bluuebunny/crossref_metadata_2025 huggingface dataset:
The prostate cancer immunome: In silico functional analysis of antigenic proteins from microarray profiling with IgG
Authors: Luna‐Coronell Johana A. , Vierlinger Klemens , Gamperl Magdalena , Hofbauer Johann , Berger Ingrid , Weinhäusel Andreas
Published: March 2016

The study of the immunome of prostate cancer (PCa) and characterization of autoantibody signature from differentially reactive antigens can uncover disease stage proteins, reveal enriched networks and even expose aberrant cellular mechanisms during the disease process. By conducting plasma IgG profiling on protein microarrays presenting 5449 unique human proteins expressed in 15 417 E. coli human cDNA expression clones, we elucidated 471 (21 higher reactive in PCa) differentially reactive antigens in 50 PCa versus 49 patients with benign prostate hyperplasia (BPH) at initial diagnosis. Functional analyzes show that the immune‐profile of PCa compared to BPH control samples is significantly enriched in features targeting Cellular assembly, Cell death and pathways involved in Cell cycle, translation, and assembly of proteins as EIF2 signaling, PCa related genes as AXIN1 and TP53, and ribosomal proteins (e.g. RPS10). An overlap of 61 (out of 471) DIRAGs with the published 1545 antigens from the SEREX database has been found, however those were higher reactive in BPH. Clinical relevance is shown when antibody‐reactivities against eight proteins were significantly (p < 0.001) correlated with Gleason‐score. Herewith we provide a biological and pathophysiological characterization of the immunological layer of cancerous (PCa) versus benign (BPH) disease, derived from antibody profiling on protein microarrays.
Microfluidic Synthesis of Size‐Controlled and Morphologically Homogeneous Lead Trinitroresorcinate Produced by Segmented Flow
Authors: Zhou Nan , Zhu Peng , Rong Yi , Xia Huanming , Shen Ruiqi , Ye Yinghua , Lv Shenglin
Published: March 2016

Size‐controlled and morphologically homogeneous lead trinitroresorcinate (LTNR) particles were synthesized in aqueous solutions using segmented flow. The experimental setup consisted of syringe pumps connected with silicone tubing to a segmented flow microfluidic platform made of polymethyl methacrylate (PMMA) containing silicone‐based microchannels immersed in a thermostatted bath. As a starting point for the optimization of the experimental conditions, LTNR particles were first synthesized through conventional batch synthesis. The optimized batch conditions were adapted to segmented flow arrangements. Characterization studies on LTNR formed through batch and segmented flow methods were carried out, and it was found that in the latter LTNR particles exhibited superior particle morphology and narrower particle size distribution. In addition, the heat release of LTNR prepared by segmented flow increased by 353.52 J g−1 in comparison to that formed through batch synthesis. Finally, it was found demonstrated that segmented flow methods result in a 13 % increase in yield for the synthesis of LTNR. This study demonstrated the feasibility of synthesising primary explosives using a segmented flow microfluidic platform.
Soft Theorems from String Theory
Authors: Di Vecchia Paolo , Marotta Raffaele , Mojaza Matin
Published: March 2016

Soft behaviour of closed string amplitudes involving dilatons, gravitons and anti‐symmetric tensors, is studied in the framework of bosonic string theory. The leading double soft limit of gluons is analysed as well, starting from scattering amplitudes computed in the open bosonic string. Field theory expressions are then obtained by sending the string tension to infinity. The presented results have been derived in the papers of Ref [1].
Deforming D‐brane models on orbifolds
Authors: Koltermann Isabel , Blaszczyk Michael , Honecker Gabriele
Published: March 2016

We review the stabilisation of complex structure moduli in Type IIA orientifolds, especially on with discrete torsion, via deformations of orbifold singularities. While D6‐branes in SO(2N) and USp(2N) models always preserve supersymmetry and thus give rise to flat directions, in an exemplary Pati‐Salam model with only U(N) gauge groups ten out of the 15 deformation moduli can be stabilised at the orbifold point.
Challenges in advanced characterization techniques for high Voc thin‐film tandem solar cells
Authors: Ventosinos Federico , Fakes Boulos , Johnson Erik V.
Published: March 2016

In this work we focus on two techniques developed to extract the individual open circuit voltages (Voc) of tandem devices, as well as their sub‐cell current–voltage (I–V) characteristics. These were developed to work on the micromorph cell, the subcells of which have only a limited region of overlapping photoresponse due to the very different band gaps of its constituent cells, which allows for selective illumination. However, it is not known if such techniques will work in tandem structures consisting of high Voc structures (compared to the micromorph device), such as combinations of hydrogenated amorphous silicon oxide (a‐SiO:H), polymorphous silicon (pm‐Si:H), and amorphous silicon (a‐Si:H) in a‐SiO:H/pmSi:H a‐Si:H/pm‐Si:H device stacks. These novel structures have proven to suffer from less light induced degradation (LID), which is one of the main drawbacks of devices using a‐Si:H. The presence of similar band gaps (difference of less than 150 mV in both cases) and overlapping external quantum efficiencies (EQEs) above 500 nm implies that some of the hypotheses used may not be valid for high Voc devices. In this work we show the difficulties that arise when using these characterization techniques in such devices.
One–pot synthesis of ethyl‐3‐aryl‐2‐(1H‐tetrazol‐5‐yl)acrylates and 3‐(1H‐tetrazol‐5‐yl)coumarins via tandem [2+3] dipolar cycloaddition reaction‐Knoevenagel condensation
Authors: Jafari Chermahini Zahra , Najafi Chermahini Alireza , Dabbagh Hossein A. , Teimouri Abbas
Published: March 2016

A simple, one‐pot, three‐component, two‐step tandem method has been developed for the synthesis of ethyl‐3‐aryl‐2‐(1H‐tetrazol‐5‐yl)acrylates that may have biologically importance from ethyl cyanoacetate, sodium azide and a series of aromatic aldehydes with different substituents. Reactions were performed using ammonium chloride as the catalyst and dimethylformamide as the solvent. The results indicated that electron withdrawing groups in the phenyl ring leads to comparatively more yield. When we used the salicylaldehyde precursors, the corresponding coumarin derivatives containing tetrazole group were formed in good yields. All the synthesized compounds were fully characterized by 1H, 13C NMR, FT‐IR and mass spectroscopic techniques and elemental analysis. The obtained results rationalized by proposing a suitable mechanism. Efficient and simple reaction conditions, easy isolation process and very good yields are the advantages of this strategy for the synthesis of tetrazole compounds.
Furanolabdanoid–based 1,2,4‐oxadiazoles: Synthesis and cytotoxic activity
Authors: Mironov Maxim E. , Pokrovsky Mikhail A. , Kharitonov Yurii V. , Shakirov Makhmut M. , Pokrovsky Andrey G. , Shults Elvira E.
Published: March 2016

Several 15,16‐epoxy‐8,13,14‐labdatriene derivatives modified at the C‐16 position with a 1,2,4‐oxadiazole ring with various substituent in the 5‐th position, were obtained via multistep synthesis from 16‐formyl derivatives of natural diterpenoid lambertianic acid. The cytotoxicity of furanolabdanoid‐based 1,2,4‐oxadiazoles was evaluated against human cancer cells (CEM‐13, MT‐4, U‐937, MCF‐7, MDA‐MB‐231, MEL‐8) using the conventional MTT assays. All the tested diterpenoid‐oxadiazole hybrids displayed better cytotoxic activity then lambertianic acid. The activity and selectivity to the cell line increased even further in the compounds containing a chloromethyl substituent in the 5‐th position of the 1,2,4‐oxadiazole ring. Two of the synthesized compounds exhibited high cytotoxic activity against lymphoblastoid cell line CEM‐13 (GI50 0.08‐0.34 μM), which was higher that than of the comparative drug Doxorubicin. The antitumor mechanism may be related to apoptosis induction in U‐937, MCF‐7, and CEM‐13 cells.
Preterm delivery and elevated maternal total vascular resistance: signs of suboptimal cardiovascular adaptation to pregnancy?
Authors: Valensise H. , Farsetti D. , Lo Presti D. , Pisani I. , Tiralongo G. M. , Gagliardi G. , Vasapollo B. , Novelli G. P.
Published: March 2016

Objective

To evaluate the maternal hemodynamic profile in women with a diagnosis of threatened preterm delivery (TPD) in order to understand the possible pathophysiologic mechanism leading to an increased lifetime risk for future cardiovascular disease.

Methods

Patients with a diagnosis of TPD were enrolled and assessed using a non‐invasive method (USCOM®) for the determination of hemodynamic parameters. Vaginal and rectal swabs were taken, cervical length, blood inflammatory indices, fetal blood‐vessel Doppler velocimetry were measured and gestational age at the time of delivery and neonatal outcomes were noted.

Results

A total of 68 patients were enrolled and included in the analysis. The population was divided into two groups according to total vascular resistance (TVR): Group A with a TVR of ≤ 1000 dynes × s/cm5 (n = 48) and Group B with a TVR of > 1000 dynes × s/cm5 (n = 20). C‐reactive protein (CRP) was higher in Group B than in Group A, suggesting a systemic inflammation status. Group B delivered earlier (32 + 4 weeks vs 38 + 2 weeks; P < 0.01) and neonatal outcome was worse than in Group A. Significantly lower values of cardiac output, stroke volume, peak velocity of flow, velocity time integral, minute distance, stroke volume index, cardiac index, stroke work, cardiac power, inotropy index and potential‐to‐kinetic energy ratio were observed in Group B than in Group A.

Conclusions

Women with a diagnosis of TPD showing TVR values of > 1000 dynes × s/cm5 and elevated levels of CRP are at high risk of preterm delivery. An impaired maternal cardiovascular adaptation during pregnancy in these patients might suggest a possible higher risk for subsequent future cardiovascular disease. Copyright © 2016 ISUOG. Published by John Wiley & Sons Ltd.
Anion Directed Self‐Assembly of One‐Dimensional and Two‐Dimensional Coordination Polymers Containing Bridging Diphosphine Ligands
Authors: Shawkataly Omar Bin , Sani Nur Fatiha Amat , Rosli Mohd. M. , Razali Mohd. R.
Published: March 2016

The reactions of 1,2‐bis(diphenylphosphanyl)ethane (dppe) with different silver(I) salts facilitated the formation of 1D and 2D coordination polymers, [Ag(dppe)(OAc)]n·nH2O (1) and [Ag2(dppe)1.5(NO3)2]n (2), respectively. The complexes were characterized by elemental analysis, ATR‐IR spectroscopy, 1H NMR, 13C NMR, and 31P NMR spectroscopy, and single‐crystal X‐ray diffraction. Structural analysis revealed that complex 1 exhibits a 1D infinite wavy structure, in which each silver(I) ion is bridged by dppe ligands. Structure 2 has a 2D topologically promising architecture that displays a 6.6.6 graphitic net, which corresponds to hnd topology. The nitrate ions and dppe ligands are in a μ2 bridging mode and support the formation of this net. Moreover, significant π–π interactions between the phenyl rings in the apertures of (6,3) grid stabilized complex 2.
Low Levels of Vitamin D have a Deleterious Effect on the Articular Cartilage in a Rat Model
Authors: Pascual-Garrido Cecilia , Angeline Michael E. , Ma Richard , Chahla Jorge , Voigt Cliff , Deng Xiang Hua , Nguyen Joseph , Warren Russell F. , Rodeo Scott A.
Published: March 2016

Background

Vitamin D appears to play an important role in bone and cartilage metabolism since its receptors are widely found in human articular chondrocytes. Thus, effects of variation of vitamin D may directly impact cartilage and bone biology.

Questions/Purposes

The aims of this study are to compare (1) articular cartilage structure and composition and (2) trabecular and cortical bone microstructure in rats with normal versus insufficient vitamin D levels.

Methods

Twenty-five mature, male Sprague-Dawley rats were allocated to two groups: (1) control arm (vitamin D replete—12 rats) and (2) an experimental arm (vitamin D deficient—13 rats). Vitamin D deficiency was induced using a vitamin D-deficient diet and UV light restriction. Rats were sacrificed after 4 weeks vitamin D deficiency was confirmed. The right knee was harvested for analysis of both the medial (MFC) and lateral femoral condyles (LFC). A region of interest was established on both condyles to correlate subchondral bone architecture and the overlying cartilage. Histological analysis was performed and graded using the modified Mankin score. Subchondral and cortical bony architecture was evaluated with micro-CT.

Results

After 4 weeks, the vitamin D-deficient group had statistically significant changes in cartilage structure in both the MFC and LFC [1.55 ± 0.6 vs. 4.23 ± 4.1 ( p = 0.035) and 1.55 ± 0.6 vs. 3.53 ± 2.4 ( p = 0.009), respectively]. Micro-CT analysis revealed no correlation between subchondral bone values and the overlying cartilage Mankin score ( p = 0.460). No significant difference was evident between the subchondral bone of the control and study group.

Conclusions

Low levels of vitamin D have a deleterious effect on the cartilage. Given the high prevalence of vitamin D deficiency in the general population, these findings raise important questions about the potential role of vitamin D in articular cartilage health.
Summative peer marking?
Authors: O’Neill Lotte , Morcke Anne Mette
Published: March 2016

None
Alternative splicing and nonsense‐mediated mRNA decay enforce neural specific gene expression
Authors: Zheng Sika
Published: March 2016

Alternative pre‐mRNA splicing is a fundamental regulatory process for most mammalian multi‐exon genes to increase proteome diversity. Nonsense‐mediated mRNA decay (NMD) is a conserved mRNA surveillance mechanism to mitigate deleterious effects caused by gene mutations or transcriptional errors. Coupling alternative splicing and NMD (AS‐NMD), in which alternative splicing switches between translational and NMD isoforms, results in fine‐tuning overall gene expression to, in turn, expand the functional activities of these two post‐transcriptional regulatory processes. AS‐NMD is known for maintaining homeostatic expression of many RNA‐binding proteins. We further show that AS‐NMD is a conserved mechanism among mammals to induce developmental expression of the synaptic scaffold protein PSD‐95. Comparing gene sequences between human Psd‐95 and its ancestral orthologues indicates that AS‐NMD regulation of mammalian Psd‐95 is a product of selective pressure and that it enforces neural‐specific expression of PSD‐95 proteins in mammals. Invertebrate homolog of Psd‐95 is not subjected to AS‐NMD regulation and its protein product does not exhibit neural‐specific expression. Given the prevalence of alternative splicing regulation in the mammalian nervous system, neural‐specific expression of many other genes could be controlled by AS‐NMD in a similar manner. We discuss the implication of these discoveries, as well as the challenges in generalizing the regulation and functional activity of AS‐NMD.
Bureaucratic Benefit-Cost Analysis and Policy Controversy
Authors: Scott Ryan P. , Scott Tyler A. , Zerbe Richard
Published: March 2016

Critiques of benefit-cost analysis (BCA) are usually made on theoretical or methodological grounds; however, understanding how BCA is actually used in decision-making processes is critical if BCA is to inform policy-making. Our paper examines how the implementation of BCA within policy decision-making processes can serve to increase, rather than alleviate, controversy. This runs contrary to the standard assumption that BCA improves decision-making by providing objective data that serves as a basis for policy consensus. To frame this issue, we engage the literature on the role of science in policy decisions and the role of bureaucrats in understanding and implementing policy research. We introduce the concept of “Bureaucratic BCA” as a framework for the practical application of BCA; Bureaucratic BCA does not refer to BCA specifically conducted by bureaucrats or a lesser, technically inferior version of BCA, but rather acknowledges that BCA plays an interactive role within bureaucratic decision-making processes rather than simply serving as a sterilized information input. We show how the dynamics of BCA within the policy process can make BCA a source of controversy and waste rather than an aid to policy efficiency. In light of the Bureaucratic BCA framework, we provide recommendations as to how BCA can be implemented more productively.
‘Mr Smith Goes To Brussels’: Third Country Lobbying and the Making of EU Law and Policy
Authors: KORKEA-AHO Emilia
Published: March 2016

The EU’s openness towards stakeholders is central to the legitimacy of its law-making. With the rapid globalisation of EU legislative activities, openness towards actors from third countries requires analysis. With reference to the notion of ‘lobbying’, this article outlines a framework for identifying the role of third country actors in EU policy processes. The two arguments brought forward suggest that third country lobbying is facilitated by the openness of Union law- and policy-making, and that third country actors contribute to EU decision-making at all stages. The article concludes with a set of questions that third country lobbying raises concerning the EU’s legitimate law-making authority in Europe and beyond.
Settling of heated particles in homogeneous turbulence
Authors: Frankel Ari , Pouransari H. , Coletti F. , Mani A.
Published: March 2016

We study the case of inertial particles heated by thermal radiation while settling by gravity through a turbulent transparent gas. We consider dilute and optically thin regimes in which each particle receives the same heat flux. Numerical simulations of forced homogeneous turbulence are performed taking into account the two-way coupling of both momentum and temperature between the dispersed and continuous phases. Particles much smaller than the smallest flow scales are considered and the point-particle approximation is adopted. The particle Stokes number (based on the Kolmogorov time scale) is of order unity, while the nominal settling velocity is up to an order of magnitude larger than the Kolmogorov velocity, marking a critical difference with previous two-way coupled simulations. It is found that non-heated particles enhance turbulence when their settling velocity is sufficiently high compared to the Kolmogorov velocity. Energy spectra show that the non-heated particle settling impacts both the very small and very large flow scales, while the intermediate scales are weakly affected. When heated, particles shed plumes of buoyant gas, further modifying the turbulence structure. At the considered radiation intensities, clustering is strong but the classic mechanism of preferential concentration is modified, while preferential sweeping is eliminated or even reversed. Particle heating also causes a significant reduction of the mean settling velocity, which is caused by rising buoyant plumes in the vicinity of particle clusters. The turbulent kinetic energy is affected non-monotonically as the radiation intensity is increased due to the competing effects of the downward gravitational force and the upward buoyancy force. The thermal radiation influences all scales of the turbulence. The effects of settling and buoyancy on the turbulence anisotropy are also discussed.
The Rhetoric of Sincerity: Cicero and Smith on Propriety and Political Context
Authors: KAPUST DANIEL J. , SCHWARZE MICHELLE A.
Published: March 2016

The study of rhetoric has recently undergone a revival in political theory as a response to deliberative democratic approaches that value reason over affect in the political sphere. Most rhetorical revivalists look to Aristotle and develop accounts of ethos (character) that privilege the epistemic dimensions of trust, while overlooking the importance that considerations of propriety play in shaping the political speech of democratic leaders. We reconsider the rhetorical approach by integrating the regulative standards suggested by two political thinkers who also were theorists of rhetoric: Cicero and Adam Smith. Committed to character's role in collective judgment, Cicero and Smith both hold that sincerity and context shape decorum or propriety: Leaders rely on decorum to shape their rhetorical appeals, and audiences look to the fit between speech and character to gauge moral trustworthiness. Smith, however, goes beyond Cicero to develop a rhetorical theory more relevant for democracies by highlighting the importance of political context for rhetorical appeals and evaluations. We conclude by suggesting that attention to these components of decorum moves beyond Aristotelian accounts of rhetorical character in a way that is consistent with much empirical research on how voters judge the character of elected officials.
GENERAL STABILITY OF THE EXPONENTIAL AND LOBAČEVSKIǏ FUNCTIONAL EQUATIONS
Authors: CHUNG JAEYOUNG
Published: March 2016

Let $S$ be a semigroup possibly with no identity and $f:S\rightarrow \mathbb{C}$. We consider the general superstability of the exponential functional equation with a perturbation $\unicode[STIX]{x1D713}$ of mixed variables $$\begin{eqnarray}\displaystyle |f(x+y)-f(x)f(y)|\leq \unicode[STIX]{x1D713}(x,y)\quad \text{for all }x,y\in S. & & \displaystyle \nonumber\end{eqnarray}$$ In particular, if $S$ is a uniquely $2$-divisible semigroup with an identity, we obtain the general superstability of Lobačevskiǐ’s functional equation with perturbation $\unicode[STIX]{x1D713}$$$\begin{eqnarray}\displaystyle \biggl|f\biggl(\frac{x+y}{2}\biggr)^{2}-f(x)f(y)\biggr|\leq \unicode[STIX]{x1D713}(x,y)\quad \text{for all }x,y\in S. & & \displaystyle \nonumber\end{eqnarray}$$
The International Congress of Orientalists
Authors: Shaw Stanford J.
Published: March 2016

The XXVII International Congress of Orientalists was held at the University of Michigan, Ann Arbor, Michigan, from August 13 through August 19, 1967. This was the first time the Congress was held in the United States or, for that matter, in the Western Hemisphere. Before the Congress convened, fears were expressed that the distance of Ann Arbor from the East Coast of the United States, and that of the United States from the older centers of Oriental studies, would appreciably reduce attendance. In fact, however, more than 2500 scholars attended, a considerable increase over the previous Congress, demonstrating the tremendous development of Oriental studies in the United States during the previous two decades, and also the effectiveness of the Organizing Committee’s effort to assist the transportation of foreign scholars by means of subsidized airplane flights from Tokyo as well as principal centers in Europe.
Clinical significance of psychotic experiences in the context of sleep disturbance or substance use
Authors: DeVylder J. E. , Kelleher I.
Published: March 2016

Background

Psychotic experiences (PE) are commonly reported in the general population, where they are associated with elevated clinical need and functional impairment. Research studies typically exclude PE that occur in the context of sleep or substance use (PE-SS), based on the assumption that they are normative within these contexts. This is the first study to formally test clinical and functional outcomes associated with PE that occur in the context of sleep or substance use.

Method

Data from the Collaborative Psychiatric Epidemiology Surveys (n = 11 776) were used to assess the associations between both PE and PE-SS and a broad range of outcomes, including psychiatric co-morbidity, suicidal behavior, mental health treatment utilization and World Health Organization (WHO) domains of function, using logistic regression analyses. Lifetime PE and PE-SS were mutually exclusive categories, assessed using the WHO Composite International Diagnostic Interview psychosis screen.

Results

PE were associated with all 10 clinical and functional outcomes. Similarly, respondents reporting PE-SS had greater clinical need and impaired function relative to controls, which was significant for seven of the 10 outcome variables. When directly compared, the PE and PE-SS groups differed only in their associations with role function (greater impairment for PE) and self-care (greater impairment for PE-SS).

Conclusions

PE-SS were associated with a broad range of clinical and functional outcomes in this large general population sample. These associations were similar to those found for PE. Future studies should investigate relative differences between sleep- and substance-induced PE.
SUPERFICIAL FIBRES OF GENERIC PROJECTIONS
Authors: Ran Ziv
Published: March 2016

We consider a general fibre of given length in a generic projection of a variety. Under the assumption that the fibre is of local embedding dimension 2 or less, an assumption which can be checked in many cases, we prove that the fibre is reduced and its image on the projected variety is an ordinary multiple point.
Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters
Authors: Gülay Arda , Musovic Sanin , Albrechtsen Hans-Jørgen , Al-Soud Waleed Abu , Sørensen Søren J , Smets Barth F
Published: March 2016

Here, we document microbial communities in rapid gravity filtration units, specifically serial rapid sand filters (RSFs), termed prefilters (PFs) and after- filters (AFs), fed with anoxic groundwaters low in organic carbon to prepare potable waters. A comprehensive 16S rRNA-based amplicon sequencing survey revealed a core RSF microbiome comprising few bacterial taxa (29–30 genera) dominated by Nitrospirae, Proteobacteria and Acidobacteria, with a strikingly high abundance (75–87±18%) across five examined waterworks in Denmark. Lineages within the Nitrospira genus consistently comprised the second most and most abundant fraction in PFs (27±23%) and AFs (45.2±23%), respectively, and were far more abundant than typical proteobacterial ammonium-oxidizing bacteria, suggesting a physiology beyond nitrite oxidation for Nitrospira. Within the core taxa, sequences closely related to types with ability to oxidize ammonium, nitrite, iron, manganese and methane as primary growth substrate were identified and dominated in both PFs (73.6±6%) and AFs (61.4±21%), suggesting their functional importance. Surprisingly, operational taxonomic unit richness correlated strongly and positively with sampling location in the drinking water treatment plant (from PFs to AFs), and a weaker negative correlation held for evenness. Significant spatial heterogeneity in microbial community composition was detected in both PFs and AFs, and was higher in the AFs. This is the first comprehensive documentation of microbial community diversity in RSFs treating oligotrophic groundwaters. We have identified patterns of local spatial heterogeneity and dispersal, documented surprising energy–diversity relationships, observed a large and diverse Nitrospira fraction and established a core RSF microbiome.
Beyond the Black Queen Hypothesis
Authors: Mas Alix , Jamshidi Shahrad , Lagadeuc Yvan , Eveillard Damien , Vandenkoornhuyse Philippe
Published: March 2016

The Black Queen Hypothesis, recently proposed to explain an evolution of dependency based on gene loss, is gaining ground. This paper focuses on how the evolution of dependency transforms interactions and the community. Using agent-based modeling we suggest that species specializing in the consumption of a common good escape competition and therefore favor coexistence. This evolutionary trajectory could open the way for novel long-lasting interactions and a need to revisit the classically accepted assembly rules. Such evolutionary events also reshape the structure and dynamics of communities, depending on the spatial heterogeneity of the common good production. Let Black be the new black!
Biofilm plasmids with a rhamnose operon are widely distributed determinants of the ‘swim-or-stick’ lifestyle in roseobacters
Authors: Michael Victoria , Frank Oliver , Bartling Pascal , Scheuner Carmen , Göker Markus , Brinkmann Henner , Petersen Jörn
Published: March 2016

Alphaproteobacteria of the metabolically versatile Roseobacter group (Rhodobacteraceae) are abundant in marine ecosystems and represent dominant primary colonizers of submerged surfaces. Motility and attachment are the prerequisite for the characteristic ‘swim-or-stick’ lifestyle of many representatives such as Phaeobacter inhibens DSM 17395. It has recently been shown that plasmid curing of its 65-kb RepA-I-type replicon with >20 genes for exopolysaccharide biosynthesis including a rhamnose operon results in nearly complete loss of motility and biofilm formation. The current study is based on the assumption that homologous biofilm plasmids are widely distributed. We analyzed 33 roseobacters that represent the phylogenetic diversity of this lineage and documented attachment as well as swimming motility for 60% of the strains. All strong biofilm formers were also motile, which is in agreement with the proposed mechanism of surface attachment. We established transposon mutants for the four genes of the rhamnose operon from P. inhibens and proved its crucial role in biofilm formation. In the Roseobacter group, two-thirds of the predicted biofilm plasmids represent the RepA-I type and their physiological role was experimentally validated via plasmid curing for four additional strains. Horizontal transfer of these replicons was documented by a comparison of the RepA-I phylogeny with the species tree. A gene content analysis of 35 RepA-I plasmids revealed a core set of genes, including the rhamnose operon and a specific ABC transporter for polysaccharide export. Taken together, our data show that RepA-I-type biofilm plasmids are essential for the sessile mode of life in the majority of cultivated roseobacters.
Local diversity of heathland Cercozoa explored by in-depth sequencing
Authors: Harder Christoffer Bugge , Rønn Regin , Brejnrod Asker , Bass David , Al-Soud Waleed Abu , Ekelund Flemming
Published: March 2016

Cercozoa are abundant free-living soil protozoa and quantitatively important in soil food webs; yet, targeted high-throughput sequencing (HTS) has not yet been applied to this group. Here we describe the development of a targeted assay to explore Cercozoa using HTS, and we apply this assay to measure Cercozoan community response to drought in a Danish climate manipulation experiment (two sites exposed to artificial drought, two unexposed). Based on a comparison of the hypervariable regions of the 18S ribosomal DNA of 193 named Cercozoa, we concluded that the V4 region is the most suitable for group-specific diversity analysis. We then designed a set of highly specific primers (encompassing ~270 bp) for 454 sequencing. The primers captured all major cercozoan groups; and >95% of the obtained sequences were from Cercozoa. From 443 350 high-quality short reads (>300 bp), we recovered 1585 operational taxonomic units defined by >95% V4 sequence similarity. Taxonomic annotation by phylogeny enabled us to assign >95% of our reads to order level and ~85% to genus level despite the presence of a large, hitherto unknown diversity. Over 40% of the annotated sequences were assigned to Glissomonad genera, whereas the most common individually named genus was the euglyphid Trinema. Cercozoan diversity was largely resilient to drought, although we observed a community composition shift towards fewer testate amoebae.
Stratified coastal ocean interactions with tropical cyclones
Authors: Glenn S. M. , Miles T. N. , Seroka G. N. , Xu Y. , Forney R. K. , Yu F. , Roarty H. , Schofield O. , Kohut J.
Published: March 2016

Hurricane-intensity forecast improvements currently lag the progress achieved for hurricane tracks. Integrated ocean observations and simulations during hurricane Irene (2011) reveal that the wind-forced two-layer circulation of the stratified coastal ocean, and resultant shear-induced mixing, led to significant and rapid ahead-of-eye-centre cooling (at least 6 °C and up to 11 °C) over a wide swath of the continental shelf. Atmospheric simulations establish this cooling as the missing contribution required to reproduce Irene’s accelerated intensity reduction. Historical buoys from 1985 to 2015 show that ahead-of-eye-centre cooling occurred beneath all 11 tropical cyclones that traversed the Mid-Atlantic Bight continental shelf during stratified summer conditions. A Yellow Sea buoy similarly revealed significant and rapid ahead-of-eye-centre cooling during Typhoon Muifa (2011). These findings establish that including realistic coastal baroclinic processes in forecasts of storm intensity and impacts will be increasingly critical to mid-latitude population centres as sea levels rise and tropical cyclone maximum intensities migrate poleward.
Structural basis of allosteric and synergistic activation of AMPK by furan-2-phosphonic derivative C2 binding
Authors: Langendorf Christopher G. , Ngoei Kevin R. W. , Scott John W. , Ling Naomi X. Y. , Issa Sam M. A. , Gorman Michael A. , Parker Michael W. , Sakamoto Kei , Oakhill Jonathan S. , Kemp Bruce E.
Published: March 2016

The metabolic stress-sensing enzyme AMP-activated protein kinase (AMPK) is responsible for regulating metabolism in response to energy supply and demand. Drugs that activate AMPK may be useful in the treatment of metabolic diseases including type 2 diabetes. We have determined the crystal structure of AMPK in complex with its activator 5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid (C2), revealing two C2-binding sites in the γ-subunit distinct from nucleotide sites. C2 acts synergistically with the drug A769662 to activate AMPK α1-containing complexes independent of upstream kinases. Our results show that dual drug therapies could be effective AMPK-targeting strategies to treat metabolic diseases.
Simulating the Kibble-Zurek mechanism of the Ising model with a superconducting qubit system
Authors: Gong Ming , Wen Xueda , Sun Guozhu , Zhang Dan-Wei , Lan Dong , Zhou Yu , Fan Yunyi , Liu Yuhao , Tan Xinsheng , Yu Haifeng , Yu Yang , Zhu Shi-Liang , Han Siyuan , Wu Peiheng
Published: March 2016

The Kibble-Zurek mechanism (KZM) predicts the density of topological defects produced in the dynamical processes of phase transitions in systems ranging from cosmology to condensed matter and quantum materials. The similarity between KZM and the Landau-Zener transition (LZT), which is a standard tool to describe the dynamics of some non-equilibrium physics in contemporary physics, is being extensively exploited. Here we demonstrate the equivalence between KZM in the Ising model and LZT in a superconducting qubit system. We develop a time-resolved approach to study quantum dynamics of LZT with nano-second resolution. By using this technique, we simulate the key features of KZM in the Ising model with LZT, e.g., the boundary between the adiabatic and impulse regions, the freeze-out phenomenon in the impulse region, especially, the scaling law of the excited state population as the square root of the quenching speed. Our results provide the experimental evidence of the close connection between KZM and LZT, two textbook paradigms to study the dynamics of the non-equilibrium phenomena.
Herbivory in the soft coral Sinularia flexibilis (Alcyoniidae)
Authors: Piccinetti Chiara C. , Ricci Roberta , Pennesi Chiara , Radaelli Giuseppe , Totti Cecilia , Norici Alessandra , Giordano Mario , Olivotto Ike
Published: March 2016

Our work provides strong support for the hypothesis that Sinularia flexibilis ingests diatoms such as Thalassiosira pseudonana. We assessed algal ingestion by S. flexibilis through estimates of algal removal, histological analyses, scanning electron microscopy observations and gene expression determination (18S and silicon transporter 1) by real time PCR. Cell counts are strongly suggestive of algal removal by the coral; light and scanning microscopy provide qualitative evidence for the ingestion of T. pseudonana by S. flexibilis, while molecular markers did not prove to be sufficiently selective/specific to give clear results. We thus propose that previous instances of inability of corals to ingest algae are reconsidered using different technical approach, before concluding that coral herbivory is not a general feature.
Metal-Diazo Radicals of α-Carbonyl Diazomethanes
Authors: Li Feifei , Xiao Longqiang , Liu Lijian
Published: March 2016

Metal-diazo radicals of α-carbonyl diazomethanes are new members of the radical family and are precursors to metal-carbene radicals. Herein, using electron paramagnetic resonance spectroscopy with spin-trapping, we detect diazo radicals of α-carbonyl diazomethanes, induced by [RhICl(cod)]2, [CoII(por)] and PdCl2, at room temperature. The unique quintet signal of the Rh-diazo radical was observed in measurements of α-carbonyl diazomethane adducts of [RhICl(cod)]2 in the presence of 5,5-dimethyl-pyrroline-1-N-oxide (DMPO). DFT calculations indicated that 97.2% of spin density is localized on the diazo moiety. Co- and Pd-diazo radicals are EPR silent but were captured by DMPO to form spin adducts of DMPO-N∙ (triplet-of-sextets signal). The spin-trapping also provides a powerful tool for detection of metal-carbene radicals, as evidenced by the DMPO-trapped carbene radicals (DMPO-C∙, sextet signal) and 2-methyl-2-nitrosopropane-carbene adducts (MNP-C∙, doublet-of-triplets signal). The transformation of α-carbonyl diazomethanes to metal-carbene radicals was confirmed to be a two-step process via metal-diazo radicals.
Characterization of organic matter of plants from lakes by thermal analysis in a N2 atmosphere
Authors: Guo Fei , Wu Fengchang , Mu Yunsong , Hu Yan , Zhao Xiaoli , Meng Wei , Giesy John P. , Lin Ying
Published: March 2016

Organic matter (OM) has been characterized using thermal analysis in O2 atmospheres, but it is not clear if OM can be characterized using slow thermal degradation in N2 atmospheres (STDN). This article presents a new method to estimate the behavior of OM in anaerobic environment. Seventeen different plants from Tai Lake (Ch: Taihu), China were heated to 600 °C at a rate of 10 °C min−1 in a N2 atmosphere and characterized by use of differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA). DSC chromatograms were compared with 9 standard compounds. Seven peaks were observed in DSC chromatograms, 2 main peaks strongly correlated with biochemical indices and one main peak was a transitional stage. Energy absorbed by a peak at approximately 200 °C and total organic carbon were well correlated, while energy absorbed at approximately 460 °C was negatively correlated with lignin content. Presence of peaks at approximately 350 and 420 °C varied among plant biomass sources, providing potential evidence for biomass identification. Methods of STDN reported here were rapid and accurate ways to quantitatively characterize OM, which may provide useful information for understanding anaerobic behaviors of natural organic matters.
Experimental Investigation of Temperature-Dependent Gilbert Damping in Permalloy Thin Films
Authors: Zhao Yuelei , Song Qi , Yang See-Hun , Su Tang , Yuan Wei , Parkin Stuart S. P. , Shi Jing , Han Wei
Published: March 2016

The Gilbert damping of ferromagnetic materials is arguably the most important but least understood phenomenological parameter that dictates real-time magnetization dynamics. Understanding the physical origin of the Gilbert damping is highly relevant to developing future fast switching spintronics devices such as magnetic sensors and magnetic random access memory. Here, we report an experimental study of temperature-dependent Gilbert damping in permalloy (Py) thin films of varying thicknesses by ferromagnetic resonance. From the thickness dependence, two independent contributions to the Gilbert damping are identified, namely bulk damping and surface damping. Of particular interest, bulk damping decreases monotonically as the temperature decreases, while surface damping shows an enhancement peak at the temperature of ~50 K. These results provide an important insight to the physical origin of the Gilbert damping in ultrathin magnetic films.
Direct Visualization of the Two-step Nucleation Model by Fluorescence Color Changes during Evaporative Crystallization from Solution
Authors: Ito Fuyuki , Suzuki Yukino , Fujimori Jun-ichi , Sagawa Takehiro , Hara Mitsuo , Seki Takahiro , Yasukuni Ryohei , Chapelle Marc Lamy de la
Published: March 2016

The two-step nucleation model for crystal nuclei formation explains several experimental and theoretical results better than the classical nucleation theory. We report here direct visualization of the two-step nucleation model for organic molecular crystallization. Evaporative crystallization from a solution of a dibenzoylmethane boron complex that displays mechanofluorochromism, a fluorescence color change induced by mechanical perturbation, was probed by fluorescence change. The dependence of fluorescence change on dispersion concentration of the complex in a polymer matrix was also investigated. We detected transitional emission from the amorphous cluster state prior to crystallization. This is the first demonstration of the two-step nucleation model based on fluorescence color changes.
Photomodulation of fluoride ion binding through anion-π interactions using a photoswitchable azobenzene system
Authors: Rananaware Anushri , Samanta Mousumi , Bhosale Rajesh S. , Kobaisi Mohammad Al , Roy Biswajit , Bheemireddy Varun , Bhosale Sidhanath V. , Bandyopadhyay Subhajit , Bhosale Sheshanath V.
Published: March 2016

The discovery of photoswitchable azobenzene-systems that undergo trans-to-cis photoisomerisation was a milestone in supramolecular chemistry. Such photoswitches have possible applications in data storage, stimuli responsive delivery systems and molecular machines due to fast and selective switching. However, the light induced cis isomer of azobenzene is rather unstable and reverts thermally and photochemically to the thermodynamically stable trans configuration. We report, for the first time, controlled photoswitching of an azo-naphthalenediimide (azo-NDI) which can be achieved upon binding of fluoride ions through anion-π interaction. This NDI-F–NDI “sandwich” stabilises the cis configuration through the generation of an NDI•− radical anion and a dianionic, NDI2− species that becomes unusually stable in the cis form. The sandwiched cis form reverts to the trans form only upon decomplexation of F−. A model pollutant was successfully degraded using the photogenerated NDI-F–NDI sandwich. This opens a wide range of applications in molecular and supramolecular nanotechnology.
Castration influences intestinal microflora and induces abdominal obesity in high-fat diet-fed mice
Authors: Harada Naoki , Hanaoka Ryo , Horiuchi Hiroko , Kitakaze Tomoya , Mitani Takakazu , Inui Hiroshi , Yamaji Ryoichi
Published: March 2016

Late-onset hypogonadism (i.e. androgen deficiency) raises the risk for abdominal obesity in men. The mechanism for this obesity is unclear. Here, we demonstrated that hypogonadism after castration caused abdominal obesity in high-fat diet (HFD)-fed, but not in standard diet (SD)-fed, C57BL/6J mice. Furthermore, the phenotype was not induced in mice treated with antibiotics that disrupt the intestinal microflora. In HFD-fed mice, castration increased feed efficiency and decreased fecal weight per food intake. Castration also induced in an increase of visceral fat mass only in the absence of antibiotics in HFD-fed mice, whereas subcutaneous fat mass was increased by castration irrespective of antibiotics. Castration reduced the expression in the mesenteric fat of both adipose triglyceride lipase and hormone-sensitive lipase in HFD-fed mice, which was not observed in the presence of antibiotics. Castration decreased thigh muscle (i.e. quadriceps and hamstrings) mass, elevated fasting blood glucose levels and increased liver triglyceride levels in a HFD-dependent manner, whereas these changes were not observed in castrated mice treated with antibiotics. The Firmicutes/Bacteroidetes ratio and Lactobacillus species increased in the feces of HFD-fed castrated mice. These results show that androgen (e.g. testosterone) deficiency can alter the intestinal microbiome and induce abdominal obesity in a diet-dependent manner.
Catalytic activity and thermal stability of horseradish peroxidase encapsulated in self-assembled organic nanotubes
Authors: Lu Qin , Kim Youngchan , Bassim Nabil , Raman Nisha , Collins Greg E.
Published: March 2016

The confined nanospace of organic nanotubes protects enzymes against thermal denaturation and preserves catalytic activity following prolonged elevated temperature exposure.
An unprecedented benzannulation of oxindoles with enalcarbenoids: a regioselective approach to functionalized carbazoles
Authors: Rathore Kuldeep Singh , Lad Bapurao Sudam , Chennamsetti Haribabu , Katukojvala Sreenivas
Published: March 2016

An unusual rhodium-catalyzed tandem reaction of oxindoles with diazoenals involving the cleavage of sp2 C–O and sp2 C–C bonds resulted in the formation of 1-hydroxy-2-acylcarbazoles.
Mechanical phenotyping of primary human skeletal stem cells in heterogeneous populations by real-time deformability cytometry
Authors: Xavier Miguel , Rosendahl Philipp , Herbig Maik , Kräter Martin , Spencer Daniel , Bornhäuser Martin , Oreffo Richard O. C. , Morgan Hywel , Guck Jochen , Otto Oliver
Published: March 2016

Mechanical measurements of skeletal stem cells using RT-DC reveal a distinct sub-population within the human bone marrow.
Advanced removal of toluene in aerosol by adsorption and photocatalytic degradation of silver-doped TiO2/PU under visible light irradiation
Authors: Pham Thanh-Dong , Lee Byeong-Kyu , Pham-Cong De
Published: March 2016

We synthesized a novel Ag–TiO2/PU material for the effective removal of gaseous toluene by both adsorption and photocatalytic degradation.
A novel functional group difference-based selective etching strategy for the synthesis of hollow organic silica nanospheres
Authors: Zeng Fanlong , Chen Lianxi , Li Jie , Ye Xinshan , Yu Huogen , Liu Zhenhui
Published: March 2016

CTES@TCPTES were synthesized by CTES and TCPTES, and then TC-HSNSs could be fabricated with the basic etching agent based on stability difference between core and shell.
Chemistry and biology of microsomal prostaglandin E2 synthase-1 (mPGES-1) inhibitors as novel anti-inflammatory agents: recent developments and current status
Authors: Khurana Puneet , Jachak Sanjay M.
Published: March 2016

Prostaglandin (PG) E2, a key mediator of inflammatory pain and fever, is biosynthesized from PGH2 by mPGES-1.
Atomistic investigation into the mechanical behaviour of crystalline and amorphous TiO2 nanotubes
Authors: Xu Yanan , Wang Mingchao , Hu Ning , Bell John , Yan Cheng
Published: March 2016

The mechanical properties of titanium dioxide (TiO2) nanotubes are studied based on molecular dynamics simulations.
An electrochemical biosensing platform based on 1-formylpyrene functionalized reduced graphene oxide for sensitive determination of phenol
Authors: Hua Zulin , Qin Qin , Bai Xue , Huang Xin , Zhang Qi
Published: March 2016

A novel electrochemical biosensing platform is proposed. New tyrosinase-based biosensor can be used to detect phenols.
Ultrafast breathing humidity sensing properties of low-dimensional Fe-doped SnO2flower-like spheres
Authors: Zhen Yuhua , Sun Fu-Hua , Zhang Min , Jia Kaili , Li Linling , Xue Qingzhong
Published: March 2016

It is demonstrated that the low-dimensional Fe-doped SnO2flower-like spheres with enhanced breathing sensing property are synthesized by a simple template- and surfactant-free hydrothermal method.
Unraveling innate substrate control in site-selective palladium-catalyzed C–H heterocycle functionalization
Authors: Choi Hwanho , Min Minsik , Peng Qian , Kang Dahye , Paton Robert S. , Hong Sungwoo
Published: March 2016

Pd(ii)-catalyzed direct arylation of chromones and enaminones gives divergent site-selectivities. Computational and experimental studies reveal a switch in mechanism, from a C3-selective CMD mechanism to a C2-selective carbopalladation pathway. This model accounts for the opposite selectivities of enaminone and chromone, and also correctly predicts selectivities for the C–H functionalization of heteroaromatic substrates as a function of the coupling partner.