bluuebunny/crossref_metadata_2025 huggingface dataset:
EPR of synthetic diamond heavily doped with phosphorus
Authors: Nadolinny Vladimir , Komarovskikh Andrey , Palyanov Yuri , Sokol Alexander
Published: July 2015

In this work, diamond synthesized under high‐pressure high‐temperature (HPHT) conditions in the phosphorus‐carbon system with addition of aluminum has been studied by electron paramagnetic resonance (EPR). It is established that microcrystals with different defect concentrations are formed. Nitrogen‐phosphorus defects NP3 are observed in some microcrystals, although pure phosphorus paramagnetic centers NP8 and NP9 are detected in other microcrystals. The NP8 center has an electron spin S = 1/2, gxx = gyy = 2.0016, gzz = 2.0048, and hyperfine structure (HFS) of one phosphorus atom Axx = Ayy = 3.2 mT, Azz = 5.6 mT. The NP9 center has an electron spin S = 1/2, gxx = gyy = 2.0038, gzz = 2.0030, and HFS of two inequivalent phosphorus atoms A(P1)xx = A(P1)yy = 8.8 mT, A(P1)zz = 13.6 mT, A(P2)xx = A(P2)yy = 2.2 mT, A(P2)zz = 1.4 mT. The structures of the NP8 and NP9 centers are discussed. Concentration of phosphorus impurity in some microcrystals is high enough to detect conductivity electrons. Subsequent annealing of the samples at 2273 K leads to the disappearance of the NP3, NP8, and NP9 spectra; the NP4 spectrum is observed.
Transperitoneal robotic resection of benign primary retroperitoneal tumors: can it be widely used?
Authors: Zhang Tian , Wang Xinjing , Zhao Liangchao , Liu Fei , Chen Hao , Deng Xiaxing , Peng Chenghong , Shen Baiyong
Published: July 2015

Background

This article was aimed to show the safety, flexibility and other advantages of transperitoneal robot‐assisted resection of benign primary retroperitoneal tumors.

Methods

Ten patients underwent robotic surgeries, and 31 underwent laparotomy surgeries from 2012 to 2014. The perioperative data, including tumor size, operation time, and other parameters were analyzed.

Results

The tumor sizes of the two groups were not different (robotic group vs laparotomy group: 5.47 vs 5.32 cm, respectively; P = 0.777). The differences in the blood loss (robotic group vs laparotomy group: 80.00 vs. 146.08 mL, respectively; P = 0.021), time of oral intake (robotic group vs laparotomy group: 2.12 vs. 3.42 d, respectively; P = 0.045) and post‐operation hospital stay (robotic group vs laparotomy group: 5.40 vs. 8.77 d, respectively; P = 0.004) were statistically significant and lower in the robotic group.

Conclusion

Robot‐assisted resection of benign retroperitoneal tumors is flexible and safe and provides better protection when complex lesions are removed. Copyright © 2015 John Wiley & Sons, Ltd.
Identity‐based signcryption from lattices
Authors: Yan Jianhua , Wang Licheng , Dong Mianxiong , Yang Yixian , Yao Wenbin
Published: July 2015

Signcryption as a cryptographic primitive can carry out signature and encryption simultaneously at a remarkably reduced cost. Identity‐based cryptography is more convenient than public key infrastructure‐based cryptography in certificate management. As a result, identity‐based signcryption has been studied extensively, and many efficient and provably secure constructions have been proposed. However, most of these schemes are based on intractability assumptions from number theory, and these assumptions have been threatened by the booming quantum computation. Therefore, a recent trend in cryptography is to construct cryptosystems that are based on lattice‐based intractability assumptions because of their plausible features of quantum attack resistance. In this paper, several identity‐based signcryption schemes from lattice hardness assumptions are proposed. In the standard model, these schemes are indistinguishable against inner adaptively chosen ciphertext attacks (IND‐CCA2) and strongly unforgeable against inner chosen message attacks. In our construction, it does not matter whether the original encryption scheme used to construct signcryption is deterministic or probabilistic; the resulted signcryption schemes can reach IND‐CCA2 security. To achieve this, we carefully combine three techniques—the identity‐based encryption from lattice due to Agrawal–Boneh–Boyen (EUROCRYPT 2010), the framework of lattice‐based short signature due to Boyen (Public Key Cryptography 2010), and the Canetti–Halevi–Katz (abbr. CHK) technique, with necessary and tailored optimization—for transforming an (ℓ + 1)‐level indistinguishable under chosen plaintext attack secure hierarchical identity‐based encryption (HIBE) into an ℓ level IND‐CCA2 secure HIBE scheme. In addition, our security proof also contains a more efficient simulation tool that might have separate interest in cryptographic applications. Copyright © 2015 John Wiley & Sons, Ltd.
K‐anonymity against neighborhood attacks in weighted social networks
Authors: Liu Chuan‐Gang , Liu I‐Hsien , Yao Wun‐Sheng , Li Jung‐Shian
Published: July 2015

Nowadays, with the advance of Internet technology, social network is getting popular, which combines the virtual network and the real world. People employ this network to communicate with all social things of their interest, including shopping, making friends, sharing experiences of life, and so on. In social networks, the social data expands rapidly and the malicious users can easily get the social data. With the social information, they could conjecture the relationship among social network data via the systematical analysis tool. Hence, the personal privacy data in social network may be exposed to some unknown risks, and recently, these issues arising in such a network catch much attention. The protection of personal privacy social data becomes an important and urgent research in social networks. One of personal privacy social information is the relations between the individuals and their social groups, namely human relationships.

Neighborhood attacks are incident to the exposure of human relationships. Previous studies try to conceal human relationships information with well‐known k‐anonymity protection to resist this attack in social networks. However, those researches do not take care of those attacks in weighted social network, which does not make sense due to the fact that people should have different relationships with different persons. In such weighted social network, the edge denotes the human relationship and the weight denotes the degree of this human relationship in social networks. Our study focuses on the k‐anonymity protection scheme in weighted social networks, and our scheme can achieve k‐anonymity protection under the expected conditions, less virtual edges added and fewer weights changed. Through the analysis with MATLAB tool, we show that our k‐anonymity algorithm can achieve high anonymity protection rate under various k‐anonymity policies. Copyright © 2015 John Wiley & Sons, Ltd.
Lightweight security against combined IE and SSDF attacks in cooperative spectrum sensing for cognitive radio networks
Authors: Sucasas Victor , Althunibat Saud , Radwan Ayman , Marques Hugo , Rodriguez Jonathan , Vahid Seiamak , Tafazolli Rahim , Granelli Fabrizio
Published: July 2015

Cognitive radio is envisaged as a promising solution to cope with the problem of spectrum scarcity. In cognitive radio networks, users can sense the medium and opportunistically use available frequency bands. Users can cooperate in order to increase the reliability of the sensing process, which is called cooperative spectrum sensing (CSS). However, cooperative paradigms are threatened by the behavior of malicious users. Two types of attacks represent the main threats for CSS network operation, namely, spectrum sensing data falsification (SSDF) and incumbent emulation (IE). These two types of attacks have received a considerable amount of attention in the literature, but they have always been studied separately. In this paper, we propose a novel mechanism based on lightweight cryptography that considers both SSDF and IE attacks combined in a CSS network for the first time. Lightweight cryptography, in contrast to previous techniques used (such as intrusion detection or reputation systems), provides higher resilience to such attacks when a high number of mobile malicious users exist, providing better energy efficiency. Analytical and simulation results show the outperformance of the proposed algorithm compared with previous mechanisms, in terms of lower false alarm probability (i.e., higher chance of using the free frequency bands) and hence better energy ratings. Copyright © 2015 John Wiley & Sons, Ltd.
Estimating fixed‐end rotations of reinforced concrete members at yielding and ultimate
Authors: Mergos Panagiotis E. , Kappos Andreas J.
Published: July 2015

Strain penetration of the longitudinal reinforcement in reinforced concrete (RC) members at the joints and/or footings results in fixed‐end rotations at the member ends. Several experimental studies have shown that fixed‐end rotations caused by strain penetration contribute significantly (up to 50 %) to the total displacement capacity of RC members. Hence, accurate determination of these fixed‐end rotations at yielding and ultimate limit states is of primary importance when defining the structural response of RC members. The purpose of this study is to present the theoretical background to and the assumptions made for the most common relationships found in the literature for determining strain penetration‐induced fixed‐end rotations at yielding and ultimate. Furthermore, new simple relationships are proposed on the basis of realistic and mechanically based assumptions. Comparisons between the existing and proposed relationships demonstrate the limitations of the former. Finally, the proposed relationships are calibrated against experimental measurements of RC column specimens subjected to cyclic loading with recorded fixed‐end rotations due to strain penetration in the adjacent joints and/or footings.
Vibrational Raman Shifts and Aromaticity: The Case of Oligothiophenes
Authors: Casado Juan , Hernández Víctor , López Navarrete Juan T.
Published: July 2015

A general description of the use of the Raman spectra of polyconjugated molecules to infer their electronic and molecular properties and how these change in a number of situations is illustrated with several examples, with particular emphasis on oligothiophene molecules. The most noticeable features of the Raman spectra of these molecules and the main theoretical models developed for their understanding have been revised and explained in terms related to π‐electron delocalization intimately connected with the aromatic and quinoidal characters.
Successful pregnancy by vitrified–warmed embryo transfer for a woman with Kallmann syndrome
Authors: Shimoda Misato , Iwayama Hiroshi , Ishiyama Mai , Nakatani Ayano , Yamashita Masanori
Published: July 2015

Purpose

Kallmann syndrome is a genetic disorder characterized by hypogonadotropic hypogonadism and anosmia. We report the case of a 31‐year‐old woman with Kallmann syndrome who successfully gave birth after intracytoplasmic sperm injection (ICSI) and vitrified–warmed embryo transfer, despite relatively ineffective ovarian stimulation.

Method

A 30 year‐old woman with primary amenorrhea wished to achieve pregnancy. Diagnostic testing results were consistent with Kallmann syndrome. Follicular stimulation was started with human menopausal gonadotropin (hMG; 150 IU/day). After 28 days of treatment, 4 follicles were observed (total hMG; 4200 IU), with a dominant follicle diameter of 23 mm. Ovum pick‐up was performed and 2 oocytes, one at metaphase II (MII) and one at the germinal vesicle stage, were obtained. Piezo‐ICSI was performed on the MII oocyte and an 8‐cell stage embryo was cryopreserved on day 3. Subsequently, embryo transfer was performed after endometrial preparation.

Result

A gestational sac and embryo heart activity were confirmed by ultrasonographic monitoring, and a healthy male infant weighing 3246 g was delivered by Caesarean section after 41 weeks 3 days of gestation.

Conclusion

This is the first report of a healthy delivery after vitrified–warmed embryo transfer for a woman with Kallmann syndrome. Our experience suggests that ICSI and vitrified–warmed embryo transfer are effective for women with Kallmann syndrome.
Human Mpn1 promotes post‐transcriptional processing and stability of U6atac
Authors: Shchepachev Vadim , Wischnewski Harry , Soneson Charlotte , Arnold Andreas W. , Azzalin Claus M.
Published: July 2015

Mpn1 is an exoribonuclease that modifies the spliceosomal small nuclear RNA (snRNA) U6 by trimming its oligouridine tail and introducing a cyclic phosphate group (>p). Mpn1 deficiency induces U6 3′ end misprocessing, accelerated U6 decay and pre‐mRNA splicing defects. Mutations in the human MPN1 gene are associated with the genodermatosis Clericuzio‐type poikiloderma with neutropenia (PN). Here we present the deep sequencing of the >p‐containing transcriptomes of mpn1Δ fission yeast and PN cells. While in yeast U6 seems to be the only substrate of Mpn1, human Mpn1 also processes U6atac snRNA. PN cells bear unstable U6atac species with aberrantly long and oligoadenylated 3′ ends. Our data corroborate the link between Mpn1 and snRNA stability suggesting that PN could derive from pre‐mRNA splicing aberrations.
Assessment of cardiometabolic risk in children in population studies: underpinning developmental origins of health and disease mother–offspring cohort studies
Authors: Huang R.-C. , Prescott Susan L. , Godfrey Keith M. , Davis Elizabeth A.
Published: July 2015

Pregnancy and birth cohorts have been utilised extensively to investigate the developmental origins of health and disease, particularly in relation to understanding the aetiology of obesity and related cardiometabolic disorders. Birth and pregnancy cohorts have been utilised extensively to investigate this area of research. The aim of the present review was twofold: first to outline the necessity of measuring cardiometabolic risk in children; and second to outline how it can be assessed. The major outcomes thought to have an important developmental component are CVD, insulin resistance and related metabolic outcomes. Conditions such as the metabolic syndrome, type 2 diabetes and CHD all tend to have peak prevalence in middle-aged and older individuals but assessments of cardiometabolic risk in childhood and adolescence are important to define early causal factors and characterise preventive measures. Typically, researchers investigating prospective cohort studies have relied on the thesis that cardiovascular risk factors, such as dyslipidaemia, hypertension and obesity, track from childhood into adult life. The present review summarises some of the evidence that these factors, when measured in childhood, may be of value in assessing the risk of adult cardiometabolic disease, and as such proceeds to describe some of the methods for assessing cardiometabolic risk in children.
Recommended intakes of vitamin D to optimise health, associated circulating 25-hydroxyvitamin D concentrations, and dosing regimens to treat deficiency: workshop report and overview of current literature
Authors: Balvers Michiel G. J. , Brouwer-Brolsma Elske M. , Endenburg Silvia , de Groot Lisette C. P. G. M. , Kok Frans J. , Gunnewiek Jacqueline Klein
Published: July 2015

Vitamin D is a fat-soluble hormone that traditionally has been linked to bone health. Recently, its involvement has been extended to other (extra-skeletal) disease areas, such as cancer, CVD, energy metabolism and autoimmune diseases. Vitamin D deficiency is a worldwide problem, and several recommendation-setting bodies have published guidelines for adequate vitamin D intake and status. However, recommendations from, for example, the Health Council of the Netherlands do not provide advice on how to treat vitamin D deficiency, a condition that is often encountered in the clinic. In addition, these recommendations provide guidelines for the maintenance of ‘minimum levels’, and do not advise on ‘optimum levels’ of vitamin D intake/status to further improve health. The NutriProfiel project, a collaboration between the Gelderse Vallei Hospital (Ede, the Netherlands) and the Division of Human Nutrition of Wageningen University (Wageningen, the Netherlands), was initiated to formulate a protocol for the treatment of vitamin deficiency and for the maintenance of optimal vitamin D status. To discuss the controversies around treatment of deficiency and optimal vitamin D status and intakes, a workshop meeting was organised with clinicians, scientists and dietitians. In addition, a literature review was conducted to collect recent information on optimal intake of vitamins, their optimal circulating concentrations, and effective dosing regimens to treat deficiency. This information has been translated into the NutriProfiel advice, which is outlined in this article.
PEBBLE GAMES AND LINEAR EQUATIONS
Authors: GROHE MARTIN , OTTO MARTIN
Published: July 2015

We give a new, simplified and detailed account of the correspondence between levels of the Sherali–Adams relaxation of graph isomorphism and levels of pebble-game equivalence with counting (higher-dimensional Weisfeiler–Lehman colour refinement). The correspondence between basic colour refinement and fractional isomorphism, due to Tinhofer [22; 23] and Ramana, Scheinerman and Ullman [17], is re-interpreted as the base level of Sherali–Adams and generalised to higher levels in this sense by Atserias and Maneva [1] and Malkin [14], who prove that the two resulting hierarchies interleave. In carrying this analysis further, we here give (a) a precise characterisation of the level k Sherali–Adams relaxation in terms of a modified counting pebble game; (b) a variant of the Sherali–Adams levels that precisely match the k-pebble counting game; (c) a proof that the interleaving between these two hierarchies is strict. We also investigate the variation based on boolean arithmetic instead of real/rational arithmetic and obtain analogous correspondences and separations for plain k-pebble equivalence (without counting). Our results are driven by considerably simplified accounts of the underlying combinatorics and linear algebra.
REAL HYPERSURFACES OF NON-FLAT COMPLEX SPACE FORMS WITH GENERALIZED ξ-PARALLEL JACOBI STRUCTURE OPERATOR
Authors: THEOFANIDIS TH.
Published: July 2015

The aim of the present paper is the classification of real hypersurfaces M equipped with the condition Al = lA, l = R(., ξ)ξ, restricted in a subspace of the tangent space TpM of M at a point p. This class is large and difficult to classify, therefore a second condition is imposed: (∇ξl)X = ω(X)ξ + ψ(X)lX, where ω(X), ψ(X) are 1-forms. The last condition is studied for the first time and is much weaker than ∇ξl = 0 which has been studied so far. The Jacobi Structure Operator satisfying this weaker condition can be called generalized ξ-parallel Jacobi Structure Operator.
Inoderma and related genera in Arthoniaceae with elevated white pruinose pycnidia or sporodochia
Authors: Frisch Andreas , Ohmura Yoshihito , Ertz Damien , Thor Göran
Published: July 2015

The genus Inoderma (Ach.) Gray is lectotypified with Inoderma byssaceum and resurrected for a small group of species in Arthoniaceae with elevated, white pruinose pycnidia, immersed to adnate white pruinose apothecia and a weakly gelatinized hymenium. Inoderma nipponicum is described from Japan, I. afromontanum from Uganda and the European Lecanactis subabietina is transferred to the genus. Sporodophoron is described for a small group of species in Arthoniaceae related to Inoderma but with a unique type of sporodochia instead of pycnidia. Sterile specimens of this new genus resemble species of Tylophoron but differ in the rounded angular to elliptical to short cylindrical, 0–2-septate sporodochial conidia with unevenly thickened walls which are formed apically in zigzag-shaped and occasionally branched chains. Sporodophoron further differs in thallus chemistry and is genetically distinct. Tylophoron americanum and Schismatomma cretaceum are transferred to Sporodophoron, and the new species S. gossypinum from Japan and S. primorskiense from eastern Russia are described. The genus Glomerulophoron is described for a single species from Mauritius, G. mauritiae, differing from Sporodophoron in the tightly coiled chains of sporodochial conidia and being genetically distinct. A phylogenetic tree showing the position of Inoderma, Sporodophoron and Glomerulophoron in Arthoniaceae is presented. A key to all species of Arthoniaceae with sporodochia or elevated white pruinose pycnidia is presented. Arthothelium spectabile, the type of the large heterogeneous genus Arthothelium, is confirmed for the cryptothecioid subclade in Arthoniaceae.
Relativistic Gaussian laser beam self-focusing in collisional quantum plasmas
Authors: Zare S. , Rezaee S. , Yazdani E. , Anvari A. , Sadighi-Bonabi R.
Published: July 2015

Propagation of Gaussian X-ray laser beam is presented in collisional quantum plasma and the beam width oscillation is studied along the propagation direction. It is noticed that due to energy absorption in collisional plasma, the laser energy drops to an amount less than the critical value of the self-focusing effect and consequently, the laser beam defocuses. It is found that the oscillation amplitude of the laser spot size enhances while passing through collisional plasma. For the greater values of collision frequency, the beam width oscillates with higher amplitude and defocuses in a shallower plasma depth. Also, it is realized that in a dense plasma environment, the laser self-focusing occurs earlier with the higher oscillation amplitude, smaller laser spot size and more oscillations.
“Not Rural but Not Urban”: Community Governance in China's Urban Villages
Authors: Tang Beibei
Published: July 2015

China's urbanization has created a large number of urban villages which, although they have been transferred to urban administration, have maintained their collective economies. Using a comparative perspective, this article investigates how villagers, the village collectives and the urban administration organize community governance in three urban villages on the fringes of the cities of Guangzhou, Wuhan and Shenyang. The findings suggest that successful village collective shareholding companies play a leading role in community governance by providing villagers with economic and social welfare, subsidizing community administration services, and mobilizing residents. The comparative analysis also shows that village shareholding companies employ different mechanisms based on the varied histories of their village collective economies, the ability of the village collectives to mobilize resources, and the degree to which the village collectives are engaged in the grassroots administrative structure. The article argues that the “not rural but not urban” governance mode of the urban villages illustrates China's fragmented urbanization planning. At the same time, it illuminates the dynamics of state–society relations during China's urbanization and how landless villagers and village collectives respond to urban transformation by adopting different strategies to preserve their individual and collective interests.
Relationship of polar bodies morphology to embryo quality and pregnancy outcome
Authors: Zhou Wenhui , Fu Lei , Sha Wei , Chu Dapeng , Li Yuan
Published: July 2015

The aim of this study was to explore whether the morphology of polar bodies (PBs) estimated at 16–18 h after insemination can be used as an additional marker for predicting human embryo quality or pregnancy outcome. The data from 355 patients who received standardin vitrofertilization (IVF) or intracytoplasmic sperm injection (ICSI) treatment after controlled ovarian hyperstimulation were recruited. Normal fertilized 3048 zygotes from 382 cycles were divided into two groups, PBs intact or fragmented, according to the morphology of PBs assessed at 16–18 h after insemination. Embryo quality and pregnancy outcome were compared between the two groups. It was shown that the day 3 (D3) good embryo rate, good quality blastocyst rate and available embryo rate of the PBs intact group were all significantly higher than that of the corresponding fragmented groups. However, no significant differences in pregnancy rate (PR) or implantation rate (IR) were observed between the intact and fragmented groups. Although PBs morphology estimated at 16–18 h after insemination had little effect on PR or IR in fresh embryo transfer cycles, a better embryo quality can be achieved in the PB-intact group, which is valuable for embryo selection.
A New Social Risk? Social-Scientific Knowledge and Work-Life Balance in Twentieth-Century Finland
Authors: Eräranta Kirsi
Published: July 2015

Work-life balance, or the reconciliation of work and family, has been discussed recently as a “new social risk” in comparative research on the welfare state. According to this discussion, the social security systems of traditional welfare states were built after World War II in order to protect (male) breadwinners against the “old social risks” such as the loss of income due to old age, sickness, accident, or unemployment. Scholars have argued, however, that these postwar policies have been inadequate for dealing with the new types of risks that resulted from complex changes in employment practices and family life. This article reflects critically upon the conceptualization of work-life balance as a new social risk by focusing on one of the Nordic countries, which have come to be known for their policies that combine (female) parenthood and paid work. In particular, it analyzes the problematization and governance of work-family reconciliation in twentieth-century Finland. Overall, the article argues that social scientific knowledge played a key role in the ways in which work-life balance was rendered intelligible and manageable as a social policy issue.
Rektusdiastase und Schwangerschaft
Authors: Kimmich Nina , Haslinger Christian , Kreft Martina , Zimmermann Roland
Published: July 2015

Zusammenfassung. Eine Rektusdiastase in der Schwangerschaft ist mit einer Prävalenz von 30–70% ein sehr häufig anzutreffendes Phänomen. Es bestehen hierbei funktionelle sowie vor allem kosmetische Einschränkungen. Goldstandard in der Diagnostik in der Schwangerschaft ist die Transabdominalsonografie. Die häufigste Lokalisation ist periumbilikal zu finden, eine Persistenz postpartal ist in bis zu 60% der Fälle gegeben. Sowohl konservative (physiotherapeutische) als auch chirurgische Behandlungen sind bis zu einem gewissen Grad effektiv, die Rezidivraten, vor allem nach chirurgischer Therapie, aber relativ unklar. Problematisch ist bei der gesamten Thematik jedoch die Tatsache, dass in puncto Schwangerschaft keine Normwerte der Rektusdiastase existieren, keine evidenzbasierten Therapieschemata bestehen und dass es kaum Studien bzw. nur solche mässiger Qualität zu der gesamten Thematik gibt.
Patterned arrays of lateral heterojunctions within monolayer two-dimensional semiconductors
Authors: Mahjouri-Samani Masoud , Lin Ming-Wei , Wang Kai , Lupini Andrew R. , Lee Jaekwang , Basile Leonardo , Boulesbaa Abdelaziz , Rouleau Christopher M. , Puretzky Alexander A. , Ivanov Ilia N. , Xiao Kai , Yoon Mina , Geohegan David B.
Published: July 2015

The formation of semiconductor heterojunctions and their high-density integration are foundations of modern electronics and optoelectronics. To enable two-dimensional crystalline semiconductors as building blocks in next-generation electronics, developing methods to deterministically form lateral heterojunctions is crucial. Here we demonstrate an approach for the formation of lithographically patterned arrays of lateral semiconducting heterojunctions within a single two-dimensional crystal. Electron beam lithography is used to pattern MoSe2 monolayer crystals with SiO2, and the exposed locations are selectively and totally converted to MoS2 using pulsed laser vaporization of sulfur to form MoSe2/MoS2 heterojunctions in predefined patterns. The junctions and conversion process are studied by Raman and photoluminescence spectroscopy, atomically resolved scanning transmission electron microscopy and device characterization. This demonstration of lateral heterojunction arrays within a monolayer crystal is an essential step for the integration of two-dimensional semiconductor building blocks with different electronic and optoelectronic properties for high-density, ultrathin devices.
Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening
Authors: Neumann M. A. , van de Streek J. , Fabbiani F. P. A. , Hidber P. , Grassmann O.
Published: July 2015

Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib.
Interaction-induced decay of a heteronuclear two-atom system
Authors: Xu Peng , Yang Jiaheng , Liu Min , He Xiaodong , Zeng Yong , Wang Kunpeng , Wang Jin , Papoular D. J. , Shlyapnikov G. V. , Zhan Mingsheng
Published: July 2015

Two-atom systems in small traps are of fundamental interest for understanding the role of interactions in degenerate cold gases and for the creation of quantum gates in quantum information processing with single-atom traps. One of the key quantities is the inelastic relaxation (decay) time when one of the atoms or both are in a higher hyperfine state. Here we measure this quantity in a heteronuclear system of 87Rb and 85Rb in a micro optical trap and demonstrate experimentally and theoretically the presence of both fast and slow relaxation processes, depending on the choice of the initial hyperfine states. This experimental method allows us to single out a particular relaxation process thus provides an extremely clean platform for collisional physics studies. Our results have also implications for engineering of quantum states via controlled collisions and creation of two-qubit quantum gates.
Predicting the stability of large structured food webs
Authors: Allesina Stefano , Grilli Jacopo , Barabás György , Tang Si , Aljadeff Johnatan , Maritan Amos
Published: July 2015

The stability of ecological systems has been a long-standing focus of ecology. Recently, tools from random matrix theory have identified the main drivers of stability in ecological communities whose network structure is random. However, empirical food webs differ greatly from random graphs. For example, their degree distribution is broader, they contain few trophic cycles, and they are almost interval. Here we derive an approximation for the stability of food webs whose structure is generated by the cascade model, in which ‘larger’ species consume ‘smaller’ ones. We predict the stability of these food webs with great accuracy, and our approximation also works well for food webs whose structure is determined empirically or by the niche model. We find that intervality and broad degree distributions tend to stabilize food webs, and that average interaction strength has little influence on stability, compared with the effect of variance and correlation.
Constraints on soluble aerosol iron flux to the Southern Ocean at the Last Glacial Maximum
Authors: Conway T.M. , Wolff E.W. , Röthlisberger R. , Mulvaney R. , Elderfield H.E.
Published: July 2015

Relief of iron (Fe) limitation in the Southern Ocean during ice ages, with potentially increased carbon storage in the ocean, has been invoked as one driver of glacial–interglacial atmospheric CO2 cycles. Ice and marine sediment records demonstrate that atmospheric dust supply to the oceans increased by up to an order of magnitude during glacial intervals. However, poor constraints on soluble atmospheric Fe fluxes to the oceans limit assessment of the role of Fe in glacial–interglacial change. Here, using novel techniques, we present estimates of water- and seawater-soluble Fe solubility in Last Glacial Maximum (LGM) atmospheric dust from the European Project for Ice Coring in Antarctica (EPICA) Dome C and Berkner Island ice cores. Fe solubility was very variable (1–42%) during the interval, and frequently higher than typically assumed by models. Soluble aerosol Fe fluxes to Dome C at the LGM (0.01–0.84 mg m−2 per year) suggest that soluble Fe deposition to the Southern Ocean would have been ≥10 × modern deposition, rivalling upwelling supply.
A draft network of ligand–receptor-mediated multicellular signalling in human
Authors: Ramilowski Jordan A. , Goldberg Tatyana , Harshbarger Jayson , Kloppmann Edda , Lizio Marina , Satagopam Venkata P. , Itoh Masayoshi , Kawaji Hideya , Carninci Piero , Rost Burkhard , Forrest Alistair R. R.
Published: July 2015

Cell-to-cell communication across multiple cell types and tissues strictly governs proper functioning of metazoans and extensively relies on interactions between secreted ligands and cell-surface receptors. Herein, we present the first large-scale map of cell-to-cell communication between 144 human primary cell types. We reveal that most cells express tens to hundreds of ligands and receptors to create a highly connected signalling network through multiple ligand–receptor paths. We also observe extensive autocrine signalling with approximately two-thirds of partners possibly interacting on the same cell type. We find that plasma membrane and secreted proteins have the highest cell-type specificity, they are evolutionarily younger than intracellular proteins, and that most receptors had evolved before their ligands. We provide an online tool to interactively query and visualize our networks and demonstrate how this tool can reveal novel cell-to-cell interactions with the prediction that mast cells signal to monoblastic lineages via the CSF1–CSF1R interacting pair.
Anion-Responsive Metallopolymer Hydrogels for Healthcare Applications
Authors: Zhang Jiuyang , Yan Jing , Pageni Parasmani , Yan Yi , Wirth Adam , Chen Yun-Ping , Qiao Yali , Wang Qian , Decho Alan W. , Tang Chuanbing
Published: July 2015

Metallopolymers combine a processable, versatile organic polymeric skeleton with functional metals, providing multiple functions and methodologies in materials science. Taking advantage of cationic cobaltocenium as the key building block, organogels could be simply switched to hydrogels via a highly efficient ion exchange. With the unique ionic complexion ability, cobaltocenium moieties provide a robust soft substrate for recycling antibiotics from water. The essential polyelectrolyte nature offers the metallopolymer hydrogels to kill multidrug resistant bacteria. The multifunctional characteristics of these hydrogels highlight the potential for metallopolymers in the field of healthcare and environmental treatment.
Prediction of Links and Weights in Networks by Reliable Routes
Authors: Zhao Jing , Miao Lili , Yang Jian , Fang Haiyang , Zhang Qian-Ming , Nie Min , Holme Petter , Zhou Tao
Published: July 2015

Link prediction aims to uncover missing links or predict the emergence of future relationships from the current network structure. Plenty of algorithms have been developed for link prediction in unweighted networks, but only a few have been extended to weighted networks. In this paper, we present what we call a “reliable-route method” to extend unweighted local similarity indices to weighted ones. Using these indices, we can predict both the existence of links and their weights. Experiments on various real-world networks suggest that our reliable-route weighted resource-allocation index performs noticeably better than others with respect to weight prediction. For existence prediction it is either the highest or very close to the highest. Further analysis shows a strong positive correlation between the clustering coefficient and prediction accuracy. Finally, we apply our method to the prediction of missing protein-protein interactions and their confidence scores from known PPI networks. Once again, our reliable-route method shows the highest accuracy.
Pushing back the limits of Raman imaging by coupling super-resolution and chemometrics for aerosols characterization
Authors: Offroy Marc , Moreau Myriam , Sobanska Sophie , Milanfar Peyman , Duponchel Ludovic
Published: July 2015

The increasing interest in nanoscience in many research fields like physics, chemistry and biology, including the environmental fate of the produced nano-objects, requires instrumental improvements to address the sub-micrometric analysis challenges. The originality of our approach is to use both the super-resolution concept and multivariate curve resolution (MCR-ALS) algorithm in confocal Raman imaging to surmount its instrumental limits and to characterize chemical components of atmospheric aerosols at the level of the individual particles. We demonstrate the possibility to go beyond the diffraction limit with this algorithmic approach. Indeed, the spatial resolution is improved by 65% to achieve 200 nm for the considered far-field spectrophotometer. A multivariate curve resolution method is then coupled with super-resolution in order to explore the heterogeneous structure of submicron particles for describing physical and chemical processes that may occur in the atmosphere. The proposed methodology provides new tools for sub-micron characterization of heterogeneous samples using far-field (i.e. conventional) Raman imaging spectrometer.
Functional Loss of Bmsei Causes Thermosensitive Epilepsy in Contractile Mutant Silkworm, Bombyx mori
Authors: Nie Hongyi , Cheng Tingcai , Huang Xiaofeng , Zhou Mengting , Zhang Yinxia , Dai Fangyin , Mita Kazuei , Xia Qingyou , Liu Chun
Published: July 2015

The thermoprotective mechanisms of insects remain largely unknown. We reported the Bombyx mori contractile (cot) behavioral mutant with thermo-sensitive seizures phenotype. At elevated temperatures, the cot mutant exhibit seizures associated with strong contractions, rolling, vomiting and a temporary lack of movement. We narrowed a region containing cot to ~268 kb by positional cloning and identified the mutant gene as Bmsei which encoded a potassium channel protein. Bmsei was present in both the cell membrane and cytoplasm in wild-type ganglia but faint in cot. Furthermore, Bmsei was markedly decreased upon high temperature treatment in cot mutant. With the RNAi method and injecting potassium channel blockers, the wild type silkworm was induced the cot phenotype. These results demonstrated that Bmsei was responsible for the cot mutant phenotype and played an important role in thermoprotection in silkworm. Meanwhile, comparative proteomic approach was used to investigate the proteomic differences. The results showed that the protein of Hsp-1 and Tn1 were significantly decreased and increased on protein level in cot mutant after thermo-stimulus, respectively. Our data provide insights into the mechanism of thermoprotection in insect. As cot phenotype closely resembles human epilepsy, cot might be a potential model for the mechanism of epilepsy in future.
A versatile class of prototype dynamical systems for complex bifurcation cascades of limit cycles
Authors: Sándor Bulcsú , Gros Claudius
Published: July 2015

A general class of prototype dynamical systems is introduced, which allows to study the generation of complex bifurcation cascades of limit cycles, including bifurcations breaking spontaneously a symmetry of the system, period doubling and homoclinic bifurcations and transitions to chaos induced by sequences of limit cycle bifurcations. The prototype systems are adaptive, with friction forces f(V(x)) being functionally dependent exclusively on the mechanical potential V(x), characterized in turn by a finite number of local minima. We discuss several low-dimensional systems, with friction forces f(V) which are linear, quadratic or cubic polynomials in the potential V. We point out that the zeros of f(V) regulate both the relative importance of energy uptake and dissipation respectively, serving at the same time as bifurcation parameters, hence allowing for an intuitive interpretation of the overall dynamical behavior. Starting from simple Hopf- and homoclinic bifurcations, complex sequences of limit cycle bifurcations are observed when the energy uptake gains progressively in importance.
Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio
Authors: Clausson Carl-Magnus , Arngården Linda , Ishaq Omer , Klaesson Axel , Kühnemund Malte , Grannas Karin , Koos Björn , Qian Xiaoyan , Ranefall Petter , Krzywkowski Tomasz , Brismar Hjalmar , Nilsson Mats , Wählby Carolina , Söderberg Ola
Published: July 2015

Rolling circle amplification (RCA) for generation of distinct fluorescent signals in situ relies upon the self-collapsing properties of single-stranded DNA in commonly used RCA-based methods. By introducing a cross-hybridizing DNA oligonucleotide during rolling circle amplification, we demonstrate that the fluorophore-labeled RCA products (RCPs) become smaller. The reduced size of RCPs increases the local concentration of fluorophores and as a result, the signal intensity increases together with the signal-to-noise ratio. Furthermore, we have found that RCPs sometimes tend to disintegrate and may be recorded as several RCPs, a trait that is prevented with our cross-hybridizing DNA oligonucleotide. These effects generated by compaction of RCPs improve accuracy of visual as well as automated in situ analysis for RCA based methods, such as proximity ligation assays (PLA) and padlock probes.
A strategy for the identification of combinatorial bioactive compounds contributing to the holistic effect of herbal medicines
Authors: Long Fang , Yang Hua , Xu Yanmin , Hao Haiping , Li Ping
Published: July 2015

It has been well claimed that herbal medicines (HMs) elicit effects via a multi-compounds and multi-targets synergistic mode. However, it lacks appropriate strategies to uncover the combinatory compounds that take effect together and contribute to a certain pharmacological effect of an herb as a whole, which represents a major bottleneck in providing sound evidence in supporting the clinic benefits of HMs. Here, we proposed a strategy to the identification of combinatory compounds contributing to the anti-inflammatory activity of Cardiotonic Pill (CP). The strategy proposed herein contains four core steps, including the identification of bioequivalent combinatorial compounds, chemical family classification-based combinatorial screen, interactive mode evaluation and activity contribution index assay. Using this strategy, we have successfully identified six compounds in combination responsible for the anti-inflammatory effect of CP, whose anti-inflammatory activities were found comparable to that of the whole CP. Additionally, these six compounds take effect via an additive mode but little synergism. This study, together with our recent work in the identification of bioactive equivalent compounds combination, provides a widely applicable strategy to the identification of combinatory compounds responsible for a certain pharmacological activity of HMs.
Position-specific prediction of methylation sites from sequence conservation based on information theory
Authors: Shi Yinan , Guo Yanzhi , Hu Yayun , Li Menglong
Published: July 2015

Protein methylation plays vital roles in many biological processes and has been implicated in various human diseases. To fully understand the mechanisms underlying methylation for use in drug design and work in methylation-related diseases, an initial but crucial step is to identify methylation sites. The use of high-throughput bioinformatics methods has become imperative to predict methylation sites. In this study, we developed a novel method that is based only on sequence conservation to predict protein methylation sites. Conservation difference profiles between methylated and non-methylated peptides were constructed by the information entropy (IE) in a wider neighbor interval around the methylation sites that fully incorporated all of the environmental information. Then, the distinctive neighbor residues were identified by the importance scores of information gain (IG). The most representative model was constructed by support vector machine (SVM) for Arginine and Lysine methylation, respectively. This model yielded a promising result on both the benchmark dataset and independent test set. The model was used to screen the entire human proteome and many unknown substrates were identified. These results indicate that our method can serve as a useful supplement to elucidate the mechanism of protein methylation and facilitate hypothesis-driven experimental design and validation.
New “haploid biofilm model” unravels IRA2 as a novel regulator of Candida albicans biofilm formation
Authors: Seneviratne Chaminda Jayampath , Zeng Guisheng , Truong Thuyen , Sze Sarah , Wong Wah , Samaranayake Lakshman , Chan Fong Yee , Wang Yan-Ming , Wang Haitao , Gao Jiaxin , Wang Yue
Published: July 2015

Clinical isolates of the fungal human pathogen Candida albicans are invariably diploid and heterozygous, impeding genetic study. Recent isolation of C. albicans haploids opens opportunities to apply technologies unfeasible in diploids. However, doubts remain on whether the haploids, derived from chromosome loss, can represent the diploids. Here, we use C. albicans haploids to investigate biofilm, a key virulence attribute. We conducted the first comprehensive characterization of biofilm formation of the haploids in comparison with the diploids. We demonstrate that the haploids form biofilms with essentially the same characteristics as the diploids. Screening a haploid mutant library has uncovered novel GTPase-related genes as biofilm regulators, including IRA2 that encodes an activator of the Ras GTPase. IRA2-deletion mutants develop poorly constructed biofilm in both haploid and diploid C. albicans. Our results demonstrate that the haploids are a valid model for C. albicans biofilm research and a powerful tool for uncovering novel regulators.
Clock gene polymorphism and scheduling of migration: a geolocator study of the barn swallow Hirundo rustica
Authors: Bazzi Gaia , Ambrosini Roberto , Caprioli Manuela , Costanzo Alessandra , Liechti Felix , Gatti Emanuele , Gianfranceschi Luca , Podofillini Stefano , Romano Andrea , Romano Maria , Scandolara Chiara , Saino Nicola , Rubolini Diego
Published: July 2015

Circannual rhythms often rely on endogenous seasonal photoperiodic timers involving ‘clock’ genes andClockgene polymorphism has been associated to variation in phenology in some bird species. In the long-distance migratory barn swallowHirundo rustica, individuals bearing the rareClockallele with the largest number of C-terminal polyglutamine repeats found in this species (Q8) show a delayed reproduction and moult later. We explored the association betweenClockpolymorphism and migration scheduling, as gauged by light-level geolocators, in two barn swallow populations (Switzerland; Po Plain, Italy). Genetic polymorphism was low: 91% of the 64 individuals tracked year-round were Q7/Q7homozygotes. We compared the phenology of the rare genotypes with the phenotypic distribution of Q7/Q7homozygotes within each population. In Switzerland, compared to Q7/Q7, two Q6/Q7males departed earlier from the wintering grounds and arrived earlier to their colony in spring, while a single Q7/Q8female was delayed for both phenophases. On the other hand, in the Po Plain, three Q6/Q7individuals had a similar phenology compared to Q7/Q7. The Swiss data are suggestive for a role of genetic polymorphism at a candidate phenological gene in shaping migration traits and support the idea thatClockpolymorphism underlies phenological variation in birds.