Critical mass and the dependency of research quality on group size

Academic research groups are treated as complex systems and their cooperative behaviour is analysed from a mathematical and statistical viewpoint. Contrary to the naive expectation that the quality of a research group is simply given by the mean calibre of its individual scientists, we show that intra-group interactions play a dominant role. Our model manifests phenomena akin to phase transitions which are brought about by these interactions, and which facilitate the quantification of the notion of critical mass for research groups. We present these critical masses for many academic areas. A consequence of our analysis is that overall research performance of a given discipline is improved by supporting medium-sized groups over large ones, while small groups must strive to achieve critical mass.Comment: 16 pages, 6 figures consisting of 16 panels. Presentation and reference list improved for version

Selection of noise level in strategy adoption for spatial social dilemmas

We studied spatial Prisoner's Dilemma and Stag Hunt games where both the strategy distribution and the players' individual noise level could evolve to reach higher individual payoff. Players are located on the sites of different two-dimensional lattices and gain their payoff from games with their neighbors by choosing unconditional cooperation or defection. The way of strategy adoption can be characterized by a single $K$ (temperature-like) parameter describing how strongly adoptions depend on the payoff-difference. If we start the system from a random strategy distribution with many different player specific $K$ parameters, the simultaneous evolution of strategies and $K$ parameters drives the system to a final stationary state where only one $K$ value remains. In the coexistence phase of cooperator and defector strategies the surviving $K$ parameter is in good agreement with the noise level that ensures the highest cooperation level if uniform $K$ is supposed for all players. In this paper we give a thorough overview about the properties of this evolutionary process.Comment: 10 two-column pages, 10 figures; accepted for publication in Physical Review

Iterative Approximate Consensus in the presence of Byzantine Link Failures

This paper explores the problem of reaching approximate consensus in synchronous point-to-point networks, where each directed link of the underlying communication graph represents a communication channel between a pair of nodes. We adopt the transient Byzantine link failure model [15, 16], where an omniscient adversary controls a subset of the directed communication links, but the nodes are assumed to be fault-free. Recent work has addressed the problem of reaching approximate consen- sus in incomplete graphs with Byzantine nodes using a restricted class of iterative algorithms that maintain only a small amount of memory across iterations [22, 21, 23, 12]. However, to the best of our knowledge, we are the first to consider approximate consensus in the presence of Byzan- tine links. We extend our past work that provided exact characterization of graphs in which the iterative approximate consensus problem in the presence of Byzantine node failures is solvable [22, 21]. In particular, we prove a tight necessary and sufficient condition on the underlying com- munication graph for the existence of iterative approximate consensus algorithms under transient Byzantine link model. The condition answers (part of) the open problem stated in [16].Comment: arXiv admin note: text overlap with arXiv:1202.609

Gathering in Dynamic Rings

The gathering problem requires a set of mobile agents, arbitrarily positioned at different nodes of a network to group within finite time at the same location, not fixed in advanced. The extensive existing literature on this problem shares the same fundamental assumption: the topological structure does not change during the rendezvous or the gathering; this is true also for those investigations that consider faulty nodes. In other words, they only consider static graphs. In this paper we start the investigation of gathering in dynamic graphs, that is networks where the topology changes continuously and at unpredictable locations. We study the feasibility of gathering mobile agents, identical and without explicit communication capabilities, in a dynamic ring of anonymous nodes; the class of dynamics we consider is the classic 1-interval-connectivity. We focus on the impact that factors such as chirality (i.e., a common sense of orientation) and cross detection (i.e., the ability to detect, when traversing an edge, whether some agent is traversing it in the other direction), have on the solvability of the problem. We provide a complete characterization of the classes of initial configurations from which the gathering problem is solvable in presence and in absence of cross detection and of chirality. The feasibility results of the characterization are all constructive: we provide distributed algorithms that allow the agents to gather. In particular, the protocols for gathering with cross detection are time optimal. We also show that cross detection is a powerful computational element. We prove that, without chirality, knowledge of the ring size is strictly more powerful than knowledge of the number of agents; on the other hand, with chirality, knowledge of n can be substituted by knowledge of k, yielding the same classes of feasible initial configurations

Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases

Acetyl xylan esterases (AcXEs), also termed xylan deacetylases, are broad specificity Carbohydrate-Active Enzymes (CAZymes) that hydrolyse ester bonds to liberate acetic acid from acetylated hemicellulose (typically polymeric xylan and xylooligosaccharides). They belong to eight families within the Carbohydrate Esterase (CE) class of the CAZy database. AcXE classification is largely based on sequence-dependent phylogenetic relationships, supported in some instances with substrate specificity data. However, some sequence-based predictions of AcXE-encoding gene identity have proved to be functionally incorrect. Such ambiguities can lead to mis-assignment of genes and enzymes during sequence data-mining, reinforcing the necessity for the experimental confirmation of the functional properties of putative AcXE-encoding gene products. Although one-third of all characterized CEs within CAZy families 1–7 and 16 are AcXEs, there is a need to expand the sequence database in order to strengthen the link between AcXE gene sequence and specificity. Currently, most AcXEs are derived from a limited range of (mostly microbial) sources and have been identified via culture-based bioprospecting methods, restricting current knowledge of AcXEs to data from relatively few microbial species. More recently, the successful identification of AcXEs via genome and metagenome mining has emphasised the huge potential of culture-independent bioprospecting strategies. We note, however, that the functional metagenomics approach is still hampered by screening bottlenecks. The most relevant recent reviews of AcXEs have focused primarily on the biochemical and functional properties of these enzymes. In this review, we focus on AcXE phylogeny, classification and the future of metagenomic bioprospecting for novel AcXEs.The South African Department of Science and Technology Biocatalysis Initiative, National Research Foundation (DAC, TPM), the University of Pretoria’s Genomics Research Institute (DAC) and Research Development Program (TPM). FAA was supported by funds from the Organisation for Women in Science in the Developing World (OWSD).http://www.elsevier.com/locate/emt2017-11-30hb2016Genetic

Recent progress in understanding mode of action of acetylxylan esterases

Acetylation is one of the main obstacles to the effective enzymatic conversion of hemicelluloses to fermentable sugars. In nature, the microbial degradation of hemicellulose involves the action of deacetylating esterases that act synergistically with glycoside hydrolases. In the industrial processing of lignocelluloses biomass, alkaline pretreatments remove acetyl groups by saponification, but other non-alkaline pretreatment methods generate acetylated hemicelluloses. Complete saccharification of plant hemicelluloses can’t be achieved without the deacetylating enzymes. Recent years have witnessed considerale progress in our understanding of the mode of acetylation of hemicellulose and mode of action of microbial polysaccharide deacetylases. In this article we focus on the diversity and role of acetylxylan esterases in the breakdown of acetylxylan, the most abundant hemicellulose in nature.This work was supported by grants from the Slovak Academy of Sciences grant agency VEGA 2/0037/14, by The Slovak Research and Development Agency under the contract No. APVV-0602-12, by grant 214613 from the Norwegian Research Council and by the FP7 project Waste2Go under contract 308363 with European Commission.https://www.jstage.jst.go.jp/browse/jagam201

Anonymous Asynchronous Systems: The Case of Failure Detectors

Due the multiplicity of loci of control, a main issue distributed systems have to cope with lies in the uncertainty on the system state created by the adversaries that are asynchrony, failures, dynamicity, mobility, etc. Considering message-passing systems, this paper considers the uncertainty created by the net effect of three of these adversaries, namely, asynchrony, failures, and anonymity. This means that, in addition to be asynchronous and crash-prone, the processes have no identity. Trivially, agreement problems (e.g., consensus) that cannot be solved in presence of asynchrony and failures cannot be solved either when adding anonymity. The paper consequently proposes anonymous failure detectors to circumvent these impossibilities. It has several contributions. First it presents three classes of failure detectors (denoted AP, A∩ and A∑) and show that they are the anonymous counterparts of the classes of perfect failure detectors, eventual leader failure detectors and quorum failure detectors, respectively. The class A∑ is new and showing it is the anonymous counterpart of the class ∑ is not trivial. Then, the paper presents and proves correct a genuinely anonymous consensus algorithm based on the pair of anonymous failure detector classes (A∩, A∑) (“genuinely” means that, not only processes have no identity, but no process is aware of the total number of processes). This new algorithm is not a “straightforward extension” of an algorithm designed for non-anonymous systems. To benefit from A∑, it uses a novel message exchange pattern where each phase of every round is made up of sub-rounds in which appropriate control information is exchanged. Finally, the paper discusses the notions of failure detector class hierarchy and weakest failure detector class for a given problem in the context of anonymous systems

A novel xylan degrading β-D-xylosidase: purification and biochemical characterization

Aspergillus ochraceus, a thermotolerant fungus isolated in Brazil from decomposing materials, produced an extracellular b-xylosidase that was purified using DEAE-cellulose ion exchange chromatography, Sephadex G-100 and Biogel P-60 gel filtration. b-xylosidase is a glycoprotein (39 % carbohydrate content) and has a molecular mass of 137 kDa by SDS-PAGE, with optimal temperature and pH at 70 C and 3.0–5.5, respectively.b-xylosidase was stable in acidic pH (3.0–6.0) and 70 C for 1 h. The enzyme was activated by 5 mM MnCl2 (28 %)and MgCl2 (20 %) salts. The b-xylosidase produced by A. ochraceus preferentially hydrolyzed p-nitrophenyl-b- D-xylopyranoside, exhibiting apparent Km and Vmax values of 0.66 mM and 39 U (mg protein)-1 respectively, and to a lesser extent p-nitrophenyl-b-D-glucopyranoside. The enzyme was able to hydrolyze xylan from different sources,suggesting a novel b-D-xylosidase that degrades xylan. HPLC analysis revealed xylans of different compositions which allowed explaining the differences in specificity observed by b-xylosidase. TLC confirmed the capacity.This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), and the Conselho de Desenvolvimento Científico e Tecnológico (CNPq). J. A. J. and M. L. T. M. P are Research Fellows of CNPq. M. M. was a recipient of a FAPESP fellowship and this work is part of her Doctoral Thesis. It is also part of the project SISBIOTA CNPq: 563260/2010-6 and FAPESP: 2010/52322-3

Purification and preliminary characterization of a xylanase from Thermomyces lanuginosus strain SS-8

Thermomyces lanuginosus SS-8 was isolated from soil samples that had been collected from near self-heating plant material and its extracellular cellulase-free xylanase purified approximately 160-fold using ion exchange chromatography and continuous elution electrophoresis. This xylanase was thermoactive (optimum temperature 60 °C) at pH 6.0 and had a molecular weight of 23.79 kDa as indicated by SDS-PAGE electrophoresis. The xylanase rapidly hydrolyzed xylan directly to xylose without the production of intermediary xylo-oligosaccharides within 15 min of incubation under optimum conditions. This trait of rapidly degrading xylan to xylose as a sole end-product could have biotechnological potential in degradation of agro-wastes for bioethanol manufacturing industry

Properties of an alkali-thermo stable xylanase from Geobacillus thermodenitrificans A333 and applicability in xylooligosaccharides generation

An extracellular thermo-alkali-stable and cellulase-free xylanase from Geobacillus thermodenitrificans A333 was purified to homogeneity by ion exchange and size exclusion chromatography. Its molecular mass was 44 kDa as estimated in native and denaturing conditions by gel filtration and SDS-PAGE analysis, respectively. The xylanase (GtXyn) exhibited maximum activity at 70 °C and pH 7.5. It was stable over broad ranges of temperature and pH retaining 88 % of activity at 60 °C and up to 97 % in the pH range 7.5–10.0 after 24 h. Moreover, the enzyme was active up to 3.0 M sodium chloride concentration, exhibiting at that value 70 % residual activity after 1 h. The presence of other metal ions did not affect the activity with the sole exceptions of K+ that showed a stimulating effect, and Fe2+, Co2+ and Hg2+, which inhibited the enzyme. The xylanase was activated by non-ionic surfactants and was stable in organic solvents remaining fully active over 24 h of incubation in 40 % ethanol at 25 °C. Furthermore, the enzyme was resistant to most of the neutral and alkaline proteases tested. The enzyme was active only on xylan, showing no marked preference towards xylans from different origins. The hydrolysis of beechwood xylan and agriculture-based biomass materials yielded xylooligosaccharides with a polymerization degree ranging from 2 to 6 units and xylobiose and xylotriose as main products. These properties indicate G. thermodenitrificans A333 xylanase as a promising candidate for several biotechnological applications, such as xylooligosaccharides preparation