bluuebunny/crossref_metadata_2025 huggingface dataset:
Insights into the dynamic nature of the dsRNA-bound TLR3 complex
Authors: Gosu Vijayakumar , Son Seungwoo , Shin Donghyun , Song Ki-Duk
Published: March 2019

Toll-like receptor 3 (TLR3), an endosomal receptor crucial for immune responses upon viral invasion. The TLR3 ectodomain (ECD) is responsible for double-stranded RNA (dsRNA) recognition and mutational analysis suggested that TLR3 ECD C-terminal dimerization is essential for dsRNA binding. Moreover, the L412F polymorphism of TLR3 is associated with human diseases. Although the mouse structure of the TLR3-dsRNA complex provides valuable insights, the structural dynamic behavior of the TLR3-dsRNA complex in humans is not completely understood. Hence, in this study, we performed molecular dynamic simulations of human wild-type and mutant TLR3 complexes. Our results suggested that apoTLR3 ECD dimers are unlikely to be stable due to the distance between the monomers are largely varied during simulations. The observed interaction energies and hydrogen bonds in dsRNA-bound TLR3 wild-type and mutant complexes indicate the presence of a weak dimer interface at the TLR3 ECD C-terminal site, which is required for effective dsRNA binding. The L412F mutant exhibited similar dominant motion compared to wild-type. Additionally, we identified the distribution of crucial residues for signal propagation in TLR3-dsRNA complex through the evaluation of residue betweenness centrality (CB). The results of this study extend our understanding of TLR3-dsRNA complex, which may assist in TLR3 therapeutics.
Tryptophan hydroxylase (TRH) loss of function mutations in Daphnia deregulated growth, energetic, serotoninergic and arachidonic acid metabolic signalling pathways
Authors: Campos Bruno , Rivetti Claudia , Tauler Roma , Piña Benjamin , Barata Carlos
Published: March 2019

Serotonin has a pivotal function regulating development, growth, reproduction and behavior in animals. In this paper, we studied the deregulatory effects of the deprivation of serotonin in Daphnia magna TRH CRISPR-Cas9 mutants. Bi-allelic in-del THR mutants and, to a lesser extent, mono-allelic ones grew less, reproduced later, and produced smaller clutches than wild type clones. Transcriptomic and functional gene analyses showed a down-regulation of growth/molting and energy metabolism signaling pathways in TRH mutants, while revealing marked differences between mono- and bi-allelic clones. Bi-allelic mutants, lacking serotonin, presented the serotonergic synapse and arachidonic acid metabolic pathways down-regulated while the tryptophan to kynurenine was upregulated, thus indicating a cross-talk between the serotonergic and arachidonic acid metabolic pathways. Finally, the effects on the insulin growth factor-mediated signaling pathway were marginal. These changes in functional and metabolic pathways are consistent with previously reported effects in D. magna exposed to pharmaceuticals that inhibited arachidonic metabolism or enhanced the levels of serotonin.
Four-Year Outcome of Aflibercept for Neovascular Age-Related Macular Degeneration and polypoidal choroidal vasculopathy
Authors: Nishikawa Keiichi , Oishi Akio , Hata Masayuki , Miyake Masahiro , Ooto Sotaro , Yamashiro Kenji , Miyata Manabu , Tamura Hiroshi , Ueda-Arakawa Naoko , Takahashi Ayako , Kawashima Yu , Tsujikawa Akitaka
Published: March 2019

Intravitreal injections of anti-vascular endothelial growth factor agents such as ranibizumab and aflibercept are the first-line treatment for neovascular age-related macular degeneration (AMD). However, data about long-term outcome in real-world clinical practice is scarce. We recruited 98 AMD patients and investigated four-year visual outcome. During the four years, 25 patients dropped out. The survivors received 7.0 ± 0.1 injections during the first year and 8.0 ± 7.4 injections in the following three years. The logarithm of minimum angle of resolution (logMAR) at baseline, year one, and year four was 0.28, 0.14 (P = 0.033), and 0.22 (P = 0.697), respectively. The gain of vision was not different among AMD subtypes (typical AMD, polypoidal choroidal vasculopathy, and retinal angiomatous proliferation; P = 0.513) Among the investigated factors, the presence of external limiting membrane (ELM), the absence of vitreoretinal adhesion, and thicker choroid at baseline were associated with better logMAR values at year four (coefficient beta = −0.388, 0.201, and −0.001; P = 7.34 × 10−6; 0.01, and 0.028, respectively). In the present study, vision was retained at baseline level after the four-year treatment with aflibercept. The status of ELM, vitreoretinal adhesion, and choroidal thickness were predictive factors for final vision.
Chronic contact with realistic soil concentrations of imidacloprid affects the mass, immature development speed, and adult longevity of solitary bees
Authors: Anderson Nicholas L. , Harmon-Threatt Alexandra N.
Published: March 2019

The non-target effects of pesticides are an area of growing concern, particularly for ecologically and economically important organisms such as bees. Much of the previous research on the effects of neonicotinoids, a class of insecticide that has gained attention for non-target effects, on bees focused on the consumption of contaminated food resources by a limited number of eusocial species. However, neonicotinoids are known to accumulate and persist in soils at concentrations 2 to 60 times greater than in food resources, and may represent an important route of exposure for diverse and ecologically important ground-nesting bees. This study aimed to assess the effect of chronic contact exposure to realistic soil concentrations of imidacloprid, the most widely used neonicotinoid pesticide, on bee longevity, development speed, and body mass. Cohorts ofOsmia lignariaandMegachile rotundatawere used as proxies for ground-nesting species. We observed species- and sex-specific changes to adult longevity, development speed, and mass in response to increasing concentrations of imidacloprid. These results suggest that chronic exposure to nesting substrates contaminated with neonicotinoids may represent an important route of exposure that could have considerable physiological and ecological consequences for bees and plant-pollinator interactions.
Comparative label-free lipidomic analysis of Mycobacterium tuberculosis during dormancy and reactivation
Authors: Raghunandanan Sajith , Jose Leny , Gopinath Vipin , Kumar Ramakrishnan Ajay
Published: March 2019

Mycobacterium tuberculosis employs several strategies to combat and adapt to adverse conditions encountered inside the host. The non-replicative dormant state of the bacterium is linked to drug resistance and slower response to anti-tubercular therapy. It is known that alterations in lipid content allow dormant bacteria to acclimatize to cellular stress. Employing comparative lipidomic analysis we profiled the changes in lipid metabolism in M. tuberculosis using a modified Wayne’s model of hypoxia-induced dormancy. Further we subjected the dormant bacteria to resuscitation, and analyzed their lipidomes until the lipid profile was similar to that of normoxially grown bacteria. An enhanced degradation of cell wall-associated and cytoplasmic lipids during dormancy, and their gradual restoration during reactivation, were clearly evident. This study throws light on distinct lipid metabolic patterns that M. tuberculosis undergoes to maintain its cellular energetics during dormancy and reactivation.
A Spiking Neural Network Model of Depth from Defocus for Event-based Neuromorphic Vision
Authors: Haessig Germain , Berthelon Xavier , Ieng Sio-Hoi , Benosman Ryad
Published: March 2019

Depth from defocus is an important mechanism that enables vision systems to perceive depth. While machine vision has developed several algorithms to estimate depth from the amount of defocus present at the focal plane, existing techniques are slow, energy demanding and mainly relying on numerous acquisitions and massive amounts of filtering operations on the pixels’ absolute luminance value. Recent advances in neuromorphic engineering allow an alternative to this problem, with the use of event-based silicon retinas and neural processing devices inspired by the organizing principles of the brain. In this paper, we present a low power, compact and computationally inexpensive setup to estimate depth in a 3D scene in real time at high rates that can be directly implemented with massively parallel, compact, low-latency and low-power neuromorphic engineering devices. Exploiting the high temporal resolution of the event-based silicon retina, we are able to extract depth at 100 Hz for a power budget lower than a 200 mW (10 mW for the camera, 90 mW for the liquid lens and ~100 mW for the computation). We validate the model with experimental results, highlighting features that are consistent with both computational neuroscience and recent findings in the retina physiology. We demonstrate its efficiency with a prototype of a neuromorphic hardware system and provide testable predictions on the role of spike-based representations and temporal dynamics in biological depth from defocus experiments reported in the literature.
Involvement of TRPM2 and TRPM8 in temperature-dependent masking behavior
Authors: Ota Wataru , Nakane Yusuke , Kashio Makiko , Suzuki Yoshiro , Nakamura Kazuhiro , Mori Yasuo , Tominaga Makoto , Yoshimura Takashi
Published: March 2019

Masking is a direct behavioral response to environmental changes and plays an important role in the temporal distribution of activity. However, the mechanisms responsible for masking remain unclear. Here we identify thermosensors and a possible neural circuit regulating temperature-dependent masking behavior in mice. Analysis of mice lacking thermosensitive transient receptor potential (TRP) channels (Trpv1/3/4 and Trpm2/8) reveals that temperature-dependent masking is impaired in Trpm2- and Trpm8-null mice. Several brain regions are activated during temperature-dependent masking, including the preoptic area (POA), known as the thermoregulatory center, the suprachiasmatic nucleus (SCN), which is the primary circadian pacemaker, the paraventricular nucleus of the thalamus (PVT), and the nucleus accumbens (NAc). The POA, SCN, PVT are interconnected, and the PVT sends dense projections to the NAc, a key brain region involved in wheel-running activity. Partial chemical lesion of the PVT attenuates masking, suggesting the involvement of the PVT in temperature-dependent masking behavior.
Long non-coding RNA FAM83H-AS1 is regulated by human papillomavirus 16 E6 independently of p53 in cervical cancer cells
Authors: Barr Jamie A. , Hayes Karen E. , Brownmiller Tayvia , Harold Abby D. , Jagannathan Rajaganapathi , Lockman Paul R. , Khan Saleem , Martinez Ivan
Published: March 2019

High-risk human papillomavirus (HPV) infection is one of the first events in the process of carcinogenesis in cervical and head and neck cancers. The expression of the viral oncoproteins E6 and E7 are essential in this process by inactivating the tumor suppressor proteins p53 and Rb, respectively, in addition to their interactions with other host proteins. Non-coding RNAs, such as long non-coding RNAs (lncRNAs) have been found to be dysregulated in several cancers, suggesting an important role in tumorigenesis. In order to identify host lncRNAs affected by HPV infection, we expressed the high-risk HPV-16 E6 oncoprotein in primary human keratinocytes and measured the global lncRNA expression profile by high-throughput sequencing (RNA-seq). We found several host lncRNAs differentially expressed by E6 including GAS5, H19, and FAM83H-AS1. Interestingly, FAM83H-AS1 was found overexpressed in HPV-16 positive cervical cancer cell lines in an HPV-16 E6-dependent manner but independently of p53 regulation. Furthermore, FAM83H-AS1 was found to be regulated through the E6-p300 pathway. Knockdown of FAM83H-AS1 by siRNAs decreased cellular proliferation, migration and increased apoptosis. FAM83H-AS1 was also found to be altered in human cervical cancer tissues and high expression of this lncRNA was associated with worse overall survival, suggesting an important role in cervical carcinogenesis.
Impact of laterality and mucinous histology on relapse-free and overall survival in a registry-based colon cancer series
Authors: Negri Francesca , De Giorgi Annamaria , Gilli Annalisa , Azzoni Cinzia , Bottarelli Lorena , Gnetti Letizia , Goldoni Matteo , Manotti Laura , Sgargi Paolo , Michiara Maria , Leonardi Francesco , Rindi Guido , Cascinu Stefano , Silini Enrico Maria
Published: March 2019

Recent data suggest that tumor laterality and mucinous histology may be clinically relevant. We investigated how both variables impact on the prognosis and the response to therapies in a large population-based cohort of cancer patients. Incidence data, clinical and pathological features, and outcome were systematically collected from the Tumor Registry of Parma over the years 2004–2009. Survival data were modeled by multivariable analysis. 1358 patients affected by stage I–IV colon cancer were considered; 661 (49%) had right-sided and 697 (51%) left-sided tumors. 144 (11%) had mucinous (MAC) and 1214 (89%) non-mucinous (NMAC) histology. MACs and NMACs of the right colon showed no difference in stage distribution, whereas left colon MACs were more frequently in an advanced stage (stage IV) (p = 0.008). Stage IV right colon tumors had a poorer overall survival than stage IV left-sided colon cancers (75th percentile 20 vs 34 months, p < 0.001). At relapse, MACs were less responsive to systemic therapy and had worse survival compared with NMACs regardless of tumor side (7.1 vs 13.1 months, p = 0.018). Right-sided colon cancers had poorer survival compared to left-sided tumors; the effect was mainly attributable to NMACs. At relapse, MACs had unfavorable prognosis regardless of the primary tumor-side.
Activation of Peripheral Blood CD4+ T-Cells in IBS is not Associated with Gastrointestinal or Psychological Symptoms
Authors: Nasser Yasmin , Petes Carlene , Simmers Celine , Basso Lilian , Altier Christophe , Gee Katrina , Vanner Stephen J.
Published: March 2019

Immune activation may underlie the pathogenesis of irritable bowel syndrome (IBS), but the evidence is conflicting. We examined whether peripheral CD4+ T-cells from IBS patients demonstrated immune activation and changes in cytokine production. To gain mechanistic insight, we examined whether immune activation correlated with psychological stress and changing symptoms over time. IBS patients (n = 29) and healthy volunteers (HV; n = 29) completed symptom and psychological questionnaires. IBS patients had a significant increase in CD4+ T-cells expressing the gut homing marker integrin β7 (p = 0.023) and lymphoid marker CD62L (p = 0.026) compared to HV. Furthermore, phytohaemagglutinin stimulated CD4+ T-cells from IBS-D patients demonstrated increased TNFα secretion when compared to HV (p = 0.044). Increased psychological scores in IBS did not correlate with TNFα production, while stress hormones inhibited cytokine secretion from CD4+ T-cells of HV in vitro. IBS symptoms, but not markers of immune activation, decreased over time. CD4+ T-cells from IBS-D patients exhibit immune activation, but this did not appear to correlate with psychological stress measurements or changing symptoms over time. This could suggest that immune activation is a surrogate of an initial trigger and/or ongoing parallel peripheral mechanisms.
A basic Helix-Loop-Helix (SlARANCIO), identified from a Solanum pennellii introgression line, affects carotenoid accumulation in tomato fruits
Authors: D’Amelia Vincenzo , Raiola Assunta , Carputo Domenico , Filippone Edgardo , Barone Amalia , Rigano Maria Manuela
Published: March 2019

Carotenoid accumulation in tomato (Solanum lycopersicum) fruits is influenced by environmental stimuli and hormonal signals. However, information on the relative regulatory mechanisms are scanty since many molecular players of the carotenoid biosynthetic pathway are still unknown. Here, we reported a basic Helix-Loop-Helix transcription factor, named SlARANCIO (SlAR), whose silencing influences carotenoid accumulation in tomato fruits. The SlAR gene was found in the S. pennellii introgression line (IL) 12-4SL that holds the carotenoid QTL lyc12.1. We observed that the presence of the wild region in a cultivated genetic background led to a decrease in total carotenoid content of IL12-4SL fruits. To get insights into the function of SlAR, a quick reverse genetic approach was carried out. Virus-induced gene silencing of SlAR in S. lycopersicum M82 and MicroTom fruits reproduced the same phenotype observed in IL12-4SL, i.e. decreased content of lycopene and total carotenoids. Vice versa, the overexpression of SlAR in Nicotiana benthamiana leaves increased the content of total carotenoids and chlorophylls. Our results, combined with public transcriptomic data, highly suggest that SlAR acts indirectly on the carotenoid pathway and advances current knowledge on the molecular regulators controlling lyc12.1 and, potentially, precursors of carotenoid biosynthesis.
Genomic and metagenomic signatures of giant viruses are ubiquitous in water samples from sewage, inland lake, waste water treatment plant, and municipal water supply in Mumbai, India
Authors: Chatterjee Anirvan , Sicheritz-Pontén Thomas , Yadav Rajesh , Kondabagil Kiran
Published: March 2019

We report the detection of genomic signatures of giant viruses (GVs) in the metagenomes of three environment samples from Mumbai, India, namely, a pre-filter of a household water purifier, a sludge sample from wastewater treatment plant (WWTP), and a drying bed sample of the same WWTP. The de novo assembled contigs of each sample yielded 700 to 2000 maximum unique matches with the GV genomic database. In all three samples, the maximum number of reads aligned to Pandoraviridae, followed by Phycodnaviridae, Mimiviridae, Iridoviridae, and other Megaviruses. We also isolated GVs from every environmental sample (n = 20) we tested using co-culture of the sample with Acanthomoeba castellanii. From this, four randomly selected GVs were subjected to the genomic characterization that showed remarkable cladistic homology with the three GV families viz., Mimivirirdae (Mimivirus Bombay [MVB]), Megaviruses (Powai lake megavirus [PLMV] and Bandra megavius [BAV]), and Marseilleviridae (Kurlavirus [KV]). All 4 isolates exhibited remarkable genomic identity with respective GV families. Functionally, the genomes were indistinguishable from other previously reported GVs, encoding nearly all COGs across extant family members. Further, the uncanny genomic homogeneity exhibited by individual GV families across distant geographies indicate their yet to be ascertained ecological significance.
Minor allele of the factor V K858R variant protects from venous thrombosis only in non-carriers of factor V Leiden mutation
Authors: Ibrahim-Kosta M. , Suchon P. , Couturaud F. , Smadja D. , Olaso R. , Germain M. , Saut N. , Goumidi L. , Derbois C. , Thibord F. , Debette S. , Amouyel P. , Deleuze J. F. , van Doorn P. , Castoldi E. , Patin E. , Alessi M. C. , Trégouët D. A. , Morange P. E.
Published: March 2019

Factor V serves an important role in the regulation of blood coagulation. The rs6025 (R534Q) and rs4524 (K858R) polymorphisms in the F5 gene, are known to influence the risk of venous thrombosis. While the rare Q534 (factor V Leiden) allele is associated with an increased risk of venous thrombosis, the minor R858 allele is associated with a lower risk of disease. However, no study has deeply examined the cumulative impact of these two variations on venous thrombosis risk. We study the association of these polymorphisms with the risk of venous thrombosis in 4 French case-control populations comprising 3719 patients and 4086 controls. We demonstrate that the Q534 allele has a dominant effect over R858. Besides, we show that in individuals not carrying the Q534 allele, the protective effect of the R858 allele acts in a dominant mode. Thrombin generation-based normalized activated protein C sensitivity ratio was lower in the 858R/R homozygotes than in the 858K/K homozygotes (1.92 ± 1.61 vs 2.81 ± 1.57, p = 0.025). We demonstrate that the R858 allele of the F5 rs4524 variant protects from venous thrombosis only in non-carriers of the Q534 allele of the F5 rs6025. Its protective effect is mediated by reduced factor VIII levels and reduced activated protein C resistance.
Efficient recycling of nutrients in modern and past hypersaline environments
Authors: Isaji Y. , Kawahata H. , Ogawa N. O. , Kuroda J. , Yoshimura T. , Jiménez-Espejo F. J. , Makabe A. , Shibuya T. , Lugli S. , Santulli A. , Manzi V. , Roveri M. , Ohkouchi N.
Published: March 2019

The biogeochemistry of hypersaline environments is strongly influenced by changes in biological processes and physicochemical parameters. Although massive evaporation events have occurred repeatedly throughout Earth history, their biogeochemical cycles and global impact remain poorly understood. Here, we provide the first nitrogen isotopic data for nutrients and chloropigments from modern shallow hypersaline environments (solar salterns, Trapani, Italy) and apply the obtained insights to δ15N signatures of the Messinian salinity crisis (MSC) in the late Miocene. Concentrations and δ15N of chlorophyll a, bacteriochlorophyll a, nitrate, and ammonium in benthic microbial mats indicate that inhibition of nitrification suppresses denitrification and anammox, resulting in efficient ammonium recycling within the mats and high primary productivity. We also suggest that the release of 15N-depleted NH3(gas) with increasing salinity enriches ammonium 15N in surface brine (≈34.0‰). Such elevated δ15N is also recorded in geoporphyrins isolated from sediments of the MSC peak (≈20‰), reflecting ammonium supply sufficient for sustaining phototrophic primary production. We propose that efficient nutrient supply combined with frequent bottom-water anoxia and capping of organic-rich sediments by evaporites of the Mediterranean MSC could have contributed to atmospheric CO2 reduction during the late Miocene.
Effect of ripasudil on diabetic macular edema
Authors: Minami Yoshiro , Song Young-seok , Ishibazawa Akihiro , Omae Tsuneaki , Ro-mase Tomoko , ishiko Satoshi , Yoshida Akitoshi
Published: March 2019

The current study aimed to address whether ripasudil, a Rho-associated coiled-coil containing protein kinase (ROCK) inhibitor developed to treat glaucoma and ocular hypertension (OH), improves diabetic macular edema (DME) since it is known that ROCK upregulates vascular endothelial growth factor. We retrospectively investigated the foveal thickness (FT) measured by spectral-domain optical coherence tomography, visual acuity (VA), and intraocular pressure (IOP) in 12 eyes with DME that received ripasudil treatment for primary open-angle glaucoma or OH and compared them with 14 eyes that received no treatment. One month after ripasudil therapy, the mean FT decreased significantly from 439 ± 72 µm to 395 ± 62 µm (P = 0.003); this change was significantly different from that in the controls, in which the mean FT increased by 1 ± 39 µm (P = 0.01). Ripasudil also caused a significant decrease in IOP from 17.3 ± 5.2 mmHg to 14.6 ± 4.0 mmHg (P = 0.02); this change was significantly greater than that in the controls, in which IOP changed by 0.0 ± 1.6 mmHg (P < 0.008). There was no significant difference in the VA changes between groups. Our results suggested that ripasudil may have positive effects on both IOP and DME.
Surveying of acid-tolerant thermophilic lignocellulolytic fungi in Vietnam reveals surprisingly high genetic diversity
Authors: Thanh Vu Nguyen , Thuy Nguyen Thanh , Huong Han Thi Thu , Hien Dinh Duc , Hang Dinh Thi My , Anh Dang Thi Kim , Hüttner Silvia , Larsbrink Johan , Olsson Lisbeth
Published: March 2019

Thermophilic fungi can represent a rich source of industrially relevant enzymes. Here, 105 fungal strains capable of growing at 50 °C and pH 2.0 were isolated from compost and decaying plant matter. Maximum growth temperatures of the strains were in the range 50 °C to 60 °C. Sequencing of the internal transcribed spacer (ITS) regions indicated that 78 fungi belonged to 12 species of Ascomycota and 3 species of Zygomycota, while no fungus of Basidiomycota was detected. The remaining 27 strains could not be reliably assigned to any known species. Phylogenetically, they belonged to the genusThielavia, but they represented 23 highly divergent genetic groups different from each other and from the closest known species by 12 to 152 nucleotides in the ITS region. Fungal secretomes of all 105 strains produced during growth on untreated rice straw were studied for lignocellulolytic activity at different pH and temperatures. The endoglucanase and xylanase activities differed substantially between the different species and strains, but in general, the enzymes produced by the novelThielaviaspp. strains exhibited both higher thermal stability and tolerance to acidic conditions. The study highlights the vast potential of an untapped diversity of thermophilic fungi in the tropics.
A trimetallic organometallic precursor for efficient water oxidation
Authors: Madadkhani Sepideh , Aghakhanpour Reza Babadi , Singh Jitendra Pal , Bagheri Robabeh , Chae Keun Hwa , Song Zhenlun , Najafpour Mohammad Mahdi
Published: March 2019

Herein, we report an iron/nickel/zinc mixed oxide as a catalyst for the electrochemical water oxidation. This catalyst was synthesized by a straightforward method for the synthesis of an iron/nickel/zinc mixed oxide through the calcination of a Fe/Ni/Zn organometallic compound. The calcined product contains Fe and Ni as crucial ions for water oxidation, accompanied by the presence of Zn ions. The removal of Zn ions from the mixed oxide provides more active sites on the surface of the catalyst. The composition of the compound was characterized by some common methods and found to be an efficient water-oxidizing catalyst. The catalyst on FTO at pH = 13 yields a current density of 12 mA/cm2at 1.2 V (vs. Ag│AgCl). After 5 hours at 1.1 V, the electrode not only shows no decrease in performance, but also shows an increase from 4 to 7 mA/cm2in the water oxidation activity. Tafel plot, for the electrode at pH = 13 in KOH solution (0.1 M) showed linearity for the graph of lg j vs. V with both relatively low (220.4 mV per decade) and high overpotentials (903.7 mV per decade).
Deciphering host-parasitoid interactions and parasitism rates of crop pests using DNA metabarcoding
Authors: Sow Ahmadou , Brévault Thierry , Benoit Laure , Chapuis Marie-Pierre , Galan Maxime , Coeur d’acier Armelle , Delvare Gérard , Sembène Mbacké , Haran Julien
Published: March 2019

An accurate estimation of parasitism rates and diversity of parasitoids of crop insect pests is a prerequisite for exploring processes leading to efficient natural biocontrol. Traditional methods such as rearing have been often limited by taxonomic identification, insect mortality and intensive work, but the advent of high-throughput sequencing (HTS) techniques, such as DNA metabarcoding, is increasingly seen as a reliable and powerful alternative approach. Little has been done to explore the benefits of such an approach for estimating parasitism rates and parasitoid diversity in an agricultural context. In this study, we compared the composition of parasitoid species and parasitism rates between rearing and DNA metabarcoding of host eggs and larvae of the millet head miner, Heliocheilus albipunctella De Joannis (Lepidoptera, Noctuidae), collected from millet fields in Senegal. We first assessed the detection threshold for the main ten endoparasitoids, by sequencing PCR products obtained from artificial dilution gradients of the parasitoid DNAs in the host moth. We then assessed the potential of DNA metabarcoding for diagnosing parasitism rates in samples collected from the field. Under controlled conditions, our results showed that relatively small quantities of parasitoid DNA (0.07 ng) were successfully detected within an eight-fold larger quantity of host DNA. Parasitoid diversity and parasitism rate estimates were always higher for DNA metabarcoding than for host rearing. Furthermore, metabarcoding detected multi-parasitism, cryptic parasitoid species and differences in parasitism rates between two different sampling sites. Metabarcoding shows promise for gaining a clearer understanding of the importance and complexity of host-parasitoid interactions in agro-ecosystems, with a view to improving pest biocontrol strategies.
Chemically deposited palladium nanoparticles on graphene for hydrogen sensor applications
Authors: Tang Xiaohui , Haddad Pierre-Antoine , Mager Nathalie , Geng Xin , Reckinger Nicolas , Hermans Sophie , Debliquy Marc , Raskin Jean-Pierre
Published: March 2019

Graphene decorated by palladium (Pd) nanoparticles has been investigated for hydrogen sensor applications. The density of Pd nanoparticles is critical for the sensor performance. We develop a new chemical method to deposit high-density, small-size and uniformly-distributed Pd nanoparticles on graphene. With this method, Pd precursors are connected to the graphene by π-π bonds without introducing additional defects in the hexagonal carbon lattice. Our method is simple, cheap, and compatible with complementary metal-oxide semiconductor (CMOS) technology. This method is used to fabricate hydrogen sensors on 3-inch silicon wafers. The sensors show high performance at room temperature. Particularly, the sensors present a shorter recovery time under light illumination. The sensing mechanism is explained and discussed. The proposed deposition method facilitates mass fabrication of the graphene sensors and allows integration with CMOS circuits for practical applications.
Metal-coated microsphere monolayers as surface plasmon resonance sensors operating in both transmission and reflection modes
Authors: Farcau Cosmin
Published: March 2019

Metal-coated microsphere monolayers (MCM) are a class of plasmonic crystals consisting of noble metal films over arrays of self-assembled colloidal microspheres. Despite their ease of fabrication and tunable plasmonic response, their optical sensing potential has been scarcely explored. Here, silver coated polystyrene sphere monolayers are proposed as surface plasmon resonance sensors capable of functioning in both transmission (T) and reflection (R) readout modes. An original and key point is the use of ~200 nm colloids, smaller than in MCM studied before. It allowed us to reveal a previously unobserved, additional/secondary Enhanced Optical Transmission band, which can be exploited in sensing, with higher sensitivity than the better-known main transmission band. The reflection configuration however, is almost an order of magnitude more efficient for sensing than the transmission one. We also evidenced a strong impact of the adsorbate location on the metal surface on the sensing efficiency. Electric field distribution analysis is performed to explain these results. Proof-of-concept experiments on the detection of 11-MUA molecular monolayers, performed in both readout modes, confirm the behaviors observed through FDTD simulations. Results in this paper can serve as guidelines for designing optimized sensors based on metal-coated colloidal monolayers, and more generally for plasmonic sensors based on metal nanostructured films.
Temporal Dynamics of Visual Attention Allocation
Authors: Moon Jongmin , Choe Seonggyu , Lee Seul , Kwon Oh-Sang
Published: March 2019

We often temporally prepare our attention for an upcoming event such as a starter pistol. In such cases, our attention should be properly allocated around the expected moment of the event to process relevant sensory input efficiently. In this study, we examined the dynamic changes of attention levels near the expected moment by measuring contrast sensitivity to a target that was temporally cued by a five-second countdown. We found that the overall attention level decreased rapidly after the expected moment, while it stayed relatively constant before it. Results were not consistent with the predictions of existing explanations of temporal attention such as the hazard rate or the stimulus-driven oscillations. A control experiment ruled out the possibility that the observed pattern was due to biased time perception. In a further experiment with a wider range of cue-stimulus-intervals, we observed that attention level increased until the last 500 ms of the interval range, and thereafter, started to decrease. Based on the performances of a generative computational model, we suggest that our results reflect the nature of temporal attention that takes into account the subjectively estimated hazard rate and the probability of relevant events occurring in the near future.
FGF signal is not required for hepatoblast differentiation of human iPS cells
Authors: Toba Yukiko , Kiso Ayumi , Nakamae Souichiro , Sakurai Fuminori , Takayama Kazuo , Mizuguchi Hiroyuki
Published: March 2019

Human induced pluripotent stem cell-derived hepatocyte-like cells are expected to be utilized in pharmaceutical research and regenerative medicine. In general, human induced pluripotent stem (iPS) cells are differentiated into hepatocyte-like cells through definitive endoderm cells and hepatoblast-like cells using various growth factors that are essential for liver development. Although recombinant bone morphogenetic proteins (BMPs) and fibroblast growth factors (FGFs) are widely used in the hepatoblast differentiation, hepatoblast differentiation process has not been fully modified. In this study, we examined the roles of BMPs and FGFs in the hepatoblast differentiation from human iPS cells. Surprisingly, the gene expression levels of hepatoblast markers were upregulated by the removal of FGFs. In addition, the percentages of hepatoblast markers-positive cells were increased by the removal of FGFs. Furthermore, the hepatocyte differentiation potency was also significantly increased by the removal of FGFs. To examine whether FGF signals are completely unnecessary for the hepatoblast differentiation, the expression levels of endogenous FGF ligands and receptors were examined. The definitive endoderm cells highly expressed the FGF ligand, FGF2, and the FGF receptor, FGFR1. To examine the role of endogenous FGF signals, an FGFR inhibitor was treated during the hepatoblast differentiation. The hepatoblast differentiation was promoted by using FGFR inhibitor, suggesting that endogenous FGF signals are also unnecessary for the hepatoblast differentiation. In conclusion, we found that FGF signals are not essential for hepatoblast differentiation. We believe that our finding will be useful for generating functional hepatocyte-like cells for medical applications.
Femtosecond laser-based nanosurgery reveals the endogenous regeneration of single Z-discs including physiological consequences for cardiomyocytes
Authors: Müller Dominik , Hagenah Dorian , Biswanath Santoshi , Coffee Michelle , Kampmann Andreas , Zweigerdt Robert , Heisterkamp Alexander , Kalies Stefan M. K.
Published: March 2019

A highly organized cytoskeleton architecture is the basis for continuous and controlled contraction in cardiomyocytes (CMs). Abnormalities in cytoskeletal elements, like the Z-disc, are linked to several diseases. It is challenging to reveal the mechanisms of CM failure, endogenous repair, or mechanical homeostasis on the scale of single cytoskeletal elements. Here, we used a femtosecond (fs) laser to ablate single Z-discs in human pluripotent stem cells (hPSC) -derived CMs (hPSC-CM) and neonatal rat CMs. We show, that CM viability was unaffected by the loss of a single Z-disc. Furthermore, more than 40% of neonatal rat and 68% of hPSC-CMs recovered the Z-disc loss within 24 h. Significant differences to control cells, after the Z-disc loss, in terms of cell perimeter, x- and y-expansion and calcium homeostasis were not found. Only 14 days in vitro old hPSC-CMs reacted with a significant decrease in cell area, x- and y-expansion 24 h past nanosurgery. This demonstrates that CMs can compensate the loss of a single Z-disc and recover a regular sarcomeric pattern during spontaneous contraction. It also highlights the significant potential of fs laser-based nanosurgery to physically micro manipulate CMs to investigate cytoskeletal functions and organization of single elements.
Effect of size and charge asymmetry on aggregation kinetics of oppositely charged nanoparticles
Authors: Singh Kulveer , Raghav Anubhav , Jha Prateek K. , Satapathi Soumitra
Published: March 2019

We report a theoretical and experimental study of the aggregation kinetics of oppositely charged nanoparticles. Kinetic Monte Carlo simulations are performed for symmetric, charge-asymmetric and size-asymmetric systems of oppositely charged nanoparticles. Simulation results show that both the weight and number average aggregate size kinetics exhibit power law scaling with different exponents for small and intermediate time of evolution. The qualitative behavior of the symmetric and the size asymmetric system are the same, but the charge asymmetric system shows anomalous behavior for intermediate to high particle concentrations. We also observe a strong dependence of power law exponents on the particle concentration. Radius of gyration of the cluster that indicates how nanoparticles inside a cluster are distributed around the center of mass of the cluster shows a non-monotonic time evolution with pronounced peak at higher particle concentration. The dependence of particle concentration on aggregation kinetics as observed by predictive numerical simulation is further verified experimentally by monitoring the time evolution of aggregate size of nanoparticles assemblies of Poly (methacrylic acid) (PMMA) nanoparticles functionalized with oppositely charged ligands. These size and charge tunable asymmetric polymeric nanoparticles were synthesized by modified miniemulsion technique. The integrated approach for studying nanoparticles aggregation as described here renders new insights into super structure formation and morphology optimization which can be potentially useful in the design of new materials, such as organic photovoltaics.
Resting hyperinflation and emphysema on the clinical course of COPD
Authors: Kim Yeon Wook , Lee Chang-Hoon , Hwang Hun-Gyu , Kim Yu-Il , Kim Deog Kyeom , Oh Yeon-Mok , Lee Sang Haak , Kim Ki Uk , Lee Sang-Do
Published: March 2019

The aim of this study is to clarify whether the combined evaluation of resting hyperinflation and emphysema confers any additional advantages in terms of predicting clinical outcomes in chronic obstructive pulmonary disease (COPD) patients. We included COPD patients from the Korean Obstructive Lung Disease (KOLD) cohort. Patients with a residual volume/total lung capacity (RV/TLC) over the upper limit of normal were defined as having resting hyperinflation, and those with an emphysema index >10% were defined as having emphysema. We investigated the impacts of resting hyperinflation and emphysema on exacerbations and mortality. A total of 310 COPD patients were analyzed over a mean of 61.1 months. After adjustment for covariates, resting hyperinflation was an independent predictor of earlier exacerbation (HR = 1.66, CI = 1.24–2.22), more frequent exacerbation (IRR = 1.35, CI = 1.01–1.81), and higher mortality (HR = 2.45, CI = 1.16–5.17) risk. Emphysema was also significantly associated with earlier exacerbation (HR = 1.64, CI = 1.15–2.35), and higher mortality (HR = 3.13, CI = 1.06–9.27) risk. Participants with both resting hyperinflation and emphysema had an additively higher risk of earlier exacerbations (HR = 1.71, 95% CI = 1.26–2.33) and mortality (HR = 3.75, 95% CI = 1.81–7.73) compared with those in other groups. In conclusion, resting hyperinflation and emphysema had additional worse impacts on exacerbations and mortality in COPD patients.
Optimal leaf water status regulation of plants in drylands
Authors: Ratzmann Gregor , Zakharova Liubov , Tietjen Britta
Published: March 2019

Leaf water potential regulation is a key process in whole plant and ecosystem functioning. While low water potentials induced by open stomata may initially be associated with greater CO2 supply and a higher water flux from the rhizosphere to the canopy, they also inhibit cell growth, photosynthesis and ultimately water supply. Here, we show that plants regulate their leaf water potential in an optimal manner under given constraints using a simple leaf water status regulation model and data from a global dryland leaf water potential database. Model predictions agree strongly with observations across locations and species and are further supported by experimental data. Leaf water potentials non-linearly decline with soil water potential, underlining the shift from maximizing water supply to avoiding stress with declining water availability. Our results suggest that optimal regulation of the leaf water status under varying water supply and stress tolerance is a ubiquitous property of plants in drylands. The proposed model moreover provides a novel quantitative framework describing how plants respond to short- and long-term changes in water availability and may help elaborating models of plant and ecosystem functioning.
Preparation of peroxidase and phenolics using discarded sweet potato old stems
Authors: Yang Liu , Xi Yi , Luo Xiang-Yu , Ni He , Li Hai-Hang
Published: March 2019

Sweet potato (Ipomoea batatas L.) is the sixth most important food crop in the world. The industry discarded huge amount of sweet potato stems, rich of peroxidases and phenolics. A simple procedure was developed to make peroxidases and phenolics from sweet potato old stems. Dried stem powder was loaded into columns with water and eluted sequentially with water and 50% ethanol. Peroxidases (91%) were extracted in 5.5-fold water extracts and 87% phenolics were extracted in 4.4-fold ethanol extracts. Purified peroxidases powder was yielded at 3.1 g (8.6 unit/mg) per kilogram stems by PEG6000/Na2SO4 aqueous two-phase purification from the water extracts (93.2% recovery), followed by ethanol precipitation and vacuum freeze-drying. The purified peroxidase had high activity in transforming tea catechins into theaflavins. Phenolics powder containing 43% phenolics and 27% flavonoids was yielded at 76.9 g per kilogram stems after vacuum-concentrating the ethanol extracts. This method can make valuable functional products using the sweet potato waste.
Designing Rashba–Dresselhaus effect in magnetic insulators
Authors: Kawano Masataka , Onose Yoshinori , Hotta Chisa
Published: March 2019

One of the major strategies to control magnetism in spintronics is to utilize the coupling between electron spin and its orbital motion. The Rashba and Dresselhaus spin–orbit couplings induce magnetic textures of band electrons called spin momentum locking, which produces a spin torque by the injection of electric current. However, joule heating had been a bottleneck for device applications. Here, we propose a theory to generate further rich spin textures in insulating antiferromagnets with broken spatial inversion symmetry (SIS), which is easily controlled by a small magnetic field. In antiferromagnets, the ordered moments host two species of magnons that serve as internal degrees of freedom in analogy with electron spins. The Dzyaloshinskii–Moriya interaction introduced by the SIS breaking couples the two-magnon-degrees of freedom with the magnon momentum. We present a systematic way to design such texture and to detect it via magnonic spin current for the realization of antiferromagnetic memory.
Chromatographic analysis of peptidoglycan samples with the aid of a chemometric technique: introducing a novel analytical procedure to classify bacterial cell wall collection
Authors: Kumar Keshav , Cava Felipe
Published: March 2019

The present work introduces a simple analytical procedure using self-organising map (SOM) analysis to analyse the large number of complex chromatographic data sets from bacterial peptidoglycan samples.
Double-headed nanosystems for oral drug delivery
Authors: Kaur G. , Arora M. , Ganugula R. , Kumar M. N. V. Ravi
Published: March 2019

We demonstrate a novel strategy to engineer double-headed nanosystems by chemical modification of the carboxyl terminal polyester with a linker that offers tripodal arrangement of ligands on the particle surfaces.
Dietary lysozyme supplementation contributes to enhanced intestinal functions and gut microflora of piglets
Authors: Xiong Xia , Zhou Jian , Liu Hongnan , Tang Yulong , Tan Bie , Yin Yulong
Published: March 2019

Lysozyme plays a significant role in defense against bacterial pathogens and in regulating the interactions between gut microbiota and host immune systems.
Spinodal stratification in ultrathin micellar foam films
Authors: Yilixiati Subinuer , Wojcik Ewelina , Zhang Yiran , Sharma Vivek
Published: March 2019

We report the discovery and analysis of spinodal stratification, a hitherto unreported mechanism underlying drainage and rupture of micellar foam films, that presents unexplored opportunities for understanding and controlling the stability, lifetime and properties of ubiquitous foams.
An ultrafast quantum thermometer from graphene quantum dots
Authors: Sehrawat Poonam , Abid Abid , Islam S. S.
Published: March 2019

We report an ultra-sensitive temperature sensor derived from graphene quantum dots (GQDs) embedded in a self-standing reduced graphene oxide (RGO) film.
Improving the electron transport performance by changing side chains in sulfur-containing azaacenes: a combined theoretical investigation on free molecules and an adsorption system
Authors: Wen Keke , Pan Xiao , Feng Songyan , Wu Wenpeng , Guo Xugeng , Zhang Jinglai
Published: March 2019

The properties of designed sulfur-containing azaacene electron transport materials by changing side chains are theoretically investigated.
A Raman spectral probe on polar w-ZnS nanostructures and surface optical phonon modes in nanowires
Authors: Prasad Neena , Karthikeyan Balasubramanian
Published: March 2019

In the present study, different morphologies of ZnS nanostructures have been synthesized through a hydrothermal method and their Raman spectral modes are investigated.
Dynamic adsorption of toluene on amino-functionalized SBA-15 type spherical mesoporous silica
Authors: Zhou Huiping , Gao Shaomin , Zhang Wenwen , An Zhaohui , Chen Donghui
Published: March 2019

Amino-functionalized spherical mesoporous silicas were successfully prepared via a convenient treatment method by using APTES, which was used for the adsorption treatment of toluene gas, showing obvious advantages.
Enhanced performance of PTB7-Th:PCBM based active layers in ternary organic solar cells
Authors: Lakhotiya Govinda , Belsare Namdeo , Arbuj Sudhir , Kale Bharat , Rana Abhimanyu
Published: March 2019

The present study aims at understanding the role of incorporating Cu2S nanocrystals (NCs) as a third component in ternary organic solar cells.
A sandwich-type catalytic composite reassembled with a birnessite layer and metalloporphyrin as a water oxidation catalyst
Authors: Liu Fan , Wang Liming , Yang Weijun , Liu Enqing , Huang Can
Published: March 2019

Sandwich-type MnTAPP@bir was synthesized by re-assembly of exfoliated birnessite and MnTAPP, and exhibited superior OER performance.
Simultaneous bifunctional application of solid-state lighting and ratiometric optical thermometer based on double perovskite LiLaMgWO6:Er3+ thermochromic phosphors
Authors: Ran Weiguang , Noh Hyeon Mi , Park Sung Heum , Lee Bo Ram , Kim Jung Hwan , Jeong Jung Hyun , Shi Jinsheng , Liu Guangzeng
Published: March 2019

Both efficient light emitting diodes and highly sensitive (2.24% K−1) ratiometric thermometer were obtained based on the LiLaMgWO6:Er3+ thermochromic phosphor.
Mechanism and stereoselectivity in NHC-catalyzed β-functionalization of saturated carboxylic ester
Authors: Li Yan , Zhang Zhiqiang
Published: March 2019

To understand the mechanism and origin of stereoselectivity of [3 + 2] annulation reaction between a carboxylic ester and an isatin catalyzed by N-heterocyclic carbene (NHC), density functional theory (DFT) calculations have been carried out.
Formation of polarization needle-like domain and its unusual switching in compositionally graded ferroelectric thin films: an improved phase field model
Authors: Van Lich Le , Dinh Van-Hai
Published: March 2019

New phase field model to reveal switching mechanism of needle domain in compositionally graded ferroelectric thin film.