Narrow optical linewidths in erbium implanted in TiO2_2

Atomic and atom-like defects in the solid-state are widely explored for quantum computers, networks and sensors. Rare earth ions are an attractive class of atomic defects that feature narrow spin and optical transitions that are isolated from the host crystal, allowing incorporation into a wide range of materials. However, the realization of long electronic spin coherence times is hampered by magnetic noise from abundant nuclear spins in the most widely studied host crystals. Here, we demonstrate that Er$^{3+}$ ions can be introduced via ion implantation into TiO$_2$, a host crystal that has not been studied extensively for rare earth ions and has a low natural abundance of nuclear spins. We observe efficient incorporation of the implanted Er$^{3+}$ into the Ti$^{4+}$ site (40% yield), and measure narrow inhomogeneous spin and optical linewidths (20 and 460 MHz, respectively) that are comparable to bulk-doped crystalline hosts for Er$^{3+}$. This work demonstrates that ion implantation is a viable path to studying rare earth ions in new hosts, and is a significant step towards realizing individually addressed rare earth ions with long spin coherence times for quantum technologies

Reconstructing the Mind's Eye: fMRI-to-Image with Contrastive Learning and Diffusion Priors

We present MindEye, a novel fMRI-to-image approach to retrieve and reconstruct viewed images from brain activity. Our model comprises two parallel submodules that are specialized for retrieval (using contrastive learning) and reconstruction (using a diffusion prior). MindEye can map fMRI brain activity to any high dimensional multimodal latent space, like CLIP image space, enabling image reconstruction using generative models that accept embeddings from this latent space. We comprehensively compare our approach with other existing methods, using both qualitative side-by-side comparisons and quantitative evaluations, and show that MindEye achieves state-of-the-art performance in both reconstruction and retrieval tasks. In particular, MindEye can retrieve the exact original image even among highly similar candidates indicating that its brain embeddings retain fine-grained image-specific information. This allows us to accurately retrieve images even from large-scale databases like LAION-5B. We demonstrate through ablations that MindEye's performance improvements over previous methods result from specialized submodules for retrieval and reconstruction, improved training techniques, and training models with orders of magnitude more parameters. Furthermore, we show that MindEye can better preserve low-level image features in the reconstructions by using img2img, with outputs from a separate autoencoder. All code is available on GitHub.Comment: Project Page at https://medarc-ai.github.io/mindeye-website/. Code at https://github.com/MedARC-AI/fMRI-reconstruction-NSD

Experimental infection of cattle with Mycobacterium tuberculosis isolates shows the attenuation of the human tubercle bacillus for cattle

The Mycobacterium tuberculosis complex (MTBC) is the collective term given to the group of bacteria that cause tuberculosis (TB) in mammals. It has been reported that M. tuberculosis H37Rv, a standard reference MTBC strain, is attenuated in cattle compared to Mycobacterium bovis. However, as M. tuberculosis H37Rv was isolated in the early 1930s, and genetic variants are known to exist, we sought to revisit this question of attenuation of M. tuberculosis for cattle by performing a bovine experimental infection with a recent M. tuberculosis isolate. Here we report infection of cattle using M. bovis AF2122/97, M. tuberculosis H37Rv, and M. tuberculosis BTB1558, the latter isolated in 2008 during a TB surveillance project in Ethiopian cattle. We show that both M. tuberculosis strains caused reduced gross and histopathology in cattle compared to M. bovis. Using M. tuberculosis H37Rv and M. bovis AF2122/97 as the extremes in terms of infection outcome, we used RNA-Seq analysis to explore differences in the peripheral response to infection as a route to identify biomarkers of progressive disease in contrast to a more quiescent, latent infection. Our work shows the attenuation of M. tuberculosis strains for cattle, and emphasizes the potential of the bovine model as a ‘One Health’ approach to inform human TB biomarker development and post-exposure vaccine development

TABADO: "Evaluation of a smoking cessation program among Adolescents in Vocational Training Centers": Study protocol

<p>Abstract</p> <p>Background</p> <p>Most of the efforts to reduce teenagers' tobacco addiction have focused on smoking prevention and little on smoking cessation. A smoking cessation program (TABADO study), associating pharmacologic and cognitive-behavioural strategy, on a particularly vulnerable population (vocational trainees), was developed. This study aims to evaluate the efficacy of the program which was offered to all smokers in a population aged 15 to 20 years in Vocational Training Centers (VTC). This paper presents the TABADO study protocol.</p> <p>Methods</p> <p>The study is quasi-experimental, prospective, evaluative and comparative and takes place during the 2 years of vocational training. The final population will be composed of 2000 trainees entering a VTC in Lorraine, France, during the 2008-2009 period. The intervention group (1000 trainees) benefited from the TABADO program while no specific intervention took place in the "control" group (1000 trainees) other than the treatment and education services usually available. Our primary outcome will be the tobacco abstinence rate at 12 months.</p> <p>Discussion</p> <p>If the program proves effective, it will be a new tool in the action against smoking in populations that have been seldom targeted until now. In addition, the approach could be expanded to other young subjects from socially disadvantaged backgrounds in the context of a public health policy against smoking among adolescents.</p> <p>Trial registration</p> <p>Clinical trial identification number is NTC00973570.</p

Measuring global ocean heat content to estimate the earth energy imbalance

The energy radiated by the Earth toward space does not compensate the incoming radiation from the Sun leading to a small positive energy imbalance at the top of the atmosphere (0.4–1 Wm–2). This imbalance is coined Earth’s Energy Imbalance (EEI). It is mostly caused by anthropogenic greenhouse gas emissions and is driving the current warming of the planet. Precise monitoring of EEI is critical to assess the current status of climate change and the future evolution of climate. But the monitoring of EEI is challenging as EEI is two orders of magnitude smaller than the radiation fluxes in and out of the Earth system. Over 93% of the excess energy that is gained by the Earth in response to the positive EEI accumulates into the ocean in the form of heat. This accumulation of heat can be tracked with the ocean observing system such that today, the monitoring of Ocean Heat Content (OHC) and its long-term change provide the most efficient approach to estimate EEI. In this community paper we review the current four state-of-the-art methods to estimate global OHC changes and evaluate their relevance to derive EEI estimates on different time scales. These four methods make use of: (1) direct observations of in situ temperature; (2) satellite-based measurements of the ocean surface net heat fluxes; (3) satellite-based estimates of the thermal expansion of the ocean and (4) ocean reanalyses that assimilate observations from both satellite and in situ instruments. For each method we review the potential and the uncertainty of the method to estimate global OHC changes. We also analyze gaps in the current capability of each method and identify ways of progress for the future to fulfill the requirements of EEI monitoring. Achieving the observation of EEI with sufficient accuracy will depend on merging the remote sensing techniques with in situ measurements of key variables as an integral part of the Ocean Observing System

A Spontaneous Mutation of the Rat Themis Gene Leads to Impaired Function of Regulatory T Cells Linked to Inflammatory Bowel Disease

Spontaneous or chemically induced germline mutations, which lead to Mendelian phenotypes, are powerful tools to discover new genes and their functions. Here, we report an autosomal recessive mutation that occurred spontaneously in a Brown-Norway (BN) rat colony and was identified as causing marked T cell lymphopenia. This mutation was stabilized in a new rat strain, named BNm for “BN mutated.” In BNm rats, we found that the T cell lymphopenia originated in the thymus, was intrinsic to CD4 T lymphocytes, and was associated with the development of an inflammatory bowel disease. Furthermore, we demonstrate that the suppressive activity of both peripheral and thymic CD4+ CD25bright regulatory T cells (Treg) is defective in BNm rats. Complementation of mutant animals with BN Treg decreases disease incidence and severity, thus suggesting that the impaired Treg function is involved in the development of inflammatory bowel disease in BNm rats. Moreover, the cytokine profile of effector CD4 T cells is skewed toward Th2 and Th17 phenotypes in BNm rats. Linkage analysis and genetic dissection of the CD4 T cell lymphopenia in rats issued from BNm×DA crosses allowed the localization of the mutation on chromosome 1, within a 1.5 megabase interval. Gene expression and sequencing studies identified a frameshift mutation caused by a four-nucleotide insertion in the Themis gene, leading to its disruption. This result is the first to link Themis to the suppressive function of Treg and to suggest that, in Themis-deficient animals, defect of this function is involved in intestinal inflammation. Thus, this study highlights the importance of Themis as a new target gene that could participate in the pathogenesis of immune diseases characterized by chronic inflammation resulting from a defect in the Treg compartment

Metabolic Compartmentation – A System Level Property of Muscle Cells: Real Problems of Diffusion in Living Cells

Problems of quantitative investigation of intracellular diffusion and compartmentation of metabolites are analyzed. Principal controversies in recently published analyses of these problems for the living cells are discussed. It is shown that the formal theoretical analysis of diffusion of metabolites based on Fick's equation and using fixed diffusion coefficients for diluted homogenous aqueous solutions, but applied for biological systems in vivo without any comparison with experimental results, may lead to misleading conclusions, which are contradictory to most biological observations. However, if the same theoretical methods are used for analysis of actual experimental data, the apparent diffusion constants obtained are orders of magnitude lower than those in diluted aqueous solutions. Thus, it can be concluded that local restrictions of diffusion of metabolites in a cell are a system-level properties caused by complex structural organization of the cells, macromolecular crowding, cytoskeletal networks and organization of metabolic pathways into multienzyme complexes and metabolons. This results in microcompartmentation of metabolites, their channeling between enzymes and in modular organization of cellular metabolic networks. The perspectives of further studies of these complex intracellular interactions in the framework of Systems Biology are discussed

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field