Image analysis and empirical modeling of gene and protein expression

Protein gradients and gene expression patterns are major determinants in the differentiation and fate map of the developing embryo. Here we discuss computational methods to quantitatively measure the positions of gene expression domains and the gradients of protein expression along the dorsal–ventral axis in the Drosophila embryo. Our methodology involves three layers of data. The first layer, or the primary data, consists of z-stack confocal images of embryos processed by in situ hybridization and/or antibody stainings. The secondary data are relationships between location, usually an x-axis coordinate, and fluorescent intensity of gene or protein detection. Tertiary data comprise the optimal parameters that arise from fits of the secondary data to empirical models. The tertiary data are useful to distill large datasets of imaged embryos down to a tractable number of conceptually useful parameters. This analysis allows us to detect subtle phenotypes and is adaptable to any set of genes or proteins with a canonical pattern. For example, we show how insights into the Dorsal transcription factor protein gradient and its target gene ventral-neuroblasts defective (vnd) were obtained using such quantitative approaches

Calcium signals are necessary to establish auxin transporter polarity in a plant stem cell niche

In plants mechanical signals pattern morphogenesis through the polar transport of the hormone auxin and through regulation of interphase microtubule (MT) orientation. To date, the mechanisms by which such signals induce changes in cell polarity remain unknown. Through a combination of time-lapse imaging, and chemical and mechanical perturbations, we show that mechanical stimulation of the SAM causes transient changes in cytoplasmic calcium ion concentration (Ca^(2+)) and that transient Ca^(2+) response is required for downstream changes in PIN-FORMED 1 (PIN1) polarity. We also find that dynamic changes in Ca^(2+) occur during development of the SAM and this Ca^(2+) response is required for changes in PIN1 polarity, though not sufficient. In contrast, we find that Ca^(2+) is not necessary for the response of MTs to mechanical perturbations revealing that Ca^(2+) specifically acts downstream of mechanics to regulate PIN1 polarity response

A silent gigantic solitary fibrous tumor of the pleura: case report

Solitary fibrous tumor of the pleura is a rare mesenchymal tumor, representing less than 5% of all neoplasms associated with the pleura. A 57-year-old man had general malaise without chest symptoms for 1 month. A chest roentgenogram and computed tomography showed a giant mass in the left thorax. Although the tumor compressed the descending aorta and other mediastinal structures strongly, thereby shifting them to the right side, the patient had no symptoms except malaise. The tumor was successfully resected via two separate thoracotomies. The tumor was measured (20 cm × 19 cm × 15 cm) and weighed (2150 g). The tumor was histologically and immunohistochemically diagnosed as benign. Although SFT is benign, a long follow-up period is essential as even patients with complete resection are at risk of recurrence many years after surgery

Direct Measurement of Nuclear Dependence of Charged Current Quasielastic-like Neutrino Interactions using MINERvA

Charged-current $\nu_{\mu}$ interactions on carbon, iron, and lead with a final state hadronic system of one or more protons with zero mesons are used to investigate the influence of the nuclear environment on quasielastic-like interactions. The transfered four-momentum squared to the target nucleus, $Q^2$, is reconstructed based on the kinematics of the leading proton, and differential cross sections versus $Q^2$ and the cross-section ratios of iron, lead and carbon to scintillator are measured for the first time in a single experiment. The measurements show a dependence on atomic number. While the quasielastic-like scattering on carbon is compatible with predictions, the trends exhibited by scattering on iron and lead favor a prediction with intranuclear rescattering of hadrons accounted for by a conventional particle cascade treatment. These measurements help discriminate between different models of both initial state nucleons and final state interactions used in the neutrino oscillation experiments

First evidence of coherent K+K^{+} meson production in neutrino-nucleus scattering

Neutrino-induced charged-current coherent kaon production, $\nu_{\mu}A\rightarrow\mu^{-}K^{+}A$, is a rare, inelastic electroweak process that brings a $K^+$ on shell and leaves the target nucleus intact in its ground state. This process is significantly lower in rate than neutrino-induced charged-current coherent pion production, because of Cabibbo suppression and a kinematic suppression due to the larger kaon mass. We search for such events in the scintillator tracker of MINERvA by observing the final state $K^+$, $\mu^-$ and no other detector activity, and by using the kinematics of the final state particles to reconstruct the small momentum transfer to the nucleus, which is a model-independent characteristic of coherent scattering. We find the first experimental evidence for the process at $3\sigma$ significance.Comment: added ancillary file with information about the six kaon candidate

Single neutral pion production by charged-current νˉμ\bar{\nu}_\mu interactions on hydrocarbon at ⟨Eν⟩=\langle E_\nu \rangle = 3.6 GeV

Single neutral pion production via muon antineutrino charged-current interactions in plastic scintillator (CH) is studied using the \minerva detector exposed to the NuMI low-energy, wideband antineutrino beam at Fermilab. Measurement of this process constrains models of neutral pion production in nuclei, which is important because the neutral-current analog is a background for $\bar{\nu}_e$ appearance oscillation experiments. The differential cross sections for $\pi^0$ momentum and production angle, for events with a single observed $\pi^0$ and no charged pions, are presented and compared to model predictions. These results comprise the first measurement of the $\pi^0$ kinematics for this process.Comment: 6 pages, 5 figures, submitted to Physics Letters