Automatic Labeling of Special Diagnostic Mammography Views from Images and DICOM Headers.

Applying state-of-the-art machine learning techniques to medical images requires a thorough selection and normalization of input data. One of such steps in digital mammography screening for breast cancer is the labeling and removal of special diagnostic views, in which diagnostic tools or magnification are applied to assist in assessment of suspicious initial findings. As a common task in medical informatics is prediction of disease and its stage, these special diagnostic views, which are only enriched among the cohort of diseased cases, will bias machine learning disease predictions. In order to automate this process, here, we develop a machine learning pipeline that utilizes both DICOM headers and images to predict such views in an automatic manner, allowing for their removal and the generation of unbiased datasets. We achieve AUC of 99.72% in predicting special mammogram views when combining both types of models. Finally, we apply these models to clean up a dataset of about 772,000 images with expected sensitivity of 99.0%. The pipeline presented in this paper can be applied to other datasets to obtain high-quality image sets suitable to train algorithms for disease detection

Genetic determinants of co-accessible chromatin regions in activated T cells across humans.

Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4+ T cells in up to 105 healthy donors. We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the three-dimensional chromatin organization measured by in situ Hi-C in T cells. Fifteen percent of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (local-ATAC-QTLs). Local-ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression

Receptor-like cytoplasmic kinase MARIS functions downstream of CrRLK1L-dependent signaling during tip growth

Growing plant cells need to rigorously coordinate external signals with internal processes. For instance, the maintenance of cell wall (CW) integrity requires the coordination of CW sensing with CW remodeling and biosynthesis to avoid growth arrest or integrity loss. Despite the involvement of receptor-like kinases (RLKs) of the Catharanthus roseus RLK1-like (CrRLK1L) subfamily and the reactive oxygen species-producing NADPH oxidases, it remains largely unknown how this coordination is achieved. ANXUR1 (ANX1) and ANX2, two redundant members of the CrRLK1L subfamily, are required for tip growth of the pollen tube (PT), and their closest homolog, FERONIA, controls root-hair tip growth. Previously, we showed that ANX1 overexpression mildly inhibits PT growth by oversecretion of CW material, whereas pollen tubes of anx1 anx2 double mutants burst spontaneously after germination. Here, we report the identification of suppressor mutants with improved fertility caused by the rescue of anx1 anx2 pollen tube bursting. Mapping of one these mutants revealed an R240C nonsynonymous substitution in the activation loop of a receptor-like cytoplasmic kinase (RLCK), which we named MARIS (MRI). We show that MRI is a plasma membrane-localized member of the RLCK-VIII subfamily and is preferentially expressed in both PTs and root hairs. Interestingly, mri-knockout mutants display spontaneous PT and root-hair bursting. Moreover, expression of the MRI(R240C) mutant, but not its wild-type form, partially rescues the bursting phenotypes of anx1 anx2 PTs and fer root hairs but strongly inhibits wild-type tip growth. Thus, our findings identify a novel positive component of the CrRLK1L-dependent signaling cascade that coordinates CW integrity and tip growth

A calcium dialog mediated by the FERONIA Signal transduction pathway controls plant sperm delivery

Sperm delivery for double fertilization of flowering plants relies on interactions between the pollen tube (PT) and two synergids, leading to programmed cell death (PCD) of the PT and one synergid. The mechanisms underlying the communication among these cells during PT reception is unknown. We discovered that the synergids control this process by coordinating their distinct calcium signatures in response to the calcium dynamics and growth behavior of the PT. Induced and spontaneous aberrant calcium responses in the synergids abolish the two coordinated PCD events. Components of the FERONIA (FER) signaling pathway are required for initiating and modulating these calcium responses and for coupling the PCD events. Intriguingly, the calcium signatures are interchangeable between the two synergids, implying that their fates of death and survival are determined by reversible interactions with the PT. Thus, complex intercellular interactions involving a receptor kinase pathway and calcium-mediated signaling control sperm delivery in plants

<i>rbohH rbohJ</i> mutant pollen display <i>anxur</i>-like phenotypes.

<p>(A) Quantification of pollen germination and PT rupture percentages (top histogram) and seed per siliques (bottom histogram) for WT, single, and double <i>rboh</i> as well as <i>anx1 anx2</i> mutant plants. Data are mean ± standard error of the mean (SEM) of three independent experiments with more than 150 pollen grains or ten siliques per genotype and experiment. (B) Representative overview images of WT and <i>rbohH rbohJ</i> pollen grown <i>in vitro</i> for 5 h. Up to 80% of germinated pollen from <i>rbohH rbohJ</i> ruptured with clear traces of cytoplasmic content that was released into the medium (top right), while the remaining germinated grains produce PTs that will burst later on (bottom right, arrowheads) as opposed to WT PTs that grow normally (bottom left). Scale bar = 50 µm. (C) Photographs of siliques from WT, <i>rbohH rbohJ</i>, and <i>anx1 anx2</i> plants. Scale bar = 500 µm. (D) Representative images of aniline blue staining of a WT pistil pollinated with WT pollen (left), a <i>rbohH rbohJ</i> pistil with WT pollen (middle), and a WT pistil with <i>rbohH rbohJ</i> pollen (right). Eighteen hours after manual pollination, WT PTs (left and middle panels) had grown through the entire pistil to reach the female gametophytes. In contrast, most of the <i>rbohH rbohJ</i> mutant PTs (right) were arrested in the transmitting tract. White arrows indicate the tip of the longest PT. Scale bar = 5 mm.</p

ANX RLK over-expressing pollen tubes do not exhibit endocytosis defects but display an increased rate of exocytosis.

<p>(A) Representative single median plane images of a normally growing PT of the ANX1-YFP complemented line (top) and a slow growing PT of the ANX1-YFP over-expressing line (bottom) treated for 5 min with FM4-64 (2 µM). FM4-64 derived fluorescence was quantified in the apical PM (region 1) and the apical cytoplasm (region 2) for <i>n</i>>25 PTs of each line. Note that there are more endocytotic and secretory vesicles in the apical cytoplasm of over-expressing PTs. See also corresponding <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001719#pbio.1001719.s018" target="_blank">Video S2</a> and (B). Scale bar = 5 µm. (B) Quantitative analysis of relative FM4-64 fluorescence in the apical PM <i>versus</i> the apical cytoplasm in growing PTs of one ANX1-YFP complemented and two over-expressing lines. Data are presented as mean values ± standard deviation (SD) (<i>n</i>>25 each). Double asterisks indicate significant differences from the complemented line according to a Student's <i>t</i> test with <i>p</i><0.01. (C) Representative time-course imaging of FRAP for a complemented (left) and an over-expressing growing PT (right). Refer to <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001719#pbio.1001719.s019" target="_blank">Video S3</a> for more examples. Scale bar = 5 µm. (D) Quantitative analysis of FRAP time-courses of growing PTs of the complemented line (left, <i>n</i> = 18) and two over-expressing lines (right, <i>n</i>>17 for each). Relative intensity of apical PM-localized ANX1-YFP compared with fluorescence prior to photobleaching was used to quantify the rate of fluorescence recovery. FRAP signals are shown as mean values ± SD. The relative intensity after recovery for 10 s after photobleaching (I_10sec) is indicated. See also corresponding <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001719#pbio.1001719.s012" target="_blank">Table S1</a>.</p

ANX1-YFP over-expression phenotypes are dependent on functional <i>RbohH</i> and <i>RbohJ</i>.

<p>(A) Quantification of pollen germination and PT rupture for <i>rbohH-1 rbohJ-2</i>, ANX1-YFP in WT (line #4), ANX1-YFP in <i>anx1-2 anx2-2</i> (complemented line), and ANX1-YFP in <i>rbohH-1 rbohJ-2</i> plants. Data are mean ± standard error of the mean (SEM) of three independent experiments with more than 150 pollen grains per genotype and experiment. (B) Representative time-course imaging of FRAP for a <i>rbohH-1 rbohJ-2</i> PT expressing ANX1-YFP. Scale bar = 5 µm. (C) Quantitative analysis of FRAP time-courses for growing PTs of ANX1-YFP in <i>rbohH-1 rbohJ-2</i> (<i>n</i> = 24). Relative intensity of apical PM-localized ANX1-YFP compared with fluorescence prior to photobleaching was used to quantify the rate of fluorescence recovery. FRAP signals are shown as mean values ± standard deviation (SD). The relative intensity after recovery for 10 s after photobleaching (I_10sec) is indicated. See also corresponding <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001719#pbio.1001719.s012" target="_blank">Table S1</a>.</p