bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancing photoluminescence yields in lead halide perovskites by photon recycling and light out-coupling
Authors: Richter Johannes M. , Abdi-Jalebi Mojtaba , Sadhanala Aditya , Tabachnyk Maxim , Rivett Jasmine P.H. , Pazos-Outón Luis M. , Gödel Karl C. , Price Michael , Deschler Felix , Friend Richard H.
Published: December 2016

In lead halide perovskite solar cells, there is at least one recycling event of electron–hole pair to photon to electron–hole pair at open circuit under solar illumination. This can lead to a significant reduction in the external photoluminescence yield from the internal yield. Here we show that, for an internal yield of 70%, we measure external yields as low as 15% in planar films, where light out-coupling is inefficient, but observe values as high as 57% in films on textured substrates that enhance out-coupling. We analyse in detail how externally measured rate constants and photoluminescence efficiencies relate to internal recombination processes under photon recycling. For this, we study the photo-excited carrier dynamics and use a rate equation to relate radiative and non-radiative recombination events to measured photoluminescence efficiencies. We conclude that the use of textured active layers has the ability to improve power conversion efficiencies for both LEDs and solar cells.
Ecological networks are more sensitive to plant than to animal extinction under climate change
Authors: Schleuning Matthias , Fründ Jochen , Schweiger Oliver , Welk Erik , Albrecht Jörg , Albrecht Matthias , Beil Marion , Benadi Gita , Blüthgen Nico , Bruelheide Helge , Böhning-Gaese Katrin , Dehling D. Matthias , Dormann Carsten F. , Exeler Nina , Farwig Nina , Harpke Alexander , Hickler Thomas , Kratochwil Anselm , Kuhlmann Michael , Kühn Ingolf , Michez Denis , Mudri-Stojnić Sonja , Plein Michaela , Rasmont Pierre , Schwabe Angelika , Settele Josef , Vujić Ante , Weiner Christiane N. , Wiemers Martin , Hof Christian
Published: December 2016

Impacts of climate change on individual species are increasingly well documented, but we lack understanding of how these effects propagate through ecological communities. Here we combine species distribution models with ecological network analyses to test potential impacts of climate change on >700 plant and animal species in pollination and seed-dispersal networks from central Europe. We discover that animal species that interact with a low diversity of plant species have narrow climatic niches and are most vulnerable to climate change. In contrast, biotic specialization of plants is not related to climatic niche breadth and vulnerability. A simulation model incorporating different scenarios of species coextinction and capacities for partner switches shows that projected plant extinctions under climate change are more likely to trigger animal coextinctions than vice versa. This result demonstrates that impacts of climate change on biodiversity can be amplified via extinction cascades from plants to animals in ecological networks.
Measurement of transverse emittance and coherence of double-gate field emitter array cathodes
Authors: Tsujino Soichiro , Das Kanungo Prat , Monshipouri Mahta , Lee Chiwon , Miller R.J. Dwayne
Published: December 2016

Achieving small transverse beam emittance is important for high brightness cathodes for free electron lasers and electron diffraction and imaging experiments. Double-gate field emitter arrays with on-chip focussing electrode, operating with electrical switching or near infrared laser excitation, have been studied as cathodes that are competitive with photocathodes excited by ultraviolet lasers, but the experimental demonstration of the low emittance has been elusive. Here we demonstrate this for a field emitter array with an optimized double-gate structure by directly measuring the beam characteristics. Further we show the successful application of the double-gate field emitter array to observe the low-energy electron beam diffraction from suspended graphene in minimal setup. The observed low emittance and long coherence length are in good agreement with theory. These results demonstrate that our all-metal double-gate field emitters are highly promising for applications that demand extremely low-electron bunch-phase space volume and large transverse coherence.
Biallelic JAK1 mutations in immunodeficient patient with mycobacterial infection
Authors: Eletto Davide , Burns Siobhan O. , Angulo Ivan , Plagnol Vincent , Gilmour Kimberly C. , Henriquez Frances , Curtis James , Gaspar Miguel , Nowak Karolin , Daza-Cajigal Vanessa , Kumararatne Dinakantha , Doffinger Rainer , Thrasher Adrian J. , Nejentsev Sergey
Published: December 2016

Mutations in genes encoding components of the immune system cause primary immunodeficiencies. Here, we study a patient with recurrent atypical mycobacterial infection and early-onset metastatic bladder carcinoma. Exome sequencing identified two homozygous missense germline mutations, P733L and P832S, in the JAK1 protein that mediates signalling from multiple cytokine receptors. Cells from this patient exhibit reduced JAK1 and STAT phosphorylation following cytokine stimulations, reduced induction of expression of interferon-regulated genes and dysregulated cytokine production; which are indicative of signalling defects in multiple immune response pathways including Interferon-γ production. Reconstitution experiments in the JAK1-deficient cells demonstrate that the impaired JAK1 function is mainly attributable to the effect of the P733L mutation. Further analyses of the mutant protein reveal a phosphorylation-independent role of JAK1 in signal transduction. These findings clarify JAK1 signalling mechanisms and demonstrate a critical function of JAK1 in protection against mycobacterial infection and possibly the immunological surveillance of cancer.
Electronically decoupled stacking fault tetrahedra embedded in Au(111) films
Authors: Schouteden Koen , Amin-Ahmadi Behnam , Li Zhe , Muzychenko Dmitry , Schryvers Dominique , Van Haesendonck Chris
Published: December 2016

Stacking faults are known as defective structures in crystalline materials that typically lower the structural quality of the material. Here, we show that a particular type of defect, that is, stacking fault tetrahedra (SFTs), exhibits pronounced quantized electronic behaviour, revealing a potential synthetic route to decoupled nanoparticles in metal films. We report on the electronic properties of SFTs that exist in Au(111) films, as evidenced by scanning tunnelling microscopy and confirmed by transmission electron microscopy. We find that the SFTs reveal a remarkable decoupling from their metal surroundings, leading to pronounced energy level quantization effects within the SFTs. The electronic behaviour of the SFTs can be described well by the particle-in-a-box model. Our findings demonstrate that controlled preparation of SFTs may offer an alternative way to achieve well-decoupled nanoparticles of high crystalline quality in metal thin films without the need of thin insulating layers.
Shortcut to adiabatic control of soliton matter waves by tunable interaction
Authors: Li Jing , Sun Kun , Chen Xi
Published: December 2016

We propose a method for shortcut to adiabatic control of soliton matter waves in harmonic traps. The tunable interaction controlled by Feshbach resonance is inversely designed to achieve fast and high-fidelity compression of soliton matter waves as compared to the conventional adiabatic compression. These results pave the way to control the nonlinear dynamics for matter waves and optical solitons by using shortcuts to adiabaticity.
Low abundance of Archaeorhizomycetes among fungi in soil metatranscriptomes
Authors: Choma Michal , Bárta Jiří , Šantrůčková Hana , Urich Tim
Published: December 2016

The Archaeorhizomycetes are recently discovered fungi with poorly resolved ecology. Even their abundance in soil fungal communities is currently disputed. Here we applied a PCR-independent, RNA-based metatranscriptomic approach to determine their abundance among fungi in eleven different soils across Europe. Using small subunit (SSU) ribosomal RNA transcripts as marker, we detected Archaeorhizomycetes in 17 out of 28 soil metatranscriptomes. They had average relative SSU rRNA abundance of 2.0% with a maximum of 9.4% among fungal SSU rRNAs. Network analysis revealed that they co-occur with arbuscular mycorrhizal Glomerales, which is in line with their previously suggested association with plant roots. Moreover, Archaeorhizomycetes ranked among the potential keystone taxa. This metatranscriptomic survey exemplifies the usage of non-targeted molecular approaches for the study of soil fungi. It provides PCR- and DNA-independent evidence for the low abundance of Archaeorhizomycetes in soil fungal communities, although they might be non-negligible players despite their low abundance.
Geometrical vortex lattice pinning and melting in YBaCuO submicron bridges
Authors: Papari G. P. , Glatz A. , Carillo F. , Stornaiuolo D. , Massarotti D. , Rouco V. , Longobardi L. , Beltram F. , Vinokur V. M. , Tafuri F.
Published: December 2016

Since the discovery of high-temperature superconductors (HTSs), most efforts of researchers have been focused on the fabrication of superconducting devices capable of immobilizing vortices, hence of operating at enhanced temperatures and magnetic fields. Recent findings that geometric restrictions may induce self-arresting hypervortices recovering the dissipation-free state at high fields and temperatures made superconducting strips a mainstream of superconductivity studies. Here we report on the geometrical melting of the vortex lattice in a wide YBCO submicron bridge preceded by magnetoresistance (MR) oscillations fingerprinting the underlying regular vortex structure. Combined magnetoresistance measurements and numerical simulations unambiguously relate the resistance oscillations to the penetration of vortex rows with intermediate geometrical pinning and uncover the details of geometrical melting. Our findings offer a reliable and reproducible pathway for controlling vortices in geometrically restricted nanodevices and introduce a novel technique of geometrical spectroscopy, inferring detailed information of the structure of the vortex system through a combined use of MR curves and large-scale simulations.
How to Enhance Gas Removal from Porous Electrodes?
Authors: Kadyk Thomas , Bruce David , Eikerling Michael
Published: December 2016

This article presents a structure-based modeling approach to optimize gas evolution at an electrolyte-flooded porous electrode. By providing hydrophobic islands as preferential nucleation sites on the surface of the electrode, it is possible to nucleate and grow bubbles outside of the pore space, facilitating their release into the electrolyte. Bubbles that grow at preferential nucleation sites act as a sink for dissolved gas produced in electrode reactions, effectively suctioning it from the electrolyte-filled pores. According to the model, high oversaturation is necessary to nucleate bubbles inside of the pores. The high oversaturation allows establishing large concentration gradients in the pores that drive a diffusion flux towards the preferential nucleation sites. This diffusion flux keeps the pores bubble-free, avoiding deactivation of the electrochemically active surface area of the electrode as well as mechanical stress that would otherwise lead to catalyst degradation. The transport regime of the dissolved gas, viz. diffusion control vs. transfer control at the liquid-gas interface, determines the bubble growth law.
Electromagnetic Performances Analysis of an Ultra-wideband and Flexible Material Antenna in Microwave Breast Imaging: To Implement A Wearable Medical Bra
Authors: Rahman Ashiqur , Islam Mohammad Tariqul , Singh Mandeep Jit , Kibria Salehin , Akhtaruzzaman Md.
Published: December 2016

In this paper, we report a compact and ultra-wide band antenna on a flexible substrate using the 5-(4-(perfluorohexyl)phenyl)thiophene-2-carbaldehyde compound for microwave imaging. In contrast to other microwave based imaging systems, such as an array of 16 antennas, we proposed a bi-static radar based imaging system consisting of two omnidirectional antennas, which reduces complexity and the overall dimension. The proposed compact antennas are 20 × 14 mm2 and designed for operating at frequencies from 4 to 6 GHz. To allow for implantation into a bra, the electromagnetic performances of the antennas must be considered in bending conditions. In comparison with the recently reported flexible antennas, we demonstrated both electromagnetic performance and imaging reconstruction for bending conditions. For the proof of concept, the electromagnetic performances both at flat and bending conditions have been verified using a homogeneous multilayer model of the human breast phantom. Our results demonstrate that the antenna, even at bending conditions, exhibits an excellent omni-directional radiation pattern with an average efficiency above 70% and average gain above 1 dBi, within the operational frequency band. The comprehensive aim of the realized antenna is to design a biodegradable and wearable antenna-based bra for early breast cancer detection in the future.
Relationship between quantum speed limit time and memory time in a photonic-band-gap environment
Authors: Wang J. , Wu Y. N. , Mo M. L. , Zhang H. Z.
Published: December 2016

Non-Markovian effect is found to be able to decrease the quantum speed limit (QSL) time, and hence to enhance the intrinsic speed of quantum evolution. Although a reservoir with larger degree of non-Markovianity may seem like it should cause smaller QSL times, this seemingly intuitive thinking may not always be true. We illustrate this by investigating the QSL time of a qubit that is coupled to a two-band photonic-band-gap (PBG) environment. We show how the QSL time is influenced by the coherent property of the reservoir and the band-gap width. In particular, we find that the decrease of the QSL time is not attributed to the increasing non-Markovianity, while the memory time of the environment can be seen as an essential reflection to the QSL time. So, the QSL time provides a further insight and sharper identification of memory time in a PBG environment. We also discuss a feasible experimental realization of our prediction.
Drosophila microRNA-34 Impairs Axon Pruning of Mushroom Body γ Neurons by Downregulating the Expression of Ecdysone Receptor
Authors: Lai Yen-Wei , Chu Sao-Yu , Wei Jia-Yi , Cheng Chu-Ya , Li Jian-Chiuan , Chen Po-Lin , Chen Chun-Hong , Yu Hung-Hsiang
Published: December 2016

MicroRNA-34 (miR-34) is crucial for preventing chronic large-scale neurite degeneration in the aged brain of Drosophila melanogaster. Here we investigated the role of miR-34 in two other types of large-scale axon degeneration in Drosophila: axotomy-induced axon degeneration in olfactory sensory neurons (OSNs) and developmentally related axon pruning in mushroom body (MB) neurons. Ectopically overexpressed miR-34 did not inhibit axon degeneration in OSNs following axotomy, whereas ectopically overexpressed miR-34 in differentiated MB neurons impaired γ axon pruning. Intriguingly, the miR-34-induced γ axon pruning defect resulted from downregulating the expression of ecdysone receptor B1 (EcR-B1) in differentiated MB γ neurons. Notably, the separate overexpression of EcR-B1 or a transforming growth factor- β receptor Baboon, whose activation can upregulate the EcR-B1 expression, in MB neurons rescued the miR-34-induced γ axon pruning phenotype. Future investigations of miR-34 targets that regulate the expression of EcR-B1 in MB γ neurons are warranted to elucidate pathways that regulate axon pruning, and to provide insight into mechanisms that control large-scale axon degeneration in the nervous system.
CsMAP34, a teleost MAP with dual role: A promoter of MASP-assisted complement activation and a regulator of immune cell activity
Authors: Li Mo-fei , Li Jun , Sun Li
Published: December 2016

In teleost fish, the immune functions of mannan-binding lectin (MBL) associated protein (MAP) and MBL associated serine protease (MASP) are scarcely investigated. In the present study, we examined the biological properties both MAP (CsMAP34) and MASP (CsMASP1) molecules from tongue sole (Cynoglossus semilaevis). We found that CsMAP34 and CsMASP1 expressions occurred in nine different tissues and were upregulated by bacterial challenge. CsMAP34 protein was detected in blood, especially during bacterial infection. Recombinant CsMAP34 (rCsMAP34) bound C. semilaevis MBL (rCsBML) when the latter was activated by bacteria, while recombinant CsMASP1 (rCsMASP1) bound activated rCsBML only in the presence of rCsMAP34. rCsMAP34 stimulated the hemolytic and bactericidal activities of serum complement, whereas anti-CsMAP34 antibody blocked complement activities. Knockdown of CsMASP1 in C. semilaevis resulted in significant inhibition of complement activities. Furthermore, rCsMAP34 interacted directly with peripheral blood leukocytes (PBL) and enhanced the respiratory burst, acid phosphatase activity, chemotactic activity, and gene expression of PBL. These results indicate for the first time that a teleost MAP acts one hand as a regulator that promotes the lectin pathway of complement activation via its ability to recruit MBL to MASP, and other hand as a modulator of immune cell activity.
Class B β-arrestin2-dependent CCR5 signalosome retention with natural antibodies to CCR5
Authors: Venuti Assunta , Pastori Claudia , Pennisi Rosamaria , Riva Agostino , Sciortino Maria Teresa , Lopalco Lucia
Published: December 2016

CCR5 stimulation with natural ligands, such as RANTES, classically induces short-term internalization with transient activation of β-arrestins and rapidly recycling on the cell surface. Here we discovered that, in T cells, natural CCR5 antibodies induce a CCR5-negative phenotype with the involvement of β-arrestin2, which leads to the formation of a stable CCR5 signalosome with both β-arrestin2 and ERK1. The activation of β-arrestin2 is necessary to CCR5 signaling for the signalosome formation and stabilization. When all stimuli were washed out, β-arrestin1 silencing favors the activity of β-arrestin2 for the CCR5 signalosome retention. Interestingly, CCR5 turn from Class A trafficking pattern, normally used for its internalization with natural modulating molecules (i.e. RANTES), into a long lasting Class B type specifically induced by stimulation with natural anti-CCR5 antibodies. This new CCR5 pathway is relevant not only to study in depth the molecular basis of all pathologies where CCR5 is involved but also to generate new antidody-based therapeutics.
HtrA2 suppresses autoimmune arthritis and regulates activation of STAT3
Authors: Lee Seung Hoon , Moon Young-Mee , Seo Hyeon-Beom , Kim Se-Young , Kim Eun-Kyung , Yi Junyeong , Nam Min-Kyung , Min Jun-Ki , Park Sung-Hwan , Rhim Hyangshuk , Cho Mi-La
Published: December 2016

Rheumatoid arthritis (RA) is an autoimmune disease that is related to the induction of T helper (Th)17 cells, which secrete interleukin-17, and activation of the signal transducer and activator of transcription (STAT) 3. The expression of high-temperature requirement protein A (HtrA) 2, a serine protease involved in apoptosis, was decreased in RA patients nonresponsive to drug treatment of RA. The aim of this study was to determine whether overexpression of HtrA2 has a therapeutic effect on RA. Th17 differentiation, osteoclastogenesis, and lymphocyte activation are increased in motor neuron degeneration (mnd)2 mice, which lack HtrA2 activity because of a missense mutation (Ser276Cys) in the protease domain of HtrA2. The inhibitor of HtrA2 also increased Th17 differentiation. On the other hand, HtrA2 induced cleavage of STAT3 and overexpression of HtrA2 attenuated CIA in a mouse model. HtrA2 overexpression inhibited plaque development as well as the differentiation of Th17 in ApoE−/− mice after immunization with proteoglycans to induce a hyperlipidemia-based RA animal model. The therapeutic function of HtrA2 in inflammatory diseases is linked with Th17 development and the STAT3 pathway in splenocytes. These results suggest that HtrA2 participates in immunomodulatory activity where the upregulation of HtrA2 may shed light on therapeutic approaches to RA and hyperlipidemia.
Everyday bat vocalizations contain information about emitter, addressee, context, and behavior
Authors: Prat Yosef , Taub Mor , Yovel Yossi
Published: December 2016

Animal vocal communication is often diverse and structured. Yet, the information concealed in animal vocalizations remains elusive. Several studies have shown that animal calls convey information about their emitter and the context. Often, these studies focus on specific types of calls, as it is rarely possible to probe an entire vocal repertoire at once. In this study, we continuously monitored Egyptian fruit bats for months, recording audio and video around-the-clock. We analyzed almost 15,000 vocalizations, which accompanied the everyday interactions of the bats, and were all directed toward specific individuals, rather than broadcast. We found that bat vocalizations carry ample information about the identity of the emitter, the context of the call, the behavioral response to the call, and even the call’s addressee. Our results underline the importance of studying the mundane, pairwise, directed, vocal interactions of animals.
Structural Insights on PHA Binding Protein PhaP from Aeromonas hydrophila
Authors: Zhao Hongyu , Wei Hui , Liu Xi , Yao Zhenyu , Xu Manyu , Wei Daixu , Wang Jiawei , Wang Xinquan , Chen Guo-Qiang
Published: December 2016

Phasins or PhaPs are a group of amphiphilic proteins that are found attached to the surface of microbial polyhydroxyalkanoate (PHA) granules. They have both structural and regulatory functions and can affect intracellular PHA accumulation and mediate protein folding. The molecular basis for the diverse functions of the PhaPs has not been fully understood due to the lack of the structural knowledge. Here we report the structural and biochemical studies of the PhaP cloned from Aeromonas hydrophila (PhaPAh), which is utilized in protein and tissue engineering. The crystal structure of PhaPAh was revealed to be a tetramer with 8 α-helices adopting a coiled-coil structure. Each monomer has a hydrophobic and a hydrophilic surface, rendering the surfactant properties of the PhaPAh monomer. Based on the crystal structure, we predicted three key amino acid residues and obtained mutants with enhanced stability and improved emulsification properties. The first PhaP crystal structure, as reported in this study, is an important step towards a mechanistic understanding of how PHA is formed in vivo and why PhaP has such unique surfactant properties. At the same time, it will facilitate the study of other PhaP members that may have significant biotechnological potential as bio-surfactants and amphipathic coatings.
Characterization of dorsal root ganglion neurons cultured on silicon micro-pillar substrates
Authors: Repić Tihana , Madirazza Katarina , Bektur Ezgi , Sapunar Damir
Published: December 2016

Our study focuses on characterization of dorsal root ganglion (DRG) neurons cultured on silicon micro-pillar substrates (MPS) with the ultimate goal of designing micro-electrode arrays (MEAs) for successful electrophysiological recordings of DRG neurons. Adult and neonatal DRG neurons were cultured on MPS and glass coverslips for 7 days in vitro. DRG neuronal distribution and morphometric analysis, including neurite alignment and length, was performed on MPS areas with different pillar width and spacing. We showed that MPS provide an environment for growth of adult and neonatal DRG neurons as permissive as control glass surfaces. Neonatal DRG neurons were present on MPS areas with narrow pillar spacing, while adult neurons preferred wider pillar spacing. Compared to the control glass surfaces the neonatal and adult DRG neurons in regions with narrow pillar spacing range developed a smaller number of longer neurites. In the same area, neurites were preferentially oriented along three directional axes at 30°, 90° and 150°. MPS architecture influenced growth directionality of all main DRG neuronal subtypes. We can conclude that specific micro-pillar substrate topography affects the morphology of DRG neurons. This knowledge can enable development of MEAs with precisely defined physical features for various neuroscience applications.
Common germline variants within the CDKN2A/2B region affect risk of pancreatic neuroendocrine tumors
Authors: Campa Daniele , Capurso Gabriele , Pastore Manuela , Talar-Wojnarowska Renata , Milanetto Anna Caterina , Landoni Luca , Maiello Evaristo , Lawlor Rita T. , Malecka-Panas Ewa , Funel Niccola , Gazouli Maria , De Bonis Antonio , Klüter Harald , Rinzivillo Maria , Delle Fave Gianfranco , Hackert Thilo , Landi Stefano , Bugert Peter , Bambi Franco , Archibugi Livia , Scarpa Aldo , Katzke Verena , Dervenis Christos , Liço Valbona , Furlanello Sara , Strobel Oliver , Tavano Francesca , Basso Daniela , Kaaks Rudolf , Pasquali Claudio , Gentiluomo Manuel , Rizzato Cosmeri , Canzian Federico
Published: December 2016

Pancreatic neuroendocrine tumors (PNETs) are heterogeneous neoplasms which represent only 2% of all pancreatic neoplasms by incidence, but 10% by prevalence. Genetic risk factors could have an important role in the disease aetiology, however only a small number of case control studies have been performed yet. To further our knowledge, we genotyped 13 SNPs belonging to the pleiotropic CDKN2A/B gene region in 320 PNET cases and 4436 controls, the largest study on the disease so far. We observed a statistically significant association between the homozygotes for the minor allele of the rs2518719 SNP and an increased risk of developing PNET (ORhom = 2.08, 95% CI 1.05–4.11, p = 0.035). This SNP is in linkage disequilibrium with another polymorphic variant associated with increased risk of several cancer types. In silico analysis suggested that the SNP could alter the sequence recognized by the Neuron-Restrictive Silencer Factor (NRSF), whose deregulation has been associated with the development of several tumors. The mechanistic link between the allele and the disease has not been completely clarified yet but the epidemiologic evidences that link the DNA region to increased cancer risk are convincing. In conclusion, our results suggest rs2518719 as a pleiotropic CDKN2A variant associated with the risk of developing PNETs.
Impaired Hepatic Adaptation to Chronic Cholestasis induced by Primary Sclerosing Cholangitis
Authors: Milkiewicz Malgorzata , Klak Marta , Kempinska-Podhorodecka Agnieszka , Wiechowska-Kozlowska Anna , Urasinska Elzbieta , Blatkiewicz Malgorzata , Wunsch Ewa , Elias Elwyn , Milkiewicz Piotr
Published: December 2016

Pathogenesis of primary sclerosing cholangitis (PSC) may involve impaired bile acid (BA) homeostasis. We analyzed expressions of factors mediating enterohepatic circulation of BA using ileal and colonic (ascending and sigmoid) biopsies obtained from patients with PSC with and without ulcerative colitis (UC) and explanted PSC livers. Two-fold increase of BA-activated farnesoid X receptor (FXR) protein levels were seen in ascending and sigmoid colon of PSC patients with correspondingly decreased apical sodium-dependent BA transporter (ASBT) gene expression. This was associated with increased OSTβ protein levels in each part of analyzed gut. An intestinal fibroblast growth factor (FGF19) protein expression was significantly enhanced in ascending colon. Despite increased hepatic nuclear receptors (FXR, CAR, SHP), and FGF19, neither CYP7A1 suppression nor CYP3A4 induction were observed. The lack of negative regulation of BA synthesis may be accountable for lower levels of cholesterol observed in PSC in comparison to primary biliary cholangitis (PBC). In conclusion, chronic cholestasis in PSC induces adaptive changes in expression of BA transporters and FXR in the intestine. However hepatic impairment of expected in chronic cholestasis downregulation of CYP7A1 and upregulation of CYP3A4 may promote BA-induced liver injury in PSC.
Gas entrapment and microbial N2O reduction reduce N2O emissions from a biochar-amended sandy clay loam soil
Authors: Harter Johannes , Guzman-Bustamante Ivan , Kuehfuss Stefanie , Ruser Reiner , Well Reinhard , Spott Oliver , Kappler Andreas , Behrens Sebastian
Published: December 2016

Nitrous oxide (N2O) is a potent greenhouse gas that is produced during microbial nitrogen transformation processes such as nitrification and denitrification. Soils represent the largest sources of N2O emissions with nitrogen fertilizer application being the main driver of rising atmospheric N2O concentrations. Soil biochar amendment has been proposed as a promising tool to mitigate N2O emissions from soils. However, the underlying processes that cause N2O emission suppression in biochar-amended soils are still poorly understood. We set up microcosm experiments with fertilized, wet soil in which we used 15N tracing techniques and quantitative polymerase chain reaction (qPCR) to investigate the impact of biochar on mineral and gaseous nitrogen dynamics and denitrification-specific functional marker gene abundance and expression. In accordance with previous studies our results showed that biochar addition can lead to a significant decrease in N2O emissions. Furthermore, we determined significantly higher quantities of soil-entrapped N2O and N2 in biochar microcosms and a biochar-induced increase in typical and atypical nosZ transcript copy numbers. Our findings suggest that biochar-induced N2O emission mitigation is based on the entrapment of N2O in water-saturated pores of the soil matrix and concurrent stimulation of microbial N2O reduction resulting in an overall decrease of the N2O/(N2O + N2) ratio.
Experimental Demonstration of a Highly Efficient Fan-out Polarization Grating
Authors: Wan Chenhao , Chen Jian , Tang Xiahui , Zhan Qiwen
Published: December 2016

Highly efficient fan-out elements are crucial in coherent beam combining architectures especially in coupled laser resonators where the beam passes through the fan-out element twice per round trip. Although the theoretical efficiency is usually less than 86%, the Dammann gratings are ubiquitously utilized in a variety of types of coherent beam combining systems due to the facile design and fabrication. In the current paper, we experimentally demonstrate a highly efficient fan-out polarization grating. It is the first time to our knowledge that all the three space-variant parameters of a polarization grating are simultaneously optimized to achieve the function of multi-beam splitting. Besides the high fan-out efficiency, the ability to control the polarization states of individual split beams is another advantage of this polarization grating. The novel polarization grating is promising to find applications in laser beam combining systems.
Biochemical and structural characterization of a novel halotolerant cellulase from soil metagenome
Authors: Garg Roma , Srivastava Ritika , Brahma Vijaya , Verma Lata , Karthikeyan Subramanian , Sahni Girish
Published: December 2016

Cellulase catalyzes the hydrolysis of β-1,4-linkages of cellulose to produce industrially relevant monomeric subunits. Cellulases find their applications in pulp and paper, laundry, food and feed, textile, brewing industry and in biofuel production. These industries always have great demand for cellulases that can work efficiently even in harsh conditions such as high salt, heat, and acidic environments. While, cellulases with high thermal and acidic stability are already in use, existence of a high halotolerant cellulase is still elusive. Here, we report a novel cellulase Cel5R, obtained from soil metagenome that shows high halotolerance and thermal stability. The biochemical and functional characterization of Cel5R revealed its endoglucanase activity and high halostability. In addition, the crystal structure of Cel5R determined at 2.2 Å resolution reveals a large number of acidic residues on the surface of the protein that contribute to the halophilic nature of this enzyme. Moreover, we demonstrate that the four free and non-conserved cysteine residues (C65, C90, C231 and C273) contributes to the thermal stability of Cel5R by alanine scanning experiments. Thus, the newly identified endoglucanase Cel5R is a promising candidate for various industrial applications.
Strong-field ionization of clusters using two-cycle pulses at 1.8 μm
Authors: Schütte Bernd , Ye Peng , Patchkovskii Serguei , Austin Dane R. , Brahms Christian , Strüber Christian , Witting Tobias , Ivanov Misha Yu. , Tisch John W. G. , Marangos Jon P.
Published: December 2016

The interaction of intense laser pulses with nanoscale particles leads to the production of high-energy electrons, ions, neutral atoms, neutrons and photons. Up to now, investigations have focused on near-infrared to X-ray laser pulses consisting of many optical cycles. Here we study strong-field ionization of rare-gas clusters (103 to 105 atoms) using two-cycle 1.8 μm laser pulses to access a new interaction regime in the limit where the electron dynamics are dominated by the laser field and the cluster atoms do not have time to move significantly. The emission of fast electrons with kinetic energies exceeding 3 keV is observed using laser pulses with a wavelength of 1.8 μm and an intensity of 1 × 1015 W/cm2, whereas only electrons below 500 eV are observed at 800 nm using a similar intensity and pulse duration. Fast electrons are preferentially emitted along the laser polarization direction, showing that they are driven out from the cluster by the laser field. In addition to direct electron emission, an electron rescattering plateau is observed. Scaling to even longer wavelengths is expected to result in a highly directional current of energetic electrons on a few-femtosecond timescale.
Label-free, multi-scale imaging of ex-vivo mouse brain using spatial light interference microscopy
Authors: Min Eunjung , Kandel Mikhail E. , Ko CheMyong J , Popescu Gabriel , Jung Woonggyu , Best-Popescu Catherine
Published: December 2016

Brain connectivity spans over broad spatial scales, from nanometers to centimeters. In order to understand the brain at multi-scale, the neural network in wide-field has been visualized in detail by taking advantage of light microscopy. However, the process of staining or addition of fluorescent tags is commonly required, and the image contrast is insufficient for delineation of cytoarchitecture. To overcome this barrier, we use spatial light interference microscopy to investigate brain structure with high-resolution, sub-nanometer pathlength sensitivity without the use of exogenous contrast agents. Combining wide-field imaging and a mosaic algorithm developed in-house, we show the detailed architecture of cells and myelin, within coronal olfactory bulb and cortical sections, and from sagittal sections of the hippocampus and cerebellum. Our technique is well suited to identify laminar characteristics of fiber tract orientation within white matter, e.g. the corpus callosum. To further improve the macro-scale contrast of anatomical structures, and to better differentiate axons and dendrites from cell bodies, we mapped the tissue in terms of its scattering property. Based on our results, we anticipate that spatial light interference microscopy can potentially provide multiscale and multicontrast perspectives of gross and microscopic brain anatomy.
Global microbial carbonate proliferation after the end-Devonian mass extinction: Mainly controlled by demise of skeletal bioconstructors
Authors: Yao Le , Aretz Markus , Chen Jitao , Webb Gregory E. , Wang Xiangdong
Published: December 2016

Microbial carbonates commonly flourished following mass extinction events. The end-Devonian (Hangenberg) mass extinction event is a first-order mass extinction on the scale of the ‘Big Five’ extinctions. However, to date, it is still unclear whether global microbial carbonate proliferation occurred after the Hangenberg event. The earliest known Carboniferous stromatolites on tidal flats are described from intertidal environments of the lowermost Tournaisian (Qianheishan Formation) in northwestern China. With other early Tournaisian microbe-dominated bioconstructions extensively distributed on shelves, the Qianheishan stromatolites support microbial carbonate proliferation after the Hangenberg extinction. Additional support comes from quantitative analysis of the abundance of microbe-dominated bioconstructions through the Famennian and early Tournaisian, which shows that they were globally distributed (between 40° latitude on both sides of the palaeoequator) and that their abundance increased distinctly in the early Tournaisian compared to the latest Devonian (Strunian). Comparison of variations in the relative abundance of skeleton- versus microbe-dominated bioconstructions across the Hangenberg and ‘Big Five’ extinctions suggests that changes in abundance of skeletal bioconstructors may play a first-order control on microbial carbonate proliferation during extinction transitions but that microbial proliferation is not a general necessary feature after mass extinctions.
Effect of high-flux, low-energy He+ ion irradiation on Ta as a plasma-facing material
Authors: Novakowski T. J. , Tripathi J. K. , Hassanein A.
Published: December 2016

The goal of this work is to assess Ta as a potential plasma-facing material for future fusion reactors in terms of its response to high-flux, low-energy He+ ion irradiation. Ta samples were irradiated with 100 eV He+ ions at various fluences up to 3.5 × 1025 ions m−2 while simultaneously heated at constant temperatures in the range 823–1223 K. SEM studies show that irradiated Ta surfaces undergo significant morphology changes that have a strong dependence on both ion fluence and sample temperature. Optical reflectivity complements SEM and demonstrates a vertical growth of surface structures with increasing fluence. Ex situ XPS and XRD both show significant oxidation of the irradiated Ta surfaces, giving further qualitative information on the extent of surface modification. Overall, these irradiation-induced structures on Ta are similar to early-stage “fuzz” structures observed in W. However, Ta exhibits a higher fluence threshold for structure formation. While Ta may have less desirable bulk properties (e.g., thermal conductivity) when compared to W, its higher resilience to He+ ion-induced surface modification suggests that surface thermal and mechanical properties may not degrade as quickly in extreme fusion environments; this quality may be a redeeming factor for Ta as a plasma-facing material.
Real-time qPCR improves meningitis pathogen detection in invasive bacterial-vaccine preventable disease surveillance in Fiji
Authors: Dunne Eileen M. , Mantanitobua Silivia , Singh Shalini P. , Reyburn Rita , Tuivaga Evelyn , Rafai Eric , Tikoduadua Lisi , Porter Barbara , Satzke Catherine , Strachan Janet E. , Fox Kimberly K. , Jenkins Kylie M. , Jenney Adam , Baro Silo , Mulholland E. Kim , Kama Mike , Russell Fiona M.
Published: December 2016

As part of the World Health Organization Invasive Bacterial-Vaccine Preventable Diseases (IB-VPD) surveillance in Suva, Fiji, cerebrospinal fluid (CSF) samples from suspected meningitis patients of all ages were examined by traditional methods (culture, Gram stain, and latex agglutination for bacterial antigen) and qPCR for Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae. Of 266 samples tested, pathogens were identified in 47 (17.7%). S. pneumoniae was the most common pathogen detected (n = 17) followed by N. meningitidis (n = 13). The use of qPCR significantly increased detection of IB-VPD pathogens (P = 0.0001): of 35 samples that were qPCR positive for S. pneumoniae, N. meningitidis, and H. influenzae, only 10 were culture positive. This was particularly relevant for N. meningitidis, as only 1/13 cases was culture positive. Molecular serotyping by microarray was used to determine pneumococcal serotypes from 9 of 16 (56%) of samples using DNA directly extracted from CSF specimens. Results indicate that qPCR significantly increases detection of S. pneumoniae, N. meningitidis, and H. influenzae in CSF, and that application of molecular diagnostics is a feasible way to enhance local and global surveillance for IB-VPD.
Scaffold Free Bio-orthogonal Assembly of 3-Dimensional Cardiac Tissue via Cell Surface Engineering
Authors: Rogozhnikov Dmitry , O’Brien Paul J. , Elahipanah Sina , Yousaf Muhammad N.
Published: December 2016

There has been tremendous interest in constructing in vitro cardiac tissue for a range of fundamental studies of cardiac development and disease and as a commercial system to evaluate therapeutic drug discovery prioritization and toxicity. Although there has been progress towards studying 2-dimensional cardiac function in vitro, there remain challenging obstacles to generate rapid and efficient scaffold-free 3-dimensional multiple cell type co-culture cardiac tissue models. Herein, we develop a programmed rapid self-assembly strategy to induce specific and stable cell-cell contacts among multiple cell types found in heart tissue to generate 3D tissues through cell-surface engineering based on liposome delivery and fusion to display bio-orthogonal functional groups from cell membranes. We generate, for the first time, a scaffold free and stable self assembled 3 cell line co-culture 3D cardiac tissue model by assembling cardiomyocytes, endothelial cells and cardiac fibroblast cells via a rapid inter-cell click ligation process. We compare and analyze the function of the 3D cardiac tissue chips with 2D co-culture monolayers by assessing cardiac specific markers, electromechanical cell coupling, beating rates and evaluating drug toxicity.
Circulating tumor cell detection in hepatocellular carcinoma based on karyoplasmic ratios using imaging flow cytometry
Authors: Liu Zixin , Guo Weixing , Zhang Dandan , Pang Yanan , Shi Jie , Wan Siqin , Cheng Kai , Wang Jiaqi , Cheng Shuqun
Published: December 2016

Circulating tumor cells (CTCs) originate from tumor tissues and are associated with cancer prognosis. However, existing technologies for CTC detection are limited owing to a lack of specific or accurate biomarkers. Here, we developed a new method for CTC detection based on the karyoplasmic ratio, without biomarkers. Consecutive patients with liver cancer or non-cancer liver diseases were recruited. CTCs in blood samples were analyzed by imaging flow cytometry based on the karyoplasmic ratio as well as EpCAM and CD45. Microvascular invasion (MVI), tumor recurrence, and survival were recorded for all patients. A total of 56.2 ± 23.8/100,000 cells with high karyoplasmic ratios (HKR cells) were detected in cancer patients, which was higher than the number of HKR cells in the non-cancer group (7.6 ± 2.2/100,000). There was also a difference in HKR cells between liver cancer patients with and without MVI. Based on a receiver operating characteristic curve analysis, the threshold was 21.8 HKR cells per 100,000 peripheral blood mononuclear cells, and the area under the curve was higher than those of traditional methods (e.g., CD45 and EpCAM staining). These results indicate that the new CTC detection method was more sensitive and reliable than existing methods. Accordingly, it may improve clinical CTC detection.
Genetic architecture differences between pediatric and adult-onset inflammatory bowel diseases in the Polish population
Authors: Ostrowski Jerzy , Paziewska Agnieszka , Lazowska Izabella , Ambrozkiewicz Filip , Goryca Krzysztof , Kulecka Maria , Rawa Tomasz , Karczmarski Jakub , Dabrowska Michalina , Zeber-Lubecka Natalia , Tomecki Roman , Kluska Anna , Balabas Aneta , Piatkowska Magdalena , Paczkowska Katarzyna , Kierkus Jaroslaw , Socha Piotr , Lodyga Michal , Rydzewska Grazyna , Klopocka Maria , Mierzwa Grazyna , Iwanczak Barbara , Krzesiek Elzbieta , Bak-Drabik Katarzyna , Walkowiak Jaroslaw , Klincewicz Beata , Radwan Piotr , Grzybowska-Chlebowczyk Urszula , Landowski Piotr , Jankowska Agnieszka , Korczowski Bartosz , Starzynska Teresa , Albrecht Piotr , Mikula Michal
Published: December 2016

Most inflammatory bowel diseases (IBDs) are classic complex disorders represented by common alleles. Here we aimed to define the genetic architecture of pediatric and adult-onset IBDs for the Polish population. A total of 1495 patients were recruited, including 761 patients with Crohn’s disease (CD; 424 pediatric), 734 patients with ulcerative colitis (UC; 390 pediatric), and 934 healthy controls. Allelotyping employed a pooled-DNA genome-wide association study (GWAS) and was validated by individual genotyping. Whole exome sequencing (WES) was performed on 44 IBD patients diagnosed before 6 years of age, 45 patients diagnosed after 40 years of age, and 18 healthy controls. Altogether, out of 88 selected SNPs, 31 SNPs were replicated for association with IBD. A novel BRD2 (rs1049526) association reached significance of P = 5.2 × 10−11 and odds ratio (OR) = 2.43. Twenty SNPs were shared between pediatric and adult patients; 1 and 7 were unique to adult-onset and pediatric-onset IBD, respectively. WES identified numerous rare and potentially deleterious variants in IBD-associated or innate immunity-associated genes. Deleterious alleles in both groups were over-represented among rare variants in affected children. Our GWAS revealed differences in the polygenic architecture of pediatric- and adult-onset IBD. A significant accumulation of rare and deleterious variants in affected children suggests a contribution by yet unexplained genetic components.
The presence of Anf/Hesx1 homeobox gene in lampreys suggests that it could play an important role in emergence of telencephalon
Authors: Bayramov Andrey V. , Ermakova Galina V. , Eroshkin Fedor M. , Kucheryavyy Alexandr V. , Martynova Natalia Y. , Zaraisky Andrey G.
Published: December 2016

Accumulated evidence indicates that the core genetic mechanisms regulating early patterning of the brain rudiment in vertebrates are very similar to those operating during development of the anterior region of invertebrate embryos. However, the mechanisms underlying the morphological differences between the elaborate vertebrate brain and its simpler invertebrate counterpart remain poorly understood. Recently, we hypothesized that the emergence of the most anterior unit of the vertebrate brain, the telencephalon, could be related to the appearance in vertebrates’ ancestors of a unique homeobox gene, Anf/Hesx1(further Anf), which is absent from all invertebrates and regulates the earliest steps of telencephalon development in vertebrates. However, the failure of Anf to be detected in one of the most basal extant vertebrate species, the lamprey, seriously compromises this hypothesis. Here, we report the cloning of Anf in three lamprey species and demonstrate that this gene is indeed expressed in embryos in the same pattern as in other vertebrates and executes the same functions by inhibiting the expression of the anterior general regulator Otx2 in favour of the telencephalic regulator FoxG1. These results are consistent with the hypothesis that the Anf homeobox gene may have been important in the evolution of the telencephalon.
A review of analytical techniques for quantifying microplastics in sediments
Authors: Hanvey Joanne S. , Lewis Phoebe J. , Lavers Jennifer L. , Crosbie Nicholas D. , Pozo Karla , Clarke Bradley O.
Published: December 2016

In this review the analytical techniques for measuring microplastics in sediment have been evaluated.
A three-way junction structure-based isothermal exponential amplification strategy for sensitive detection of 3′-terminal 2′-O-methylated plant microRNA
Authors: Wang Xiangdong , Wang Hui , Liu Chenghui , Wang Honghong , Li Zhengping
Published: December 2016

A versatile and general 3WJ-EXPAR strategy is developed for the sensitive detection of 3′-terminal 2′-O-methylated plant microRNAs.
Cooperative Lewis acid–onium salt catalysis as tool for the desymmetrization of meso-epoxides
Authors: Broghammer Florian , Brodbeck Daniel , Junge Thorsten , Peters René
Published: December 2016

A new concept for epoxide desymmetrizations using bifunctional Lewis acid/ammonium salt catalysts is presented for bromohydrin ester formation.