Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features.

Empirical evidence suggests that the malaria parasite Plasmodium falciparum employs a broad range of mechanisms to regulate gene transcription throughout the organism's complex life cycle. To better understand this regulatory machinery, we assembled a rich collection of genomic and epigenomic data sets, including information about transcription factor (TF) binding motifs, patterns of covalent histone modifications, nucleosome occupancy, GC content, and global 3D genome architecture. We used these data to train machine learning models to discriminate between high-expression and low-expression genes, focusing on three distinct stages of the red blood cell phase of the Plasmodium life cycle. Our results highlight the importance of histone modifications and 3D chromatin architecture in Plasmodium transcriptional regulation and suggest that AP2 transcription factors may play a limited regulatory role, perhaps operating in conjunction with epigenetic factors

Efficient Ultrasound Image Analysis Models with Sonographer Gaze Assisted Distillation.

Recent automated medical image analysis methods have attained state-of-the-art performance but have relied on memory and compute-intensive deep learning models. Reducing model size without significant loss in performance metrics is crucial for time and memory-efficient automated image-based decision-making. Traditional deep learning based image analysis only uses expert knowledge in the form of manual annotations. Recently, there has been interest in introducing other forms of expert knowledge into deep learning architecture design. This is the approach considered in the paper where we propose to combine ultrasound video with point-of-gaze tracked for expert sonographers as they scan to train memory-efficient ultrasound image analysis models. Specifically we develop teacher-student knowledge transfer models for the exemplar task of frame classification for the fetal abdomen, head, and femur. The best performing memory-efficient models attain performance within 5% of conventional models that are 1000× larger in size

Resonant-state solution of the Faddeev-Merkuriev integral equations for three-body systems with Coulomb potentials

A novel method for calculating resonances in three-body Coulombic systems is proposed. The Faddeev-Merkuriev integral equations are solved by applying the Coulomb-Sturmian separable expansion method. The $e^- e^+ e^-$ S-state resonances up to $n=5$ threshold are calculated.Comment: 6 pages, 2 ps figure

Narrow Line Cooling and Momentum-Space Crystals

Narrow line laser cooling is advancing the frontier for experiments ranging from studies of fundamental atomic physics to high precision optical frequency standards. In this paper, we present an extensive description of the systems and techniques necessary to realize 689 nm 1S0 - 3P1 narrow line cooling of atomic 88Sr. Narrow line cooling and trapping dynamics are also studied in detail. By controlling the relative size of the power broadened transition linewidth and the single-photon recoil frequency shift, we show that it is possible to continuously bridge the gap between semiclassical and quantum mechanical cooling. Novel semiclassical cooling process, some of which are intimately linked to gravity, are also explored. Moreover, for laser frequencies tuned above the atomic resonance, we demonstrate momentum-space crystals containing up to 26 well defined lattice points. Gravitationally assisted cooling is also achieved with blue-detuned light. Theoretically, we find the blue detuned dynamics are universal to Doppler limited systems. This paper offers the most comprehensive study of narrow line laser cooling to date.Comment: 14 pages, 19 figure

Coherent response of the Hodgkin-Huxley neuron in the high-input regime

We analyze the response of the Hodgkin-Huxley neuron to a large number of uncorrelated stochastic inhibitory and excitatory post-synaptic spike trains. In order to clarify the various mechanisms responsible for noise-induced spike triggering we examine the model in its silent regime. We report the coexistence of two distinct coherence resonances: the first one at low noise is due to the stimulation of "correlated" subthreshold oscillations; the second one at intermediate noise variances is instead related to the regularization of the emitted spike trains.Comment: 5 pages - 5 eps figures, contribution presented to the conference CNS 2006 held in Edinburgh (UK), to appear on Neurocomputin

Isolation and characterization of the full-length cDNA encoding a member of a novel cytochrome p450 family (CYP320A1) from the tropical freshwater snail, Biomphalaria glabrata, intermediate host for Schistosoma mansoni

Cytochrome p450s (cyp450s) are a family of structurally related proteins, with diverse functions, including steroid synthesis and breakdown of toxins. This paper reports the full-length sequence of a novel cyp450 gene, the first to be isolated from the tropical freshwater snail Biomphalaria glabrata, an important intermediate host of Schistosoma mansoni. The nucleotide sequence is 2291 bp with a predicted amino acid sequence of 584aa. The sequence demonstrates conserved cyp450 structural motifs, but is sufficiently different from previously reported cyp450 sequences to be given a new classification, CYP320A1. Initially identified as down-regulated in partially resistant snails in response to S. mansoni infection, amplification of this gene using RT-PCR in both totally resistant or susceptible snail lines when exposed to infection, and all tissues examined, suggests ubiquitous expression. Characterization of the first cyp450 from B. glabrata is significant in understanding the evolution of these metabolically important proteins

Muon Colliders

Muon Colliders have unique technical and physics advantages and disadvantages when compared with both hadron and electron machines. They should thus be regarded as complementary. Parameters are given of 4 TeV and 0.5 TeV high luminosity \mumu colliders, and of a 0.5 TeV lower luminosity demonstration machine. We discuss the various systems in such muon colliders, starting from the proton accelerator needed to generate the muons and proceeding through muon cooling, acceleration and storage in a collider ring. Problems of detector background are also discussed.Comment: 28 pages, with 12 postscript figures. To be published Proceedings of the 9th Advanced ICFA Beam Dynamics Workshop, AIP Pres

Analysis of exchange terms in a projected ERPA Theory applied to the quasi-elastic (e,e') reaction

A systematic study of the influence of exchange terms in the longitudinal and transverse nuclear response to quasi-elastic (e,e') reactions is presented. The study is performed within the framework of the extended random phase approximation (ERPA), which in conjuction with a projection method permits a separation of various contributions tied to different physical processes. The calculations are performed in nuclear matter up to second order in the residual interaction for which we take a (pi+rho)-model with the addition of the Landau-Migdal g'-parameter. Exchange terms are found to be important only for the RPA-type contributions around the quasielastic peak.Comment: 29 pages, 6 figs (3 in postscript, 3 faxed on request), epsf.st