CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005. Here, we describe CellProfiler 3.0, a new version of the ...software supporting both whole-volume and plane-wise analysis of three-dimensional (3D) image stacks, increasingly common in biomedical research. CellProfiler's infrastructure is greatly improved, and we provide a protocol for cloud-based, large-scale image processing. New plugins enable running pretrained deep learning models on images. Designed by and for biologists, CellProfiler equips researchers with powerful computational tools via a well-documented user interface, empowering biologists in all fields to create quantitative, reproducible image analysis workflows.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
ABSTRACT
We present the goals, design, and first results of the MUSE Ultra Deep Field (MUDF) survey, a large programme using the Multi Unit Spectroscopic Explorer (MUSE) instrument at the ESO Very ...Large Telescope. The MUDF survey is collecting ≈150 h on-source of integral field optical spectroscopy in a 1.5 × 1.2 arcmin2 region which hosts several astrophysical structures along the line of sight, including two bright z ≈ 3.2 quasars with close separation (≈500 kpc). Following the description of the data reduction procedures, we present the analysis of the galaxy environment and gaseous properties of seven groups detected at redshifts 0.5 < z < 1.5, spanning a large dynamic range in halo mass, $\log (M_h/\rm {M_\odot }) \approx 11 - 13.5$. For four of the groups, we find associated Mg ii absorbers tracing cool gas in high-resolution spectroscopy of the two quasars, including one case of correlated absorption in both sightlines at distance ≈480 kpc. The absorption strength associated with the groups is higher than what has been reported for more isolated galaxies of comparable mass and impact parameters. We do not find evidence for widespread cool gas giving rise to strong absorption within these groups. Combining these results with the distribution of neutral and ionized gas seen in emission in lower redshift groups, we conclude that gravitational interactions in the group environment strip gas from the galaxy haloes into the intragroup medium, boosting the cross-section of cool gas and leading to the high fraction of strong Mg ii absorbers that we detect.
Of several dozen galaxies observed spectroscopically that are candidates for having a redshift (z) in excess of seven, only five have had their redshifts confirmed via Lyman α emission, at z = 7.008, ...7.045, 7.109, 7.213 and 7.215 (refs 1-4). The small fraction of confirmed galaxies may indicate that the neutral fraction in the intergalactic medium rises quickly at z > 6.5, given that Lyman α is resonantly scattered by neutral gas. The small samples and limited depth of previous observations, however, makes these conclusions tentative. Here we report a deep near-infrared spectroscopic survey of 43 photometrically-selected galaxies with z > 6.5. We detect a near-infrared emission line from only a single galaxy, confirming that some process is making Lyman α difficult to detect. The detected emission line at a wavelength of 1.0343 micrometres is likely to be Lyman α emission, placing this galaxy at a redshift z = 7.51, an epoch 700 million years after the Big Bang. This galaxy's colours are consistent with significant metal content, implying that galaxies become enriched rapidly. We calculate a surprisingly high star-formation rate of about 330 solar masses per year, which is more than a factor of 100 greater than that seen in the Milky Way. Such a galaxy is unexpected in a survey of our size, suggesting that the early Universe may harbour a larger number of intense sites of star formation than expected.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
All cellular materials are partitioned between daughters at cell division, but by various mechanisms and with different accuracy. In the yeast Schizosaccharomyces pombe, the mitochondria are pushed ...to the cell poles by the spindle. We found that mitochondria spatially reequilibrate just before division, and that the mitochondrial volume and DNA-containing nucleoids instead segregate in proportion to the cytoplasm inherited by each daughter. However, nucleoid partitioning errors are suppressed by control at two levels: Mitochondrial volume is actively distributed throughout a cell, and nucleoids are spaced out in semiregular arrays within mitochondria. During the cell cycle, both mitochondria and nucleoids appear to be produced without feedback, creating a net control of fluctuations that is just accurate enough to avoid substantial growth defects.
We study the causes of the reported mass-dependence in the slope of the SFR−M∗ relation, the so-called main sequence of star-forming galaxies, and discuss its implication on the physical processes ...that shaped the star formation history of massive galaxies over cosmic time. We made use of the near-infrared high-resolution imaging from the Hubble Space Telescope in the CANDELS fields to perform a careful bulge-to-disk decomposition of distant galaxies and measure for the first time the slope of the SFR−Mdisk relation at z = 1. We find that this relation very closely follows the shape of the nominal SFR−M∗ correlation, still with a pronounced flattening at the high-mass end. This clearly excludes, at least at z = 1, the progressive growth of quiescent stellar bulges in star-forming galaxies as the main driver for the change of slope of the main sequence. Then, by stacking the Herschel data available in the CANDELS field, we estimated the gas mass (Mgas = MH i + MH2) and the star formation efficiency (SFE ≡ SFR/Mgas) at different positions on the SFR−M∗ relation. We find that the relatively low SFRs observed in massive galaxies (M∗> 5 × 1010 M⊙) are not caused by a reduced gas content, but by a star formation efficiency that is lower by up to a factor of 3 than in galaxies with lower stellar mass. The trend at the lowest masses is probably linked to the dominance of atomic over molecular gas. We argue that this stellar-mass-dependent SFE can explain the varying slope of the main sequence since z = 1.5, hence over 70% of the Hubble time. The drop in SFE occurs at lower masses in the local Universe (M∗> 2 × 1010 M⊙) and is not present at z = 2. Altogether, this provides evidence for a slow decrease in star formation efficiency in massive main sequence galaxies. The resulting loss of star formation is found to be rising starting from z = 2 to reach a level similar to the mass growth of the quiescent population by z = 1. We finally discuss the possible physical origin of this phenomenon.
ABSTRACT
In this work, we investigate upper limits on the global escape fraction of ionizing photons ($f_{\rm esc/global}^{\rm abs}$) from a sample of galaxies probed for Lyman-continuum (LyC) ...emission characterized as non-LyC and LyC leakers. We present a sample of nine clean non-contaminated (by low-redshift interlopers, CCD problems, and internal reflections of the instrument) galaxies that do not show significant (>3σ) LyC flux in the range 880 < λrest < 910 Å. The nine-galaxy stacked spectrum reveals no significant LyC flux with an upper limit of $f_{\rm esc}^{\rm abs} \le 0.06$. In the next step of our analysis, we join all estimates of $f_{\rm esc}^{\rm abs}$ upper limits derived from different samples of 2 ≲ z < 6 galaxies from the literature reported in last ∼20 yr and include the sample presented in this work. We find the $f_{\rm esc}^{\rm abs}$ upper limit ≤0.084 for the galaxies recognized as non-LyC leakers. After including all known detections from literature $f_{\rm esc/global}^{\rm abs}$ upper limit ≤0.088 for all galaxies examined for LyC flux. Furthermore, $f_{\rm esc}^{\rm abs}$ upper limits for different groups of galaxies indicate that the strongest LyC emitters could be galaxies classified as Lyman α emitters. We also discuss the possible existence of a correlation among the observed flux density ratio $(F_{\nu }^{\mathrm{ LyC}}/F_{\nu }^{\mathrm{ UV}})_{\rm obs}$ and Lyman α equivalent width EW(Lyα), where we confirm the existence of moderately significant correlation among galaxies classified as non-LyC leakers.
During human pregnancy, placental trophoblasts differentiate and syncytialize into syncytiotrophoblasts that sustain progesterone production 1. This process is accompanied by mitochondrial ...fragmentation and cristae remodeling 2, two facets of mitochondrial apoptosis, whose molecular mechanisms and functional consequences on steroidogenesis are unclear. Here we show that the mitochondria-shaping protein Optic atrophy 1 (Opa1) controls efficiency of steroidogenesis. During syncytialization of trophoblast BeWo cells, levels of the profission mitochondria-shaping protein Drp1 increase, and those of Opa1 and mitofusin (Mfn) decrease, leading to mitochondrial fragmentation and cristae remodeling. Manipulation of the levels of Opa1 reveal an inverse relationship with the efficiency of steroidogenesis in trophoblasts and in mouse embryonic fibroblasts where the mitochondrial steroidogenetic pathway has been engineered. In an in vitro assay, accumulation of cholesterol is facilitated in the inner membrane of isolated mitochondria lacking Opa1. Thus, Opa1-dependent inner membrane remodeling controls efficiency of steroidogenesis.
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► Mitochondrial remodeling characterize differentiation of human trophoblasts ► Expression of Opa1 decreases during trophoblast differentiation ► Lowered Opa1 increases efficiency of steroidogenesis stimulating cholesterol flux
ABSTRACT
Understanding the relationship between the underlying escape fraction of Lyman continuum (LyC) photons (fesc) emitted by galaxies and measuring the distribution of observed fesc values at ...high redshift is fundamental to the interpretation of the reionization process. In this paper, we perform a statistical exploration of the attenuation of LyC photons by neutral hydrogen in the intergalactic medium using ensembles of simulated transmission functions. We show that LyC-detected galaxies are more likely to be found in sightlines with higher than average transmission of LyC photons. This means that adopting a mean transmission at a given redshift leads to an overestimate of the true fesc for LyC-detected galaxies. We note, however, that mean values are appropriate for fesc estimates of larger parent samples that include LyC non-detected galaxies. We quantify this IGM transmission bias for LyC detections in photometric and spectroscopic surveys in the literature and show that the bias is stronger for both shallower observations and for fainter parent samples (i.e. Ly α emitters versus Lyman break galaxies). We also explore the effects of varying the underlying probability distribution function (PDF) of fesc on recovered values, showing that the underlying fesc PDF may depend on sample selection by comparing with observational surveys. This work represents a first step in improved interpretation of LyC detections in the context of understanding fesc from high-redshift galaxies.
ABSTRACT We present the largest, publicly available sample of damped Ly systems (DLAs) along the lines of sight of Swift-discovered gamma-ray bursts (GRBs) in order to investigate the environmental ...properties of long GRB hosts in the z = 1.8-6 redshift range. Compared with the most recent quasar DLA sample (QSO-DLA), our analysis shows that GRB-DLAs probe a more metal-enriched environment at , up to . In the z = 2-3 redshift range, despite the large number of lower limits, there are hints that the two populations may be more similar (only at a 90% significance level) than at higher redshifts. Also, at high-z, the GRB-DLA average metallicity seems to decline at a lower rate than the QSO-DLAs: GRB-DLA hosts may be polluted with metals at least as far as kpc from the GRB explosion site, probably due to previous star formation episodes and/or supernova explosions. This shallow metallicity trend, now extended up to , confirms previous results that GRB hosts are star-forming and have, on average, higher metallicities than the general QSO-DLA population. Finally, our host metallicity measurements are broadly consistent with the predictions derived from the hypothesis of two channels of GRB progenitors, one of which is mildly affected by a metallicity bias, although more data are needed to constrain the models at .
Mitochondria must grow with the growing cell to ensure proper cellular physiology and inheritance upon division. We measured the physical size of mitochondrial networks in budding yeast and found ...that mitochondrial network size increased with increasing cell size and that this scaling relation occurred primarily in the bud. The mitochondria-to-cell size ratio continually decreased in aging mothers over successive generations. However, regardless of the mother's age or mitochondrial content, all buds attained the same average ratio. Thus, yeast populations achieve a stable scaling relation between mitochondrial content and cell size despite asymmetry in inheritance.
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