bluuebunny/crossref_metadata_2025 huggingface dataset:
A biochemical framework for anaerobic oxidation of methane driven by Fe(III)-dependent respiration
Authors: Yan Zhen , Joshi Prachi , Gorski Christopher A. , Ferry James G.
Published: April 2018

Consumption of methane by aerobic and anaerobic microbes governs the atmospheric level of this powerful greenhouse gas. Whereas a biochemical understanding of aerobic methanotrophy is well developed, a mechanistic understanding of anaerobic methanotrophy has been prevented by the unavailability of pure cultures. Here we report a biochemical investigation of Methanosarcina acetivorans, a methane-producing species capable of anaerobic methanotrophic growth dependent on reduction of Fe(III). Our findings support a pathway anchored by Fe(III)-dependent mechanisms for energy conservation driving endergonic reactions that are key to methanotrophic growth. The pathway is remarkably similar to pathways hypothesized for uncultured anaerobic methanotrophic archaea. The results contribute to an improved understanding of the methane cycle that is paramount to understanding human interventions influencing Earth’s climate. Finally, the pathway enables advanced development and optimization of biotechnologies converting methane to value-added products through metabolic engineering of M. acetivorans.
Fine manipulation of sound via lossy metamaterials with independent and arbitrary reflection amplitude and phase
Authors: Zhu Yifan , Hu Jie , Fan Xudong , Yang Jing , Liang Bin , Zhu Xuefeng , Cheng Jianchun
Published: April 2018

Abstract

The fine manipulation of sound fields is critical in acoustics yet is restricted by the coupled amplitude and phase modulations in existing wave-steering metamaterials. Commonly, unavoidable losses make it difficult to control coupling, thereby limiting device performance. Here we show the possibility of tailoring the loss in metamaterials to realize fine control of sound in three-dimensional (3D) space. Quantitative studies on the parameter dependence of reflection amplitude and phase identify quasi-decoupled points in the structural parameter space, allowing arbitrary amplitude-phase combinations for reflected sound. We further demonstrate the significance of our approach for sound manipulation by producing self-bending beams, multifocal focusing, and a single-plane two-dimensional hologram, as well as a multi-plane 3D hologram with quality better than the previous phase-controlled approach. Our work provides a route for harnessing sound via engineering the loss, enabling promising device applications in acoustics and related fields.
Path to stable quantum spin liquids in spin-orbit coupled correlated materials
Authors: Catuneanu Andrei , Yamaji Youhei , Wachtel Gideon , Kim Yong Baek , Kee Hae-Young
Published: April 2018

The spin liquid phase is one of the prominent strongly interacting topological phases of matter whose unambiguous confirmation is yet to be reached despite intensive experimental efforts on numerous candidate materials. Recently, a new family of correlated honeycomb materials, in which strong spin-orbit coupling allows for various bond-dependent spin interactions, have been promising candidates to realize the Kitaev spin liquid. Here we study a model with bond-dependent spin interactions and show numerical evidence for the existence of an extended quantum spin liquid region, which is possibly connected to the Kitaev spin liquid state. These results are used to provide an explanation of the scattering continuum seen in neutron scattering on α-RuCl3.
The mitigating effect of repeated memory reactivations on forgetting
Authors: MacLeod Sydney , Reynolds Michael G. , Lehmann Hugo
Published: April 2018

Memory reactivation is a process whereby cueing or recalling a long-term memory makes it enter a new active and labile state. Substantial evidence suggests that during this state the memory can be updated (e.g., adding information) and can become more vulnerable to disruption (e.g., brain insult). Memory reactivations can also prevent memory decay or forgetting. However, it is unclear whether cueing recall of a feature or component of the memory can benefit retention similarly to promoting recall of the entire memory. We examined this possibility by having participants view a series of neutral images and then randomly assigning them to one of four reactivation groups: control (no reactivation), distractor (reactivation of experimental procedures), component (image category reactivation), and descriptive (effortful description of the images). The experiment also included three retention intervals: 1 h, 9 days, and 28 days. Importantly, the participants received three reactivations equally spaced within their respective retention interval. At the end of the interval, all the participants were given an in-lab free-recall test in which they were asked to write down each image they remembered with as many details as possible. The data revealed that both the participants in the descriptive reactivation and component reactivation groups remembered significantly more than the participants in the control groups, with the effect being most pronounced in the 28-day retention interval condition. These findings suggest that memory reactivation, even component reactivation of a memory, makes memories more resistant to decay.
FIV vaccine with receptor epitopes results in neutralizing antibodies but does not confer resistance to challenge
Authors: Miller Craig , Emanuelli Mauren , Fink Elizabeth , Musselman Esther , Mackie Ryan , Troyer Ryan , Elder John , VandeWoude Sue
Published: April 2018

Feline immunodeficiency virus (FIV) is the feline analogue to human immunodeficiency virus (HIV) and utilizes parallel modes of receptor-mediated entry. The FIV surface glycoprotein (SU) is an important target for induction of neutralizing antibodies, and autoantibodies to the FIV binding receptor (CD134) block infection ex vivo; thus highlighting the potential for immunotherapies which utilize anti-receptor antibodies to block viral infection. To determine whether vaccination with CD134-SU complexes could induce protection against FIV infection, cats (n = 5 per group) were immunized with soluble CD134, recombinant FIV-SU protein, and/or CD134+SU complexes. Two trials were performed with different antigen combinations and vaccination schedules. In vivo generation of anti-CD134 and anti-SU IgG antibodies was measured, and in vitro neutralization assays were conducted. Immunization induced production of anti-CD134 and anti-SU antibodies that significantly inhibited FIV infection in vitro. However, no vaccine combination protected cats from FIV infection, and neat serum from vaccinated cats enhanced FIV growth in vitro. CD134+SU vaccinated cats exhibited increased CD4:CD8 ratio immediately prior to challenge, and antibodies were much more efficiently generated against vaccine by-products versus target antigens. Results suggest vaccination against viral and cryptic receptor epitopes yields neutralizing antibodies that synergistically inhibit FIV infection in vitro. Factors contributing to vaccine failure may include: (1) Heat-labile serum factors that enhance viral replication, (2) changes in circulating target cell populations induced by vaccination, and (3) weak immunogenicity of neutralizing epitopes compared to off-target vaccine components. Results reinforce the need to monitor vaccine preparation components and avoid non-specific immune stimulation during vaccination.
Removal of Cr (III) and Ni (II) from tannery effluent using calcium carbonate coated bacterial magnetosomes
Authors: Jacob Jobin John , Varalakshmi R. , Gargi S. , Jayasri M. A. , Suthindhiran K.
Published: April 2018

Heavy metal contamination of surface water bodies and ground water has been a major problem around the world. Calcium-based adsorbents are effective but cannot be separated easily after the treatment. Magnetosomes are biogenic magnetite synthesised as highly ordered chain-like structures by magnetotactic bacteria. In this study, we have prepared magnetically controlled calcite microcrystals using magnetosomes for the adsorption experiment. The ability of magnetic calcite as adsorbent was investigated for the removal of Cr (III) and Ni (II) ions from synthetic solution. Critical parameters, such as the effect of pH, temperature, contact time, initial ion concentration, and adsorbent dose, were optimised in comparison with calcite, magnetosomes, and activated carbon for maximum metal ion removal. The study showed that equilibrium was established in 1 h for both Cr (III) and Ni (II) at a pH of 6.0 and 8.0, respectively. The adsorption process follows pseudo-second-order reaction kinetics, along with Langmuir and Freundlich adsorption isotherms. The thermodynamics of adsorption of both metal ions on magnetic calcite showed that the adsorption was spontaneous and endothermic in nature. Magnetically controlled calcite crystals successfully removed Cr (III) and Ni (II) from collected tannery effluent and separated from the solution by applying magnetic field. Maximum removal of chromium and nickel (94 and 84%) by magnetic calcite is similar to calcite crystals but higher than magnetosomes and activated carbon. The results indicated that magnetic calcite could be used as an alternative adsorbent for removing heavy metals from tannery effluent.
Fit-for-purpose block polymer membranes molecularly engineered for water treatment
Authors: Zhang Yizhou , Almodovar-Arbelo Noelia E. , Weidman Jacob L. , Corti David S. , Boudouris Bryan W. , Phillip William A.
Published: April 2018

Continued stresses on fresh water supplies necessitate the utilization of non-traditional resources to meet the growing global water demand. Desalination and hybrid membrane processes are capable of treating non-traditional water sources to the levels demanded by users. Specifically, desalination can produce potable water from seawater, and hybrid processes have the potential to recover valuable resources from wastewater while producing water of a sufficient quality for target applications. Despite the demonstrated successes of these processes, state-of-the-art membranes suffer from limitations that hinder the widespread adoption of these water treatment technologies. In this review, we discuss nanoporous membranes derived from self-assembled block polymer precursors for the purposes of water treatment. Due to their well-defined nanostructures, myriad chemical functionalities, and the ability to molecularly-engineer these properties rationally, block polymer membranes have the potential to advance water treatment technologies. We focus on block polymer-based efforts to: (1) nanomanufacture large areas of high-performance membranes; (2) reduce the characteristic pore size and push membranes into the reverse osmosis regime; and (3) design and implement multifunctional pore wall chemistries that enable solute-specific separations based on steric, electrostatic, and chemical affinity interactions. The use of molecular dynamics simulations to guide block polymer membrane design is also discussed because its ability to systematically examine the available design space is critical for rapidly translating fundamental understanding to water treatment applications. Thus, we offer a full review regarding the computational and experimental approaches taken in this arena to date while also providing insights into the future outlook of this emerging technology.
Author Correction: Exercise – induced changes in cerebrospinal fluid miRNAs in Gulf War Illness, Chronic Fatigue Syndrome and sedentary control subjects
Authors: Baraniuk James N. , Shivapurkar Narayan
Published: April 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Virus-encoded miRNAs in Ebola virus disease
Authors: Duy Janice , Honko Anna N. , Altamura Louis A. , Bixler Sandra L. , Wollen-Roberts Suzanne , Wauquier Nadia , O’Hearn Aileen , Mucker Eric M. , Johnson Joshua C. , Shamblin Joshua D. , Zelko Justine , Botto Miriam A. , Bangura James , Coomber Moinya , Pitt M. Louise , Gonzalez Jean-Paul , Schoepp Randal J. , Goff Arthur J. , Minogue Timothy D.
Published: April 2018

Ebola virus (EBOV) is a negative-strand RNA virus that replicates in the cytoplasm and causes an often-fatal hemorrhagic fever. EBOV, like other viruses, can reportedly encode its own microRNAs (miRNAs) to subvert host immune defenses. miRNAs are short noncoding RNAs that can regulate gene expression by hybridizing to multiple mRNAs, and viral miRNAs can enhance viral replication and infectivity by regulating host or viral genes. To date, only one EBOV miRNA has been examined in human infection. Here, we assayed mouse, rhesus macaque, cynomolgus macaque, and human samples infected with three EBOV variants for twelve computationally predicted viral miRNAs using RT-qPCR. Ten miRNAs aligned to EBOV variants and were detectable in the four species during disease with several viral miRNAs showing presymptomatic amplification in animal models. miRNA abundances in both the mouse and nonhuman primate models mirrored the human cohort, with miR-1-5p, miR-1-3p, and miR-T3-3p consistently at the highest levels. These striking similarities in the most abundant miRNAs during infection with different EBOV variants and hosts indicate that these miRNAs are potential valuable diagnostic markers and key effectors of EBOV pathogenesis.
Metabolomics reveals perturbations in endometrium and serum of minimal and mild endometriosis
Authors: Dutta Mainak , Singh Brajesh , Joshi Mamata , Das Debanjan , Subramani Elavarasan , Maan Meenu , Jana Saikat Kumar , Sharma Uma , Das Soumen , Dasgupta Swagata , Ray Chaitali Datta , Chakravarty Baidyanath , Chaudhury Koel
Published: April 2018

Endometriosis is a common benign gynecological disease, characterized by growth and proliferation of endometrial glands and stroma outside the uterus. With studies showing metabolic changes in various biofluids of endometriosis women, we have set upon to investigate whether endometrial tissue show differences in their metabolic profiles. 1H NMR analysis was performed on eutopic endometrial tissue of women with endometriosis and controls. Analysis was performed on spectral data and on relative concentrations of metabolites obtained from spectra using multivariate and univariate data analysis. Analysis shows that various energy, ketogenic and glucogenic metabolites have significant altered concentrations in various stages of endometriosis. In addition, altered tissue metabolites in minimal and mild stages of endometriosis were explored in serum of these patients to assess their role in disease diagnosis. For Stage I diagnosis alanine was found to have 90% sensitivity (true positives) and 58% specificity (true negatives). For Stage II diagnosis alanine, leucine, lysine, proline and phenylalanine showed significant altered levels in serum. While sensitivity of these serum metabolites varied between 69.2–100% the specificity values ranged between 58.3–91.7%. Further, a regression model generated with this panel of serum markers showed an improved sensitivity and specificity of 100% and 83%, respectively for Stage II diagnosis.
Uniqueness of Protected Areas for Conservation Strategies in the European Union
Authors: Hoffmann Samuel , Beierkuhnlein Carl , Field Richard , Provenzale Antonello , Chiarucci Alessandro
Published: April 2018

Protected areas (PAs) constitute major tools in nature conservation. In the European Union (EU), the Birds and Habitats Directives are the most important policies for conservation strategy, legally preserving Europe’s characteristic, rare, endemic and threatened biota. We used occurrence data for species listed in the directives’ Annexes to assess the uniqueness of major PAs in the EU (National Parks, Biosphere Reserves); this is important for preserving the EU’s focal species. We developed a novel, multifunctional approach to calculate different metrics of conservation value that represent different components of species diversity within the PAs, involving inventory diversity, deviation from the species–area relationship, species rarity and differentiation diversity. Applying it, we found that individual PAs frequently vary considerably in their scores on different components, which are often disconnected from PA size. PAs around the EU periphery, often containing few species, are key to conserving species that are rare in the EU. Because our analysis focuses on EU priority species and includes different components of diversity, it allows more appropriate estimation of conservation value inside PAs in context of the EU than recent, high-profile, global-level research. We offer tools to evaluate, and information to regulate, the representativeness, persistence and efficiency of PAs.
Adjuvant chemotherapy after surgery can improve clinical outcomes for patients with IB2-IIB cervical cancer with neoadjuvant chemotherapy followed by radical surgery
Authors: Sun Haiying , Huang Kecheng , Tang Fangxu , Li Xiong , Wang Xiaoli , Long Sixiang , Zhou Shasha , Suolangquzhen  , Zhang Jianwei , Ning Ruoqi , Li Shuang , Wang Shixuan , Ma Ding
Published: April 2018

The aim of the study is to evaluate the efficacy of postoperative treatments based on pathological response for cervical cancer patients who received neoadjuvant chemotherapy (NACT) followed by radical surgery. Firstly, a total of 756 cervical squamous cell cancer (SCC) patients with FIGO IB2-IIB were included in this retrospective study. Then data from a prospective cohort of 393 patients was employed for further validation. Overall survival (OS) and disease-free survival (DFS) were assessed. In the retrospective study, SCC patients who accepted adjuvant chemotherapy after radical surgery had a relatively better OS than those who received no therapy (P = 0.08, HR = 0.57). The result was more noticeable in the prospective cohort study (P = 0.006, HR = 0.28). In the combined analysis, adjuvant chemotherapy improved clinical outcomes compared with no therapy (P = 0.002 and 0.04 for OS and DFS). Particularly for patients with extra-cervical residual disease, adjuvant chemotherapy improved OS (log-rank P = 0.008, 0.004 and 0.001 in the retrospective, prospective and combined studies). Optimal response patients had good outcomes even without therapy. Our study indicates that adjuvant chemotherapy can benefit clinical outcomes for SCC patients with NACT followed by radical surgery, especially those with extra-cervical residual disease. For optimal response patients, there may be no need for further treatment. This finding needs to be validated in more future studies.
Parallel detection of theta and respiration-coupled oscillations throughout the mouse brain
Authors: Tort Adriano B. L. , Ponsel Simon , Jessberger Jakob , Yanovsky Yevgenij , Brankačk Jurij , Draguhn Andreas
Published: April 2018

Slow brain oscillations are usually coherent over long distances and thought to link distributed cell assemblies. In mice, theta (5–10 Hz) stands as one of the most studied slow rhythms. However, mice often breathe at theta frequency, and we recently reported that nasal respiration leads to local field potential (LFP) oscillations that are independent of theta. Namely, we showed respiration-coupled oscillations in the hippocampus, prelimbic cortex, and parietal cortex, suggesting that respiration could impose a global brain rhythm. Here we extend these findings by analyzing LFPs from 15 brain regions recorded simultaneously with respiration during exploration and REM sleep. We find that respiration-coupled oscillations can be detected in parallel with theta in several neocortical regions, from prefrontal to visual areas, and also in subcortical structures such as the thalamus, amygdala and ventral hippocampus. They might have escaped attention in previous studies due to the absence of respiration monitoring, the similarity with theta oscillations, and the highly variable peak frequency. We hypothesize that respiration-coupled oscillations constitute a global brain rhythm suited to entrain distributed networks into a common regime. However, whether their widespread presence reflects local network activity or is due to volume conduction remains to be determined.
Human and ecological determinants of the spatial structure of local breed diversity
Authors: Colino-Rabanal Victor J. , Rodríguez-Díaz Roberto , Blanco-Villegas María José , Peris Salvador J. , Lizana Miguel
Published: April 2018

Since domestication, a large number of livestock breeds adapted to local conditions have been created by natural and artificial selection, representing one of the most powerful ways in which human groups have constructed niches to meet their need. Although many authors have described local breeds as the result of culturally and environmentally mediated processes, this study, located in mainland Spain, is the first aimed at identifying and quantifying the environmental and human contributions to the spatial structure of local breed diversity, which we refer to as livestock niche. We found that the more similar two provinces were in terms of human population, ecological characteristics, historical ties, and geographic distance, the more similar the composition of local breeds in their territories. Isolation by human population distance showed the strongest effect, followed by isolation by the environment, thus supporting the view of livestock niche as a socio-cultural product adapted to the local environment, in whose construction humans make good use of their ecological and cultural inheritances. These findings provide a useful framework to understand and to envisage the effects of climate change and globalization on local breeds and their livestock niches.
A fast-converging iterative method based on weighted feedback for multi-distance phase retrieval
Authors: Guo Cheng , Shen Cheng , Li Qiang , Tan Jiubin , Liu Shutian , Kan Xinchi , Liu Zhengjun
Published: April 2018

Multiple distance phase retrieval methods hold great promise for imaging and measurement due to their less expensive and compact setup. As one of their implementations, the amplitude-phase retrieval algorithm (APR) can achieve stable and high-accuracy reconstruction. However, it suffers from the slow convergence and the stagnant issue. Here we propose an iterative modality named as weighted feedback to solve this problem. With the plug-ins of single and double feedback, two augmented approaches, i.e. the APRSF and APRDF algorithms, are demonstrated to increase the convergence speed with a factor of two and three in experiments. Furthermore, the APRDF algorithm can extend the multiple distance phase retrieval to the partially coherent illumination and enhance the imaging contrast of both amplitude and phase, which actually relaxes the light source requirement. Thus the weighted feedback enables a fast-converging and high-contrast imaging scheme for the iterative phase retrieval.
Heterologous DNA prime-protein boost immunization with RecA and FliD offers cross-clade protection against leptospiral infection
Authors: Raja Veerapandian , Sobana Sankaran , Mercy Charles Solomon Akino , Cotto Bianca , Bora Durlav Prasad , Natarajaseenivasan Kalimuthusamy
Published: April 2018

The emergence of >300 serovars ofLeptospiraconfounded the use of generalized bacterin, the whole cell lysate, as vaccines to control leptospirosis. Because of substantial genetic and geographic heterogeneity among circulating serovars, one vaccine strain per serovar cannot be efficacious against all the serovars. We have performed heterologous DNA prime-protein boost vaccination challenge studies in hamsters usingin vivoexpressed, leptospiral recombinase A (RecA) and flagellar hook associated protein (FliD). We prepared the monovalent recombinant protein, plasmid DNA, and DNA prime protein boost adjuvant vaccines. The whole cell bacterin served as a control. Our data show that (i) RecA and FliD have multiple immunogenic B and T-cell epitopes with highly conserved domains among most prevalent pathogenicLeptospiraspp., (ii) humoral and cell mediated immune responses were induced remarkably, (iii) provides significant protection against homologous (Autumnalis strain N2) and cross-clade heterologous (Canicola strain PAI-1) challenge infection for the heterologous prime-protein boost (∼91–100%) and, the DNA vaccine (∼75–83%). Recombinant protein vaccine shows only partial protection (∼58–66%), (iv) RecA prime-protein boost vaccine shows sterilizing immunity, with heterologous protection. This RecA/FliD prime-protein boost strategy holds potential for vaccination against animal leptospirosis and for a better control of zoonotic transmission.
Alternative polyadenylation drives genome-to-phenome information detours in the AMPKα1 and AMPKα2 knockout mice
Authors: Zhang Shuwen , Zhang Yangzi , Zhou Xiang , Fu Xing , Michal Jennifer J. , Ji Guoli , Du Min , Davis Jon F. , Jiang Zhihua
Published: April 2018

Currently available mouse knockout (KO) lines remain largely uncharacterized for genome-to-phenome (G2P) information flows. Here we test our hypothesis that altered myogenesis seen in AMPKα1- and AMPKα2-KO mice is caused by use of alternative polyadenylation sites (APSs). AMPKα1 and AMPKα2 are two α subunits of adenosine monophosphate-activated protein kinase (AMPK), which serves as a cellular sensor in regulation of many biological events. A total of 56,483 APSs were derived from gastrocnemius muscles. The differentially expressed APSs (DE-APSs) that were down-regulated tended to be distal. The DE-APSs that were related to reduced and increased muscle mass were down-regulated in AMPKα1-KO mice, but up-regulated in AMPKα2-KO mice, respectively. Five genes: Car3 (carbonic anhydrase 3), Mylk4 (myosin light chain kinase family, member 4), Neb (nebulin), Obscn (obscurin) and Pfkm (phosphofructokinase, muscle) utilized different APSs with potentially antagonistic effects on muscle function. Overall, gene knockout triggers genome plasticity via use of APSs, completing the G2P processes. However, gene-based analysis failed to reach such a resolution. Therefore, we propose that alternative transcripts are minimal functional units in genomes and the traditional central dogma concept should be now examined under a systems biology approach.
Elf3 Contributes to Cartilage Degradation in vivo in a Surgical Model of Post-Traumatic Osteoarthritis
Authors: Wondimu Elisabeth B. , Culley Kirsty L. , Quinn Justin , Chang Jun , Dragomir Cecilia L. , Plumb Darren A. , Goldring Mary B. , Otero Miguel
Published: April 2018

The E-74 like factor 3 (ELF3) is a transcription factor induced by inflammatory factors in various cell types, including chondrocytes. ELF3 levels are elevated in human cartilage from patients with osteoarthritis (OA), and ELF3 contributes to the IL-1β-induced expression of genes encoding Mmp13, Nos2, and Ptgs2/Cox2 in chondrocytes in vitro. Here, we investigated the contribution of ELF3 to cartilage degradation in vivo, using a mouse model of OA. To this end, we generated mouse strains with cartilage-specific Elf3 knockout (Col2Cre:Elf3f/f) and Comp-driven Tet-off-inducible Elf3 overexpression (TRE-Elf3:Comp-tTA). To evaluate the contribution of ELF3 to OA, we induced OA in 12-week-old Col2Cre:Elf3f/f and 6-month-old TRE-Elf3:Comp-tTA male mice using the destabilization of the medial meniscus (DMM) model. The chondrocyte-specific deletion of Elf3 led to decreased levels of IL-1β- and DMM-induced Mmp13 and Nos2 mRNA in vitro and in vivo, respectively. Histological grading showed attenuation of cartilage loss in Elf3 knockout mice compared to wild type (WT) littermates at 8 and 12 weeks following DMM surgery that correlated with reduced collagenase activity. Accordingly, Elf3 overexpression led to increased cartilage degradation post-surgery compared to WT counterparts. Our results provide evidence that ELF3 is a central contributing factor for cartilage degradation in post-traumatic OA in vivo.
The Hippo Signaling Transducer TAZ Regulates Mammary Gland Morphogenesis and Carcinogen-induced Mammary Tumorigenesis
Authors: Denson Kayla E. , Mussell Ashley L. , Shen He , Truskinovsky Alexander , Yang Nuo , Parashurama Natesh , Chen Yanmin , Frangou Costa , Yang Fajun , Zhang Jianmin
Published: April 2018

Hippo signaling pathway is an evolutionarily conserved pathway that controls organ size by regulating cell proliferation, apoptosis and stem cell self-renewal. TAZ (transcriptional coactivator with the PDZ-binding motif) is a key downstream effector of the mammalian Hippo pathway. Here, using a transgenic mouse model with mammary-gland-specific expression of constitutively active TAZ, we found that TAZ induction in mammary epithelial cells was associated with an increase in mammary glandular size, which probably resulted from adipocyte hypertrophy. Consistent with its known oncogenic potential, we observed tumor formation in TAZ transgenic mice after administration of the carcinogen 7,12-dimethylbenzanthracene (DMBA) and demonstrated that tumorigenesis was reliant on the presence of TAZ. Our findings establish a previously unknown roles of TAZ in regulating both mammary gland morphogenesis as well as carcinogen-induced mammary tumor formation.
Encapsulating Networks of Droplet Interface Bilayers in a Thermoreversible Organogel
Authors: Challita Elio J. , Najem Joseph S. , Monroe Rachel , Leo Donald J. , Freeman Eric C.
Published: April 2018

The development of membrane-based materials that exhibit the range and robustness of autonomic functions found in biological systems remains elusive. Droplet interface bilayers (DIBs) have been proposed as building blocks for such materials, owing to their simplicity, geometry, and capability for replicating cellular phenomena. Similar to how individual cells operate together to perform complex tasks and functions in tissues, networks of functionalized DIBs have been assembled in modular/scalable networks. Here we present the printing of different configurations of picoliter aqueous droplets in a bath of thermoreversible organogel consisting of hexadecane and SEBS triblock copolymers. The droplets are connected by means of lipid bilayers, creating a network of aqueous subcompartments capable of communicating and hosting various types of chemicals and biomolecules. Upon cooling, the encapsulating organogel solidifies to form self-supported liquid-in-gel, tissue-like materials that are robust and durable. To test the biomolecular networks, we functionalized the network with alamethicin peptides and alpha-hemolysin (αHL) channels. Both channels responded to external voltage inputs, indicating the assembly process does not damage the biomolecules. Moreover, we show that the membrane properties may be regulated through the deformation of the surrounding gel.
Subsurface Endospore-Forming Bacteria Possess Bio-Sealant Properties
Authors: Basha Sreenivasulu , Lingamgunta Lakshman Kumar , Kannali Jayakumar , Gajula Swarna Kumari , Bandikari Ramesh , Dasari Sreenivasulu , Dalavai Veena , Chinthala Paramageetham , Gundala Prasada Babu , Kutagolla Peera , Balaji Vinodh Kumar
Published: April 2018

Concrete is a strong and fairly inexpensive building substance, but has several disadvantages like cracking that allows corrosion, thus reducing its lifespan. To mitigate these complications, long-lasting microbial self-healing cement is an alternative that is eco-friendly and also actively repairs cracks. The present paper describes the detailed experimental investigation on compressive strength of cement mortars, mixed with six alkaliphilic bacteria, isolated from subsurface mica mines of high alkalinity. The experiments showed that the addition of alkaliphilic isolates at different cell concentrations (104 and 106 cells/ml) enhanced the compressive strength of cement mortar, because the rapid growth of bacteria at high alkalinity precipitates calcite crystals that lead to filling of pores and densifying the concrete mix. Thus, Bacillus subtilis (SVUNM4) showed the highest compressive strength (28.61%) of cement mortar at 104 cells/ml compared to those of other five alkaliphilic isolates (Brevibacillus sp., SVUNM15-22.1%; P. dendritiformis, SVUNM11-19.9%; B. methylotrophicus, SVUNM9-16%; B. licheniformis, SVUNM14-12.7% and S. maltophilia, SVUNM13-9.6%) and controlled cement mortar as well. This method resulted in the filling of cracks in concrete with calcite (CaCO3), which was observed by scanning electron microscopy (SEM). Our results showed that the alkaliphilic bacterial isolates used in the study are effective in self-healing and repair of concrete cracks.
Ghost Imaging Based on Deep Learning
Authors: He Yuchen , Wang Gao , Dong Guoxiang , Zhu Shitao , Chen Hui , Zhang Anxue , Xu Zhuo
Published: April 2018

Even though ghost imaging (GI), an unconventional imaging method, has received increased attention by researchers during the last decades, imaging speed is still not satisfactory. Once the data-acquisition method and the system parameters are determined, only the processing method has the potential to accelerate image-processing significantly. However, both the basic correlation method and the compressed sensing algorithm, which are often used for ghost imaging, have their own problems. To overcome these challenges, a novel deep learning ghost imaging method is proposed in this paper. We modified the convolutional neural network that is commonly used in deep learning to fit the characteristics of ghost imaging. This modified network can be referred to as ghost imaging convolutional neural network. Our simulations and experiments confirm that, using this new method, a target image can be obtained faster and more accurate at low sampling rate compared with conventional GI method.
Biological Insights Into Muscular Strength: Genetic Findings in the UK Biobank
Authors: Tikkanen Emmi , Gustafsson Stefan , Amar David , Shcherbina Anna , Waggott Daryl , Ashley Euan A. , Ingelsson Erik
Published: April 2018

We performed a large genome-wide association study to discover genetic variation associated with muscular strength, and to evaluate shared genetic aetiology with and causal effects of muscular strength on several health indicators. In our discovery analysis of 223,315 individuals, we identified 101 loci associated with grip strength (P <5 × 10−8). Of these, 64 were associated (P < 0.01 and consistent direction) also in the replication dataset (N = 111,610). eQTL analyses highlighted several genes known to play a role in neuro-developmental disorders or brain function, and the results from meta-analysis showed a significant enrichment of gene expression of brain-related transcripts. Further, we observed inverse genetic correlations of grip strength with cardiometabolic traits, and positive correlation with parents’ age of death and education. We also showed that grip strength had shared biological pathways with indicators of frailty, including cognitive performance scores. By use of Mendelian randomization, we provide evidence that higher grip strength is protective of both coronary heart disease (OR = 0.69, 95% CI 0.60–0.79, P < 0.0001) and atrial fibrillation (OR = 0.75, 95% CI 0.62–0.90, P = 0.003). In conclusion, our results show shared genetic aetiology between grip strength, and cardiometabolic and cognitive health; and suggest that maintaining muscular strength could prevent future cardiovascular events.
Reversal of memory and neuropsychiatric symptoms and reduced tau pathology by selenium in 3xTg-AD mice
Authors: Van der Jeugd Ann , Parra-Damas Arnaldo , Baeta-Corral Raquel , Soto-Faguás Carlos M. , Ahmed Tariq , LaFerla Frank M. , Giménez-Llort Lydia , D’Hooge Rudi , Saura Carlos A.
Published: April 2018

Accumulation of amyloid-β plaques and tau contribute to the pathogenesis of Alzheimer’s disease (AD), but it is unclear whether targeting tau pathology by antioxidants independently of amyloid-β causes beneficial effects on memory and neuropsychiatric symptoms. Selenium, an essential antioxidant element reduced in the aging brain, prevents development of neuropathology in AD transgenic mice at early disease stages. The therapeutic potential of selenium for ameliorating or reversing neuropsychiatric and cognitive behavioral symptoms at late AD stages is largely unknown. Here, we evaluated the effects of chronic dietary sodium selenate supplementation for 4 months in female 3xTg-AD mice at 12–14 months of age. Chronic sodium selenate treatment efficiently reversed hippocampal-dependent learning and memory impairments, and behavior- and neuropsychiatric-like symptoms in old female 3xTg-AD mice. Selenium significantly decreased the number of aggregated tau-positive neurons and astrogliosis, without globally affecting amyloid plaques, in the hippocampus of 3xTg-AD mice. These results indicate that selenium treatment reverses AD-like memory and neuropsychiatric symptoms by a mechanism involving reduction of aggregated tau and/or reactive astrocytes but not amyloid pathology. These results suggest that sodium selenate could be part of a combined therapeutic approach for the treatment of memory and neuropsychiatric symptoms in advanced AD stages.
Automated sorting of neuronal trees in fluorescent images of neuronal networks using NeuroTreeTracer
Authors: Kayasandik Cihan , Negi Pooran , Laezza Fernanda , Papadakis Manos , Labate Demetrio
Published: April 2018

Fluorescence confocal microscopy has become increasingly more important in neuroscience due to its applications in image-based screening and profiling of neurons. Multispectral confocal imaging is useful to simultaneously probe for distribution of multiple analytes over networks of neurons. However, current automated image analysis algorithms are not designed to extract single-neuron arbors in images where neurons are not separated, hampering the ability map fluorescence signals at the single cell level. To overcome this limitation, we introduce NeuroTreeTracer – a novel image processing framework aimed at automatically extracting and sorting single-neuron traces in fluorescent images of multicellular neuronal networks. This method applies directional multiscale filters for automated segmentation of neurons and soma detection, and includes a novel tracing routine that sorts neuronal trees in the image by resolving network connectivity even when neurites appear to intersect. By extracting each neuronal tree, NeuroTreetracer enables to automatically quantify the spatial distribution of analytes of interest in the subcellular compartments of individual neurons. This software is released open-source and freely available with the goal to facilitate applications in neuron screening and profiling.
Assessing the benefits of early pandemic influenza vaccine availability: a case study for Ontario, Canada
Authors: Champredon David , Laskowski Marek , Charland Nathalie , Moghadas Seyed M.
Published: April 2018

New vaccine production technologies can significantly shorten the timelines for availability of a strain-specific vaccine in the event of an influenza pandemic. We sought to evaluate the potential benefits of early vaccination in reducing the clinical attack rate (CAR), taking into account the timing and speed of vaccination roll-out. Various scenarios corresponding to the transmissibility of a pandemic strain and vaccine prioritization strategies were simulated using an agent-based model of disease spread in Ontario, the largest Canadian province. We found that the relative reduction of the CAR reached 60% (90%CI: 44–100%) in a best-case scenario, in which the pandemic strain was moderately transmissible, vaccination started 4 weeks before the first imported case, the vaccine administration rate was 4 times higher than its average for seasonal influenza, and the vaccine efficacy was up to 90%. But the relative reductions in the CAR decreased significantly when the vaccination campaign was delayed or the administration rate reduced. In urban settings with similar characteristics to our population study, early availability and high rates of vaccine administration has the potential to substantially reduce the number of influenza cases. Low rates of vaccine administration or uptake can potentially offset the benefits of early vaccination.
How experience modulates semantic memory for food: evidence from elderly adults and centenarians
Authors: Vignando Miriam , Aiello Marilena , Foroni Francesco , Marcon Gabriella , Tettamanti Mauro , Rumiati Raffaella I.
Published: April 2018

In order to make sense of the objects we encounter in everyday life we largely rely on previous knowledge stored in our semantic memory. Semantic memory is considered dependent on lifelong experience and cultural knowledge. So far, a few studies have investigated the role of expertise on the organization of semantic memory, whereas life-long experience has largely been overlooked. In this study, we investigated this issue using food concepts. In particular, we administered different semantic tasks using food (natural and transformed) and non-food (living and non-living things) as stimuli to participants belonging to three different age cohorts (56–74, 75–91, 100–108), who were also asked to report on the dietary habits held throughout their life. In addition, we investigated to what extent psycholinguistic variables influence the semantic performance of different age cohorts. Results showed that Centenarians recognized natural food better than transformed food, while the other two groups showed the opposite pattern. According to our analyses, experience is responsible for this effect in Centenarians, as their dietary habits seem to suggest. Moreover, significant correlations between picture naming and age of acquisition, familiarity and frequency were observed. This study indicates that lifelong experience can shape conceptual knowledge of food concepts, and that semantic memory is less resilient to aging than initially thought.
Author Correction: Soil biota in vineyards are more influenced by plants and soil quality than by tillage intensity or the surrounding landscape
Authors: Buchholz Jacob , Querner Pascal , Paredes Daniel , Bauer Thomas , Strauss Peter , Guernion Muriel , Scimia Jennifer , Cluzeau Daniel , Burel Françoise , Kratschmer Sophie , Winter Silvia , Potthoff Martin , Zaller Johann G.
Published: April 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Environmental Pollution and Related Hazards at Agbara Industrial Area, Ogun State
Authors: Z. O. Ojekunle , O. O. E. Jinadu , T. A. Afolabi , A. M. Taiwo
Published: April 2018

This study aimed at assessing the environmental pollution and related hazards of industries at Agbara, Ogun State, Nigeria. A total of five sampling points were identified and selected at random. Environmental samples were collected on a weekly basis for duration of 10 weeks. Air pollutants measured were CO2, CO, NO, NOx, VOCs, H2S, SO2, NH3, PM2.5 andPM10 using standard procedure. Dust and plant samples were also collected and analyzed for heavy metals (Pb, Cr, Cd, Cu and Zn) using the Atomic Absorption Spectrophotometer (AAS). Data was evaluated for descriptive and inferential statistics using SPSS for Windows version 22.0. Air pollution data were also subjected to SPE-risk model. The results of highest measured air parameters were: CO (5.50 ± 2.32 ppm), CO2 (3.00 ± 2.05%), NOx (0.90 ± 0.32 ppm), NO (0.60 ± 0.52 ppm), PM10 (0.40 ± 0.52 mg/m3) and PM2.5 (0.20 ± 0.42 mg/m3). The results of heavy metal concentrations in dust samples were: 57.40 ± 13.28 mg/kg for Cu, 45.36 ± 12.37 mg/kg for Cr, 22.80 ± 17.36 mg/kg for Zn, 13.76 ± 3.08 mg/kg for Pb and 0.32 ± 0.36 mg/kg for Cd. Metal concentrations in plants were: Cu (70.07 ± 16.24 mg/kg), Zn (67.69 ± 14.50 mg/kg), Cr (22.46 ± 9.35 mg/kg), Pb (13.76 ± 3.08 mg/kg) and Cd (2.25 ± 3.04 mg/kg). This study revealed the concentrations of CO2, NOx and NO higher than the World Health Organization (WHO) permissible standards while Pb, Cu, Cr, Cd and Zn values in dust samples were also found above the National Environmental Standards and Regulations Enforcement Agency (NESREA) and the WHO standards. Results of SPE-RISK model indicated that CO2, CO, Pb, Cu and Zn posed the greatest health risks, while the Principal Component Analysis (PCA) indentified pollutant sources from industrial and vehicle exhaust.
Adaptive response of neonatal sepsis-derived Group B Streptococcus to bilirubin
Authors: Hansen Richard , Gibson Sophie , De paiva Alves Eduardo , Goddard Mark , MacLaren Andrew , Karcher Anne Marie , Berry Susan , Collie-Duguid Elaina S. R. , El-Omar Emad , Munro Mike , Hold Georgina L.
Published: April 2018

Hyperbilirubinemia is so common in newborns as to be termed physiological. The most common bacteria involved in early-onset neonatal sepsis areStreptococcus agalactiae, commonly called Group BStreptococcus(GBS). Whilst previous studies show bilirubin has antioxidant properties and is beneficial in endotoxic shock, little thought has been given to whether bilirubin might have antibacterial properties. In this study, we performed a transcriptomic and proteomic assessment of GBS cultured in the presence/absence of bilirubin. Our analysis revealed that increasing levels of bilirubin (>100 µmol/L) negatively correlated with GBS growth (18% reduction from 0–400 µmol/L on plate model, p < 0.001; 33% reduction from 0–100 µmol/L in liquid model, p = 0.02). Transcriptome analysis demonstrated 19 differentially expressed genes, almost exclusively up-regulated in the presence of bilirubin. Proteomic analysis identified 12 differentially expressed proteins, half over-expressed in the presence of bilirubin. Functional analysis using Gene Ontology and KEGG pathways18revealed a differential expression of genes involved in transport and carbohydrate metabolism, suggesting bilirubin may impact on substrate utilisation. The data improve our understanding of the mechanisms modulating GBS survival in neonatal hyperbilirubinemia and suggest physiological jaundice may have an evolutionary role in protection against early-onset neonatal sepsis.
Effects of pre-existing orthopoxvirus-specific immunity on the performance of Modified Vaccinia virus Ankara-based influenza vaccines
Authors: Altenburg Arwen F. , van Trierum Stella E. , de Bruin Erwin , de Meulder Dennis , van de Sandt Carolien E. , van der Klis Fiona R. M. , Fouchier Ron A. M. , Koopmans Marion P. G. , Rimmelzwaan Guus F. , de Vries Rory D.
Published: April 2018

The replication-deficient orthopoxvirus modified vaccinia virus Ankara (MVA) is a promising vaccine vector against various pathogens and has an excellent safety record. However, pre-existing vector-specific immunity is frequently suggested to be a drawback of MVA-based vaccines. To address this issue, mice were vaccinated with MVA-based influenza vaccines in the presence or absence of orthopoxvirus-specific immunity. Importantly, protective efficacy of an MVA-based influenza vaccine against a homologous challenge was not impaired in the presence of orthopoxvirus-specific pre-existing immunity. Nonetheless, orthopoxvirus-specific pre-existing immunity reduced the induction of antigen-specific antibodies under specific conditions and completely prevented induction of antigen-specific T cell responses by rMVA-based vaccination. Notably, antibodies induced by vaccinia virus vaccination, both in mice and humans, were not capable of neutralizing MVA. Thus, when using rMVA-based vaccines it is important to consider the main correlate of protection induced by the vaccine, the vaccine dose and the orthopoxvirus immune status of vaccine recipients.
Author Correction: Impact of nanoparticles on the Bacillus subtilis (3610) competence
Authors: Eymard-Vernain Elise , Luche Sylvie , Rabilloud Thierry , Lelong Cécile
Published: April 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.