Semantically Informed Multiview Surface Refinement

We present a method to jointly refine the geometry and semantic segmentation of 3D surface meshes. Our method alternates between updating the shape and the semantic labels. In the geometry refinement step, the mesh is deformed with variational energy minimization, such that it simultaneously maximizes photo-consistency and the compatibility of the semantic segmentations across a set of calibrated images. Label-specific shape priors account for interactions between the geometry and the semantic labels in 3D. In the semantic segmentation step, the labels on the mesh are updated with MRF inference, such that they are compatible with the semantic segmentations in the input images. Also, this step includes prior assumptions about the surface shape of different semantic classes. The priors induce a tight coupling, where semantic information influences the shape update and vice versa. Specifically, we introduce priors that favor (i) adaptive smoothing, depending on the class label; (ii) straightness of class boundaries; and (iii) semantic labels that are consistent with the surface orientation. The novel mesh-based reconstruction is evaluated in a series of experiments with real and synthetic data. We compare both to state-of-the-art, voxel-based semantic 3D reconstruction, and to purely geometric mesh refinement, and demonstrate that the proposed scheme yields improved 3D geometry as well as an improved semantic segmentation

Aquatic occurrence of phytotoxins in small streams triggered by biogeography, vegetation growth stage, and precipitation

Toxic plant secondary metabolites (PSMs), so-called phytotoxins, occur widely in plant species. Many of these phytotoxins have similar mobility, persistence, and toxicity properties in the environment as anthropogenic micropollutants, which increasingly contaminate surface waters. Although recent case studies have shown the aquatic relevance of phytotoxins, the overall exposure remains unknown. Therefore, we performed a detailed occurrence analysis covering 134 phytotoxins from 27 PSM classes. Water samples from seven small Swiss streams with catchment areas from 1.7 to 23 km(2) and varying land uses were gathered over several months to investigate seasonal impacts. They were complemented with samples from different biogeographical regions to cover variations in vegetation. A broad SPE-LC-HRMS/MS method was applied with limits of detection below 5 ng/L for over 80% of the 134 included phytotoxins. In total, we confirmed 39 phytotoxins belonging to 13 PSM classes, which corresponds to almost 30% of all included phytotoxins. Several alkaloids were regularly detected in the low ng/L-range, with average detection frequencies of 21%. This is consistent with the previously estimated persistence and mobility properties that indicated a high contamination potential. Coumarins were previously predicted to be unstable, however, detection frequencies were around 89%, and maximal concentrations up to 90 ng/L were measured for fraxetin produced by various trees. Overall, rainy weather conditions at full vegetation led to the highest total phytotoxin concentrations, which might potentially be most critical for aquatic organisms

Familial hypomagnesaemia with hypercalciuria and nephrocalcinosis (FHHNC): Compound heterozygous mutation in the claudin 16 (CLDN16) gene

<p>Abstract</p> <p>Background</p> <p>Familial hypomagnesaemia with hypercalciuria and nephrocalcinosis (FHHNC) is an autosomal recessive disorder of renal calcium and magnesium wasting frequently complicated by progressive chronic renal failure in childhood or adolescence.</p> <p>Methods</p> <p>A 7 year old boy was investigated following the findings of marked renal insufficiency and nephrocalcinosis in his 18-month old sister. He too was found to have extensive nephrocalcinosis with increased fractional excretion of magnesium: 12.4% (<4%) and hypercalciuria: 5.7 mmol (< 2.5/24 hours). He had renal impairment, partial distal renal tubular acidosis and defective urinary concentrating ability. Therapy with thiazide diuretics and magnesium supplements failed to halt the progression of the disorder. Both children subsequently underwent renal transplantation. Both children's parents are unaffected and there is one unaffected sibling.</p> <p>Results</p> <p>Mutation analysis revealed 2 heterozygous mutations in the claudin 16 gene <it>(CLDN16</it>) in both affected siblings; one missense mutation in exon 4: C646T which results in an amino acid change Arg216Cys in the second extracellular loop of <it>CLDN16 </it>and loss of function of the protein and a donor splice site mutation which changes intron 4 consensus splice site from 'GT' to 'TT' resulting in decreased splice efficiency and the formation of a truncated protein with loss of 64 amino acids in the second extracellular loop.</p> <p>Conclusion</p> <p>The mutations in <it>CLDN16 </it>in this kindred affect the second extra-cellular loop of claudin 16. The clinical course and molecular findings suggest complete loss of function of the protein in the 2 affected cases and highlight the case for molecular diagnosis in individuals with FHHNC.</p

CFHTLenS: Weak lensing constraints on the ellipticity of galaxy-scale matter haloes and the galaxy-halo misalignment

We present weak lensing constraints on the ellipticity of galaxy-scale matter haloes and the galaxy-halo misalignment. Using data from the Canada-France-Hawaii Telescope Lensing Survey (CFHTLenS), we measure the weighted-average ratio of the aligned projected ellipticity components of galaxy matter haloes and their embedded galaxies, $f_\mathrm{h}$, split by galaxy type. We then compare our observations to measurements taken from the Millennium Simulation, assuming different models of galaxy-halo misalignment. Using the Millennium Simulation we verify that the statistical estimator used removes contamination from cosmic shear. We also detect an additional signal in the simulation, which we interpret as the impact of intrinsic shape-shear alignments between the lenses and their large-scale structure environment. These alignments are likely to have caused some of the previous observational constraints on $f_\mathrm{h}$ to be biased high. From CFHTLenS we find $f_\mathrm{h}=-0.04 \pm 0.25$ for early-type galaxies, which is consistent with current models for the galaxy-halo misalignment predicting $f_\mathrm{h}\simeq 0.20$. For late-type galaxies we measure $f_\mathrm{h}=0.69_{-0.36}^{+0.37}$ from CFHTLenS. This can be compared to the simulated results which yield $f_\mathrm{h}\simeq 0.02$ for misaligned late-type models.Comment: 21 pages, 3 tables, 9 figures. This replacement matches the version accepted for publication in MNRA

A Novel Rapid DNA Microarray Assay Enables Identification of 37 Mycoplasma Species and Highlights Multiple Mycoplasma Infections

Mycoplasmas comprise a conglomerate of pathogens and commensals occurring in humans and animals. The genus Mycoplasma alone contains more than 120 species at present, and new members are continuously being discovered. Therefore, it seems promising to use a single highly parallel detection assay rather than develop separate tests for each individual species. In this study, we have designed a DNA microarray carrying 70 oligonucleotide probes derived from the 23S rRNA gene and 86 probes from the tuf gene target regions. Following a PCR amplification and biotinylation step, hybridization on the array was shown to specifically identify 31 Mycoplasma spp., as well as 3 Acholeplasma spp. and 3 Ureaplasma spp. Members of the Mycoplasma mycoides cluster can be recognized at subgroup level. This procedure enables parallel detection of Mollicutes spp. occurring in humans, animals or cell culture, from mono- and multiple infections, in a single run. The main advantages of the microarray assay include ease of operation, rapidity, high information content, and affordability. The new test's analytical sensitivity is equivalent to that of real-time PCR and allows examination of field samples without the need for culture. When 60 field samples from ruminants and birds previously analyzed by denaturing-gradient gel electrophoresis (DGGE) were tested by the microarray assay both tests identified the same agent in 98.3% of the cases. Notably, microarray testing revealed an unexpectedly high proportion (35%) of multiple mycoplasma infections, i.e., substantially more than DGGE (15%). Two of the samples were found to contain four different Mycoplasma spp. This phenomenon deserves more attention, particularly its implications for epidemiology and treatment

CFHTLenS tomographic weak lensing: Quantifying accurate redshift distributions

The Canada-France-Hawaii Telescope Lensing Survey (CFHTLenS) comprises deep multi-colour (u*g'r'i'z') photometry spanning 154 square degrees, with accurate photometric redshifts and shape measurements. We demonstrate that the redshift probability distribution function summed over galaxies provides an accurate representation of the galaxy redshift distribution accounting for random and catastrophic errors for galaxies with best fitting photometric redshifts z_p < 1.3. We present cosmological constraints using tomographic weak gravitational lensing by large-scale structure. We use two broad redshift bins 0.5 < z_p <= 0.85 and 0.85 < z_p <= 1.3 free of intrinsic alignment contamination, and measure the shear correlation function on angular scales in the range ~1-40 arcmin. We show that the problematic redshift scaling of the shear signal, found in previous CFHTLS data analyses, does not afflict the CFHTLenS data. For a flat Lambda-CDM model and a fixed matter density Omega_m=0.27, we find the normalisation of the matter power spectrum sigma_8=0.771 \pm 0.041. When combined with cosmic microwave background data (WMAP7), baryon acoustic oscillation data (BOSS), and a prior on the Hubble constant from the HST distance ladder, we find that CFHTLenS improves the precision of the fully marginalised parameter estimates by an average factor of 1.5-2. Combining our results with the above cosmological probes, we find Omega_m=0.2762 \pm 0.0074 and sigma_8=0.802 \pm 0.013.Comment: 17 pages, 12 figures, submitted to MNRA

Modest de novo Reactivation of Single HIV-1 Proviruses in Peripheral CD4+ T Cells by Romidepsin

A cure for human immunodeficiency virus (HIV-1) is restricted by the continued presence of a latent reservoir of memory CD4+ T cells with proviruses integrated into their DNA despite suppressive antiretroviral therapy (ART). A predominant strategy currently pursued in HIV-1 cure-related research is the “kick and kill” approach, where latency reversal agents (LRAs) are used to reactivate transcription from integrated proviruses. The premise of this approach is that “kicking” latent virus out of hiding allows the host immune system to recognize and kill infected cells. Clinical trials investigating the efficacy of LRAs, such as romidepsin, have shown that these interventions do induce transient spikes in viral RNA in HIV-1-infected individuals. However, since these trials failed to significantly reduce viral reservoir size or significantly delay time to viral rebound during analytical treatment interruptions, it is questioned how much each individual latent provirus is actually “kicked” to produce viral transcripts and/or proteins by the LRA. Here, we developed sensitive and specific digital droplet PCR-based assays with single-provirus level resolution. Combining these assays allowed us to interrogate the level of viral RNA transcripts from single proviruses in individuals on suppressive ART with or without concomitant romidepsin treatment. Small numbers of proviruses in peripheral blood memory CD4+ T cells were triggered to become marginally transcriptionally active upon romidepsin treatment. These novel assays can be applied retrospectively and prospectively in HIV-1 cure-related clinical trials to gain crucial insights into LRA efficacy at the single provirus level

A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells

Growth and differentiation of multicellular systems is orchestrated by spatially restricted gene expression programs in specialized subpopulations. The targeted manipulation of such processes by synthetic tools with high-spatiotemporal resolution could, therefore, enable a deepened understanding of developmental processes and open new opportunities in tissue engineering. Here, we describe the first red/far-red light-triggered gene switch for mammalian cells for achieving gene expression control in time and space. We show that the system can reversibly be toggled between stable on- and off-states using short light pulses at 660 or 740 nm. Red light-induced gene expression was shown to correlate with the applied photon number and was compatible with different mammalian cell lines, including human primary cells. The light-induced expression kinetics were quantitatively analyzed by a mathematical model. We apply the system for the spatially controlled engineering of angiogenesis in chicken embryos. The system's performance combined with cell- and tissue-compatible regulating red light will enable unprecedented spatiotemporally controlled molecular interventions in mammalian cells, tissues and organism

Radiographic abnormalities, bladder interventions, and bladder surgery in the first decade of life in children with spina bifida

Background Spina bifida (SB) patients are at increased risk for hydronephrosis, bladder storage and emptying problems, and renal failure that may require multiple bladder surgeries. Methods We retrospectively reviewed patients born with SB 2005–2009, presenting to our institution within 1 year of birth. Outcomes at 8–11 years old included final renal/bladder ultrasound (RBUS) results, clean intermittent catheterization (CIC) use, anticholinergic use, surgical interventions, and final renal function. We excluded those without follow-up past age 8 and/or no RBUS or fluoroscopic urodynamic images (FUI) within the first year of life. Imaging was independently reviewed by four pediatric urologists blinded to radiologists’ interpretation and initial findings compared with final outcomes. Results Of 98 children, 62 met inclusion criteria (48% male, 76% shunted). Median age at last follow-up was 9.6 years. Upon initial imaging, 74% had hydronephrosis (≥ SFU grade 1), decreasing to 5% at 10 years (p < 0.0001). Initially, 9% had ≥ SFU grade 3 hydronephrosis, decreasing to 2% (p = 0.13). CIC and anticholinergic use increased from 61% and 37% to 87% and 86%, respectively (p = 0.001 and p < 0.0001, respectively). With follow-up, 55% had surgical intervention and 23% had an augmentation. Of children with a serum creatinine/cystatin-C at 8–11 years old, one had confirmed chronic kidney disease (stage 2). Conclusions Despite initial high incidence of hydronephrosis, this was low grade and resolved in the first decade of life. Additionally, the 8–11-year incidence of kidney disease and upper tract changes was low due to aggressive medical management