Training Auto-encoder-based Optimizers for Terahertz Image Reconstruction

Terahertz (THz) sensing is a promising imaging technology for a wide variety of different applications. Extracting the interpretable and physically meaningful parameters for such applications, however, requires solving an inverse problem in which a model function determined by these parameters needs to be fitted to the measured data. Since the underlying optimization problem is nonconvex and very costly to solve, we propose learning the prediction of suitable parameters from the measured data directly. More precisely, we develop a model-based autoencoder in which the encoder network predicts suitable parameters and the decoder is fixed to a physically meaningful model function, such that we can train the encoding network in an unsupervised way. We illustrate numerically that the resulting network is more than 140 times faster than classical optimization techniques while making predictions with only slightly higher objective values. Using such predictions as starting points of local optimization techniques allows us to converge to better local minima about twice as fast as optimization without the network-based initialization.Comment: This is a pre-print of a conference paper published in German Conference on Pattern Recognition (GCPR) 201

Inhaled nitric oxide in premature infants: effect on tracheal aspirate and plasma nitric oxide metabolites

ObjectiveInhaled nitric oxide (iNO) is a potential new therapy for prevention of bronchopulmonary dysplasia and brain injury in premature infants. This study examined dose-related effects of iNO on NO metabolites as evidence of NO delivery.Study designA subset of 102 premature infants in the NO CLD trial, receiving 24 days of iNO (20 p.p.m. decreasing to 2 p.p.m.) or placebo, were analyzed. Tracheal aspirate (TA) and plasma samples collected at enrollment and at intervals during study gas were analyzed for NO metabolites.ResultiNO treatment increased NO metabolites in TA at 20 and 10 p.p.m. (1.7- to 2.3-fold vs control) and in plasma at 20, 10, and 5 p.p.m. (1.6- to 2.3-fold). In post hoc analysis, treated infants with lower metabolite levels at entry had an improved clinical outcome.ConclusioniNO causes dose-related increases in NO metabolites in the circulation as well as lung fluid, as evidenced by TA analysis, showing NO delivery to these compartments

From Isotropic to Anisotropic Side Chain Representations: Comparison of Three Models for Residue Contact Estimation

The criterion to determine residue contact is a fundamental problem in deriving knowledge-based mean-force potential energy calculations for protein structures. A frequently used criterion is to require the side chain center-to-center distance or the -to- atom distance to be within a pre-determined cutoff distance. However, the spatially anisotropic nature of the side chain determines that it is challenging to identify the contact pairs. This study compares three side chain contact models: the Atom Distance criteria (ADC) model, the Isotropic Sphere Side chain (ISS) model and the Anisotropic Ellipsoid Side chain (AES) model using 424 high resolution protein structures in the Protein Data Bank. The results indicate that the ADC model is the most accurate and ISS is the worst. The AES model eliminates about 95% of the incorrectly counted contact-pairs in the ISS model. Algorithm analysis shows that AES model is the most computational intensive while ADC model has moderate computational cost. We derived a dataset of the mis-estimated contact pairs by AES model. The most misjudged pairs are Arg-Glu, Arg-Asp and Arg-Tyr. Such a dataset can be useful for developing the improved AES model by incorporating the pair-specific information for the cutoff distance

Manovacuometria realizada por meio de traqueias de diferentes comprimentos

Manovacuometry is a simple, fast, and non-invasive test, with maximal inspiratory pressure (MIP) and maximal expiratory pressure (MEP) obtained to assist respiratory muscle assessment. Currently, there is a wide variety of models and brands of manovacuometers with different trachea diameters and lengths. However, the interference of these models in the measurements obtained by these equipments needs to be investigated. Thus, this study mainly aimed to verify the influence of tracheal length on maximal respiratory pressures (MRP), obtained by an analog manovacuometer, in healthy individuals. Our secondary objective was to verify the correlation between measurements. Fifty individuals, aged 18 to 30, of both sexes, were evaluated by spirometry and manovacuometry. MIP and MEP were performed using tracheas with same internal diameter (0.5 cm) and 30 cm, 60 cm, and 90 cm length. Significantly lower MIP values were observed when comparing a 90 cm trachea to 30 and 60 cm tracheas (Friedman’s ANOVA test and Wilcoxon test with Bonferroni adjustment). Tracheas with 30, 60, and 90 cm length and same diameter did not affect MIP and MEP values, except the 90 cm trachea for MIP values, which may interfere in the physical therapy clinical practice. Further studies are required to analyze the need for standardizing the trachea length used in manovacuometers.La manovacuometría es una prueba sencilla, rápida y no invasiva por la cual se obtienen la presión inspiratoria máxima (PImax) y la presión espiratoria máxima (PEmax), con el objetivo de ayudar en el examen muscular respiratorio. Hoy día se encuentran una gran variedad de modelos y marcas de manovacuometros, con diferentes diámetros y longitudes de las tráqueas, pero hacen falta estudios sobre la interferencia de estos modelos en las mediciones por este instrumento. En este texto se propone examinar en sujetos sanos, en primer lugar, la influencia en la longitud de las tráqueas en las presiones respiratorias máximas, obtenidas por manovacuometros analógicos, y en segundo lugar comprobar la existencia de correlación entre las mediciones. Se evaluaron a cincuenta sujetos entre 18 y 30 años de edad, tanto varones como mujeres, empleando la espirometría y la manovacuometría. Se midió la PImax y la PEmax empleando tráqueas de mismo diámetro interno (0,5 cm) y con longitudes de 30, 60 e 90 cm. Se observaron valores significativamente menores de PImax con la tráquea de longitud de 90 cm en comparación con las PImax con las tráqueas de 30 y 60 cm (prueba de Friedman’s ANOVA, la de Wilcoxon con ajustes de Bonferroni). Las tráqueas de 30, 60 y 90 cm de longitud y mismo diámetro no influyeron en los valores de la PEmax y de la PImax, con excepción de la tráquea de 90 cm en los valores de la PImax, lo que puede interferir la práctica clínica fisioterapéutica. Se necesitan más estudios para evaluar la necesidad de estándares de la longitud de tráqueas empleadas en manovacuometros.A manovacuometria é um teste simples, rápido e não invasivo por meio do qual a pressão inspiratória máxima (PImáx) e a pressão expiratória máxima (PEmáx) são obtidas, a fim de auxiliar na avaliação muscular respiratória. Atualmente, há grande variedade de modelos e marcas de manovacuômetros, com diferentes diâmetros e comprimentos de traqueias, no entanto, a interferência desses modelos nas medidas obtidas por esses equipamentos necessita de investigação. Desta forma, o objetivo primário deste estudo foi verificar a influência do comprimento de traqueias nas pressões respiratórias máximas, obtidas por meio de manovacuômetro analógico, em indivíduos saudáveis e, secundariamente, se há correlação entre as medidas. Foram avaliados 50 indivíduos, de 18 a 30 anos, de ambos os sexos, por meio da espirometria e manovacuometria. As PImáx e PEmáx foram realizadas com uso de traqueias de mesmo diâmetro interno (0,5 cm) e comprimentos de 30, 60 e 90 cm. Foram observados valores significativamente menores de PImáx obtidos com a traqueia de comprimento de 90 cm comparados às PImáx obtidas com as traqueias de 30 e 60 cm (teste de Friedman’s ANOVA com teste de Wilcoxon com ajuste de Bonferroni). As traqueias de 30, 60 e 90 cm de comprimento e mesmo diâmetro não influenciaram os valores de PEmáx e PImáx, exceto a traqueia de 90 cm para os valores de PImáx, o que pode interferir na prática clínica fisioterapêutica. Novos estudos são necessários para analisar a necessidade de padronização do comprimento da traqueia utilizada em manovacuômetros

lincRNAs act in the circuitry controlling pluripotency and differentiation

Although thousands of large intergenic non-coding RNAs (lincRNAs) have been identified in mammals, few have been functionally characterized, leading to debate about their biological role. To address this, we performed loss-of-function studies on most lincRNAs expressed in mouse embryonic stem (ES) cells and characterized the effects on gene expression. Here we show that knockdown of lincRNAs has major consequences on gene expression patterns, comparable to knockdown of well-known ES cell regulators. Notably, lincRNAs primarily affect gene expression in trans. Knockdown of dozens of lincRNAs causes either exit from the pluripotent state or upregulation of lineage commitment programs. We integrate lincRNAs into the molecular circuitry of ES cells and show that lincRNA genes are regulated by key transcription factors and that lincRNA transcripts bind to multiple chromatin regulatory proteins to affect shared gene expression programs. Together, the results demonstrate that lincRNAs have key roles in the circuitry controlling ES cell state.Broad InstituteHarvard UniversityNational Human Genome Research Institute (U.S.)Merkin Family Foundation for Stem Cell Researc

Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses

<p>Abstract</p> <p>Background</p> <p>Pneumonia and myocarditis are the most commonly reported diseases due to <it>Histophilus somni</it>, an opportunistic pathogen of the reproductive and respiratory tracts of cattle. Thus far only a few genes involved in metabolic and virulence functions have been identified and characterized in <it>H. somni </it>using traditional methods. Analyses of the genome sequences of several <it>Pasteurellaceae </it>species have provided insights into their biology and evolution. In view of the economic and ecological importance of <it>H. somni</it>, the genome sequence of pneumonia strain 2336 has been determined and compared to that of commensal strain 129Pt and other members of the <it>Pasteurellaceae</it>.</p> <p>Results</p> <p>The chromosome of strain 2336 (2,263,857 bp) contained 1,980 protein coding genes, whereas the chromosome of strain 129Pt (2,007,700 bp) contained only 1,792 protein coding genes. Although the chromosomes of the two strains differ in size, their average GC content, gene density (total number of genes predicted on the chromosome), and percentage of sequence (number of genes) that encodes proteins were similar. The chromosomes of these strains also contained a number of discrete prophage regions and genomic islands. One of the genomic islands in strain 2336 contained genes putatively involved in copper, zinc, and tetracycline resistance. Using the genome sequence data and comparative analyses with other members of the <it>Pasteurellaceae</it>, several <it>H. somni </it>genes that may encode proteins involved in virulence (<it>e.g</it>., filamentous haemaggutinins, adhesins, and polysaccharide biosynthesis/modification enzymes) were identified. The two strains contained a total of 17 ORFs that encode putative glycosyltransferases and some of these ORFs had characteristic simple sequence repeats within them. Most of the genes/loci common to both the strains were located in different regions of the two chromosomes and occurred in opposite orientations, indicating genome rearrangement since their divergence from a common ancestor.</p> <p>Conclusions</p> <p>Since the genome of strain 129Pt was ~256,000 bp smaller than that of strain 2336, these genomes provide yet another paradigm for studying evolutionary gene loss and/or gain in regard to virulence repertoire and pathogenic ability. Analyses of the complete genome sequences revealed that bacteriophage- and transposon-mediated horizontal gene transfer had occurred at several loci in the chromosomes of strains 2336 and 129Pt. It appears that these mobile genetic elements have played a major role in creating genomic diversity and phenotypic variability among the two <it>H. somni </it>strains.</p

A Large-Scale Multi-ancestry Genome-wide Study Accounting for Smoking Behavior Identifies Multiple Significant Loci for Blood Pressure

Genome-wide association analysis advanced understanding of blood pressure (BP), a major risk factor for vascular conditions such as coronary heart disease and stroke. Accounting for smoking behavior may help identify BP loci and extend our knowledge of its genetic architecture. We performed genome-wide association meta-analyses of systolic and diastolic BP incorporating gene-smoking interactions in 610,091 individuals. Stage 1 analysis examined similar to 18.8 million SNPs and small insertion/deletion variants in 129,913 individuals from four ancestries (European, African, Asian, and Hispanic) with follow-up analysis of promising variants in 480,178 additional individuals from five ancestries. We identified 15 loci that were genome-wide significant (p <5 x 10(-8)) in stage 1 and formally replicated in stage 2. A combined stage 1 and 2 meta-analysis identified 66 additional genome-wide significant loci (13, 35, and 18 loci in European, African, and trans-ancestry, respectively). A total of 56 known BP loci were also identified by our results (p <5 x 10(-8)). Of the newly identified loci, ten showed significant interaction with smoking status, but none of them were replicated in stage 2. Several loci were identified in African ancestry, highlighting the importance of genetic studies in diverse populations. The identified loci show strong evidence for regulatory features and support shared pathophysiology with cardiometabolic and addiction traits. They also highlight a role in BP regulation for biological candidates such as modulators of vascular structure and function (CDKN1B, BCAR1-CFDP1, PXDN, EEA1), ciliopathies (SDCCAG8, RPGRIP1L), telomere maintenance (TNKS, PINX1, AKTIP), and central dopaminergic signaling MSRA, EBF2).Peer reviewe

Potassium and Sodium Transport in Yeast

[EN] As the proper maintenance of intracellular potassium and sodium concentrations is vital for cell growth, all living organisms have developed a cohort of strategies to maintain proper monovalent cation homeostasis. In the model yeast Saccharomyces cerevisiae, potassium is accumulated to relatively high concentrations and is required for many aspects of cellular function, whereas high intracellular sodium/potassium ratios are detrimental to cell growth and survival. The fact that S. cerevisiae cells can grow in the presence of a broad range of concentrations of external potassium (10 M–2.5 M) and sodium (up to 1.5 M) indicates the existence of robust mechanisms that have evolved to maintain intracellular concentrations of these cations within appropriate limits. In this review, current knowledge regarding potassium and sodium transporters and their regulation will be summarized. 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Stochastic flowering phenology in Dactylis Glomerata populations described by Markov chain modelling

Understanding the relationship between flowering patterns and pollen dispersal is important in climate change modelling, pollen forecasting, forestry and agriculture. Enhanced understanding of this connection can be gained through detailed spatial and temporal flowering observations on a population level, combined with modelling simulating the dynamics. Species with large distribution ranges, long flowering seasons, high pollen production and naturally large populations can be used to illustrate these dynamics. Revealing and simulating species-specific demographic and stochastic elements in the flowering process will likely be important in determining when pollen release is likely to happen in flowering plants. Spatial and temporal dynamics of eight populations of Dactylis glomerata were collected over the course of two years to determine high-resolution demographic elements. Stochastic elements were accounted for using Markov Chain approaches in order to evaluate tiller-specific contribution to overall population dynamics. Tiller-specific developmental dynamics were evaluated using three different RV matrix correlation coefficients. We found that the demographic patterns in population development were the same for all populations with key phenological events differing only by a few days over the course of the seasons. Many tillers transitioned very quickly from non-flowering to full flowering, a process that can be replicated with Markov Chain modelling. Our novel approach demonstrates the identification and quantification of stochastic elements in the flowering process of D. glomerata, an element likely to be found in many flowering plants. The stochastic modelling approach can be used to develop detailed pollen release models for Dactylis, other grass species and probably other flowering plants