bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and determinants of anaemia among children aged 0–59 months in a rural region of Armenia: a case–control study
Authors: Demirchyan Anahit , Petrosyan Varduhi , Sargsyan Viktoria , Hekimian Kim 
Published: September 2015

AbstractObjectiveDespite the trend of increasing prevalence of childhood anaemia in Armenia, no studies exploring its risk factors have been conducted in the country. The present study aimed to investigate the prevalence and determinants of childhood anaemia in rural Armenia.DesignBlood Hb level was measured among a representative sample of children using the HemoCue Hb201+ analyser. The revealed cases with anaemia were compared with randomly selected non-anaemic controls. Mothers of cases and controls were interviewed. Logistic and linear regression models were fitted to identify the risk factors of anaemia and low Hb level, respectively.SettingTalin communities, Aragatsotn Province, Armenia.SubjectsChildren under 5 years of age in Talin region.ResultsOf the 729 studied children, 32·4 % were anaemic with 14·7 % having moderate/severe anaemia. Infants were the most affected group with 51·1 % being anaemic before 6 months and 67·9 % at 6–12 months of age. Fitted regression models identified the following predictors of anaemia: younger age, male gender, shorter birth length, anaemia during pregnancy, lower meal frequency per day, lack of meat in the diet, using dung cakes for heating and living in a community that received an incomplete set of nutrition interventions.ConclusionsThe study identified several modifiable risk factors that could be targeted to reduce childhood anaemia in rural Armenia and, possibly, in rural areas in other low-/middle-income countries. The suggested interventions include prevention and treatment of anaemia during pregnancy, provision of adequate complementary feeding to children with inclusion of meat in their daily diet and reduction of their exposure to biomass fuel smoke.
Hyperspectral light sheet microscopy
Authors: Jahr Wiebke , Schmid Benjamin , Schmied Christopher , Fahrbach Florian O. , Huisken Jan 
Published: September 2015

AbstractTo study the development and interactions of cells and tissues, multiple fluorescent markers need to be imaged efficiently in a single living organism. Instead of acquiring individual colours sequentially with filters, we created a platform based on line-scanning light sheet microscopy to record the entire spectrum for each pixel in a three-dimensional volume. We evaluated data sets with varying spectral sampling and determined the optimal channel width to be around 5 nm. With the help of these data sets, we show that our setup outperforms filter-based approaches with regard to image quality and discrimination of fluorophores. By spectral unmixing we resolved overlapping fluorophores with up to nanometre resolution and removed autofluorescence in zebrafish and fruit fly embryos.
A multimodal MRI dataset of professional chess players
Authors: Li Kaiming , Jiang Jing , Qiu Lihua , Yang Xun , Huang Xiaoqi , Lui Su , Gong Qiyong 
Published: September 2015

AbstractChess is a good model to study high-level human brain functions such as spatial cognition, memory, planning, learning and problem solving. Recent studies have demonstrated that non-invasive MRI techniques are valuable for researchers to investigate the underlying neural mechanism of playing chess. For professional chess players (e.g., chess grand masters and masters or GM/Ms), what are the structural and functional alterations due to long-term professional practice, and how these alterations relate to behavior, are largely veiled. Here, we report a multimodal MRI dataset from 29 professional Chinese chess players (most of whom are GM/Ms), and 29 age matched novices. We hope that this dataset will provide researchers with new materials to further explore high-level human brain functions.
Regional paleofire regimes affected by non-uniform climate, vegetation and human drivers
Authors: Blarquez Olivier , Ali Adam A. , Girardin Martin P. , Grondin Pierre , Fréchette Bianca , Bergeron Yves , Hély Christelle 
Published: September 2015

AbstractClimate, vegetation and humans act on biomass burning at different spatial and temporal scales. In this study, we used a dense network of sedimentary charcoal records from eastern Canada to reconstruct regional biomass burning history over the last 7000 years at the scale of four potential vegetation types: open coniferous forest/tundra, boreal coniferous forest, boreal mixedwood forest and temperate forest. The biomass burning trajectories were compared with regional climate trends reconstructed from general circulation models, tree biomass reconstructed from pollen series and human population densities. We found that non-uniform climate, vegetation and human drivers acted on regional biomass burning history. In the open coniferous forest/tundra and dense coniferous forest, the regional biomass burning was primarily shaped by gradual establishment of less climate-conducive burning conditions over 5000 years. In the mixed boreal forest an increasing relative proportion of flammable conifers in landscapes since 2000 BP contributed to maintaining biomass burning constant despite climatic conditions less favourable to fires. In the temperate forest, biomass burning was uncoupled with climatic conditions and the main driver was seemingly vegetation until European colonization, i.e. 300 BP. Tree biomass and thus fuel accumulation modulated fire activity, an indication that biomass burning is fuel-dependent and notably upon long-term co-dominance shifts between conifers and broadleaf trees.
Experimental Demonstration of a Synthetic Lorentz Force by Using Radiation Pressure
Authors: Šantić N. , Dubček T. , Aumiler D. , Buljan H. , Ban T. 
Published: September 2015

AbstractSynthetic magnetism in cold atomic gases opened the doors to many exciting novel physical systems and phenomena. Ubiquitous are the methods used for the creation of synthetic magnetic fields. They include rapidly rotating Bose-Einstein condensates employing the analogy between the Coriolis and the Lorentz force and laser-atom interactions employing the analogy between the Berry phase and the Aharonov-Bohm phase. Interestingly, radiation pressure - being one of the most common forces induced by light - has not yet been used for synthetic magnetism. We experimentally demonstrate a synthetic Lorentz force, based on the radiation pressure and the Doppler effect, by observing the centre-of-mass motion of a cold atomic cloud. The force is perpendicular to the velocity of the cold atomic cloud and zero for the cloud at rest. Our novel concept is straightforward to implement in a large volume, for a broad range of velocities and can be extended to different geometries.
Ultralow threading dislocation density in GaN epilayer on near-strain-free GaN compliant buffer layer and its applications in hetero-epitaxial LEDs
Authors: Shih Huan-Yu , Shiojiri Makoto , Chen Ching-Hsiang , Yu Sheng-Fu , Ko Chung-Ting , Yang Jer-Ren , Lin Ray-Ming , Chen Miin-Jang 
Published: September 2015

AbstractHigh threading dislocation (TD) density in GaN-based devices is a long unresolved problem because of the large lattice mismatch between GaN and the substrate, which causes a major obstacle for the further improvement of next-generation high-efficiency solid-state lighting and high-power electronics. Here, we report InGaN/GaN LEDs with ultralow TD density and improved efficiency on a sapphire substrate, on which a near strain-free GaN compliant buffer layer was grown by remote plasma atomic layer deposition. This “compliant” buffer layer is capable of relaxing strain due to the absorption of misfit dislocations in a region within ~10 nm from the interface, leading to a high-quality overlying GaN epilayer with an unusual TD density as low as 2.2 × 105 cm−2. In addition, this GaN compliant buffer layer exhibits excellent uniformity up to a 6” wafer, revealing a promising means to realize large-area GaN hetero-epitaxy for efficient LEDs and high-power transistors.
RETRACTED ARTICLE: MircoRNA-33a inhibits epithelial-to-mesenchymal transition and metastasis and could be a prognostic marker in non-small cell lung cancer
Authors: Yang Lihua , Yang Jie , Li Jingqiu , Shen Xingkai , Le Yanping , Zhou Chengwei , Wang Shaomin , Zhang Shun , Xu Dazhi , Gong Zhaohui 
Published: September 2015

AbstractUnderstanding the molecular mechanism by which epithelial mesenchymal transition (EMT)-mediated cancer metastasis and how microRNA (miRNA) regulates lung cancer progression via Twist1-activated EMT may provide potential therapeutic targets for cancer therapy. Here we found that miR-33a, an intronic miRNA located within the sterol regulatory element-binding protein 2 (SREBP-2) gene, is expressed at low levels in metastatic non-small cell lung cancer (NSCLC) cells and is inversely correlated with Twist1 expression. Conversely, miR-33a knockdown induces EMT and miR-33a overexpression blocks EMT by regulating of Twist1 expression in NSCLC cells. Bioinformatical prediction and luciferase reporter assay confirm that Twist1 is a direct target of miR-33a. Additionally, Twist1 knockdown blocks EMT-related metastasis and forced expression of miR-33a inhibits lung cancer metastasis in a xenograft animal model. Clinically, miR-33a is found to be at low levels in NSCLC patients and down-regulation of miR-33a predicts a poor prognosis. These findings suggest that miR-33a targets Twist1 and inhibits invasion and metastasis in NSCLC. Thus, miR-33a might be a potential prognostic marker and of therapeutic relevance for NSCLC metastasis intervention.
Inversed Vernier effect based single-mode laser emission in coupled microdisks
Authors: Li Meng , Zhang Nan , Wang Kaiyang , Li Jiankai , Xiao Shumin , Song Qinghai 
Published: September 2015

AbstractRecently, on-chip single-mode laser emissions in coupled microdisks have attracted considerable research attention due to their wide applications. While most of single-mode lasers in coupled microdisks or microrings have been qualitatively explained by either Vernier effect or inversed Vernier effect, none of them have been experimentally confirmed. Here, we studied the mechanism of single-mode laser operation in coupled microdisks. We found that the mode numbers had been significantly reduced to nearly single-mode within a large pumping power range from threshold to gain saturation. The detail laser spectra showed that the largest gain and the first lasing peak were mainly generated by one disk and the laser intensity was proportional to the wavelength detuning of two set of modes. The corresponding theoretical analysis showed that the experimental observations were dominated by internal coupling within one cavity, which was similar to the recently explored inversed Vernier effect in two coupled microrings. We believe our finding will be important for understanding the previous experimental findings and the development of on-chip single-mode laser.
The roles of Eu during the growth of eutectic Si in Al-Si alloys
Authors: Li Jiehua , Hage Fredrik , Wiessner Manfred , Romaner Lorenz , Scheiber Daniel , Sartory Bernhard , Ramasse Quentin , Schumacher Peter 
Published: September 2015

AbstractControlling the growth of eutectic Si and thereby modifying the eutectic Si from flake-like to fibrous is a key factor in improving the properties of Al-Si alloys. To date, it is generally accepted that the impurity-induced twinning (IIT) mechanism and the twin plane re-entrant edge (TPRE) mechanism as well as poisoning of the TPRE mechanism are valid under certain conditions. However, IIT, TPRE or poisoning of the TPRE mechanism cannot be used to interpret all observations. Here, we report an atomic-scale experimental and theoretical investigation on the roles of Eu during the growth of eutectic Si in Al-Si alloys. Both experimental and theoretical investigations reveal three different roles: (i) the adsorption at the intersection of Si facets, inducing IIT mechanism, (ii) the adsorption at the twin plane re-entrant edge, inducing TPRE mechanism or poisoning of the TPRE mechanism and (iii) the segregation ahead of the growing Si twins, inducing a solute entrainment within eutectic Si. This investigation not only demonstrates a direct experimental support to the well-accepted poisoning of the TPRE and IIT mechanisms, but also provides a full picture about the roles of Eu atoms during the growth of eutectic Si, including the solute entrainment within eutectic Si.
Compact microstrip tri‐band lowpass‐bandpass filter
Authors: Xu Jin 
Published: September 2015

A compact microstrip tri‐band lowpass‐bandpass filter is described. Two different sets of λ/4 uniform‐impedance open stubs generate the desired transmission zeros (TZs) to divide a lowpass frequency response based on a radial stub loaded high‐impedance microstrip line into a tri‐band lowpass‐bandpass frequency response. A lowpass passband with a 3 dB cutoff frequency of 0.66 GHz, and two bandpass passbands centred at 1.57 and 2.45 GHz for global positioning system and wireless local area network applications are obtained in this design. The fabricated tri‐band lowpass‐bandpass filter occupies a compact circuit area of 0.065 λgc × 0.085 λgc. Seven TZs around the three passbands result in high band‐to‐band isolation, good passband selectivity and a wide upper stopband.
Characteristics of digitised millimetre‐wave metal reflectarray antennas
Authors: Yi Minwoo , Lee Woosang , So Joonho 
Published: September 2015

Reflectarray antennas composed of rectangular grooves with a digitised phase‐shift element are designed for the millimetre‐wave region. The digitised metal antennas have been realised by quantising the phase shift of each rectangular groove. For 4 bit quantised antennas, the far‐field patterns are very similar to those of the non‐digitised case and especially show that the measured gain of the 2 bit reflectarray is only 1 dB lower than that of a non‐digitised reflectarray antenna. These results will contribute to saving manufacturing cost and time and the guidance of the phase shifter for an active metal reflectarray antenna for millimetre‐wave wireless networking or imaging systems.
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis
Authors: Ye Yuzhen , Tang Haixu 
Published: August 2015

Abstract
Motivation: Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture of microbial species) and other meta-omics approaches hold even greater promise for providing additional insights into functional and regulatory characteristics of the microbial communities. Current metatranscriptomics projects are often carried out without matched metagenomic datasets (of the same microbial communities). For the projects that produce both metatranscriptomic and metagenomic datasets, their analyses are often not integrated. Metagenome assemblies are far from perfect, partially explaining why metagenome assemblies are not used for the analysis of metatranscriptomic datasets.
Results: Here, we report a reads mapping algorithm for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k -mers ( k -mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. We developed an application of this mapping algorithm: a reference-based approach to metatranscriptome assembly using graphs of metagenome assembly as the reference. Our results show that this new approach (called TAG) helps to assemble substantially more transcripts that otherwise would have been missed or truncated because of the fragmented nature of the reference metagenome.
Availability and implementation: TAG was implemented in C++ and has been tested extensively on the Linux platform. It is available for download as open source at http://omics.informatics.indiana.edu/TAG .
Contact: yye@indiana.edu
Computing secure sets in graphs using answer set programming
Authors: Abseher Michael , Bliem Bernhard , Charwat Günther , Dusberger Frederico , Woltran Stefan 
Published: September 2015

Abstract
The notion of secure sets is a rather new concept in the area of graph theory. Applied to social network analysis, the goal is to identify groups of entities that can repel any attack or influence from the outside. In this article, we tackle this problem by utilizing Answer Set Programming (ASP). It is known that verifying whether a set is secure in a graph is already co-NP-hard. Therefore, the problem of enumerating all secure sets is challenging for ASP and its systems. In particular, encodings for this problem seem to require disjunction and also recursive aggregates. Here, we provide such encodings and analyse their performance using the Clingo system. Furthermore, we study several problem variants, including multiple secure or insecure sets, and weighted graphs.
Genome scaffolding with PE-contaminated mate-pair libraries
Authors: Sahlin Kristoffer , Chikhi Rayan , Arvestad Lars 
Published: August 2015

AbstractScaffolding is often an essential step in a genome assembly process, in which contigs are ordered and oriented using read pairs from a combination of paired-ends libraries and longer-range mate-pair libraries. Although a simple idea, scaffolding is unfortunately hard to get right in practice. One source of problem is so-called PE-contamination in mate-pair libraries, in which a non-negligible fraction of the read pairs get the wrong orientation and a much smaller insert size than what is expected. This contamination has been discussed in previous work on integrated scaffolders in end-to-end assemblers such as Allpaths-LG and MaSuRCA but the methods relies on the fact that the orientation is observable,e.g.,by finding the junction adapter sequence in the reads. This is not always the case, making orientation and insert size of a read pair stochastic. Furthermore, work on modeling PE-contamination has so far been disregarded in stand-alone scaffolders and the effect that PE-contamination has on scaffolding quality has not been examined before.We have addressed PE-contamination in an update of our scaffolder BESST. We formulate the problem as an Integer Linear Program (ILP) and use characteristics of the problem, such as contig lengths and insert size, to efficiently solve the ILP using a linear amount (with respect to the number of contigs) of Linear Programs. Our results show significant improvement over both integrated and standalone scaffolders. The impact of modeling PE-contamination is quantified by comparison with the previous BESST model. We also show how other scaffolders are vulnerable to PE-contaminated libraries, resulting in increased number of misassemblies, more conservative scaffolding, and inflated assembly sizes.The model is implemented in BESST. Source code and usage instructions are found athttps://github.com/ksahlin/BESST. BESST can also be downloaded using PyPI.
The mysterious orphans ofMycoplasmataceae
Authors: Tatarinova Tatiana V. , Lysnyansky Inna , Nikolsky Yuri V. , Bolshoy Alexander 
Published: August 2015

AbstractBackgroundThe length of a protein sequence is largely determined by its function, i.e. each functional group is associated with an optimal size. However, comparative genomics revealed that proteins’ length may be affected by additional factors. In 2002 it was shown that in bacteriumEscherichia coliand the archaeonArchaeoglobus fulgidus,protein sequences with no homologs are, on average, shorter than those with homologs [1]. Most experts now agree that the length distributions are distinctly different between protein sequences with and without homologs in bacterial and archaeal genomes. In this study, we examine this postulate by a comprehensive analysis of all annotated prokaryotic genomes and focusing on certain exceptions.ResultsWe compared lengths’ distributions of “having homologs proteins” (HHPs) and “non-having homologs proteins” (orphans or ORFans) in all currently annotated completely sequenced prokaryotic genomes. As expected, the HHPs and ORFans have strikingly different length distributions in almost all genomes. As previously established, the HHPs, indeed, are, on average, longer than the ORFans, and the length distributions for the ORFans have a relatively narrow peak, in contrast to the HHPs, whose lengths spread over a wider range of values. However, about thirty genomes do not obey these rules. Practically all genomes ofMycoplasmaandUreaplasmahave atypical ORFans distributions, with the mean lengths of ORFan larger than the mean lengths of HHPs. These genera constitute over 80% of atypical genomes.ConclusionsWe confirmed on a ubiquitous set of genomes the previous observation that HHPs and ORFans have different gene length distributions. We also showed thatMycoplasmataceaegenomes have very distinctive distributions of ORFans lengths. We offer several possible biological explanations of this phenomenon.
Phylogenetic community structure metrics and null models: a review with new methods and software
Authors: Miller Eliot T. , Farine Damien R. , Trisos Christopher H. 
Published: August 2015

AbstractCompetitive exclusion and habitat filtering are believed to have an important influence on the assembly of ecological communities, but ecologists and evolutionary biologists have not reached a consensus on how to quantify patterns that would reveal the action of these processes. No fewer than 22 phylogenetic community structure metrics and nine null models can be combined, providing 198 approaches to test for such patterns. Choosing statistically appropriate approaches is currently a daunting task. First, given random community assembly, we assessed similarities among metrics and among null models in their behavior across communities varying in species richness. Second, we developed spatially explicit, individual-based simulations where communities were assembled either at random, by competitive exclusion or by habitat filtering. Third, we quantified the performance (type I and II error rates) of all 198 approaches against each of the three assembly processes. Many metrics and null models are functionally equivalent, more than halving the number of unique approaches. Moreover, an even smaller subset of metric and null model combinations is suitable for testing community assembly patterns. Metrics like mean pairwise phylogenetic distance and phylogenetic diversity were better able to detect simulated community assembly patterns than metrics like phylogenetic abundance evenness. A null model that simulates regional dispersal pressure on the community of interest outperformed all others. We introduce a flexible new R package,metricTester, to facilitate robust analyses of method performance. The package is programmed in parallel to readily accommodate integration of new row-wise matrix calculations (metrics) and matrix-wise randomizations (null models) to generate expectations and quantify error rates of proposed methods.