Upregulation of the Nrf2 antioxidant pathway characterizes the transition from productive to latent infection in CD4+ T cells

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BlinkML: Efficient Maximum Likelihood Estimation with Probabilistic Guarantees

The rising volume of datasets has made training machine learning (ML) models a major computational cost in the enterprise. Given the iterative nature of model and parameter tuning, many analysts use a small sample of their entire data during their initial stage of analysis to make quick decisions (e.g., what features or hyperparameters to use) and use the entire dataset only in later stages (i.e., when they have converged to a specific model). This sampling, however, is performed in an ad-hoc fashion. Most practitioners cannot precisely capture the effect of sampling on the quality of their model, and eventually on their decision-making process during the tuning phase. Moreover, without systematic support for sampling operators, many optimizations and reuse opportunities are lost. In this paper, we introduce BlinkML, a system for fast, quality-guaranteed ML training. BlinkML allows users to make error-computation tradeoffs: instead of training a model on their full data (i.e., full model), BlinkML can quickly train an approximate model with quality guarantees using a sample. The quality guarantees ensure that, with high probability, the approximate model makes the same predictions as the full model. BlinkML currently supports any ML model that relies on maximum likelihood estimation (MLE), which includes Generalized Linear Models (e.g., linear regression, logistic regression, max entropy classifier, Poisson regression) as well as PPCA (Probabilistic Principal Component Analysis). Our experiments show that BlinkML can speed up the training of large-scale ML tasks by 6.26x-629x while guaranteeing the same predictions, with 95% probability, as the full model.Comment: 22 pages, SIGMOD 201

Cuticular chemoprofile of the fruit fly drosophila subobscura (diptera, drosophilidae)

In insects, cuticular hydrocarbon (CHC) profile is involved in many important biological functions and may vary in different conditions. Among fruit fly species, Drosophila subobscura is one of the most frequently used in genetic, ecological and evolutionary research, because of its rich chromosomal polymorphism, specific behavioral repertoires and habitat preferences. In this work, we identified and quantified cuticular chemoprofile of D. subobscura. Using gas chromatography (GC) and gas chromatography coupled with mass spectrometry (GC-MS), 25 chemical compounds were found in males and 23 compounds were found in females. Further, ANOVA confirmed significant sexual dimorphism in cuticular chemoprofile amounts. Knowledge of cuticular chemistry could contribute to further research in D. subobscura, starting from behavioral, up to ecological, since this species is recognized as an important model system for the study and monitoring of global climate changes

3-D Ultrastructure of O. tauri: Electron Cryotomography of an Entire Eukaryotic Cell

The hallmark of eukaryotic cells is their segregation of key biological functions into discrete, membrane-bound organelles. Creating accurate models of their ultrastructural complexity has been difficult in part because of the limited resolution of light microscopy and the artifact-prone nature of conventional electron microscopy. Here we explored the potential of the emerging technology electron cryotomography to produce three-dimensional images of an entire eukaryotic cell in a near-native state. Ostreococcus tauri was chosen as the specimen because as a unicellular picoplankton with just one copy of each organelle, it is the smallest known eukaryote and was therefore likely to yield the highest resolution images. Whole cells were imaged at various stages of the cell cycle, yielding 3-D reconstructions of complete chloroplasts, mitochondria, endoplasmic reticula, Golgi bodies, peroxisomes, microtubules, and putative ribosome distributions in-situ. Surprisingly, the nucleus was seen to open long before mitosis, and while one microtubule (or two in some predivisional cells) was consistently present, no mitotic spindle was ever observed, prompting speculation that a single microtubule might be sufficient to segregate multiple chromosomes

New insights into the magmatic-hydrothermal system and volatile budget of Lastarria volcano, Chile: Integrated results from the 2014 IAVCEI CCVG 12th Volcanic Gas Workshop.

Recent geophysical evidence for large-scale regional crustal inflation and localized crustal magma intrusion has made Lastarria volcano (northern Chile) the target of numerous geological, geophysical, and geochemical studies. The chemical composition of volcanic gases sampled during discrete campaigns from Lastarria volcano indicated a well-developed hydrothermal system from direct fumarole samples in A.D. 2006, 2008, and 2009, and shallow magma degassing using measurements from in situ plume sampling techniques in 2012. It is unclear if the differences in measured gas compositions and resulting interpretations were due to artifacts of the different sampling methods employed, short-term excursions from baseline due to localized changes in stress, or a systematic change in Lastarria's magmatic-hydrothermal system between 2009 and 2012. Integrated results from a two-day volcanic gas sampling and measurement campaign during the 2014 International Association of Volcanology and Chemistry of the Earth's Interior (IAVCEI) Commission on the Chemistry of Volcanic Gases (CCVG) 12th Gas Workshop are used here to compare and evaluate current gas sampling and measurement techniques, refine the existing subsurface models for Lastarria volcano, and provide new constraints on its magmatic-hydrothermal system and total degassing budget. While compositional differences among sampling methods are present, distinct compositional changes are observed, which if representative of longterm trends, indicate a change in Lastarria's overall magmatic-hydrothermal system. The composition of volcanic gases measured in 2014 contained high proportions of relatively magma- and water-soluble gases consistent with degassing of shallow magma, and in agreement with the 2012 gas composition. When compared with gas compositions measured in 2006-2009, higher relative H2O/CO2 ratios combined with lower relative CO2/St and H2O/St and stable HCl/St ratios (where St is total S [SO2 + H2S]) are observed in 2012 and 2014. These compositional changes suggest variations in the magmatic-hydrothermal system between 2009 and 2012, with possible scenarios to explain these trends including: (1) decompression-induced degassing due to magma ascent within the shallow crust; (2) crystallization-induced degassing of a stalled magma body; (3) depletion of the hydrothermal system due to heating, changes in local stress, and/or minimal precipitation; and/or (4) acidification of the hydrothermal system. These scenarios are evaluated and compared against the geophysical observations of continuous shallow inflation at ~8 km depth between 1997 and 2016, and near-surface ( < 1 km) inflation between 2000 and 2008, to further refine the existing subsurface models. Higher relative H2O/CO2 observed in 2012 and 2014 is not consistent with the depletion or acidification of a hydrothermal system, while all other observations are consistent with the four proposed models. Based on these observations, we find that scenarios 1 or 2 are the most likely to explain the geochemical and geophysical observations, and propose that targeted shallow interferometric synthetic-aperture radar (InSAR) studies could help discriminate between these two scenarios. Lastly, we use an average SO2 flux of 604 \ub1 296 t/d measured on 22 November 2014, along with the average gas composition and diffuse soil CO2 flux measurements, to estimate a total volatile flux from Lastarria volcano in 2014 of ~12,400 t/d, which is similar to previous estimates from 2012

Cryo-electron tomography of cells: connecting structure and function

Cryo-electron tomography (cryo-ET) allows the visualization of cellular structures under close-to-life conditions and at molecular resolution. While it is inherently a static approach, yielding structural information about supramolecular organization at a certain time point, it can nevertheless provide insights into function of the structures imaged, in particular, when supplemented by other approaches. Here, we review the use of experimental methods that supplement cryo-ET imaging of whole cells. These include genetic and pharmacological manipulations, as well as correlative light microscopy and cryo-ET. While these methods have mostly been used to detect and identify structures visualized in cryo-ET or to assist the search for a feature of interest, we expect that in the future they will play a more important role in the functional interpretation of cryo-tomograms

Cuticular chemoprofile of the fruit fly drosophila subobscura (diptera, drosophilidae)

In insects, cuticular hydrocarbon (CHC) profile is involved in many important biological functions and may vary in different conditions. Among fruit fly species, Drosophila subobscura is one of the most frequently used in genetic, ecological and evolutionary research, because of its rich chromosomal polymorphism, specific behavioral repertoires and habitat preferences. In this work, we identified and quantified cuticular chemoprofile of D. subobscura. Using gas chromatography (GC) and gas chromatography coupled with mass spectrometry (GC-MS), 25 chemical compounds were found in males and 23 compounds were found in females. Further, ANOVA confirmed significant sexual dimorphism in cuticular chemoprofile amounts. Knowledge of cuticular chemistry could contribute to further research in D. subobscura, starting from behavioral, up to ecological, since this species is recognized as an important model system for the study and monitoring of global climate changes

Characterisation of flame-generated soot and soot-in-oil using electron tomography volume reconstructions and comparison with traditional 2D-TEM measurements

This work characterises soot nanoparticles by electron tomography using Weighted Back Projection algorithm and appraises the uncertainties in two-dimensional calculations by comparison with 3D parameters for flame-generated soot and diesel soot-in-oil. Bright field TEM was used to capture 2D images of soot. Large uncertainties exist in 2D-measured morphological parameters. The flame-generated particle showed an extensive 3D structure while the soot-in-oil was notably two-dimensional. Morphological parameters of flame-generated soot and diesel soot-in-oil were different; primary particles, volume, and surface area varied significantly over the range of viewing angle, with differences as large as 60%. 2D flame-generated soot volume underestimated 3D measurements by 38%; soot-in-oil 2D and 3D-derived volumes were within 4%. 2D calculations of fractal dimension generally underestimate the 3D value