HTPheno: An image analysis pipeline for high-throughput plant phenotyping

<p>Abstract</p> <p>Background</p> <p>In the last few years high-throughput analysis methods have become state-of-the-art in the life sciences. One of the latest developments is automated greenhouse systems for high-throughput plant phenotyping. Such systems allow the non-destructive screening of plants over a period of time by means of image acquisition techniques. During such screening different images of each plant are recorded and must be analysed by applying sophisticated image analysis algorithms.</p> <p>Results</p> <p>This paper presents an image analysis pipeline (HTPheno) for high-throughput plant phenotyping. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening. HTPheno is applied to analyse two barley cultivars.</p> <p>Conclusions</p> <p>HTPheno, an open source image analysis pipeline, supplies a flexible and adaptable ImageJ plugin which can be used for automated image analysis in high-throughput plant phenotyping and therefore to derive new biological insights, such as determination of fitness.</p

First results from the VIRIAL survey: the stellar content of UVJUVJ-selected quiescent galaxies at 1.5<z<21.5 < z < 2 from KMOS

We investigate the stellar populations of 25 massive, galaxies ($\log[M_\ast/M_\odot] \geq 10.9$) at $1.5 < z < 2$ using data obtained with the K-band Multi-Object Spectrograph (KMOS) on the ESO VLT. Targets were selected to be quiescent based on their broadband colors and redshifts using data from the 3D-HST grism survey. The mean redshift of our sample is $\bar{z} = 1.75$, where KMOS YJ-band data probe age- and metallicity-sensitive absorption features in the rest-frame optical, including the $G$ band, Fe I, and high-order Balmer lines. Fitting simple stellar population models to a stack of our KMOS spectra, we derive a mean age of $1.03^{+0.13}_{-0.08}$ Gyr. We confirm previous results suggesting a correlation between color and age for quiescent galaxies, finding mean ages of $1.22^{+0.56}_{-0.19}$ Gyr and $0.85^{+0.08}_{-0.05}$ Gyr for the reddest and bluest galaxies in our sample. Combining our KMOS measurements with those obtained from previous studies at $0.2 < z < 2$ we find evidence for a $2-3$ Gyr spread in the formation epoch of massive galaxies. At $z < 1$ the measured stellar ages are consistent with passive evolution, while at $1 < z \lesssim2$ they appear to saturate at $\sim$1 Gyr, which likely reflects changing demographics of the (mean) progenitor population. By comparing to star-formation histories inferred for "normal" star-forming galaxies, we show that the timescales required to form massive galaxies at $z \gtrsim 1.5$ are consistent with the enhanced $\alpha$-element abundances found in massive local early-type galaxies.Comment: 6 pages, 5 figures, accepted for publication in ApJ

Hot Disks And Delayed Bar Formation

We present observational evidence for the inhibition of bar formation in dispersion-dominated (dynamically hot) galaxies by studying the relationship between galactic structure and host galaxy kinematics in a sample of 257 galaxies between 0.1 $<$ z $\leq$ 0.84 from the All-Wavelength Extended Groth Strip International Survey (AEGIS) and the Deep Extragalactic Evolutionary Probe 2 (DEEP2) survey. We find that bars are preferentially found in galaxies that are massive and dynamically cold (rotation-dominated) and on the stellar Tully-Fisher relationship, as is the case for barred spirals in the local Universe. The data provide at least one explanation for the steep ($\times$3) decline in the overall bar fraction from z=0 to z=0.84 in L$^*$ and brighter disks seen in previous studies. The decline in the bar fraction at high redshift is almost exclusively in the lower mass (10 $<$ log M$_{*}$(\Msun)$<$ 11), later-type and bluer galaxies. A proposed explanation for this "downsizing" of the bar formation / stellar structure formation is that the lower mass galaxies may not form bars because they could be dynamically hotter than more massive systems from the increased turbulence of accreting gas, elevated star formation, and/or increased interaction/merger rate at higher redshifts. The evidence presented here provides observational support for this hypothesis. However, the data also show that not every disk galaxy that is massive and cold has a stellar bar, suggesting that mass and dynamic coldness of a disk are necessary but not sufficient conditions for bar formation -- a secondary process, perhaps the interaction history between the dark matter halo and the baryonic matter, may play an important role in bar formation.Comment: In press, ApJ, 13 pages, 5 figures (3 color

ALMA observations of Elias 2–24: a protoplanetary disk with multiple gaps in the Ophiuchus molecular cloud

We present ALMA 1.3 mm continuum observations at 0. 2 (25 au) resolution of Elias 2–24, one of the largest and brightest protoplanetary disks in the Ophiuchus Molecular Cloud, and we report the presence of three partially resolved concentric gaps located at ∼20, 52, and 87 au from the star. We perform radiative transfer modeling of the disk to constrain its surface density and temperature radial profile and place the disk structure in the context of mechanisms capable of forming narrow gaps such as condensation fronts and dynamical clearing by actively forming planets. In particular, we estimate the disk temperature at the locations of the gaps to be 23, 15, and 12 K (at 20, 52, and 87 au, respectively), very close to the expected snowlines of CO (23–28 K) and N2 (12–15 K). Similarly, by assuming that the widths of the gaps correspond to 4–8× the Hill radii of forming planets (as suggested by numerical simulations), we estimate planet masses in the range of 0.2 1.5 – MJup, 1.0 8.0 – MJup, and 0.02 0.15 – MJup for the inner, middle, and outer gap, respectively. Given the surface density profile of the disk, the amount of “missing mass” at the location of each one of these gaps (between 4 and 20 MJup) is more than sufficient to account for the formation of such planets.Fil: Cieza, Lucas A.. Universidad Diego Portales; ChileFil: Casassus, Simon. Universidad de Chile; ChileFil: Pérez, Sebastian. Universidad de Chile; ChileFil: Hales, Antonio. Alma Observatory; ChileFil: Cárcamo, Miguel. Universidad de Chile; ChileFil: Ansdell, Megan. University of California at Berkeley; Estados UnidosFil: Avenhaus, Henning. Universitat Zurich; SuizaFil: Bayo, Amelia. Universidad de Valparaiso; ChileFil: Bertrang, Gesa H.-M.. Universidad Diego Portales; ChileFil: Cánovas, Hector. Agencia Espacial Europea; EspañaFil: Christiaens, Valentin. Universidad de Chile; ChileFil: Dent, William. Alma Observatory; ChileFil: Ferrero, Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Gamen, Roberto Claudio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Olofsson, Johan. Universidad de Valparaiso; ChileFil: Orcajo, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Osses, Axel. Universidad de Chile; ChileFil: Peña Ramirez, Karla. Universidad de Antofagasta; ChileFil: Principe, David. Massachusetts Institute of Technology; Estados UnidosFil: Ruíz Rodríguez, Dary. Rochester Institute Of Technology; Estados UnidosFil: Schreiber, Matthias R.. Universidad de Valparaiso; ChileFil: Plas, Gerrit van der. Univ. Grenoble Alpes; SuizaFil: Williams, Jonathan P.. Institute For Astronomy, University Of Hawaii; Estados UnidosFil: Zurlo, Alice. Universidad Diego Portales; Chil

In Celiac Disease, a Subset of Autoantibodies against Transglutaminase Binds Toll-Like Receptor 4 and Induces Activation of Monocytes

BACKGROUND: Celiac disease is a small intestine inflammatory disorder with multiple organ involvement, sustained by an inappropriate immune response to dietary gluten. Anti-transglutaminase antibodies are a typical serological marker in patients with active disease, and may disappear during a gluten-free diet treatment. Involvement of infectious agents and innate immunity has been suggested but never proven. Molecular mimicry is one of the mechanisms that links infection and autoimmunity. METHODS AND FINDINGS: In our attempt to clarify the pathogenesis of celiac disease, we screened a random peptide library with pooled sera of patients affected by active disease after a pre-screening with the sera of the same patients on a gluten-free diet. We identified a peptide recognized by serum immunoglobulins of patients with active disease, but not by those of patients on a gluten-free diet. This peptide shares homology with the rotavirus major neutralizing protein VP-7 and with the self-antigens tissue transglutaminase, human heat shock protein 60, desmoglein 1, and Toll-like receptor 4. We show that antibodies against the peptide affinity-purified from the sera of patients with active disease recognize the viral product and self-antigens in ELISA and Western blot. These antibodies were able to induce increased epithelial cell permeability evaluated by transepithelial flux of [(3)H] mannitol in the T84 human intestinal epithelial cell line. Finally, the purified antibodies induced monocyte activation upon binding Toll-like receptor 4, evaluated both by surface expression of activation markers and by production of pro-inflammatory cytokines. CONCLUSIONS: Our findings show that in active celiac disease, a subset of anti-transglutaminase IgA antibodies recognize the viral protein VP-7, suggesting a possible involvement of rotavirus infection in the pathogenesis of the disease, through a mechanism of molecular mimicry. Moreover, such antibodies recognize self-antigens and are functionally active, able to increase intestinal permeability and induce monocyte activation. We therefore provide evidence for the involvement of innate immunity in the pathogenesis of celiac disease through a previously unknown mechanism of engagement of Toll-like receptor 4

Guided Zygomatic Implantology for Oral Cancer Rehabilitation: A Case Report

Oral rehabilitation after maxillary oncological resection is challenging. This case report presents the rehabilitation of a 65-year-old Caucasian male adenoid cystic carcinoma patient using a myo-cutaneous thigh flap, zygomatic implant placement, and an immediate fixed provisional prosthesis made with computer-aided technologies. The patient presented complaints of asymptomatic enlarged swelling of 5-mm on the right hard hemi-palate. There was an oro-antral communication deriving from a previous local excision. Preoperative radiographs showed the involvement of the right maxilla, maxillary sinus, and nose with a suspect involvement of the maxillary division of the trigeminal nerve. Treatment was planned through a fully digital workflow. A partial maxillectomy was performed endoscopically, and maxilla was reconstructed using an anterolateral thigh free flap. Two zygomatic implants were inserted simultaneously. A provisional fix full-arch prosthesis was manufactured preoperatively through a fully digital workflow and was placed in the operating room. Following post-operative radiotherapy, the patient received a final hybrid prosthesis. During the follow-up period of two years, the patient reported good function, aesthetics, and significant enhancement in quality of life. According to the results of this case, the protocol represented can be a promising alternative for oral cancer patients with large defects, and can lead to an improved quality of life

Smell and taste alterations in Covid-19: a cross-sectional analysis of different cohorts

Olfactory (OD) and gustatory (GD) dysfunction have been proven to be a typical symptom of SARS-CoV-2 infection. However, their prevalence in different patient populations still needs to be clarified

Chiral symmetry breaking as open string tachyon condensation

We consider a general framework to study holographically the dynamics of fundamental quarks in a confining gauge theory. Flavors are introduced by placing a set of (coincident) branes and antibranes on a background dual to a confining color theory. The spectrum contains an open string tachyon and its condensation describes the U(N_f)_L x U(N_f)_R -> U(N_f)_V symmetry breaking. By studying worldvolume gauge transformations of the flavor brane action, we obtain the QCD global anomalies and an IR condition that allows to fix the quark condensate in terms of the quark mass. We find the expected N_f^2 Goldstone bosons (for m_q=0), the Gell-Mann-Oakes-Renner relation (for m_q small) and the \eta' mass. Remarkably, the linear confinement behavior for the masses of highly excited spin-1 mesons, m_n^2 ~ n is naturally reproduced.Comment: 30 pages + 5 appendices, 2 figure