CBA: cluster-guided batch alignment for single cell RNA-seq

The power of single-cell RNA sequencing (scRNA-seq) in detecting cell heterogeneity or developmental process is becoming more and more evident every day. The granularity of this knowledge is further propelled when combining two batches of scRNA-seq into a single large dataset. This strategy is however hampered by technical differences between these batches. Typically, these batch effects are resolved by matching similar cells across the different batches. Current approaches, however, do not take into account that we can constrain this matching further as cells can also be matched on their cell type identity. We use an auto-encoder to embed two batches in the same space such that cells are matched. To accomplish this, we use a loss function that preserves: (1) cell-cell distances within each of the two batches, as well as (2) cell-cell distances between two batches when the cells are of the same cell-type. The cell-type guidance is unsupervised, i.e., a cell-type is defined as a cluster in the original batch. We evaluated the performance of our cluster-guided batch alignment (CBA) using pancreas and mouse cell atlas datasets, against six state-of-the-art single cell alignment methods: Seurat v3, BBKNN, Scanorama, Harmony, LIGER, and BERMUDA. Compared to other approaches, CBA preserves the cluster separation in the original datasets while still being able to align the two datasets. We confirm that this separation is biologically meaningful by identifying relevant differential expression of genes for these preserved clusters.Molecular Technology and Informatics for Personalised Medicine and Healt

Relaxation of surface charge on rotating dielectric spheres: Implications on dynamic electrorheological effects

We have examined the effect of an oscillatory rotation of a polarized dielectric particle. The rotational motion leads to a re-distribution of the polarization charge on the surface of the particle. We show that the time averaged steady-state dipole moment is along the field direction, but its magnitude is reduced by a factor which depends on the angular velocity of rotation. As a result, the rotational motion of the particle reduces the electrorheological effect. We further assume that the relaxation of polarized charge is arised from a finite conductivity of the particle or host medium. We calculate the relaxation time based on the Maxwell-Wagner theory, suitably generalized to include the rotational motion. Analytic expressions for the reduction factor and the relaxation time are given and their dependence on the angular velocity of rotation will be discussed.Comment: Accepted for publications by Phys. Rev.

Equivalence Theorem and Probing the Electroweak Symmetry Breaking Sector

We examine the Lorentz non-invariance ambiguity in longitudinal weak-boson scatterings and the precise conditions for the validity of the Equivalence Theorem (ET). {\it Safe} Lorentz frames for applying the ET are defined, and the intrinsic connection between the longitudinal weak-boson scatterings and probing the symmetry breaking sector is analyzed. A universal precise formulation of the ET is presented for both the Standard Model and the Chiral Lagrangian formulated Electro-Weak Theories. It is shown that in electroweak theories with strongly interacting symmetry breaking sector, the longitudinal weak-boson scattering amplitude {\it under proper conditions} can be replaced by the corresponding Goldstone-boson scattering amplitude in which all the internal weak-boson lines and fermion loops are ignored.Comment: 20 pages, in LaTeX, to appear in Phys. Rev. D (1995). A few minor corrections were made to clarify our viewpoint of the Equivalence Theorem and compare our conclusion with those in the literatur

The superconductivity at 18 K in LiFeAs system

A new iron arsenide superconducting system LiFeAs was found that crystallizes into a tetragonal structure with space group P4/nmm. The superconductivity with Tc up to 18 K was observed in the compounds. This simple 111 type layered iron arsenide superconductor can be viewed as an analogue of the infinite layer structure of copper oxides.Comment: 11 pages 3 Figure

A Damage Mechanics Approach to Fatigue Assessment in Offshore Structures

This article is intended to describe the development of a fatigue damage model capable of assessing fatigue damage in offshore structures. This is achieved by for mulating a set of damage coupled constitutive and evolution equations which make the for mulation of a unified approach possible under both low and high cycle fatigue damage and consistent with the structural dynamic response of the changing/deteriorating material be haviors. The structural analysis for the whole designed period, say about 30 years, can be carried out with the aid of the proposed analytical procedure, in which the fundamental characteristics of sea wave statistics responsible for the structural dynamic response can be sufficiently considered. An offshore structure subject to complex ocean environment is described by a general stochastic system which embeds a group of stochastic subsystems, each characterizing a duty cycle. An effective analytical method is established by introduc ing the concept of duty strain range with a clear mathematical definition and its analytical solution which covers all possible spectral parameters. The history-dependent damage is also included in the damage model so that the overload effects can be analyzed. It should be pointed out that the whole procedure can be fully computerized such that the practical or engineering significance of varying design variables can be readily highlighted.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/67255/2/10.1177_105678959300200405.pd

Machine Learning in Automated Text Categorization

The automated categorization (or classification) of texts into predefined categories has witnessed a booming interest in the last ten years, due to the increased availability of documents in digital form and the ensuing need to organize them. In the research community the dominant approach to this problem is based on machine learning techniques: a general inductive process automatically builds a classifier by learning, from a set of preclassified documents, the characteristics of the categories. The advantages of this approach over the knowledge engineering approach (consisting in the manual definition of a classifier by domain experts) are a very good effectiveness, considerable savings in terms of expert manpower, and straightforward portability to different domains. This survey discusses the main approaches to text categorization that fall within the machine learning paradigm. We will discuss in detail issues pertaining to three different problems, namely document representation, classifier construction, and classifier evaluation.Comment: Accepted for publication on ACM Computing Survey

A Measurement of Psi(2S) Resonance Parameters

Cross sections for e+e- to hadons, pi+pi- J/Psi, and mu+mu- have been measured in the vicinity of the Psi(2S) resonance using the BESII detector operated at the BEPC. The Psi(2S) total width; partial widths to hadrons, pi+pi- J/Psi, muons; and corresponding branching fractions have been determined to be Gamma(total)= (264+-27) keV; Gamma(hadron)= (258+-26) keV, Gamma(mu)= (2.44+-0.21) keV, and Gamma(pi+pi- J/Psi)= (85+-8.7) keV; and Br(hadron)= (97.79+-0.15)%, Br(pi+pi- J/Psi)= (32+-1.4)%, Br(mu)= (0.93+-0.08)%, respectively.Comment: 8 pages, 6 figure

Measurements of the Mass and Full-Width of the ηc\eta_c Meson

In a sample of 58 million $J/\psi$ events collected with the BES II detector, the process J/$\psi\to\gamma\eta_c$ is observed in five different decay channels: $\gamma K^+K^-\pi^+\pi^-$, $\gamma\pi^+\pi^-\pi^+\pi^-$, $\gamma K^\pm K^0_S \pi^\mp$ (with $K^0_S\to\pi^+\pi^-$), $\gamma \phi\phi$ (with $\phi\to K^+K^-$) and $\gamma p\bar{p}$. From a combined fit of all five channels, we determine the mass and full-width of $\eta_c$ to be $m_{\eta_c}=2977.5\pm1.0 ({stat.})\pm1.2 ({syst.})$ MeV/$c^2$ and $\Gamma_{\eta_c} = 17.0\pm3.7 ({stat.})\pm7.4 ({syst.})$ MeV/$c^2$.Comment: 9 pages, 2 figures and 4 table. Submitted to Phys. Lett.

High efficient electrical stimulation of hippocampal slices with vertically aligned carbon nanofiber microbrush array

Long-term neuroprostheses for functional electrical stimulation must efficiently stimulate tissue without electrolyzing water and raising the extracellular pH to toxic levels. Comparison of the stimulation efficiency of tungsten wire electrodes (W wires), platinum microelectrode arrays (PtMEA), as-grown vertically aligned carbon nanofiber microbrush arrays (VACNF MBAs), and polypyrrole coated (PPy-coated) VACNF MBAs in eliciting field potentials in the hippocampus slice indicates that, at low stimulating voltages that preclude the electrolysis of water, only the PPy-coated VACNF MBA is able to stimulate the CA3 to CA1 pathway. Unlike the W wires, PtMEA, as-grown VACNF MBA, and the PPy-coated VACNF MBA elicit only excitatory postsynaptic potentials (EPSPs). Furthermore, the PPy-coated VACNF MBA evokes somatic action potentials in addition to EPSPs. These results highlight the PPy-coated VACNF’s advantages in lower electrode impedance, ability to stimulate tissue through a biocompatible chloride flux, and stable vertical alignment in liquid that enables access to spatially confined regions of neuronal cells