Modeling complex metabolic reactions, ecological systems, and financial and legal networks with MIANN models based on Markov-Wiener node descriptors

[Abstract] The use of numerical parameters in Complex Network analysis is expanding to new fields of application. At a molecular level, we can use them to describe the molecular structure of chemical entities, protein interactions, or metabolic networks. However, the applications are not restricted to the world of molecules and can be extended to the study of macroscopic nonliving systems, organisms, or even legal or social networks. On the other hand, the development of the field of Artificial Intelligence has led to the formulation of computational algorithms whose design is based on the structure and functioning of networks of biological neurons. These algorithms, called Artificial Neural Networks (ANNs), can be useful for the study of complex networks, since the numerical parameters that encode information of the network (for example centralities/node descriptors) can be used as inputs for the ANNs. The Wiener index (W) is a graph invariant widely used in chemoinformatics to quantify the molecular structure of drugs and to study complex networks. In this work, we explore for the first time the possibility of using Markov chains to calculate analogues of node distance numbers/W to describe complex networks from the point of view of their nodes. These parameters are called Markov-Wiener node descriptors of order kth (Wk). Please, note that these descriptors are not related to Markov-Wiener stochastic processes. Here, we calculated the Wk(i) values for a very high number of nodes (>100,000) in more than 100 different complex networks using the software MI-NODES. These networks were grouped according to the field of application. Molecular networks include the Metabolic Reaction Networks (MRNs) of 40 different organisms. In addition, we analyzed other biological and legal and social networks. These include the Interaction Web Database Biological Networks (IWDBNs), with 75 food webs or ecological systems and the Spanish Financial Law Network (SFLN). The calculated Wk(i) values were used as inputs for different ANNs in order to discriminate correct node connectivity patterns from incorrect random patterns. The MIANN models obtained present good values of Sensitivity/Specificity (%): MRNs (78/78), IWDBNs (90/88), and SFLN (86/84). These preliminary results are very promising from the point of view of a first exploratory study and suggest that the use of these models could be extended to the high-throughput re-evaluation of connectivity in known complex networks (collation)

Solventes eutéticos naturais profundos (NADES) no preparo de amostras de rocha fosfática e suplemento mineral para determinação elementar por técnicas de plasma.

NATURAL DEEP EUTECTIC SOLVENTS (NADES) IN SAMPLE PREPARATION OF PHOSPHATE ROCK AND MINERAL SUPPLEMENT FOR ELEMENTARY DETERMINATION BY PLASMA-BASED TECHNIQUES. Natural deep eutectic solvents (NADES) based on xylitol, citric acid, and malic acid were synthesized and used in ultrasound-assisted extraction (UAE) and heating-bath extraction of phosphate rock and mineral supplement samples. Arsenic, Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Na, P and Zn were determined by inductively coupled plasma mass spectrometry (ICP-MS) and inductively coupled plasma optical emission spectrometry (ICP OES). The results showed the NADES as promising solvents for extraction of inorganic matrices compared to reference values and concentrations obtained using microwave-assisted acid digestion (MW-AD). Significant differences were observed for some elements, suggesting different chemical interactions between the synthesized NADES and each monitored element. For analytes extraction of phosphate rock, UAE presented the best results for As, Cr and P. Zinc was extracted with UAE and heating bath. Concerning mineral supplement, no significant differences were observed for Ca (UAE), Cd (UAE and heating bath), K (UAE and heating bath), Mn (UAE and heating bath), Na (UAE and heating bath), and P (UAE and heating bath). The NADES is a greener and a potentially alternative for the sample preparation compared to the official methods of analysis, can being used as selective extractor solvent in conventional sample preparation methods

Electrochemically controlled growth and positioning of suspended collagen membranes

Two independently recognized in vitro polymer aggregation variables, electric field and pH, can be used in concert to produce suspended membranes from solutions of type I collagen monomers, without need of a supporting substrate. A collagen network film can form at the alkalineacidic pH interface created during the normal course of water electrolysis with parallel plate electrodes, and the anchoring location can be controlled by adjusting the bulk electrolyte pH. Electrosynthesized films remain intact upon drying and rehydration and function as ion separation membranes even in submillimeter channels. This approach could benefit lab-on-a-chip technologies for rational placement of membranes in microfluidic devices

Estimating the monthly pCO2 distribution in the north Atlantic using a self-organizing neural network

Here we present monthly, basin-wide maps of the partial pressure of carbon dioxide (pCO2) for the North Atlantic on a 1° latitude by 1° longitude grid for years 2004 through 2006 inclusive. The maps have been computed using a neural network technique which reconstructs the non-linear relationships between three biogeochemical parameters and marine pCO 2. A self organizing map (SOM) neural network has been trained using 389 000 triplets of the SeaWiFS-MODIS chlorophyll-a concentration, the NCEP/NCAR reanalysis sea surface temperature, and the FOAM mixed layer depth. The trained SOM was labelled with 137 000 underway pCO2 measurements collected in situ during 2004, 2005 and 2006 in the North Atlantic, spanning the range of 208 to 437 µatm. The root mean square error (RMSE) of the neural network fit to the data is 11.6 µatm, which equals to just above 3 per cent of an average pCO2 value in the in situ dataset. The seasonal pCO2 cycle as well as estimates of the interannual variability in the major biogeochemical provinces are presented and discussed. High resolution combined with basin-wide coverage makes the maps a useful tool for several applications such as the monitoring of basin-wide air-sea CO2 fluxes or improvement of seasonal and interannual marine CO2 cycles in future model predictions. The method itself is a valuable alternative to traditional statistical modelling techniques used in geosciences

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

UV/Optical disk reverberation lags despite a faint X-ray corona in the AGN Mrk 335

We present the first results from a 100-day Swift, NICER and ground-based X-ray/UV/optical reverberation mapping campaign of the Narrow-Line Seyfert 1 Mrk 335, when it was in an unprecedented low X-ray flux state. Despite dramatic suppression of the X-ray variability, we still observe UV/optical lags as expected from disk reverberation. Moreover, the UV/optical lags are consistent with archival observations when the X-ray luminosity was >10 times higher. Interestingly, both low- and high-flux states reveal UV/optical lags that are 6-11 times longer than expected from a thin disk. These long lags are often interpreted as due to contamination from the broad line region, however the u band excess lag (containing the Balmer jump from the diffuse continuum) is less prevalent than in other AGN. The Swift campaign showed a low X-ray-to-optical correlation (similar to previous campaigns), but NICER and ground-based monitoring continued for another two weeks, during which the optical rose to the highest level of the campaign, followed ~10 days later by a sharp rise in X-rays. While the low X-ray countrate and relatively large systematic uncertainties in the NICER background make this measurement challenging, if the optical does lead X-rays in this flare, this indicates a departure from the zeroth-order reprocessing picture. If the optical flare is due to an increase in mass accretion rate, this occurs on much shorter than the viscous timescale. Alternatively, the optical could be responding to an intrinsic rise in X-rays that is initially hidden from our line-of-sight.Comment: Accepted for publication in the Astrophysical Journal. 15 pages, 8 figures, 3 table

Gender Dimorphism in Skeletal Muscle Leptin Receptors, Serum Leptin and Insulin Sensitivity

To determine if there is a gender dimorphism in the expression of leptin receptors (OB-R170, OB-R128 and OB-R98) and the protein suppressor of cytokine signaling 3 (SOCS3) in human skeletal muscle, the protein expression of OB-R, perilipin A, SOCS3 and alpha-tubulin was assessed by Western blot in muscle biopsies obtained from the m. vastus lateralis in thirty-four men (age = 27.1±6.8 yr) and thirty-three women (age = 26.7±6.7 yr). Basal serum insulin concentration and HOMA were similar in both genders. Serum leptin concentration was 3.4 times higher in women compared to men (P<0.05) and this difference remained significant after accounting for the differences in percentage of body fat or soluble leptin receptor. OB-R protein was 41% (OB-R170, P<0.05) and 163% (OB-R128, P<0.05) greater in women than men. There was no relationship between OB-R expression and the serum concentrations of leptin or 17β-estradiol. In men, muscle OB-R128 protein was inversely related to serum free testosterone. In women, OB-R98 and OB-R128 were inversely related to total serum testosterone concentration, and OB-R128 to serum free testosterone concentration. SOCS3 protein expression was similar in men and women and was not related to OB-R. In women, there was an inverse relationship between the logarithm of free testosterone and SCOS3 protein content in skeletal muscle (r = −0.46, P<0.05). In summary, there is a gender dimorphism in skeletal muscle leptin receptors expression, which can be partly explained by the influence of testosterone. SOCS3 expression in skeletal muscle is not up-regulated in women, despite very high serum leptin concentrations compared to men. The circulating form of the leptin receptor can not be used as a surrogate measure of the amount of leptin receptors expressed in skeletal muscles