bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation between frictional force and surface roughness of orthodontic archwires
Authors: Choi Samjin , Hwang Eun‐Young , Park Hun‐Kuk , Park Young‐Guk
Published: May 2015

Lateral force microscopy measures the lateral bending of the cantilever depending on the frictional force acting between the tip and surface. The aim of this study was to investigate and compare the relationship between the surface roughness and frictional resistance of four archwire and bracket combinations consisting of the 0.016‐inch NiTi and 0.019 × 0.025‐inch stainless steel archwires interacting clinically with two representative self‐ligating brackets, active‐type Clippy‐C® ceramic self‐ligating brackets, and passive‐type Damon® stainless steel self‐ligating brackets, using the lateral force microscopy technique. A 0.016‐inch NiTi archwire interacting with passive‐type Damon® stainless steel self‐ligating brackets showed the smoothest surface roughness and the lowest frictional resistance compared to other combinations. The archwires interacting with passive‐type Damon® stainless steel self‐ligating brackets showed significantly lower surface roughness and frictional resistance than those interacting with active‐type Clippy‐C® ceramic self‐ligating brackets. The frictional force in the in vivo archwire and bracket system increased with increasing surface roughness of the archwire. This positive correlation suggests that surface roughness can be used as an evaluating marker for estimating the efficiency of orthodontic treatment, rather than the direct measurement of frictional force. SCANNING 37:399–405, 2015. © 2015 Wiley Periodicals, Inc.
Estimation of causal effects of binary treatments in unconfounded studies
Authors: Gutman Roee , Rubin Donald B.
Published: May 2015

Estimation of causal effects in non‐randomized studies comprises two distinct phases: design, without outcome data, and analysis of the outcome data according to a specified protocol. Recently, Gutman and Rubin (2013) proposed a new analysis‐phase method for estimating treatment effects when the outcome is binary and there is only one covariate, which viewed causal effect estimation explicitly as a missing data problem. Here, we extend this method to situations with continuous outcomes and multiple covariates and compare it with other commonly used methods (such as matching, subclassification, weighting, and covariance adjustment). We show, using an extensive simulation, that of all methods considered, and in many of the experimental conditions examined, our new ‘multiple‐imputation using two subclassification splines’ method appears to be the most efficient and has coverage levels that are closest to nominal. In addition, it can estimate finite population average causal effects as well as non‐linear causal estimands. This type of analysis also allows the identification of subgroups of units for which the effect appears to be especially beneficial or harmful. Copyright © 2015 John Wiley & Sons, Ltd.
Careers “From” but not “in” science: Why are aspirations to be a scientist challenging for minority ethnic students?
Authors: Wong Billy
Published: May 2015

The importance of science to the economy and for the progression of society is widely acknowledged. Yet, there are concerns that minority ethnic students in the UK are underrepresented, and even excluded, from post‐compulsory science education and careers in science. Drawing on an exploratory study of 46 semi‐structured interviews with British young people (aged 11–14) from Black Caribbean, Pakistani, Bangladeshi, Indian, and Chinese ethnic backgrounds, this paper explores why careers in science are not popular aspirations among minority ethnic students, while careers from science are highly sought after. Using sociological theories of identity, this paper argues that gender and ethnic identities can operate in multifaceted ways to influence students' careers aspirations. Being a scientist is constructed by students as a highly gendered and racialized profession, which may reflect popular discourse of scientist as typically for “white men.” Careers from science, particularly in medicine, appeared popular among some, but not all, minority ethnic groups, as being a medical staff is considered intrinsically and extrinsically rewarding. Implications of the findings for the science education of minority ethnic students are discussed. © 2015 Wiley Periodicals, Inc. J Res Sci Teach 52: 979–1002, 2015.
H‐infinity controller for frequency and voltage regulation in grid‐connected and islanded microgrid
Authors: Sheela A. , Vijayachitra S. , Revathi S.
Published: May 2015

This paper presents a study on a grid‐connected and islanded multiple distributed generation (DG) system for frequency and voltage regulation. The multiple DG system includes solar cells, wind turbine, fuel cell, and battery storage. The H‐infinity controller is used whose weighting parameters are optimized to minimize voltage and frequency deviation. The performance of the system is analyzed under different conditions for both grid‐connected and islanded modes of operation. In case of the load variations, the inner voltage and current loop react based on the H‐ infinity control strategies. The outer power loop uses the droop characteristic controller. The design is simulated using MATLAB/SIMULINK. The simulation results show that the multiple DG system can supply high‐quality power both in grid‐connected and islanded modes. Also, we show that the proposed control methodology will make the system to transit smoothly between the islanded mode and the grid‐connected mode. The results indicate that the frequency and voltage deviations meet the nominal values as per IEEE standard. © 2015 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Synthesis and Characterization of the Quaternary Thio­aluminogermanates A(AlS2)(GeS2) (A = Na, K)
Authors: Al‐Bloushi Mohammed , Davaasuren Bambar , Emwas Abdul‐Hamid , Rothenberger Alexander
Published: May 2015

The quaternary thioaluminogermanates Na(AlS2)(GeS2) (1) and K(AlS2)(GeS2) (2) crystallize in the tetragonal space group I4/mcm (no. 140) with unit cell parameters a = 7.4274(11) Å, c = 5.8560(12) Å for Na(AlS2)(GeS2) and a = 7.8826(2) Å, c = 5.8642(4) Å for K(AlS2)(GeS2). The crystal structure comprises of one‐dimensional [(AlS2)(GeS2)]– anionic chains with Al and Ge sharing the tetrahedral site. The alkali metal cations fill the square antiprismatic voids between chains. Both 1 and 2 are semiconductors with bandgap of around 3.6 eV and 3.5 eV, respectively.
Three Coordination Polymers Constructed with Zinc(II), 3,3′‐Thiodipropionic Acid, and Bipyridyl Ligands: Syntheses, Crystal Structures and Luminescent Properties
Authors: Cheng Hong‐Jian , Shen Ya‐Li , Zhang Shi‐Yi , Ji Hong‐Wei , Yin Wen‐Yu , Li Kun , Yuan Rong‐Xin
Published: May 2015

Three zinc(II) coordination polymers {[Zn(tdpa)(bpe)]·2H2O}n (1), [Zn(tdpa)(bpp)]n (2), and [Zn(tdpa)(bpypa)]n (3) were obtained by solvothermal reactions of Zn(NO3)2·6H2O with 3,3′‐thiodipropionic acid (H2tdpa) and corresponding N‐donor ligands, namely, trans‐1,2‐bis(4‐pyridyl)ethylene (bpe), 1,3‐bis(4‐pyridyl)propane (bpp), and 4,4′‐bis(4‐pyridyl)diphenylamine (bpypa) respectively. Complexes 1–3 were characterized by elemental analysis, IR spectroscopy, as well as powder and single‐crystal X‐ray diffraction. Compound 1 can be considered as a 3D supramolecular architecture based on 2D undulated (4,4) layers, which are connected through hydrogen bonding interactions. 2 possesses a twofold interpenetrating 2D network, whereas 3 exhibits a 3D supramolecular structure based on 2D (658) layers through hydrogen‐bonding interactions and π···π stacking interactions. The photoluminescent properties of 1–3 were also investigated.
Structural Characterization of Neutral Glycosphingolipids from 3T3‐L1 Adipocytes
Authors: Kojima Hisao , Suzuki Yusuke , Ito Masahiro , Kabayama Kazuya
Published: May 2015

In recent years, obesity has been considered a pathological stage of early lifestyle‐related diseases, and adipose tissue and adipocyte research has been active. Glycosphingolipids are involved in the pathogenesis of type 2 diabetes induced by insulin resistance, but the details of the glycosphingolipid molecular species composition of adipocytes have yet to be elucidated. We used 3T3‐L1 adipocytes and the 1,2‐dichloroethane‐wash method to remove triacylglycerols, which are abundant in adipocytes, and analyzed the structures of glycosphingolipids, particularly neutral glycosphingolipids, using liquid chromatography–mass spectrometry.
Tackling medical student stress: beyond individual resilience
Authors: Watling Christopher
Published: May 2015

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The evolution of cognitive load theory and its application to medical education
Authors: Leppink Jimmie , Van den Heuvel Angelique
Published: May 2015

Cognitive Load Theory (CLT) has started to find more applications in medical education research. Unfortunately, misconceptions such as lower cognitive load always being beneficial to learning and the continued use of dated concepts and methods can result in improper applications of CLT principles in medical education design and research. This review outlines how CLT has evolved and presents a synthesis of current-day CLT principles in a holistic model for medical education design. This model distinguishes three dimensions: task fidelity: from literature (lowest) through simulated patients to real patients (highest); task complexity: the number of information elements; and instructional support: from worked examples (highest) through completion tasks to autonomous task performance (lowest). These three dimensions together constitute three steps to proficient learning: (I) start with high support on low-fidelity low-complexity tasks and gradually fade that support as learners become more proficient; (II) repeat I for low-fidelity but higher-complexity tasks; and (III) repeat I and II in that order at subsequent levels of fidelity. The numbers of fidelity levels and complexity levels within fidelity levels needed depend on the aims of the course, curriculum or individual learning trajectory. This paper concludes with suggestions for future research based on this model.
Development of reverse genetics for Ibaraki virus to produce viable VP6‐tagged IBAV
Authors: Matsuo Eiko , Saeki Keiichi , Roy Polly , Kawano Junichi
Published: May 2015

Ibaraki virus (IBAV) is a member of the epizootic hemorrhagic disease virus (EHDV) serogroup, which belongs to theOrbivirusgenus of theReoviridaefamily. Although EHDV, including IBAV, represents an ongoing threat to livestock in the world, molecular mechanisms of EHDV replication and pathogenesis have been unclear. The reverse genetics (RG) system is one of the strong tools to understand molecular mechanisms of virus replication. Here, we developed a RG system for IBAV to identify the nonessential region of a minor structural protein, VP6, by generating VP6‐truncated IBAV. Moreover, several tags were inserted into the truncated region to produce VP6‐tagged IBAV. We demonstrated that all VP6‐tagged IBAV could replicate in BHK cells in the absence of any helper VP6 protein. Further, tagged‐VP6 proteins were first assembled into puncta in cells infected with VP6‐tagged IBAV. Our data suggests that, in order to initiate primary replication, IBAV VP6 is likely to accumulate in some parts of infected cells to assemble efficiently into the primary replication complex (subcore).
Asperger's and Girls: What Teachers Need to Know
Authors: Jarman Belinda , Rayner Christopher
Published: May 2015

Individuals with the pervasive developmental disorder Asperger's syndrome (AS) are generally of average or above average intelligence and attend mainstream schools. Despite their intelligence, some of the characteristics and challenges associated with AS can impact upon the quality of life they experience at school. Although both males and females are diagnosed with AS, females have been underrepresented and unrepresented in much of the AS research. Consequently, much of what is known about the school experiences of students with AS is based on studies consisting predominately of male perspectives. This article discusses what adult females with AS and parents of females with AS currently attending school wish teachers understood about AS in females. Many of the experiences described by participants indicate there is a lack of understanding about AS, both generally and specifically, in relation to females. Implications of these findings and recommendations for educators and schools are provided, and directions for future research are outlined.
Validity of an FFQ assessing the vitamin D intake of young Serbian women living in a region without food fortification: the method of triads model
Authors: Djekic-Ivankovic Marija , Weiler Hope A , Nikolic Marina , Kadvan Agnes , Gurinovic Mirjana , Mandic Ljuba M , Glibetic Maria
Published: May 2015

Objective

The objective of the present study was to examine the external validity of an FFQ designed to estimate dietary vitamin D intake compared with a plasma biomarker and three repeated 24 h dietary recalls in women of reproductive age in Serbia, where there is no exposure to food fortified with vitamin D. The method of triads was applied.

Design

In a cross-sectional study, 422 women completed the Women and Reproductive Health FFQ (WRH-FFQ) during the winter months. From a representative subgroup (n44), three 24 h dietary recalls and anthropometric parameters were collected as well as a fasting blood sample for vitamin D biomarker analyses. Correlation coefficients were calculated between each of the dietary methods. Validity coefficients, as a correlation between the measured and estimated ‘true’ exposure, were calculated using the method of triads. Bland–Altman plots were also constructed.

Setting

Three major universities in Serbia.

Subjects

Healthy young women (n422) aged 18–35 years.

Results

The WRH-FFQ estimate of vitamin D intake for all participants was 4·0 (sd3·3) µg/d and 3·1 (sd2·3) µg/d for the subgroup. Bland–Altman plots for these intakes showed high agreement. Validity coefficients for the FFQ, 24 h recall and biomarker wereρQI=0·847 (95 % CI 0·564, 0·928),ρRI=0·810 (95 % CI 0·537, 0·997) andρBI=0·499 (95 % CI 0·190, 0·840), while the correlation coefficients were 0·686, 0·422 and 0·404.

Conclusions

The FFQ applied in the present study is a valid tool for assessing dietary vitamin D intake in women living in Serbia, a region without mandatory vitamin D food fortification.
AMPK activation promotes lipid droplet dispersion on detyrosinated microtubules to increase mitochondrial fatty acid oxidation
Authors: Herms Albert , Bosch Marta , Reddy Babu J.N. , Schieber Nicole L. , Fajardo Alba , Rupérez Celia , Fernández-Vidal Andrea , Ferguson Charles , Rentero Carles , Tebar Francesc , Enrich Carlos , Parton Robert G. , Gross Steven P. , Pol Albert
Published: May 2015

Lipid droplets (LDs) are intracellular organelles that provide fatty acids (FAs) to cellular processes including synthesis of membranes and production of metabolic energy. While known to move bidirectionally along microtubules (MTs), the role of LD motion and whether it facilitates interaction with other organelles are unclear. Here we show that during nutrient starvation, LDs and mitochondria relocate on detyrosinated MT from the cell centre to adopt a dispersed distribution. In the cell periphery, LD–mitochondria interactions increase and LDs efficiently supply FAs for mitochondrial beta-oxidation. This cellular adaptation requires the activation of the energy sensor AMPK, which in response to starvation simultaneously increases LD motion, reorganizes the network of detyrosinated MTs and activates mitochondria. In conclusion, we describe the existence of a specialized cellular network connecting the cellular energetic status and MT dynamics to coordinate the functioning of LDs and mitochondria during nutrient scarcity.
Novel insights into the pathogenicity of epidemic Aeromonas hydrophila ST251 clones from comparative genomics
Authors: Pang Maoda , Jiang Jingwei , Xie Xing , Wu Yafeng , Dong Yuhao , Kwok Amy H. Y. , Zhang Wei , Yao Huochun , Lu Chengping , Leung Frederick C. , Liu Yongjie
Published: May 2015

Outbreaks in fish of motile Aeromonad septicemia (MAS) caused by Aeromonas hydrophila have caused a great concern worldwide. Here, for the first time, we provide two complete genomes of epidemic A. hydrophila strains isolated in China. To gain an insight into the pathogenicity of epidemic A. hydrophila, we performed comparative genomic analyses of five epidemic strains belonging to sequence type (ST) 251, together with the environmental strain ATCC 7966T. We found that the known virulence factors, including a type III secretion system, a type VI secretion system and lateral flagella, are not required for the high virulence of the ST251 clonal group. Additionally, our work identifies three utilization pathways for myo-inositol, sialic acid and L-fucose providing clues regarding the factors that underlie the epidemic and virulent nature of ST251 A. hydrophila. Based on the geographical distribution and biological resources of the ST251 clonal group, we conclude that ST251 is a high-risk clonal group of A. hydrophila which may be responsible for the MAS outbreaks in China and the southeastern United States.
Characterizing the size and shape of sea ice floes
Authors: Gherardi Marco , Lagomarsino Marco Cosentino
Published: May 2015

Monitoring drift ice in the Arctic and Antarctic regions directly and by remote sensing is important for the study of climate, but a unified modeling framework is lacking. Hence, interpretation of the data, as well as the decision of what to measure, represent a challenge for different fields of science. To address this point, we analyzed, using statistical physics tools, satellite images of sea ice from four different locations in both the northern and southern hemispheres and measured the size and the elongation of ice floes (floating pieces of ice). We find that (i) floe size follows a distribution that can be characterized with good approximation by a single length scale "Equation missing", which we discuss in the framework of stochastic fragmentation models and (ii) the deviation of their shape from circularity is reproduced with remarkable precision by a geometric model of coalescence by freezing, based on random Voronoi tessellations, with a single free parameter "Equation missing"expressing the shape disorder. Although the physical interpretations remain open, this advocates the parameters "Equation missing"and "Equation missing"as two independent indicators of the environment in the polar regions, which are easily accessible by remote sensing.
Classical Imaging with Undetected Photons
Authors: Shapiro Jeffrey H. , Venkatraman Dheera , Wong Franco N. C.
Published: May 2015

Barreto Lemos et al. [Nature512, 409–412 (2014)] reported an experiment in which a non-degenerate parametric downconverter and a non-degenerate optical parametric amplifier—used as a wavelength-converting phase conjugator—were employed to image object transparencies in a manner akin to ghost imaging. Their experiment, however, relied on single-photon detection, rather than the photon-coincidence measurements employed in ghost imaging with a parametric downconverter source. More importantly, their system formed images despite the photons that passed through the object never being detected. Barreto Lemos et al. interpreted their experiment as a quantum imager, as assuredly it is, owing to its downconverter’s emitting entangled signal and idler beams. We show, however, that virtually all the features of their setup can be realized in a quantum-mimetic fashion using classical-state light, specifically a pair of bright pseudothermal beams possessing a phase-sensitive cross correlation. Owing to its much higher signal-to-noise ratio, our bright-source classical imager could greatly reduce image-acquisition time compared to that of Barreto Lemos et al.‘s quantum system, while retaining the latter’s ability to image with undetected photons.
The cytochrome bd-type quinol oxidase is important for survival of Mycobacterium smegmatis under peroxide and antibiotic-induced stress
Authors: Lu Ping , Heineke Marieke H. , Koul Anil , Andries Koen , Cook Gregory M. , Lill Holger , van Spanning Rob , Bald Dirk
Published: May 2015

Targeting respiration and ATP synthesis has received strong interest as a new strategy for combatting drug-resistant Mycobacterium tuberculosis. Mycobacteria employ a respiratory chain terminating with two branches. One of the branches includes a cytochrome bc1 complex and an aa3-type cytochrome c oxidase while the other branch terminates with a cytochrome bd-type quinol oxidase. In this communication we show that genetic inactivation of cytochrome bd, but not of cytochrome bc1, enhances the susceptibility of Mycobacterium smegmatis to hydrogen peroxide and antibiotic-induced stress. The type-II NADH dehydrogenase effector clofazimine and the ATP synthase inhibitor bedaquiline were bacteriostatic against wild-type M. smegmatis, but strongly bactericidal against a cytochrome bd mutant. We also demonstrated that the quinone-analog aurachin D inhibited mycobacterial cytochrome bd at sub-micromolar concentrations. Our results identify cytochrome bd as a key survival factor in M. smegmatis during antibiotic stress. Targeting the cytochrome bd respiratory branch therefore appears to be a promising strategy that may enhance the bactericidal activity of existing tuberculosis drugs.
Salt stains from evaporating droplets
Authors: Shahidzadeh Noushine , Schut Marthe F. L. , Desarnaud Julie , Prat Marc , Bonn Daniel
Published: May 2015

The study of the behavior of sessile droplets on solid substrates is not only associated with common everyday phenomena, such as the coffee stain effect, limescale deposits on our bathroom walls , but also very important in many applications such as purification of pharmaceuticals, de-icing of airplanes, inkjet printing and coating applications. In many of these processes, a phase change happens within the drop because of solvent evaporation, temperature changes or chemical reactions, which consequently lead to liquid to solid transitions in the droplets. Here we show that crystallization patterns of evaporating of water drops containing dissolved salts are different from the stains reported for evaporating colloidal suspensions. This happens because during the solvent evaporation, the salts crystallize and grow during the drying. Our results show that the patterns of the resulting salt crystal stains are mainly governed by wetting properties of the emerging crystal as well as the pathway of nucleation and growth and are independent of the evaporation rate and thermal conductivity of the substrates.
Detection of Composite Communities in Multiplex Biological Networks
Authors: Bennett Laura , Kittas Aristotelis , Muirhead Gareth , Papageorgiou Lazaros G. , Tsoka Sophia
Published: May 2015

The detection of community structure is a widely accepted means of investigating the principles governing biological systems. Recent efforts are exploring ways in which multiple data sources can be integrated to generate a more comprehensive model of cellular interactions, leading to the detection of more biologically relevant communities. In this work, we propose a mathematical programming model to cluster multiplex biological networks, i.e. multiple network slices, each with a different interaction type, to determine a single representative partition of composite communities. Our method, known as SimMod, is evaluated through its application to yeast networks of physical, genetic and co-expression interactions. A comparative analysis involving partitions of the individual networks, partitions of aggregated networks and partitions generated by similar methods from the literature highlights the ability of SimMod to identify functionally enriched modules. It is further shown that SimMod offers enhanced results when compared to existing approaches without the need to train on known cellular interactions.
Refugial isolation and range expansions drive the genetic structure of Oxyria sinensis (Polygonaceae) in the Himalaya-Hengduan Mountains
Authors: Meng Lihua , Chen Gang , Li Zhonghu , Yang Yongping , Wang Zhengkun , Wang Liuyang
Published: May 2015

The formation of the Mekong-Salween Divide and climatic oscillations in Pleistocene were the main drivers for the contemporary diversity and genetic structure of plants in the Himalaya-Hengduan Mountains (HHM). To identify the relative roles of the two historical events in shaping population history of plants in HHM, we investigated the phylogeographic pattern of Oxyria sinensis, a perennial plant endemic to the HHM. Sixteen chloroplast haplotypes were identified and were clustered into three phylogenetic clades. The age of the major clades was estimated to be in the Pleistocene, falling into several Pleistocene glacial stages and postdating the formation of the Mekong-Salween Divide. Range expansions occurred at least twice in the early and middle Pleistocene, but the spatial genetic distribution rarely changed since the Last Glacial Maximum. Our results suggest that temporary mountain glaciers may act as barriers in promoting the lineage divergence in O. sinensis and that subsequential range expansions and secondary contacts might reshape the genetic distribution in geography and blur the boundary of population differentiation created in the earlier glacial stages. This study demonstrates that Pleistocene climatic change and mountain glaciers, rather than the Mekong-Salween Divide, play the primary role in shaping the spatial genetic structure of O. sinensis.
Changes in the composition of intestinal fungi and their role in mice with dextran sulfate sodium-induced colitis
Authors: Qiu Xinyun , Zhang Feng , Yang Xi , Wu Na , Jiang Weiwei , Li Xia , Li Xiaoxue , Liu Yulan
Published: May 2015

Intestinal fungi are increasingly believed to greatly influence gut health. However, the effects of fungi on intestinal inflammation and on gut bacterial constitution are not clear. Here, based on pyrosequencing method, we reveal that fungal compositions vary in different intestinal segments (ileum, cecum and colon), prefer different colonization locations (mucosa and feces) and are remarkably changed during intestinal inflammation in dextran sulfate sodium (DSS)-colitis mouse models compare to normal controls: Penicillium, Wickerhamomyces, Alternaria, and Candida are increased while Cryptococcus, Phialemonium, Wallemia and an unidentified Saccharomycetales genus are decreased in the guts of DSS-colitis mice. Fungi-depleted mice exhibited aggravated acute DSS-colitis associated with gain of Hallella, Barnesiella, Bacteroides, Alistipes, and Lactobacillus and loss of butyrate-producing Clostridium XIVa and Anaerostipes compare with normal control. In contrast, bacteria-depleted mice show attenuated acute DSS-colitis. Mice with severely chronic recurrent DSS-colitis show increased plasma (1,3)-β-D-glucan level and fungal translocation into the colonic mucosa, mesenteric lymph nodes and spleen. This work demonstrate the different roles of fungi in acute and chronic recurrent colitis: They are important counterbalance to bacteria in maintaining intestinal micro-ecological homeostasis and health in acutely inflamed intestines, but can harmfully translocate into abnormal sites and could aggravate disease severity in chronic recurrent colitis.
Unique somatic and malignant expression patterns implicate PIWI-interacting RNAs in cancer-type specific biology
Authors: Martinez Victor D. , Vucic Emily A. , Thu Kelsie L. , Hubaux Roland , Enfield Katey S.S. , Pikor Larissa A. , Becker-Santos Daiana D. , Brown Carolyn J. , Lam Stephen , Lam Wan L.
Published: May 2015

Human PIWI-interacting RNAs (piRNAs) are known to be expressed in germline cells, functionally silencing LINEs and SINEs. Their expression patterns in somatic tissues are largely uncharted. We analyzed 6,260 human piRNA transcriptomes derived from non-malignant and tumour tissues from 11 organs. We discovered that only 273 of the 20,831 known piRNAs are expressed in somatic non-malignant tissues. However, expression patterns of these piRNAs were able to distinguish tissue-of-origin. A total of 522 piRNAs are expressed in corresponding tumour tissues, largely distinguishing tumour from non-malignant tissues in a cancer-type specific manner. Most expressed piRNAs mapped to known transcripts, contrary to “piRNA clusters” reported in germline cells. We showed that piRNA expression can delineate clinical features, such as histological subgroups, disease stages and survival. PiRNAs common to many cancer types might represent a core gene-set that facilitates cancer growth, while piRNAs unique to individual cancer types likely contribute to cancer-specific biology.
Deep ultraviolet laser direct write for patterning sol-gel InGaZnO semiconducting micro/nanowires and improving field-effect mobility
Authors: Lin Hung-Cheng , Stehlin Fabrice , Soppera Olivier , Zan Hsiao-Wen , Li Chang-Hung , Wieder Fernand , Ponche Arnaud , Berling Dominique , Yeh Bo-Hung , Wang Kuan-Hsun
Published: May 2015

Deep-UV (DUV) laser was used to directly write indium-gallium-zinc-oxide (IGZO) precursor solution and form micro and nanoscale patterns. The directional DUV laser beam avoids the substrate heating and suppresses the diffraction effect. A IGZO precursor solution was also developed to fulfill the requirements for direct photopatterning and for achieving semi-conducting properties with thermal annealing at moderate temperature. The DUV-induced crosslinking of the starting material allows direct write of semi-conducting channels in thin-film transistors but also it improves the field-effect mobility and surface roughness. Material analysis has been carried out by XPS, FTIR, spectroscopic ellipsometry and AFM and the effect of DUV on the final material structure is discussed. The DUV irradiation step results in photolysis and a partial condensation of the inorganic network that freezes the sol-gel layer in a homogeneous distribution, lowering possibilities of thermally induced reorganization at the atomic scale. Laser irradiation allows high-resolution photopatterning and high-enough field-effect mobility, which enables the easy fabrication of oxide nanowires for applications in solar cell, display, flexible electronics and biomedical sensors.
iMSRC: converting a standard automated microscope into an intelligent screening platform
Authors: Carro Angel , Perez-Martinez Manuel , Soriano Joaquim , Pisano David G. , Megias Diego
Published: May 2015

Microscopy in the context of biomedical research is demanding new tools to automatically detect and capture objects of interest. The few extant packages addressing this need, however, have enjoyed limited uptake due to complexity of use and installation. To overcome these drawbacks, we developed iMSRC, which combines ease of use and installation with high flexibility and enables applications such as rare event detection and high-resolution tissue sample screening, saving time and resources.
Enthalpy-entropy compensation at play in human copper ion transfer
Authors: Niemiec Moritz S. , Dingeldein Artur P. G. , Wittung-Stafshede Pernilla
Published: May 2015

Copper (Cu) is an essential trace element but toxic in free form. After cell uptake, Cu is transferred, via direct protein-protein interactions, from the chaperone Atox1 to the Wilson disease protein (WD) for incorporation into Cu-dependent enzymes. Cu binds to a conserved C1XXC2 motif in the chaperone as well as in each of the cytoplasmic metal-binding domains of WD. Here, we dissect mechanism and thermodynamics of Cu transfer from Atox1 to the fourth metal binding domain of WD. Using chromatography and calorimetry together with single Cys-to-Ala variants, we demonstrate that Cu-dependent protein heterocomplexes require the presence of C1 but not C2. Comparison of thermodynamic parameters for mutant versus wild type reactions reveals that the wild type reaction involves strong entropy-enthalpy compensation. This property is explained by a dynamic inter-conversion of Cu-Cys coordinations in the wild type ensemble and may provide functional advantage by protecting against Cu mis-ligation and bypassing enthalpic traps.
Multiple MoS2 Transistors for Sensing Molecule Interaction Kinetics
Authors: Nam Hongsuk , Oh Bo-Ram , Chen Pengyu , Chen Mikai , Wi Sungjin , Wan Wenjie , Kurabayashi Katsuo , Liang Xiaogan
Published: May 2015

Atomically layered transition metal dichalcogenides (TMDCs) exhibit a significant potential to enable next-generation low-cost transistor biosensors that permit single-molecule-level quantification of biomolecules. To realize such potential biosensing capability, device-oriented research is needed for calibrating the sensor responses to enable the quantification of the affinities/kinetics of biomolecule interactions. In this work, we demonstrated MoS2-based transistor biosensors capable of detecting tumor necrosis factor – alpha (TNF-α) with a detection limit as low as 60 fM. Such a detection limit was achieved in both linear and subthreshold regimes of MoS2 transistors. In both regimes, all sets of transistors exhibited consistent calibrated responses with respect to TNF-α concentration and they resulted in a standard curve, from which the equilibrium constant of the antibody-(TNF-α) pair was extracted to be KD = 369 ± 48 fM. Based on this calibrated sensor model, the time-dependent binding kinetics was also measured and the association/dissociation rates of the antibody-(TNF-α) pair were extracted to be (5.03 ± 0.16) × 108 M−1s−1 and (1.97 ± 0.08) × 10−4 s−1, respectively. This work advanced the critical device physics for leveraging the excellent electronic/structural properties of TMDCs in biosensing applications as well as the research capability in analyzing the biomolecule interactions with fM-level sensitivities.
Decreased LKB1 predicts poor prognosis in Pancreatic Ductal Adenocarcinoma
Authors: Yang Jian-Yu , Jiang Shu-Heng , Liu De-Jun , Yang Xiao-Mei , Huo Yan-Miao , Li Jiao , Hua Rong , Zhang Zhi-Gang , Sun Yong-Wei
Published: May 2015

Liver kinase B1 (LKB1) has been identified as a critical modulator involved in cell proliferation and polarity. The purpose of the current study was to characterize the expression pattern of LKB1 and assess the clinical significance of LKB1 expression in pancreatic ductal adenocarcinoma (PDAC) patients. LKB1 mRNA expression which was analyzed in 32 PDAC lesions and matched non-tumor tissues, was downregulated in 50% (16/32) of PDAC lesions. Similar results were also obtained by analyzing three independent datasets from Oncomine. Protein expression of LKB1 was significantly reduced in 6 PDAC cell lines and downregulated in 31.3% (10/32) of PDAC lesions compared to matched non-tumorous tissues, as determined by Western blot analysis. Additionally, tissue microarray containing 205 PDAC specimens was evaluated for LKB1 expression by IHC and demonstrated that reduced expression of LKB1 in 17.6% (36/205) of PDAC tissues was significantly correlated with clinical stage, T classification, N classification, liver metastasis and vascular invasion. Importantly, Kaplan-Meier survival and Cox regression analyses were executed to evaluate the prognosis of PDAC and found that LKB1 protein expression was one of the independent prognostic factors for overall survival of PDAC patients.
A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data
Authors: Lu Qiongshi , Hu Yiming , Sun Jiehuan , Cheng Yuwei , Cheung Kei-Hoi , Zhao Hongyu
Published: May 2015

Identifying functional regions in the human genome is a major goal in human genetics. Great efforts have been made to functionally annotate the human genome either through computational predictions, such as genomic conservation, or high-throughput experiments, such as the ENCODE project. These efforts have resulted in a rich collection of functional annotation data of diverse types that need to be jointly analyzed for integrated interpretation and annotation. Here we present GenoCanyon, a whole-genome annotation method that performs unsupervised statistical learning using 22 computational and experimental annotations thereby inferring the functional potential of each position in the human genome. With GenoCanyon, we are able to predict many of the known functional regions. The ability of predicting functional regions as well as its generalizable statistical framework makes GenoCanyon a unique and powerful tool for whole-genome annotation. The GenoCanyon web server is available at http://genocanyon.med.yale.edu
Depsipeptide Intermediates Interrogate Proposed Biosynthesis of Cereulide, the Emetic Toxin of Bacillus cereus
Authors: Marxen Sandra , Stark Timo D. , Rütschle Andrea , Lücking Genia , Frenzel Elrike , Scherer Siegfried , Ehling-Schulz Monika , Hofmann Thomas
Published: May 2015

Cereulide and isocereulides A-G are biosynthesized as emetic toxins by Bacillus cereus via a non-ribosomal peptide synthetase (NRPS) called Ces. Although a thiotemplate mechanisms involving cyclo-trimerization of ready-made D-O-Leu-D-Ala-L-O-Val-L-Val via a thioesterase (TE) domain is proposed for cereulide biosynthesis, the exact mechanism is far from being understood. UPLC-TOF MS analysis of B. cereus strains in combination with 13C-labeling experiments now revealed tetra-, octa- and dodecapeptides of a different sequence, namely (L-O-Val-L-Val-D-O-Leu-D-Ala)1-3, as intermediates of cereulide biosynthesis. Surprisingly, also di-, hexa- and decadepsipeptides were identified which, together with the structures of the previously reported isocereulides E, F and G, do not correlate to the currently proposed mechanism for cereulide biosynthesis and violate the canonical NRPS biosynthetic logic. UPLC-TOF MS metabolite analysis and bioinformatic gene cluster analysis highlighted dipeptides rather than single amino or hydroxy acids as the basic modules in tetradepsipeptide assembly and proposed the CesA C-terminal C* domain and the CesB C-terminal TE domain to function as a cooperative esterification and depsipeptide elongation center repeatedly recruiting the action of the C* domain to oligomerize tetradepsipeptides prior to the release of cereulide from the TE domain by macrocyclization.
Starvation-induced collective behavior in C. elegans
Authors: Artyukhin Alexander B. , Yim Joshua J. , Cheong Cheong Mi , Avery Leon
Published: May 2015

We describe a new type of collective behavior in C. elegans nematodes, aggregation of starved L1 larvae. Shortly after hatching in the absence of food, L1 larvae arrest their development and disperse in search for food. In contrast, after two or more days without food, the worms change their behavior—they start to aggregate. The aggregation requires a small amount of ethanol or acetate in the environment. In the case of ethanol, it has to be metabolized, which requires functional alcohol dehydrogenase sodh-1. The resulting acetate is used in de novo fatty acid synthesis and some of the newly made fatty acids are then derivatized to glycerophosphoethanolamides and released into the surrounding medium. We examined several other Caenorhabditis species and found an apparent correlation between propensity of starved L1s to aggregate and density dependence of their survival in starvation. Aggregation locally concentrates worms and may help the larvae to survive long starvation. This work demonstrates how presence of ethanol or acetate, relatively abundant small molecules in the environment, induces collective behavior in C. elegans associated with different survival strategies.
Natural products with therapeutic potential in melanoma metastasis
Authors: AlQathama A. , Prieto J. M.
Published: May 2015

Natural products continue to provide lead cytotoxic compounds for cancer treatment but less attention has been given to antimigratory compounds. We here systematically and critically survey more than 30 natural products with direct in vitro and in vivo pharmacological effects on migration and/or metastasis of melanoma cells and chart the mechanisms of action for this underexploited property.
Polysaccharide from garlic straw: extraction, structural data, biological properties and application to beef meat preservation
Authors: Kallel Fatma , Driss Dorra , Bouaziz Fatma , Belghith Lilia , Zouari-Ellouzi Soumaya , Fatma chaari Fatma chaari , Haddar Anissa , Chaabouni Semia Ellouz , Ghorbel Raoudha
Published: May 2015

A novel polysaccharide (GSP) was isolated from garlic straw (Allium sativumL.) by hot water technique.
Squaramide-based tripodal ionophores for potentiometric sulfate-selective sensors with high selectivity
Authors: Liu Yueling , Qin Yu , Jiang Dechen
Published: May 2015

A class of squaramide-based tripodal molecules was employed as new ionophores for highly sensitive and selective sulfate-selective sensors.
An amperometric sensor for detection of tryptophan based on a pristine multi-walled carbon nanotube/graphene oxide hybrid
Authors: Han Junfeng , Wang Qingqing , Zhai Junfeng , Han Lei , Dong Shaojun
Published: May 2015

A pMWCNT/GO hybrid shows excellent catalytic activity towards tryptophan oxidation and can thus be used as electrode material in a biosensor for sensing tryptophan sensitively and selectively.
In situ nanoparticle sizing with zeptomole sensitivity
Authors: Batchelor-McAuley Christopher , Ellison Joanna , Tschulik Kristina , Hurst Philip L. , Boldt Regine , Compton Richard G.
Published: May 2015

We present the basis for an entirely new approach toin situ nanoparticle sizing of very small nanoparticles containing only12 zeptomoles of silvervia in situparticle coulometry.
Facile and controllable synthesis of hydroxyapatite/graphene hybrid materials with enhanced sensing performance towards ammonia
Authors: Zhang Qing , Liu Yong , Zhang Ying , Li Huixia , Tan Yanni , Luo Lanlan , Duan Junhao , Li Kaiyang , Banks Craig E.
Published: May 2015

Hydroxyapatite/graphene hybrid materials with two different morphologies exhibit high sensing ability towards ammonia at room temperature.
Sensitive detection of atrazine in tap water using TELISA
Authors: Qie Zhiwei , Bai Jialei , Xie Bin , Yuan Lin , Song Nan , Peng Yuan , Fan Xianjun , Zhou Huanying , Chen Fengchun , Li Shuang , Ning Baoan , Gao Zhixian
Published: May 2015

Sensitive detection of atrazine in tap water using a universal platform: novel TELISA.
NIR light induced H2evolution by a metal-free photocatalyst
Authors: Xia Xinyuan , Deng Ning , Cui Guanwei , Xie Junfeng , Shi Xifeng , Zhao Yingqiang , Wang Qian , Wang Wen , Tang Bo
Published: May 2015

A novel metal-free photocatalyst composed of g-C3N4and carbon quantum dots drives near-infrared induced H2generation from water.
A novel mechanochemical method for reconstructing the moisture-degraded HKUST-1
Authors: Sun Xuejiao , Li Hao , Li Yujie , Xu Feng , Xiao Jing , Xia Qibin , Li Yingwei , Li Zhong
Published: May 2015

A novel mechanochemical method was proposed to reconstruct quickly the moisture-degraded HKUST-1. The reconstructed samples show 95% surface area and 92% benzene adsorption capacity of the fresh HKUST-1.
Quantitative determination of fluoride in pure water using luminescent europium complexes
Authors: Butler Stephen J.
Published: May 2015

Two luminescent europium complexes are reported, each capable of the rapid, selective detection of fluoride in water. The probes are highly sensitive, permitting the quantitative determination of fluoride in drinking water samples, within the concentration range relevant to water fluoridation (20–210 μM).
Tuning magnetism by biaxial strain in native ZnO
Authors: Peng Chengxiao , Wang Yuanxu , Cheng Zhenxiang , Zhang Guangbiao , Wang Chao , Yang Gui
Published: May 2015

Strain conditions have little effect on the defect formation energy of Zn and O vacancies in ZnO, but they do affect the magnetism significantly.
Protein–ligand docking using fitness learning-based artificial bee colony with proximity stimuli
Authors: Uehara Shota , Fujimoto Kazuhiro J. , Tanaka Shigenori
Published: May 2015

A novel optimization algorithm FlABCps was introduced for protein–ligand docking. The performance of FlABCps was analyzed in terms of the energy landscape and the binding pocket structure of the target protein.
Modulating the magnetic behavior of Fe(ii)–MOF-74 by the high electron affinity of the guest molecule
Authors: Han Sungmin , Kim Heejin , Kim Jaehoon , Jung Yousung
Published: May 2015

The O2 adsorption on Fe–MOF-74, which has high electron affinity, can induce a largely enhanced FM coupling between the intrachain Fe centers in Fe–MOF-74 through the superexchange interaction compared to Bare Fe–MOF-74, and it also leads to a different intrachain magnetic behavior in comparison with the olefin adsorbed Fe–MOF-74.
Photoisomerization action spectroscopy: flicking the protonated merocyanine–spiropyran switch in the gas phase
Authors: Markworth Peter B. , Adamson Brian D. , Coughlan Neville J. A. , Goerigk Lars , Bieske Evan J.
Published: May 2015

Molecular ions drifting through buffer gas are exposed to tunable laser light causing a detectable change in their collision cross section and arrival time at the ion detector. The effect can be exploited to obtain action electronic spectra for selected molecular isomers in the gas phase.
Exfoliated carbon nitride nanosheets decorated with NiS as an efficient noble-metal-free visible-light-driven photocatalyst for hydrogen evolution
Authors: Lu Yongtao , Chu Dongmei , Zhu Mingshan , Du Yukou , Yang Ping
Published: May 2015

Exfoliated ultrathin C3N4nanosheets decorated with NiS as a highly efficient visible-light-driven photocatalyst for photoinduced hydrogen evolution.
Effects of different electrolytes on the electrochemical and dynamic behavior of electric double layer capacitors based on a porous silicon carbide electrode
Authors: Kim Myeongjin , Oh Ilgeun , Kim Jooheon
Published: May 2015

Controlling the structure and morphology of porous electrode materials is an effective strategy for realizing high surface area and efficient paths for ion diffusion.
Size and polydispersity trends found in gold nanoparticles synthesized by laser ablation in liquids
Authors: Tomko J. , Naddeo J. J. , Jimenez R. , Tan Y. , Steiner M. , Fitz-Gerald J. M. , Bubb D. M. , O'Malley S. M.
Published: May 2015

In this work, we compare our experimental results with the latest computational findings for the synthesis of nanoparticles via Laser Ablation in Liquids (LAL). In addition, we demonstrate the usefulness of shadowgraphy imaging of the cavitation bubble in determination of ablation thresholds and irradiation efficiency.
5-Thiocyanato-2′-deoxyuridine as a possible radiosensitizer: electron-induced formation of uracil-C5-thiyl radical and its dimerization
Authors: Zdrowowicz Magdalena , Chomicz Lidia , Żyndul Michał , Wityk Paweł , Rak Janusz , Wiegand Tyler J. , Hanson Cameron G. , Adhikary Amitava , Sevilla Michael D.
Published: May 2015

ESR along with LC-MS analyses demonstrate electron-induced S–CN and C5–SCN bond cleavage in 5-thiocyanato-2-deoxyuridine (SCNdU). Hence, SCNdU could be a potential radiosensitizer by causing intra-, interstrand, and DNA-protein crosslinking via S–S dimer formation.
Anion resonances and above-threshold dynamics of coenzyme Q0
Authors: Bull James N. , West Christopher W. , Verlet Jan R. R.
Published: May 2015

Anion resonances and associated above-threshold dynamics of co-enzyme Q0 were studied using frequency-, angle-, and time-resolved photoelectron imaging.
Electrochemical growth of CoNi and Pt–CoNi soft magnetic composites on an alkanethiol monolayer-modified ITO substrate
Authors: Escalera-López D. , Gómez E. , Vallés E.
Published: May 2015

CoNi and Pt–CoNi magnetic layers on indium-tin oxide (ITO) substrates modified by an alkanethiol self-assembled monolayer (SAM) have been electrochemically obtained as an initial stage to prepare semiconducting layer-SAM-magnetic layer hybrid structures.
In situ growth of TiO2 nanocrystals on g-C3N4 for enhanced photocatalytic performance
Authors: Li Hong , Zhou Liang , Wang Lingzhi , Liu Yongdi , Lei Juying , Zhang Jinlong
Published: May 2015

Highly dispersed TiO2 nanocrystals with (001) facets were successfully grown in situ on g-C3N4 through a facial method. The resultant composite exhibits remarkably enhanced photocatalysis compared to pure TiO2 or g-C3N4 or mechanically mixed TiO2/g-C3N4.