The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation

Muñ,oz-Fuentes, Violeta,Cacheiro, Pilar,Meehan, Terrence F.,Aguilar-Pimentel, Juan Antonio,Brown, Steve D. M.,Flenniken, Ann M.,Flicek, Paul,Galli, Antonella,Mashhadi, Hamed Haseli,Hrabě,de Springer Netherlands 2018 Conservation genetics Vol.19 No.4

<P>The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (10.1007/s10592-018-1072-9) contains supplementary material, which is available to authorized users.</P>

Rational curves, Dynkin diagrams and Fano manifolds with nef tangent bundle

Muñ,oz, Roberto,Occhetta, Gianluca,Solá,Conde, Luis E.,Watanabe, Kiwamu Springer-Verlag 2015 Mathematische Annalen Vol.361 No.3

DeepToF : off-the-shelf real-time correction of multipath interference in time-of-flight imaging

Marco, Julio,Hernandez, Quercus,Muñ,oz, Adolfo,Dong, Yue,Jarabo, Adrian,Kim, Min H.,Tong, Xin,Gutierrez, Diego Association for Computing Machinery 2017 ACM transactions on graphics Vol. No.

<P>Time-of-flight (ToF) imaging has become a widespread technique for depth estimation, allowing affordable off-the-shelf cameras to provide depth maps in real time. However, multipath interference (MPI) resulting from indirect illumination significantly degrades the captured depth. Most previous works have tried to solve this problem by means of complex hardware modifications or costly computations. In this work, we avoid these approaches and propose a new technique to correct errors in depth caused by MPI, which requires no camera modifications and takes just 10 milliseconds per frame. Our observations about the nature of MPI suggest that most of its information is available in image space; this allows us to formulate the depth imaging process as a spatially-varying convolution and use a convolutional neural network to correct MPI errors. Since the input and output data present similar structure, we base our network on an autoencoder, which we train in two stages. First, we use the encoder (convolution filters) to learn a suitable basis to represent MPI-corrupted depth images; then, we train the decoder (deconvolution filters) to correct depth from synthetic scenes, generated by using a physically-based, time-resolved renderer. This approach allows us to tackle a key problem in ToF, the lack of ground-truth data, by using a large-scale captured training set with MPI-corrupted depth to train the encoder, and a smaller synthetic training set with ground truth depth to train the decoder stage of the network. We demonstrate and validate our method on both synthetic and real complex scenarios, using an off-the-shelf ToF camera, and with only the captured, incorrect depth as input.</P>

Mechanistic study of styrene aziridination by iron( <small>IV</small> ) nitrides

Crandell, Douglas ,W.,Muñ,oz III, Salvador B.,Smith, Jeremy M.,Baik, Mu-Hyun Royal Society of Chemistry 2018 Chemical Science Vol.9 No.45

<▼1><P>A combined experimental and computational investigation reveals that styrene aziridination by an iron(<SMALL>IV</SMALL>) nitride occurs by a stepwise mechanism involving multistate character.</P></▼1><▼2><P>A combined experimental and computational investigation was undertaken to investigate the mechanism of aziridination of styrene by the tris(carbene)borate iron(<SMALL>IV</SMALL>) nitride complex, PhB(<SUP><I>t</I></SUP>BuIm)<SUB>3</SUB>Fe 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 N. While mechanistic investigations suggest that aziridination occurs <I>via</I> a reversible, stepwise pathway, it was not possible to confirm the mechanism using only experimental techniques. Density functional theory calculations support a stepwise radical addition mechanism, but suggest that a low-lying triplet (<I>S</I> = 1) state provides the lowest energy path for C–N bond formation (24.6 kcal mol<SUP>–1</SUP>) and not the singlet ground (<I>S</I> = 0) state. A second spin flip may take place in order to facilitate ring closure and the formation of the quintet (<I>S</I> = 2) aziridino product. A Hammett analysis shows that electron-withdrawing groups increase the rate of reaction <I>σ</I><SUB>p</SUB> (<I>ρ</I> = 1.2 ± 0.2). This finding is supported by the computational results, which show that the rate-determining step drops from 24.6 kcal mol<SUP>–1</SUP> to 18.3 kcal mol<SUP>–1</SUP> when (<I>p</I>-NO<SUB>2</SUB>C<SUB>6</SUB>H<SUB>4</SUB>)CH 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 CH<SUB>2</SUB> is used and slightly increases to 25.5 kcal mol<SUP>–1</SUP> using (<I>p</I>-NMe<SUB>2</SUB>C<SUB>6</SUB>H<SUB>4</SUB>)CH 00000000000

Relaxant and anti-inflammatory effect of two thalidomide analogs as PDE-4 inhibitors in pregnant rat uterus

Víctor Manuel Muñ,oz-Pérez,Eduardo Fernández-Martínez,Héctor Ponce-Monter,Mario I. Ortiz 대한생리학회-대한약리학회 2017 The Korean Journal of Physiology & Pharmacology Vol.13 No.1

The aim of this study was to evaluate the relaxant and anti-inflammatory effects of two thalidomide analogs as phosphodiesterase-4 (PDE-4) inhibitors in pregnant rat uterus. Uteri from Wistar female rats were isolated at 19 day of pregnancy. Uterine samples were used in functional studies to evaluate the inhibitory effects of the thalidomide analogs, methyl 3-(4-nitrophthalimido)-3-(3,4-dimethoxyphenyl)-propanoate (4NO2PDPMe) and methyl 3-(4-aminophthalimido)-3-(3,4-dimethoxyphenyl)-propanoate (4APDPMe), on prostaglandin-F2α (PGF2α)-induced phasic, K⁺-induced tonic, and Ca²⁺-induced contractions. Accumulation of cAMP was quantified in uterine homogenates by ELISA. Anti-inflammatory effect was assessed by using ELISA for determination of the pro-inflammatory cytokines tumor necrosis factor-α (TNFα) and interleukin (IL)-1β, and anti-inflammatory IL-10, from uterine explants stimulated with lipopolysaccharide (LPS). Nifedipine, forskolin and rolipram were used as positive controls where required. Both thalidomide analogs induced a significant inhibition of the uterine contractions induced by the pharmaco- and electro-mechanic stimuli. Nifedipine and forskolin were more potent than the analogs to inhibit the uterine contractility, but these were more potent than rolipram, and 4APDPMe was equieffective to nifedipine. Thalidomide analogs increased uterine cAMP-levels in a concentration-dependent manner. The LPS-induced TNFα and IL-1β uterine secretion was diminished in a concentration-dependent fashion by both analogs, whereas IL-10 secretion was increased significantly. The thalidomide analogs induced utero-relaxant and anti-inflammatory effects, which were associated with the increased cAMP levels as PDE-4 inhibitors in the pregnant rat uterus. Such properties place these thalidomide analogs as potentially safe and effective tocolytic agents in a field that urgently needs improved pharmacological treatments, as in cases of preterm labor.

Role of nonlinearities and initial prepatterned surfaces in nanobead formation by ion-beam bombardment of Au(001): Experiments and theory

Kim, J.-H.,Kim, J.-S.,Muñ,oz-Garcí,a, J.,Cuerno, R. American Physical Society 2013 Physical review. B, Condensed matter and materials Vol.87 No.8

Morphological reassessment and molecular assessment of Sargassum (Fucales: Phaeophyceae) species from the Gulf of California, Mexico

ANDRADE-SORCIA, GABRIELA,RIOSMENA-RODRIGUEZ, RAFAEL,MUÑ,IZ-SALAZAR, RAQUEL,LÓ,PEZ-VIVAS, JUAN MANUEL,BOO, GA HUN,LEE, KYUNG MIN,BOO, SUNG MIN Magnolia Press 2014 Phytotaxa Vol.183 No.4

<P>Systematic molecular studies have not been performed on ecologically important brown algae (Sargassum) in the Gulf of California, Mexico, where 42 specific and infraspecific names have been recorded within this genus. We conducted phylogenetic analyses of nuclear ribosomal ITS and mitochondrial cox1 and cox3 sequences, along with detailed morphological observations of Sargassum collected in the Gulf of California. We confirmed the presence of six species, five previously described-S. herporhizum, S. horridum, S. johnstonii, S. lapazeanum, and S. sinicola, as well as the newly described Sargassum ulixei sp. nov. which is characterized by terete primary axes arising from the stipe, lanceolate to elliptical sessile ecostate blades with smooth margins, cryptostomata, ellipsoidal vesicles with a short mucron, and cylindrical to ellipsoidal receptacles. The individual analyses and subsequent phylogenetic analysis recognized two groups previously described by Dawson, one as Sargassum and other as Horridum. Our studies suggest that the Gulf of California is a region with endemic Sargassum species, and is clearly distinguished from the Pacific side of Baja California, where recently introduced species are common. Based on phylogenetic relationships, we propose two geographical origins for the Sargassum from the Gulf of California: a first group originating from the proto-Gulf, related to species from the northern hemisphere (including five species); and a second group, containing S. sinicola, introduced when the southern end opened at a later stage. </P>

Type-specific human papillomavirus distribution in invasive cervical cancer in Korea, 1958-2004.

Oh, Jin-Kyoung,Alemany, Laia,Suh, Jung-Il,Rha, Seo-Hee,Muñ,oz, Nubia,Bosch, F Xavier,Quint, Wim,Lloveras, Belen,Klaustermeier, Jo Ellen,de Sanjosé,, Silvia,Shin, Hai-Rim Asian Pacific Organization for Cancer Prevention 2010 Asian Pacific journal of cancer prevention Vol.11 No.4

<P>To describe the HPV genotype distribution and to investigate the underlying secular trend in the relative contribution of HPV types 16-18 in invasive cervical cancer (ICC) over a period of 47 years (1958-2004) in South Korea.</P>

Structure-solubility relationships in fluoride-containing phosphate based bioactive glasses

Shaharyar, Yaqoot,Wein, Eric,Kim, Jung-Ju,Youngman, Randall E.,Muñ,oz, Francisco,Kim, Hae-Won,Tilocca, Antonio,Goel, Ashutosh The Royal Society of Chemistry 2015 Journal of Materials Chemistry B Vol.3 No.48

<P>The dissolution of fluoride-containing bioactive glasses critically affects their biomedical applications. Most commercial fluoride-releasing bioactive glasses have been designed in the soda-lime-silica system. However, their relatively slow chemical dissolution and the adverse effect of fluoride on their bioactivity are stimulating the study of alternative biodegradable materials with higher biodegradability, such as biodegradable phosphate-based bioactive glasses, which can be a good candidate for applications where a fast release of active ions is sought. In order to design new biomaterials with controlled degradability and high bioactivity, it is essential to understand the connection between chemical composition, molecular structure, and solubility in physiological fluids. Accordingly, in this work we have combined the strengths of various experimental techniques with Molecular Dynamics (MD) simulations, to elucidate the impact of fluoride ions on the structure and chemical dissolution of bioactive phosphate glasses in the system: 10Na2O-(45 − <I>x</I>)CaO-45P2O5-<I>x</I>CaF2, where <I>x</I> varies between 0-10 mol%. NMR and MD data reveal that the medium-range atomic-scale structure of these glasses is dominated by <I>Q</I><SUP>2</SUP> phosphate units followed by <I>Q</I><SUP>1</SUP> units, and the MD simulations further show that fluoride tends to associate with network modifier cations to form alkali/alkaline-earth rich ionic aggregates. The impact of fluoride on chemical dissolution of glasses has been studied in deionized water, acidic (pH = 3.0), neutral (pH = 7.4) and basic (pH = 9.0) buffer solutions, while the bioactivity and cytotoxicity of glasses has been studied <I>in vitro</I> through their apatite-forming ability in simulated body fluid (SBF) and cell culture tests on mesenchymal stem cells (MSCs), respectively. The macroscopic trends observed from various chemical dissolution and bioactivity studies are discussed on the basis of the effect of fluoride on the atomistic structure of glasses, such as F-induced phosphate network re-polymerization, in an attempt to establish composition-structure-property relationships for these biomaterials.</P>

Accurate in-operando study of molten carbonate fuel cell degradation processes -part I: Physiochemical processes individuation

Santoni, F.,Della Pietra, M.,Pumiglia, D.,Boigues Muñ,oz, C.,McPhail, S.J.,Cigolotti, V.,Nam, S.W.,Kang, M.G.,Yoon, S.P. Elsevier 2018 ELECTROCHIMICA ACTA Vol.291 No.-

<P><B>Abstract</B></P> <P>This work has the difficult task to deeply study the electrochemical processes that occur inside a 100 cm<SUP>2</SUP> of Molten Carbonate Fuel Cells (MCFC) impedance spectra using the high resolution of Distribution of Relaxation Time (DRT) method. Using this method, it is possible to shed light on the different physicochemical processes occurring within these cells, identifying the characteristic relaxation times by means of an appropriate experimental campaign where temperature and gas compositions in anode and cathode were varied one at a time. The quality of the recorded spectra was verified by Kramers-Kronig relation before applying DRT calculations. In this work, five distinct and separated peaks with different time constants ranging from 0.01 to 500 Hz were identified and associated with physiochemical processes of the cell. Three peaks at high frequency represent the charge transfer processes in anode and cathode active sites. The other two, located at low frequency, are associated with the gas diffusion in the electrodes and to the gas conversion process. This study represents the first application of the DRT approach to this technology allowing to understand the physicochemical origin of the individual polarization processes controlling the cell performance and the degradation. The analysis of degradation processes using the DRT method and the physiochemical processes identification presented in this paper will be shown in part II of this work.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The first application of DRT approach to MCFC impedance Spectra is presented. </LI> <LI> Five processes controlling the cell performance are individuated using DRT method. </LI> <LI> Repeatability and reproducibility of the DRT results in MCFCs are demonstrated. </LI> <LI> Three peaks with a high-frequency domain are related to Charge Transfer Processes. </LI> <LI> Two peaks with a low-frequency domain are associated with Mass Transfer Mechanisms. </LI> </UL> </P>