A computational framework to emulate the human perspective in flow cytometric data analysis

Background: In recent years, intense research efforts have focused on developing methods for automated flow cytometric data analysis. However, while designing such applications, little or no attention has been paid to the human perspective that is absolutely central to the manual gating process of identifying and characterizing cell populations. In particular, the assumption of many common techniques that cell populations could be modeled reliably with pre-specified distributions may not hold true in real-life samples, which can have populations of arbitrary shapes and considerable inter-sample variation. <p/>Results: To address this, we developed a new framework flowScape for emulating certain key aspects of the human perspective in analyzing flow data, which we implemented in multiple steps. First, flowScape begins with creating a mathematically rigorous map of the high-dimensional flow data landscape based on dense and sparse regions defined by relative concentrations of events around modes. In the second step, these modal clusters are connected with a global hierarchical structure. This representation allows flowScape to perform ridgeline analysis for both traversing the landscape and isolating cell populations at different levels of resolution. Finally, we extended manual gating with a new capacity for constructing templates that can identify target populations in terms of their relative parameters, as opposed to the more commonly used absolute or physical parameters. This allows flowScape to apply such templates in batch mode for detecting the corresponding populations in a flexible, sample-specific manner. We also demonstrated different applications of our framework to flow data analysis and show its superiority over other analytical methods. <p/>Conclusions: The human perspective, built on top of intuition and experience, is a very important component of flow cytometric data analysis. By emulating some of its approaches and extending these with automation and rigor, flowScape provides a flexible and robust framework for computational cytomics

Boson-fermion mappings for odd systems from supercoherent states

We extend the formalism whereby boson mappings can be derived from generalized coherent states to boson-fermion mappings for systems with an odd number of fermions. This is accomplished by constructing supercoherent states in terms of both complex and Grassmann variables. In addition to a known mapping for the full so(2$N$+1) algebra, we also uncover some other formal mappings, together with mappings relevant to collective subspaces.Comment: 40 pages, REVTE

Pseudo-Hermitian Hamiltonians, indefinite inner product spaces and their symmetries

We extend the definition of generalized parity $P$, charge-conjugation $C$ and time-reversal $T$ operators to nondiagonalizable pseudo-Hermitian Hamiltonians, and we use these generalized operators to describe the full set of symmetries of a pseudo-Hermitian Hamiltonian according to a fourfold classification. In particular we show that $TP$ and $CTP$ are the generators of the antiunitary symmetries; moreover, a necessary and sufficient condition is provided for a pseudo-Hermitian Hamiltonian $H$ to admit a $P$-reflecting symmetry which generates the $P$-pseudounitary and the $P$-pseudoantiunitary symmetries. Finally, a physical example is considered and some hints on the $P$-unitary evolution of a physical system are also given.Comment: 20 page

Schroedinger equation for joint bidirectional motion in time

The conventional, time-dependent Schroedinger equation describes only unidirectional time evolution of the state of a physical system, i.e., forward or, less commonly, backward. This paper proposes a generalized quantum dynamics for the description of joint, and interactive, forward and backward time evolution within a physical system. [...] Three applications are studied: (1) a formal theory of collisions in terms of perturbation theory; (2) a relativistically invariant quantum field theory for a system that kinematically comprises the direct sum of two quantized real scalar fields, such that one field evolves forward and the other backward in time, and such that there is dynamical coupling between the subfields; (3) an argument that in the latter field theory, the dynamics predicts that in a range of values of the coupling constants, the expectation value of the vacuum energy of the universe is forced to be zero to high accuracy. [...]Comment: 30 pages, no figures. Related material is in quant-ph/0404012. Differs from published version by a few added remarks on the possibility of a large-scale-average negative energy density in spac

Cytochrome oxidase subunit VI of Trypanosoma brucei is imported without a cleaved presequence and is developmentally regulated at both RNA and protein levels

Mitochondrial respiration in the African trypanosome undergoes dramatic developmental stage regulation. This requires co-ordinated control of components encoded by both the nuclear genome and the kinetoplast, the unusual mitochondrial genome of these parasites. As a model for understanding the co-ordination of these genomes, we have examined the regulation and mitochondrial import of a nuclear-encoded component of the cytochrome oxidase complex, cytochrome oxidase subunit VI (COXVI). By generating transgenic trypanosomes expressing intact or mutant forms of this protein, we demonstrate that COXVI is not imported using a conventional cleaved presequence and show that sequences at the N-terminus of the protein are necessary for correct mitochondrial sorting. Analyses of endogenous and transgenic COXVI mRNA and protein expression in parasites undergoing developmental stage differentiation demonstrates a temporal order of control involving regulation in the abundance of, first, mRNA and then protein. This represents the first dissection of the regulation and import of a nuclear-encoded protein into the cytochrome oxidase complex in these organisms, which were among the earliest eukaryotes to possess a mitochondrion

Attenuation of leukocyte sequestration by selective blockade of PECAM-1 or VCAM-1 in murine endotoxemia

Background: Molecular mechanisms regulating leukocyte sequestration into the tissue during endotoxemia and/or sepsis are still poorly understood. This in vivo study investigates the biological role of murine PECAM-1 and VCAM-1 for leukocyte sequestration into the lung, liver and striated skin muscle. Methods: Male BALB/c mice were injected intravenously with murine PECAM-1 IgG chimera or monoclonal antibody (mAb) to VCAM-1 ( 3 mg/kg body weight); controls received equivalent doses of IgG2a ( n = 6 per group). Fifteen minutes thereafter, 2 mg/kg body weight of Salmonella abortus equi endotoxin was injected intravenously. At 24 h after the endotoxin challenge, lungs, livers and striated muscle of skin were analyzed for their myeloperoxidase activity. To monitor intravital leukocyte-endothelial cell interactions, fluorescence videomicroscopy was performed in the skin fold chamber model of the BALB/c mouse at 3, 8 and 24 h after injection of endotoxin. Results: Myeloperoxidase activity at 24 h after the endotoxin challenge in lungs (12,171 +/- 2,357 mU/g tissue), livers ( 2,204 +/- 238 mU/g) and striated muscle of the skin ( 1,161 +/- 110 mU/g) was significantly reduced in both treatment groups as compared to controls, with strongest attenuation in the PECAM-1 IgG treatment group. Arteriolar leukocyte sticking at 3 h after endotoxin (230 +/- 46 cells x mm(-2)) was significantly reduced in both treatment groups. Leukocyte sticking in postcapillary venules at 8 h after endotoxin ( 343 +/- 69 cells/mm(2)) was found reduced only in the VCAM-1-mAb-treated animals ( 215 +/- 53 cells/mm(2)), while it was enhanced in animals treated with PECAM-1 IgG ( 572 +/- 126 cells/mm(2)). Conclusion: These data show that both PECAM-1 and VCAM-1 are involved in endotoxin-induced leukocyte sequestration in the lung, liver and muscle, presumably through interference with arteriolar and/or venular leukocyte sticking. Copyright (C) 2004 S. Karger AG, Basel

Tank-Circuit Assisted Coupling Method for Sympathetic Laser Cooling

We discuss the coupling of the motion of two ion species in separate Penning traps via a common tank circuit. The enhancement of the coupling assisted by the tank circuit is demonstrated by an avoided crossing behavior measurement of the motional modes of two coupled ions. We propose an intermittent laser cooling method for sympathetic cooling and provide a theoretical description. The technique enables tuning of the coupling strength between two ion species in separate traps and thus allows for efficient sympathetic cooling of an arbitrary type of single ion for high-precision Penning-trap experiments

Electrical Brain Responses in Language-Impaired Children Reveal Grammar-Specific Deficits

Background: Scientific and public fascination with human language have included intensive scrutiny of language disorders as a new window onto the biological foundations of language and its evolutionary origins. Specific language impairment (SLI), which affects over 7% of children, is one such disorder. SLI has received robust scientific attention, in part because of its recent linkage to a specific gene and loci on chromosomes and in part because of the prevailing question regarding the scope of its language impairment: Does the disorder impact the general ability to segment and process language or a specific ability to compute grammar? Here we provide novel electrophysiological data showing a domain-specific deficit within the grammar of language that has been hitherto undetectable through behavioural data alone. Methods and Findings: We presented participants with Grammatical(G)-SLI, age-matched controls, and younger child and adult controls, with questions containing syntactic violations and sentences containing semantic violations. Electrophysiological brain responses revealed a selective impairment to only neural circuitry that is specific to grammatical processing in G-SLI. Furthermore, the participants with G-SLI appeared to be partially compensating for their syntactic deficit by using neural circuitry associated with semantic processing and all non-grammar-specific and low-level auditory neural responses were normal. Conclusions: The findings indicate that grammatical neural circuitry underlying language is a developmentally unique system in the functional architecture of the brain, and this complex higher cognitive system can be selectively impaired. The findings advance fundamental understanding about how cognitive systems develop and all human language is represented and processed in the brain