania Andrea M. , Ducasse Daniel A.
Published: July 2018

Environmental species of bacteria and fungi coexist and interact showing antagonistic and mutualistic behaviors, mediated by exchange of small diffusible metabolites, driving microbial adaptation to complex communal lifestyles1. Here we show that a wild Bacilus subtilis strain undergoes heritable phenotypic variation following interaction with the soil fungal pathogen Setophoma terrestris (ST) in co-culture. Metabolomics analysis revealed a differential profile in B. subtilis before (pre-ST) and after (post-ST) interacting with the fungus, which paradoxically involved the absence of lipopeptides surfactin and plipastatin and yet acquired antifungal activity in post-ST variants. Metabolic changes were also observed in the profile of volatile compounds, with 2-heptanone and 2-octanone being the most discriminating metabolites present at higher concentrations in post-ST during its interaction with the fungus. Most strikingly, both ketones showed strong antifungal activity against S. terrestris, which was lost with the addition of exogenous surfactin to the medium. Whole-genome analyses showed that mutations in the comA and comP genes of the ComQPXA quorum-sensing system, constituted the genetic bases of post-ST conversion, which allowed the concomitant production of ketones and elimination of surfactin. These findings suggest that mutations in ComQXPA stably rewired B. subtilis metabolism towards the depletion of surfactins and the production of antifungal compounds during its antagonistic interaction with S. terrestris.
SGC-GAK-1: a chemical probe for cyclin G associated kinase (GAK)
Authors: Asquith Christopher R. M. , Berger Benedict-Tilman , Wan Jing , Bennett James M. , East Michael P. , Elkins Jonathan M. , Fedorov Oleg , Godoi Paulo H. , Hunter Debra M. , Knapp Stefan , Müller Susanne , Wells Carrow I. , Earp H. Shelton , Willson Timothy M. , Zuercher William J.
Published: July 2018

We describe SGC-GAK-1 (11), a potent, selective, and cell-active inhibitor of cyclin G associated kinase (GAK), together with a structurally-related negative control SGC-GAK-1N (14). SGC-GAK-1 is highly selective in a kinome-wide screen, but cellular engagement assays defined RIPK2 as a collateral target. We identified 18 as a potent inhibitor of RIPK2 lacking GAK activity. Together, the chemical probe set of 11, 14, and 18 can be used to interrogate the cellular biology of GAK inhibition.
Cell-type specific patterned stimulus-independent neuronal activity in theDrosophilavisual system during synapse formation
Authors: Akin Orkun , Bajar Bryce T. , Keles Mehmet F. , Frye Mark A. , Zipursky S. Lawrence
Published: July 2018

Stereotyped synaptic connections define the neural circuits of the brain. In vertebrates, stimulus-independent activity contributes to neural circuit formation. It is unknown whether this type of activity is a general feature of nervous system development. Here, we report patterned, stimulus-independent neural activity in theDrosophilavisual system during synaptogenesis. Usingin vivocalcium, voltage, and glutamate imaging, we found that all neurons participate in this spontaneous activity, which is characterized by brain-wide periodic active and silent phases. Glia are active in a complementary pattern. Each of the 15 examined of the over 100 specific neuron types in the fly visual system exhibited a unique activity signature. The activity of neurons that are synaptic partners in the adult was highly correlated during development. We propose that this cell type-specific activity coordinates the development of the functional circuitry of the adult brain.
Does the heart forget? Modulation of cardiac activity induced by inhibitory control over emotional memories
Authors: Legrand Nicolas , Etard Olivier , Vandevelde Anaïs , Pierre Mélissa , Viader Fausto , Clochon Patrice , Doidy Franck , Peschanski Denis , Eustache Francis , Gagnepain Pierre
Published: July 2018

Effort to suppress past experiences from conscious awareness can lead to forgetting. It remains largely unknown whether emotions, including their physiological causes, are also impacted by such memory suppression. In two studies, we measured in healthy participants the aftereffect of suppressing negative memories on cardiac response. Results of Study 1 revealed that an efficient control of memories was associated with a long-term inhibition of the cardiac deceleration normally induced by disgusting stimuli. Attempts to suppress sad memories, on the opposite, aggravated cardiac response, an effect that was largely related to the inability to forget this specific material. In Study 2, we found using electroencephalography that a prominent neural marker of inhibitory control, a suppression of the 5-9 Hz frequency band, was related to the subsequent inhibition of the cardiac response. These results demonstrate that suppressing memories also influence the cardiac system, opening new avenues for treating intrusive memories.
Complexity of Brain Activity and Connectivity in Functional Neuroimaging
Authors: Dimitriadis Stavros I.
Published: July 2018

Understanding the complexity of human brain dynamics and brain connectivity across the repertoire of functional neuroimaging and various conditions, is of paramount importance. Novel measures should be designed tailored to the input focusing on multichannel activity and dynamic functional brain connectivity (DFBC).

Here, we defined a novel complexity index (CI) from the field of symbolic dynamics that quantifies patterns of different words up to a length from a symbolic sequence. The CI characterizes the complexity of the brain activity.

We analysed dynamic functional brain connectivity by adopting the sliding window approach using imaginary part of phase locking value (iPLV) for EEG/ECoG/MEG and wavelet coherence (WC) for fMRI. Both intra and cross-frequency couplings (CFC) namely phase-to-amplitude were estimated using iPLV/WC at every snapshot of the DFBC. Using proper surrogate analysis, we defined the dominant intrinsic coupling mode (DICM) per pair of regions-of-interest (ROI). The spatio-temporal probability distribution of DICM were reported to reveal the most prominent coupling modes per condition and modality. Finally, a novel flexibility index is defined that quantifies the transition of DICM per pair of ROIs between consecutive time-windows.

The whole methodology was demonstrated using four neuroimaging datasets (EEG/ECoG/MEG/fMRI).

Finally, we succeeded to totally discriminate healthy controls from schizophrenic using FI and dynamic reconfiguration of DICM. Anesthesia independently of the drug caused a global decreased of complexity in all frequency bands with the exception in δ and alters the dynamic reconfiguration of DICM. CI and DICM of MEG/fMRI resting-state recordings in two spatial scales were high reliable.

Significant Statement

In the present study, we demonstrated novel indexes for the estimation of complexity in both raw brain activity and dynamic functional connectivity. To ort the universality of both indexes for the majority of functional neuroimaging modalities, we adopted open datasets from electro and magneto-encephalography, from electro-corticography and functional magnetic resonance imaging. Both indexes proved informative and reliable across repeat scan sessions. Moreover, we succeeded to totally discriminate with absolute accuracy healthy controls from schizophrenic patients. Both indexes proved sensitive to common anesthetic drugs effect in monkeys and reliable in MEG and fMRI repeat scan sessions. We first reported the notion of cross-frequency coupling in BOLD activity. Our analysis could be adapted it in any task and modality for any hypothesis driven study.
Muscle nonshivering thermogenesis in a feral mammal
Authors: Nowack Julia , Vetter Sebastian G. , Stalder Gabrielle , Painer Johanna , Kral Maria , Smith Steve , Le Minh Hien , Jurcevic Perica , Bieber Claudia , Arnold Walter , Ruf Thomas
Published: July 2018

While small mammals and neonates are able to maintain an optimal body temperature (Tb) independent of ambient conditions by producing heat via nonshivering thermogenesis (NST) in the brown adipose tissue (BAT), larger mammals and other mammals lacking BAT were long believed to rely primarily on shivering and behavioural adaptations. However, recently, a second mechanism of NST was found in skeletal muscle that could play an important role in thermoregulation of such species. Muscle NST is independent of muscle contractions and produces heat based on the activity of an ATPase pump in the sarcoplasmic reticulum (SERCA1a) and controlled by the protein sarcolipin. To evaluate whether muscle NST could indeed play an important role in thermoregulation in species lacking BAT, we investigated the thermogenic capacities of new-born wild boar piglets. During cold exposure over the first 5 days of life, total heat production was improved while shivering intensity decreased, indicating an increasing contribution of NST. Sampling skeletal muscle tissue for analyses of SERCA activity as well as gene expression of SERCA1a and sarcolipin, we found an age-related increase in all three variables as well as in Tb. Hence, the improved thermogenesis during the development of wild boars is not due to shivering but explained by the observed increase in SERCA activity. Our results suggest that muscle NST may be the primary mechanism of heat production during cold stress in large mammals lacking BAT, strengthening the hypothesis that muscle NST has likely played an important role in the evolution of endothermy.
The effects and mechanism of peiminine-induced apoptosis in human hepatocellular carcinoma HepG2 cells
Authors: Chao Xu , Wang Guoquan , Tang Yuping , Dong Changhu , Li Hong , Wang Bin , Wu Jieqiong , Zhao Jiarong
Published: July 2018

Peiminine is a compound that is isolated fromBolbostemma paniculatum(Maxim) Franquet (Cucurbitaceae family), which has demonstrated antitumor activities. Its precise molecular mechanisms underlying antitumor activity remain elusive. In this study, peiminine-induced apoptosis towards human hepatocellular carcinoma and its molecular mechanisms were investigated. MTT assay was employed to assess anticancer effects of peiminine at concentrations of 2, 4, 6, 8, 10, 12, and 14 μg/ml after 24, 48, or 72 h. Nuclear staining and flow cytometry were carried out to further assess apoptosis. Mitochondrial membrane potential evaluation and Western blot analysis were performed to investigate the mechanism of peiminine-induced apoptosis. Peiminine reduced the viability of HepG2 cells in a time- and dose-dependent manner and had an IC50of 4.58 μg/mL at 24h. Flow cytometry assessment indicated that peiminine markedly increased the cell number of apoptotic cells and the mitochondrial membrane potential dose-dependently in HepG2 cells. The results of Western blotting showed the expression of Bcl-2, procaspase-3, procaspase-8, procaspase-9, and PARP1decreased in HepG2 cells treated with peiminine, while the expression of Bax, caspase-3, caspase-8, caspase-9, and cleaved PARP1increased. The result suggest taht peiminine can induce apoptosis in human hepatocellular carcinoma HepG2 cells through both extrinsic and intrinsic apoptotic pathways.
Multiple roles of the non-structural protein 3 (nsP3) alphavirus unique domain (AUD) during Chikungunya virus genome replication and transcription
Authors: Gao Yanni , Goonawardane Niluka , Tuplin Andrew , Harris Mark
Published: July 2018

Chikungunya virus (CHIKV) is a re-emergingAlphaviruscausing fever, joint pain, skin rash, arthralgia, and occasionally death. Antiviral therapies and/or effective vaccines are urgently required. CHIKV biology is poorly understood, in particular the functions of the non-structural protein 3 (nsP3). Here we present the results of a mutagenic analysis of the alphavirus unique domain (AUD) of nsP3. Informed by the structure of the Sindbis virus AUD and an alignment of amino acid sequences of multiple alphaviruses, a series of mutations in the AUD were generated in a CHIKV sub-genomic replicon. This analysis revealed an essential role for the AUD in CHIKV RNA replication, with mutants exhibiting species- and cell-type specific phenotypes. To test if the AUD played a role in other stages of the virus lifecycle, the mutant panel was also analysed in the context of infectious CHIKV. Results indicated that, in addition to a role in RNA replication, the AUD was also required for virus assembly. Further analysis revealed that one mutant (P247A/V248A) specifically blocked transcription of the subgenomic RNA leading to a dramatic reduction in synthesis of the structural proteins and concomitant reduction in virus production. This phenotype could be explained by both a reduction in the binding of the P247A/V248A mutant nsP3 to viral genomic RNAin vivo, and the reduced affinity of the mutant AUD for the subgenomic promoter RNAin vitro.We propose that the AUD is a pleiotropic protein domain, with multiple functions during CHIKV RNA synthesis.

Author summary

Chikungunya virus (CHIKV) is an emerging threat to world health. It is transmitted by Aedes species mosquitos, and has caused massive epidemics across the globe. The virus causes fever, rash, arthritis and can sometimes be fatal. The biology of CHIKV is poorly understood, to address this deficiency we aimed to identify functions of one of the viral proteins, nsP3. We focussed on the central part of this protein, termed the alphavirus unique domain (AUD) because it is unique to the genus of viruses to which CHIKV belongs – theAlphaviruses– and not present in other related viruses. By making changes (mutations) in the AUD and analysing the effects of these changes we show that it is involved in multiple stages of the virus lifecycle. These observations identify nsP3 and the AUD in particular as a potential target for antiviral therapy or rational vaccine design.
Do city cachers store less? The effect of urbanization and exploration on spatial memory in individual scatter hoarders
Authors: Thompson Megan Joy , Morand-Ferron Julie
Published: July 2018

Urbanization has been shown to affect a variety of traits in animals, including their physiology, morphology, and behaviour, but it is less clear how cognitive traits are modified. Urban habitats contain artificially elevated food sources, such as bird feeders, that are known to affect the foraging behaviours of urban animals. As of yet however, it is not known whether urbanization and the abundance of supplemental food during the winter reduce caching behaviours and spatial memory in scatter hoarders. We aimed to examine individual variation in caching and spatial memory between and within urban and rural habitats to determine i) whether urban individuals cache less frequently and perform less accurately on a spatial task, and ii) explore, for the first time in scatter hoarders, whether slower explorers perform more accurately on a spatial task, indicating a speed-accuracy trade-off within individuals. We assessed spatial memory of wild-caught black-capped chickadees (Poecile atricapillus; N = 96) from 14 sites along an urban gradient. While the individuals that cached more food in captivity were all from rural environments, we find no clear evidence that caching intensity and spatial memory accuracy differ along an urban gradient, and find no significant relationship between spatial cognition and exploration of a novel environment within individuals. However, individuals that performed more accurately also tended to cache more frequently, suggesting for the first time that the specialization of spatial memory in scatter hoarders may also occur at the level of the individual in addition to the population and species levels.