Complex networks: the key to systems biology

Though introduced recently, complex networks research has grown steadily because of its potential to represent, characterize and model a wide range of intricate natural systems and phenomena. Because of the intrinsic complexity and systemic organization of life, complex networks provide a specially promising framework for systems biology investigation. The current article is an up-to-date review of the major developments related to the application of complex networks in biology, with special attention focused on the more recent literature. The main concepts and models of complex networks are presented and illustrated in an accessible fashion. Three main types of networks are covered: transcriptional regulatory networks, protein-protein interaction networks and metabolic networks. The key role of complex networks for systems biology is extensively illustrated by several of the papers reviewed.FAPESPCNP

Efficient Anodically Grown WO3 for Photoelectrochemical Water Splitting

Abstract The potentiostatic anodization of metallic tungsten has been investigated in different solvent/electrolyte compositions with the aim of improving the photoelectrochemical performances of the tungsten oxide layer. Among the explored electrolytes, the anodization in the NMF/H2O/NH4F solvent mixture was found to produce the most efficient WO3 photoanodes, which, combining spectral sensitivity, high electrochemically active surface and improved charge transfer kinetics, outperform, under simulated solar illumination, most of the reported nanocrystalline substrates produced by anodization in aqueous electrolytes and by sol gel methods. While the preparation of the photoelectrodes is a slow process at room temperature (20 °C), it could be greatly accelerated (x 10) by carrying out the anodization at 40-50 °C, thus proving to be a fast and convenient approach to the production of high performing WO3 photoactive substrates directly connected to a metal electron collector

A scoping investigation of eye-tracking in Electronic Gambling Machine (EGM) play

The nature of the association between Electronic Gambling Machines (EGMs) and gambling problems remains uncertain. Eye-tracking offers a potentially powerful method to understand how individuals attend to the visual displays and features of machine games as a function of machine experience, use of other commercial gambling products, the degree to which some game features capture players attention and, critically, vulnerability to problematic patterns of machine play. Characterizing machine players' attention to machine games may aid the design of harm-minimization measures such as, but not limited to, pop-up messages and visible clocks; and provide an important ancillary measure for testing their efficacy. Here, we conducted the first study to use eye-tracking to improve our understanding of how machine players attend to EGM displays in local bookmaker offices (LBOs) situated across North West England, as well as North East and North Wales. Through liaison with 4 bookmaker operators, we recruited a sample of 118 LBO customers who, first, completed a small number of questionnaires about their gambling history and other gambling activities and, then, completed a typical machine gambling session with their own money while wearing eye-tracking glasses to capture eye-movement pattern. The protocol captured regions of gaze fixation while playing (B2) roulette or (B3) slots on B category machines (Gambling Commission, 2012). The final dataset consisted of 91 eye-tracking recordings: 59 games of roulette and 57 slots games. Our principle dependent measure was the percentage of fixations of visual features and machine display locations (as areas of interest; AOIs) as an objective indicator of overt visual attention and their importance to machine players. Our data analysis included statistical correction for differences in the relative size (display area) and display duration across AOIs. To summarise, our main findings are as follows: In roulette, 56.3% of LBO machine players fixations were distributed over the chip-placement area while placing bets (in the stationary states of the game), rising to 75.1% while the roulette wheel Eye-tracking & machines Rogers & Leek; main text v2; 24th March 2017 3 spun in the moving states of the games). Machine players looked at their credit balance 7.2% of the time while placing bets, only slightly more frequently than the previous winning number at 6.8%. In slots games, the slot-reels dominated machine players' visual attention: accounting for 53.6% of fixations while placing bets, rising to 91.7% while spinning. Players' fixations of their credit-balances amounted to 14% of the total while placing bets but only 5.1% while the slot-reels spun. Fixations away from the machine were more frequent while placing bets in both roulette and slots games: 13.5% and 13.4% respectively, dropping to 2.4% and 1.1% while the wheel/slot-reels spun. Players' age and years of education were only weakly related to fixation patterns while playing roulette or slots games. Unemployed players allocated fewer fixations over the chip-placement area (both while the roulette wheel was stationary and while it spun) and over the slot-reels while placing bets; they also tended to look away from the machine more while placing bets in roulette. Frequent machine players tended to look at the roulette wheel less frequently than infrequent users while playing roulette games; involvement in other forms of gambling tended to increase attention towards credit balance but was not otherwise linked to particular patterns of fixations. Finally, problems gamblers allocated fewer fixations to the roulette wheel while placing bets and while it spun compared to non-problem gamblers; and tended to look away from the machine more frequently; in slots games, problem gamblers looked more frequently at amount-won messages. These data describe, for the first time, the distributions of machine players overt attention while navigating roulette and slots games in a commercial settings. In general, fixation counts showed the least variability for moving visual features and events that are likely to capture attention automatically, such as spinning Eye-tracking & machines Rogers & Leek; main text v2; 24th March 2017 4 roulette wheels or spinning slot-reels. However, fixations were also concentrated upon visual features and elements with relatively less attentional capture such as the chip-placement-area while placing bets in roulette and looking at credit balances in both games. Associations between patterns of fixation and both frequency of past-month expenditure on B category machines and broader gambling involvement were modest, suggesting that most of the variability in eye-movements and fixations reflects players navigation through the sequenced behaviours of placing bets and monitoring spinning roulette wheels or slot-reels in anticipation of game outcomes. Players with extensive machine experience tended to discount slightly the roulette wheel as a visual feature; while players with broader patterns of gambling activity looked at credit balances frequently, suggesting that such individuals are mindful of available credits. Players with gambling problems allocated fewer fixations over the chip-placement-area while placing bets and while watching the wheel spun compared to non-problem gamblers, suggesting that placing of bets can be accomplished with less attentional focus. These individuals were also more likely to look away from the machine altogether, suggesting that, in roulette play, gambling problems might be associated with a loosened attentional focus to events elsewhere in the shop. However, in slots games, problems gamblers' attended to the reward signals of previous games (amount-won) when placing the next bets. So far as we are aware, these data are the first to show that eye-tracking methodology has some potential to offer insights into machine-player interactions, and to provide a bias-free measure of individual differences in attention to games visual features and events as a function of their experience with gambling machines, gambling background and vulnerability to gambling-related harms. This study offers a methodology for studying and optimizing the timing, placement and content of harm-minimization messaging

Thoracic surgery in the COVID-19 era: an Italian university hospital experience

BackgroundAims of this study were to assess the results of anti-COVID19 measures applied to maintain thoracic surgery activity at an Italian University institution through a 12-month period and to assess the results as compared with an equivalent non-pandemic time span.MethodsData and results of 646 patients operated on at the department of Thoracic Surgery of the Tor Vergata University Policlinic in Rome between February 2019 and March 2021 were retrospectively analyzed. Patients were divided in 2 groups: one operated on during the COVID-19 pandemic (pandemic group) and another during the previous non-pandemic 12 months (non-pandemic group). Primary outcome measure was COVID-19 infection-free rate.ResultsThree patients developed mild COVID-19 infection early after surgery resulting in an estimated COVID-19 infection-free rate of 98%. At intergroup comparisons (non-pandemic vs. pandemic group), a greater number of patients was operated before the pandemic (352 vs. 294, p = 0.0013). In addition, a significant greater thoracoscopy/thoracotomy procedures rate was found in the pandemic group (97/151 vs. 82/81, p = 0.02) and the total number of chest drainages (104 vs. 131, p = 0.0001) was higher in the same group. At surgery, tumor size was larger (19.5 13 vs. 28.2 +/- 21; p < 0.001) and T3-T4/T1-T2 ratio was higher (16/97 vs. 30/56; p < 0.001) during the pandemic with no difference in mortality and morbidity. In addition, the number of patients lost before treatment was higher in the pandemic group (8 vs. 15; p = 0.01). Finally, in 7 patients admitted for COVID-19 pneumonia, incidental lung (N = 5) or mediastinal (N = 2) tumors were discovered at the chest computed tomography.Conclusions Estimated COVID-19 infection free rate was 98% in the COVID-19 pandemic group; there were less surgical procedures, and operated lung tumors had larger size and more advanced stages than in the non-pandemic group. Nonetheless, hospital stay was reduced with comparable mortality and morbidity. Our study results may help implement efficacy of the everyday surgical care

Tumor type M2-pyruvate-kinase levels in pleural fluid versus plasma in cancer patients: a further tool to define the need for invasive procedures

Pleural effusion is a common diagnostic problem and a challenge to the thoracic surgeon. The analysis of serum and body fluids for tumor markers is an established diagnostic procedure. Among various markers, tumors are linked to the overexpression of a glycolytic isoenzyme, M2-pyruvate-kinase (M2-PK). This preliminary study evaluated this enzyme as a tumor marker to differentiate malignant from benign pleural effusion

The four hexamerin genes in the honey bee: structure, molecular evolution and function deduced from expression patterns in queens, workers and drones

Background: Hexamerins are hemocyanin-derived proteins that have lost the ability to bind copper ions and transport oxygen; instead, they became storage proteins. The current study aimed to broaden our knowledge on the hexamerin genes found in the honey bee genome by exploring their structural characteristics, expression profiles, evolution, and functions in the life cycle of workers, drones and queens. Results: The hexamerin genes of the honey bee (hex 70a, hex 70b, hex 70c and hex 110) diverge considerably in structure, so that the overall amino acid identity shared among their deduced protein subunits varies from 30 to 42%. Bioinformatics search for motifs in the respective upstream control regions (UCRs) revealed six overrepresented motifs including a potential binding site for Ultraspiracle (Usp), a target of juvenile hormone (JH). The expression of these genes was induced by topical application of JH on worker larvae. The four genes are highly transcribed by the larval fat body, although with significant differences in transcript levels, but only hex 110 and hex 70a are re-induced in the adult fat body in a caste-and sex-specific fashion, workers showing the highest expression. Transcripts for hex 110, hex 70a and hex70b were detected in developing ovaries and testes, and hex 110 was highly transcribed in the ovaries of egg-laying queens. A phylogenetic analysis revealed that HEX 110 is located at the most basal position among the holometabola hexamerins, and like HEX 70a and HEX 70c, it shares potential orthology relationship with hexamerins from other hymenopteran species. Conclusions: Striking differences were found in the structure and developmental expression of the four hexamerin genes in the honey bee. The presence of a potential binding site for Usp in the respective 5' UCRs, and the results of experiments on JH level manipulation in vivo support the hypothesis of regulation by JH. Transcript levels and patterns in the fat body and gonads suggest that, in addition to their primary role in supplying amino acids for metamorphosis, hexamerins serve as storage proteins for gonad development, egg production, and to support foraging activity. A phylogenetic analysis including the four deduced hexamerins and related proteins revealed a complex pattern of evolution, with independent radiation in insect orders.Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)[05/03926-5; 08/00541-3

Molecular determinants of caste differentiation in the highly eusocial honeybee Apis mellifera

<p>Abstract</p> <p>Background</p> <p>In honeybees, differential feeding of female larvae promotes the occurrence of two different phenotypes, a queen and a worker, from identical genotypes, through incremental alterations, which affect general growth, and character state alterations that result in the presence or absence of specific structures. Although previous studies revealed a link between incremental alterations and differential expression of physiometabolic genes, the molecular changes accompanying character state alterations remain unknown.</p> <p>Results</p> <p>By using cDNA microarray analyses of >6,000 <it>Apis mellifera </it>ESTs, we found 240 differentially expressed genes (DEGs) between developing queens and workers. Many genes recorded as up-regulated in prospective workers appear to be unique to <it>A. mellifera</it>, suggesting that the workers' developmental pathway involves the participation of novel genes. Workers up-regulate more developmental genes than queens, whereas queens up-regulate a greater proportion of physiometabolic genes, including genes coding for metabolic enzymes and genes whose products are known to regulate the rate of mass-transforming processes and the general growth of the organism (e.g., <it>tor</it>). Many DEGs are likely to be involved in processes favoring the development of caste-biased structures, like brain, legs and ovaries, as well as genes that code for cytoskeleton constituents. Treatment of developing worker larvae with juvenile hormone (JH) revealed 52 JH responsive genes, specifically during the critical period of caste development. Using Gibbs sampling and Expectation Maximization algorithms, we discovered eight overrepresented <it>cis</it>-elements from four gene groups. Graph theory and complex networks concepts were adopted to attain powerful graphical representations of the interrelation between <it>cis</it>-elements and genes and objectively quantify the degree of relationship between these entities.</p> <p>Conclusion</p> <p>We suggest that clusters of functionally related DEGs are co-regulated during caste development in honeybees. This network of interactions is activated by nutrition-driven stimuli in early larval stages. Our data are consistent with the hypothesis that JH is a key component of the developmental determination of queen-like characters. Finally, we propose a conceptual model of caste differentiation in <it>A. mellifera </it>based on gene-regulatory networks.</p