In-situ velocity imaging of ultracold atoms using slow--light

The optical response of a moving medium suitably driven into a slow-light propagation regime strongly depends on its velocity. This effect can be used to devise a novel scheme for imaging ultraslow velocity fields. The scheme turns out to be particularly amenable to study in-situ the dynamics of collective and topological excitations of a trapped Bose-Einstein condensate. We illustrate the advantages of using slow-light imaging specifically for sloshing oscillations and bent vortices in a stirred condensate

Transverse Fresnel-Fizeau drag effects in strongly dispersive media

A light beam normally incident upon an uniformly moving dielectric medium is in general subject to bendings due to a transverse Fresnel-Fizeau light drag effect. In conventional dielectrics, the magnitude of this bending effect is very small and hard to detect. Yet, it can be dramatically enhanced in strongly dispersive media where slow group velocities in the m/s range have been recently observed taking advantage of the electromagnetically induced transparency (EIT) effect. In addition to the usual downstream drag that takes place for positive group velocities, we predict a significant anomalous upstream drag to occur for small and negative group velocities. Furthermore, for sufficiently fast speeds of the medium, higher order dispersion terms are found to play an important role and to be responsible for peculiar effects such as light propagation along curved paths and the restoration of the spatial coherence of an incident noisy beam. The physics underlying this new class of slow-light effects is thoroughly discussed

Programmable in situ amplification for multiplexed imaging of mRNA expression

In situ hybridization methods enable the mapping of mRNA expression within intact biological samples. With current approaches, it is challenging to simultaneously map multiple target mRNAs within whole-mount vertebrate embryos, representing a significant limitation in attempting to study interacting regulatory elements in systems most relevant to human development and disease. Here, we report a multiplexed fluorescent in situ hybridization method based on orthogonal amplification with hybridization chain reactions (HCR). With this approach, RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. The programmability and sequence specificity of these amplification cascades enable multiple HCR amplifiers to operate orthogonally at the same time in the same sample. Robust performance is achieved when imaging five target mRNAs simultaneously in fixed whole-mount and sectioned zebrafish embryos. HCR amplifiers exhibit deep sample penetration, high signal-to-background ratios and sharp signal localization

Cold and Ultracold Molecules: Science, Technology, and Applications

This article presents a review of the current state of the art in the research field of cold and ultracold molecules. It serves as an introduction to the Special Issue of the New Journal of Physics on Cold and Ultracold Molecules and describes new prospects for fundamental research and technological development. Cold and ultracold molecules may revolutionize physical chemistry and few body physics, provide techniques for probing new states of quantum matter, allow for precision measurements of both fundamental and applied interest, and enable quantum simulations of condensed-matter phenomena. Ultracold molecules offer promising applications such as new platforms for quantum computing, precise control of molecular dynamics, nanolithography, and Bose-enhanced chemistry. The discussion is based on recent experimental and theoretical work and concludes with a summary of anticipated future directions and open questions in this rapidly expanding research field.Comment: 82 pages, 9 figures, review article to appear in New Journal of Physics Special Issue on Cold and Ultracold Molecule

Exercising Bioengineered Skeletal Muscle In Vitro: Biopsy to Bioreactor.

The bioengineering of skeletal muscle tissue in-vitro has enabled researchers to more closely mimic the in-vivo skeletal muscle niche. The three-dimensional (3-D) structure of the tissue engineered systems employed to date enable the generation of highly aligned and differentiated myofibers within a representative biological matrix. The use of electrical stimulation to model concentric contraction, via innervation of the myofibers, and the use of mechanical loading to model passive lengthening or stretch has begun to provide a manipulable environment to investigate the cellular and molecular responses following exercise mimicking stimuli in-vitro. Currently available bioreactor systems allow either electrical stimulation or mechanical loading to be utilized at any given time. In the present manuscript, we describe in detail the methodological procedures to create 3-D bioengineered skeletal muscle using both cell lines and/or primary human muscle derived cells from a tissue biopsy, through to modeling exercising stimuli using a bioreactor that can provide both electrical stimulation and mechanical loading simultaneously within the same in-vitro system

Emerging concepts in biomarker discovery; The US-Japan workshop on immunological molecular markers in oncology

Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice