Effect of pooling samples on the efficiency of comparative studies using microarrays

Many biomedical experiments are carried out by pooling individual biological samples. However, pooling samples can potentially hide biological variance and give false confidence concerning the data significance. In the context of microarray experiments for detecting differentially expressed genes, recent publications have addressed the problem of the efficiency of sample-pooling, and some approximate formulas were provided for the power and sample size calculations. It is desirable to have exact formulas for these calculations and have the approximate results checked against the exact ones. We show that the difference between the approximate and exact results can be large. In this study, we have characterized quantitatively the effect of pooling samples on the efficiency of microarray experiments for the detection of differential gene expression between two classes. We present exact formulas for calculating the power of microarray experimental designs involving sample pooling and technical replications. The formulas can be used to determine the total numbers of arrays and biological subjects required in an experiment to achieve the desired power at a given significance level. The conditions under which pooled design becomes preferable to non-pooled design can then be derived given the unit cost associated with a microarray and that with a biological subject. This paper thus serves to provide guidance on sample pooling and cost effectiveness. The formulation in this paper is outlined in the context of performing microarray comparative studies, but its applicability is not limited to microarray experiments. It is also applicable to a wide range of biomedical comparative studies where sample pooling may be involved.Comment: 8 pages, 1 figure, 2 tables; to appear in Bioinformatic

Words are Malleable: Computing Semantic Shifts in Political and Media Discourse

Recently, researchers started to pay attention to the detection of temporal shifts in the meaning of words. However, most (if not all) of these approaches restricted their efforts to uncovering change over time, thus neglecting other valuable dimensions such as social or political variability. We propose an approach for detecting semantic shifts between different viewpoints--broadly defined as a set of texts that share a specific metadata feature, which can be a time-period, but also a social entity such as a political party. For each viewpoint, we learn a semantic space in which each word is represented as a low dimensional neural embedded vector. The challenge is to compare the meaning of a word in one space to its meaning in another space and measure the size of the semantic shifts. We compare the effectiveness of a measure based on optimal transformations between the two spaces with a measure based on the similarity of the neighbors of the word in the respective spaces. Our experiments demonstrate that the combination of these two performs best. We show that the semantic shifts not only occur over time, but also along different viewpoints in a short period of time. For evaluation, we demonstrate how this approach captures meaningful semantic shifts and can help improve other tasks such as the contrastive viewpoint summarization and ideology detection (measured as classification accuracy) in political texts. We also show that the two laws of semantic change which were empirically shown to hold for temporal shifts also hold for shifts across viewpoints. These laws state that frequent words are less likely to shift meaning while words with many senses are more likely to do so.Comment: In Proceedings of the 26th ACM International on Conference on Information and Knowledge Management (CIKM2017

Magnetic structure of the Eu2+ moments in superconducting EuFe2(As1-xPx)2 with x = 0.19

The magnetic structure of the Eu2+ moments in the superconducting EuFe2(As1-xPx)2 sample with x = 0.19 has been determined using neutron scattering. We conclude that the Eu2+ moments are aligned along the c direction below T_C = 19.0(1) K with an ordered moment of 6.6(2) mu_B in the superconducting state. An impurity phase similar to the underdoped phase exists within the bulk sample which orders antiferromagnetically below T_N = 17.0(2) K. We found no indication of iron magnetic order, nor any incommensurate magnetic order of the Eu2+ moments in the sample.Comment: Accepted for publication in Phys. Rev. B (regular article

Application and research of wireless laser methane sensor in drainage pipeline monitoring

Laser methane sensor has been widely promoted and successfully applied in coal mines as a new and effective technology building on the approach of laser-based absorption detection. Compared with the traditional catalytic methane sensor, the laser methane sensor discussed offers the important advantages of a long calibration period, high detection precision, the absence of zero drift and low power consumption, all of which are significant advantages for use in coal mining applications. By compensating for the temperature and pressure of the gases present, the accuracy of the methane sensor is evident across a wide range of temperatures and pressures, making it suitable for gas detection, including methane, in pipelines as well. The wireless laser approach which is incorporated into the methane sensor allows wireless transmission and data uploading to a cloud server through NB-IoT. This tackles the problem in gas pipeline monitoring of the length of many pipelines and thus the wide distribution of the sensors, avoiding complicated wiring and thus high associated cost. Further, remote data management can then be achieved, all of which greatly improves the flexibility and security of the management of the pipeline and the data generated

Magnetization distribution and orbital moment in the non-Superconducting Chalcogenide Compound K0.8Fe1.6Se2

We have used polarized and unpolarized neutron diffraction to determine the spatial distribution of the magnetization density induced by a magnetic field of 9 T in the tetragonal phase of K0.8Fe1.6Se2. The maximum entropy reconstruction shows clearly that most of the magnetization is confined to the region around the iron atoms whereas there is no significant magnetization associated with either Se or K atoms. The distribution of magnetization around the Fe atom is slightly nonspherical with a shape which is extended along the [0 0 1] direction in the projection. Multipolar refinement results show that the electrons which give rise to the paramagnetic susceptibility are confined to the Fe atoms and their distribution suggests that they occupy 3d t2g-type orbitals with around 66% in those of xz/yz symmetry. Detail modeling of the magnetic form factor indicates the presence of an orbital moment to the total paramagnetic moment of Fe2+Comment: 7 pages, accepted for publication in Physical Review

Spin-wave softening and Hund's coupling in ferromagnetic manganites

Using one-orbital model of hole-doped manganites, we show with the help of Holstein-Primakov transformation that finite Hund's coupling is responsible for the spin-wave softening in the ferromagnetic $B$-phase manganites. We obtain an analytical result for the spin-wave spectrum for \JH\gg t. In the limit of infinte Hund's coupling, the spectrum is the conventional nearest-neighbor Heisenberg ferromagnetic spin-wave. The o(t/\JH)-order correction is negative and thus accounts for the softening near the zone boundary.Comment: 5 pages, 3 figure

Elastic-Net Regularization: Error estimates and Active Set Methods

This paper investigates theoretical properties and efficient numerical algorithms for the so-called elastic-net regularization originating from statistics, which enforces simultaneously l^1 and l^2 regularization. The stability of the minimizer and its consistency are studied, and convergence rates for both a priori and a posteriori parameter choice rules are established. Two iterative numerical algorithms of active set type are proposed, and their convergence properties are discussed. Numerical results are presented to illustrate the features of the functional and algorithms

Fluctuating volume-current formulation of electromagnetic fluctuations in inhomogeneous media: incandecence and luminescence in arbitrary geometries

We describe a fluctuating volume--current formulation of electromagnetic fluctuations that extends our recent work on heat exchange and Casimir interactions between arbitrarily shaped homogeneous bodies [Phys. Rev. B. 88, 054305] to situations involving incandescence and luminescence problems, including thermal radiation, heat transfer, Casimir forces, spontaneous emission, fluorescence, and Raman scattering, in inhomogeneous media. Unlike previous scattering formulations based on field and/or surface unknowns, our work exploits powerful techniques from the volume--integral equation (VIE) method, in which electromagnetic scattering is described in terms of volumetric, current unknowns throughout the bodies. The resulting trace formulas (boxed equations) involve products of well-studied VIE matrices and describe power and momentum transfer between objects with spatially varying material properties and fluctuation characteristics. We demonstrate that thanks to the low-rank properties of the associatedmatrices, these formulas are susceptible to fast-trace computations based on iterative methods, making practical calculations tractable. We apply our techniques to study thermal radiation, heat transfer, and fluorescence in complicated geometries, checking our method against established techniques best suited for homogeneous bodies as well as applying it to obtain predictions of radiation from complex bodies with spatially varying permittivities and/or temperature profiles

Security of payment for Hong Kong construction industry

In Hong Kong, getting paid is not always easy and the construction industry stands as an illustration of how much effort may be needed to achieve this and how adverse impacts can escalate from payment problems. At the moment, many jurisdictions have adopted some form of legislation or practical measures to enhance the ease and security of payment in the construction industry. Experience and insights from their operations provide guidance to Hong Kong for its way forward. By studying practices and feedback in other jurisdictions, this paper outlines and reviews the options and alternatives implemented for securing payment in the construction industry in Hong Kong. In addition, it also seeks to appraise their respective practicability for Hong Kong and highlight those areas to be considered if they are to be adopted or adapted for use in the Hong Kong construction industry. The ultimate aim is to provide an objective, balanced and reasoned overview for further study and discussion among stakeholders in the Hong Kong construction industry when moving forward. This is not intended to be an exhaustive review of all means adopted to achieve security of payment but aims to discuss those methods which are more likely to be suitable to be adopted in Hong Kong in the light of the circumstances and environment prevailing there. Furthermore, this study did not investigate the many modes of procurement that are available and which may address the concern of security of payment but focuses on the traditional form of contracts in use in Hong Kong. Public-private partnerships or private finance initiatives which would call for different discussions are not covered.published_or_final_versio