A family-wide assessment of latent STAT transcription factor interactions reveals divergent dimer repertoires.

The conversion of signal transducer and activator of transcription (STAT) proteins from latent to active transcription factors is central to cytokine signaling. Triggered by their signal-induced tyrosine phosphorylation, it is the assembly of a range of cytokine-specific STAT homo- and heterodimers that marks a key step in the transition of hitherto latent proteins to transcription activators. In contrast, the constitutive self-assembly of latent STATs and how it relates to the functioning of activated STATs is understood less well. To provide a more complete picture, we developed a co-localization-based assay and tested all 28 possible combinations of the seven unphosphorylated STAT (U-STAT) proteins in living cells. We identified five U-STAT homodimers-STAT1, STAT3, STAT4, STAT5A, and STAT5B-and two heterodimers-STAT1:STAT2 and STAT5A:STAT5B-and performed semi-quantitative assessments of the forces and characterizations of binding interfaces that support them. One STAT protein-STAT6-was found to be monomeric. This comprehensive analysis of latent STAT self-assembly lays bare considerable structural and functional diversity in the ways that link STAT dimerization before and after activation.

Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats.

Many microbes in nature reside in dense, metabolically interdependent communities. We investigated the nature and extent of microbe-virus interactions in relation to microbial density and syntrophy by examining microbe-virus interactions in a biomass dense, deep-sea hydrothermal mat. Using metagenomic sequencing, we find numerous instances where phylogenetically distant (up to domain level) microbes encode CRISPR-based immunity against the same viruses in the mat. Evidence of viral interactions with hosts cross-cutting microbial domains is particularly striking between known syntrophic partners, for example those engaged in anaerobic methanotrophy. These patterns are corroborated by proximity-ligation-based (Hi-C) inference. Surveys of public datasets reveal additional viruses interacting with hosts across domains in diverse ecosystems known to harbour syntrophic biofilms. We propose that the entry of viral particles and/or DNA to non-primary host cells may be a common phenomenon in densely populated ecosystems, with eco-evolutionary implications for syntrophic microbes and CRISPR-mediated inter-population augmentation of resilience against viruses.

Controlling systemic risk: Network structures that minimize it and node properties to calculate it.

Evaluation of systemic risk in networks of financial institutions in general requires information of interinstitution financial exposures. In the framework of the DebtRank algorithm, we introduce an approximate method of systemic risk evaluation which requires only node properties, such as total assets and liabilities, as inputs. We demonstrate that this approximation captures a large portion of systemic risk measured by DebtRank. Furthermore, using Monte Carlo simulations, we investigate network structures that can amplify systemic risk. Indeed, while no topology in general sense is a priori more stable if the market is liquid (i.e., the price of transaction creation is small) [T. Roukny et al., Sci. Rep. 3, 2759 (2013)10.1038/srep02759], a larger complexity is detrimental for the overall stability [M. Bardoscia et al., Nat. Commun. 8, 14416 (2017)10.1038/ncomms14416]. Here we find that the measure of scalar assortativity correlates well with level of systemic risk. In particular, network structures with high systemic risk are scalar assortative, meaning that risky banks are mostly exposed to other risky banks. Network structures with low systemic risk are scalar disassortative, with interactions of risky banks with stable banks.

Repulsion in controversial debate drives public opinion into fifty-fifty stalemate.

Opinion formation is a process with strong implications for public policy. In controversial debates with large consequences, the public opinion is often trapped in a fifty-fifty stalemate, jeopardizing broadly accepted political decisions. Emergent effects from millions of private discussions make it hard to understand or influence this kind of opinion dynamics. Here we demonstrate that repulsion from opinions favors fifty-fifty stalemates. We study a voter model where agents can have two opinions or an undecided state in between, and where we allow for repulsion of opinions and for doubt: in pairwise discussions, undecided agents can be not only convinced, but also repelled from the opinion expressed by another agent, and decided agents may return to the undecided state. As a result, we observe that, if an agent is repelled instead of being convinced in at least one out of four interactions, as in controversial debates, the frequencies of both opinions equalize. This voter model attractor reproduces the phenomenology of repeated Brexit poll data well and provides a mechanism solely based on local interactions between agents that may explain stalemate polarization in controversial opinion formation.

A versatile platform for activity determination of cytokines and growth factors based on the human TSLP (thymic stromal lymphopoietin) receptor.

Cytokines and growth factors are signaling proteins involved in communication processes between cells. They are involved in the control of numerous essential physiological processes such as cell proliferation, gene transcription and differentiation; therefore being in the focus of basic and applied research. Many of them are also of relevance for human diseases. When observed as potential targets for pharmacological intervention and objects of structure/function studies, it is important to measure their biological activities, optionally along with potential inhibitors, in a convenient and rational manner. Such tests are frequently laborious to set up and their establishment is complicated by the necessity to employ problematic cell types and sophisticated assays. Here we present a robust and modular activity assay system which can be adapted to virtually all ligands that signal through dimerization of membrane receptors from different families. The technique rests on fusing ligand-binding domains of specific receptors to the transmembrane and intracellular components of the thymic stromal lymphopoietin (TSLP) receptor which translates signals into readily quantifiable luciferase expression in reporter cells. We show that the activation of various hematopoietic cytokine receptors, of receptor tyrosine kinases as well as of receptors bearing serine/threonine kinase domains by their respective ligands was faithfully reflected both upon transient and stable introduction of hybrid receptor and reporter gene constructs into the murine pro-B cell line Ba/F3. Moreover, we demonstrate the suitability of this platform for the functional characterization of cytokine/growth factor receptor inhibitors.

Impact and recovery process of mini flash crashes: An empirical study.

In an Ultrafast Extreme Event (or Mini Flash Crash), the price of a traded stock increases or decreases strongly within milliseconds. We present a detailed study of Ultrafast Extreme Events in stock market data. In contrast to popular belief, our analysis suggests that most of the Ultrafast Extreme Events are not necessarily due to feedbacks in High Frequency Trading: In at least 60 percent of the observed Ultrafast Extreme Events, the largest fraction of the price change is due to a single market order. In times of financial crisis, large market orders are more likely which leads to a significant increase of Ultrafast Extreme Events occurrences. Furthermore, we analyze the 100 trades following each Ultrafast Extreme Events. While we observe a tendency of the prices to partially recover, less than 40 percent recover completely. On the other hand we find 25 percent of the Ultrafast Extreme Events to be almost recovered after only one trade which differs from the usually found price impact of market orders.

A Computer-Assisted Training Approach for Performing and Charting Periodontal Examinations: A Retrospective Study.

The aim of this study was to retrospectively investigate the development of a model-based, computer-assisted training approach for performing and charting periodontal examinations in a dental clinic in Germany. The study was initiated in summer semester 2013 and repeated in two consecutive semesters (S1: 44 students, S2: 48 students, and S3: 61 students) because technical features were introduced (S2: feedback and time control; S3: input control). In each semester, new dental students who had never performed periodontal examinations participated. Students were divided into two groups and received intense training at different time points. Agreement levels were calculated at baseline, after the first group received training, and after the second group received training. Comparisons were also made among the semesters. All 153 enrolled students in the three semesters participated. The results showed that probing depth accuracy significantly decreased in S1 from baseline to training completion (79.9% to 74.5%), and the probing depth accuracy significantly increased in S2 (76.1% to 78.9%) and S3 (77.2% to 82.3%). The students who received intense training at a late stage of the tutorial showed greater improvement, especially in the case of S3. Small changes in accuracy were observed for recession (S1: 94.5% to 96.1%; S2: 93.8% to 93.9%; S3: 95.4% to 96.6%). Accuracy for furcation involvement improved significantly in S1 (46.1% to 52.0%), S2 (46.8% to 59.7%), and S3 (44.2% to 58.3%); the improvements occurred when the students received intense training. The time taken for periodontal examination decreased significantly for S2 (23.6 to 14.2 min) and S3 (25.7 to 13.9 min). This study found that when feedback was provided, the students' periodontal examinations improved in accuracy and duration.

Color-avoiding percolation.

Many real world networks have groups of similar nodes which are vulnerable to the same failure or adversary. Nodes can be colored in such a way that colors encode the shared vulnerabilities. Using multiple paths to avoid these vulnerabilities can greatly improve network robustness, if such paths exist. Color-avoiding percolation provides a theoretical framework for analyzing this scenario, focusing on the maximal set of nodes which can be connected via multiple color-avoiding paths. In this paper we extend the basic theory of color-avoiding percolation that was published in S. M. Krause et al. [Phys. Rev. X 6, 041022 (2016)]2160-330810.1103/PhysRevX.6.041022. We explicitly account for the fact that the same particular link can be part of different paths avoiding different colors. This fact was previously accounted for with a heuristic approximation. Here we propose a better method for solving this problem which is substantially more accurate for many avoided colors. Further, we formulate our method with differentiated node functions, either as senders and receivers, or as transmitters. In both functions, nodes can be explicitly trusted or avoided. With only one avoided color we obtain standard percolation. Avoiding additional colors one by one, we can understand the critical behavior of color-avoiding percolation. For unequal color frequencies, we find that the colors with the largest frequencies control the critical threshold and exponent. Colors of small frequencies have only a minor influence on color-avoiding connectivity, thus allowing for approximations.

A New Model for Training in Periodontal Examinations Using Manikins.

The aim of this study was to develop and test models for training dental students in periodontal examinations using manikins that had distinct anatomical designs but were indistinguishable in external appearance. After four models were tested for inter- and intra-examiner reliability by two experienced dentists, 26 additional models were produced. The models were tested by 35 dental students at a dental school in Germany in 2014. The testing involved completing a periodontal examination that included probing depths, gingival recessions, and furcation involvements. The primary purpose of the study was to determine whether the models could be used as a tool for periodontal examination training by the students. Levels of agreement (students and dentists) and Kappa statistics (dentists) were calculated using absolute (±0 mm) and tolerable difference (±1 mm). Over the span of two weeks, the dentists' reliability with preset values for probing depths, gingival recessions, and furcation involvements ranged from 0.29 to 0.38, 0.52 to 0.61, and 0.54 to 0.57, respectively, under absolute difference and from 0.86 to 0.90, 0.96 to 0.99, and 0.62 to 0.73, respectively, under tolerable difference. The students' proportions of agreement for probing depths and gingival recessions under absolute vs. tolerable difference were 34.8% vs. 79.9% and 71.9% vs. 94.4%, respectively. The students frequently scored values higher than the preset values, overestimated furcation involvements, and failed to differentiate the levels of furcations. The models used did not pose any systematic or technical difficulties in the pilot study. Students were unable to measure furcation involvements with acceptable agreement. Thus, these models could be used for student periodontal examination training.

Econophysics of adaptive power markets: When a market does not dampen fluctuations but amplifies them.

The average economic agent is often used to model the dynamics of simple markets, based on the assumption that the dynamics of a system of many agents can be averaged over in time and space. A popular idea that is based on this seemingly intuitive notion is to dampen electric power fluctuations from fluctuating sources (as, e.g., wind or solar) via a market mechanism, namely by variable power prices that adapt demand to supply. The standard model of an average economic agent predicts that fluctuations are reduced by such an adaptive pricing mechanism. However, the underlying assumption that the actions of all agents average out on the time axis is not always true in a market of many agents. We numerically study an econophysics agent model of an adaptive power market that does not assume averaging a priori. We find that when agents are exposed to source noise via correlated price fluctuations (as adaptive pricing schemes suggest), the market may amplify those fluctuations. In particular, small price changes may translate to large load fluctuations through catastrophic consumer synchronization. As a result, an adaptive power market may cause the opposite effect than intended: Power demand fluctuations are not dampened but amplified instead.

Spontaneous centralization of control in a network of company ownerships.

We introduce a model for the adaptive evolution of a network of company ownerships. In a recent work it has been shown that the empirical global network of corporate control is marked by a central, tightly connected "core" made of a small number of large companies which control a significant part of the global economy. Here we show how a simple, adaptive "rich get richer" dynamics can account for this characteristic, which incorporates the increased buying power of more influential companies, and in turn results in even higher control. We conclude that this kind of centralized structure can emerge without it being an explicit goal of these companies, or as a result of a well-organized strategy.

Expression analysis and specific blockade of the receptor for human thymic stromal lymphopoietin (TSLP) by novel antibodies to the human TSLPRα receptor chain.

Thymic stromal lymphopoietin (TSLP) is an interleukin-7 (IL-7)-like cytokine with a pivotal role in development and maintenance of atopic diseases such as allergic asthma and atopic dermatitis. Moreover, recent studies show an involvement of TSLP in the progression of various cancers. TSLP signaling is mediated by the TSLP receptor (TSLPR), a heterodimeric type I cytokine receptor. It consists of the IL-7 receptor alpha chain (IL-7Rα), which is shared with the IL-7 receptor, and the TSLPRα chain as a specific subunit. Blocking signal release by TSLP without affecting IL-7 function is a potentially interesting option for the treatment of atopic diseases or certain tumors. By employing the extracellular domain of human TSLPRα chain (hTSLPRα(ex)) as an antigen, we generated a set of monoclonal antibodies. Several binders to native and/or denatured receptor protein were identified and characterized by cytometry and Western blot analysis. A screen based on a STAT3-driven reporter gene assay in murine pro-B cells expressing a functional hTSLPR yielded two hybridoma clones with specific antagonistic properties towards hTSLP, but not IL-7. Kinetic studies measuring blockade of hTSLP-dependent STAT phosphorylation in a TSLP-responsive cell line revealed an inhibitory constant in the nanomolar range.

Opinion formation model for markets with a social temperature and fear.

In the spirit of behavioral finance, we study the process of opinion formation among investors using a variant of the two-dimensional voter model with a tunable social temperature. Further, a feedback acting on the temperature is introduced, such that social temperature reacts to market imbalances and thus becomes time dependent. In this toy market model, social temperature represents nervousness of agents toward market imbalances representing speculative risk. We use the knowledge about the discontinuous generalized voter model phase transition to determine critical fixed points. The system exhibits metastable phases around these fixed points characterized by structured lattice states, with intermittent excursions away from the fixed points. The statistical mechanics of the model is characterized, and its relation to dynamics of opinion formation among investors in real markets is discussed.

Mean-field-like behavior of the generalized voter-model-class kinetic Ising model.

We analyze a kinetic Ising model with suppressed bulk noise, which is a prominent representative of the generalized voter model phase transition. On the one hand, we discuss the model in the context of social systems and opinion formation in the presence of a tunable social temperature. On the other hand, we characterize the abrupt phase transition. The system shows nonequilibrium dynamics in the presence of absorbing states. We slightly change the system to get a stationary-state model variant exhibiting the same kind of phase transition. Using a Fokker-Planck description and comparing to mean-field calculations, we investigate the phase transition, finite-size effects, and the effect of the absorbing states resulting in a dynamic slowing down.

Signal transduction by the atopy-associated human thymic stromal lymphopoietin (TSLP) receptor depends on Janus kinase function.

Thymic stromal lymphopoietin (TSLP) is an interleukin-(IL)-7-like cytokine with emerging pathological importance for the development of atopic diseases such as allergic asthma bronchiale. The TSLP receptor (TSLPR), a heterodimeric type I cytokine receptor, shares the IL-7R alpha-subunit with the IL-7 receptor system. The specific TSLPR alpha-chain shows similarities with the gammac receptor chain, but has some unusual features within the receptor family in both its ligand-binding and cytoplasmic domain. The murine TSLPR signals via the signal transducers and activators of transcription STAT5 and STAT3, but is unique among cytokine receptors in that it activates STATs without the involvement of Janus (JAK) tyrosine kinases, but instead utilizes the Src type kinase Tec. Here, we show by Western blotting and reporter gene experiments in combination with the application of a specific JAK inhibitor that the human TSLP receptor, in contrast, requires the function of JAK1 and JAK2 for STAT activation. Moreover, we demonstrate that the human TSLPR mediates gene regulation not only through STAT5 and STAT3 but has also the potential to mediate transcription via STAT1. Our work should help to understand more thoroughly how TSLP triggers inflammatory responses in the course of atopic diseases.

Specific inhibition of interleukin-13 activity by a recombinant human single-chain immunoglobulin domain directed against the IL-13 receptor alpha1 chain.

Interleukin-13 (IL-13) is a T-cell-derived pleiotropic cytokine of particular medical importance because of its critical role in the development of allergic asthma. The effects of IL-13 on its target cells are mediated through a dimeric transmembrane receptor (IL-13R), which shares the IL-4Ralpha subunit with the IL-4R system, but contains as a specific component the IL-13Ralpha1 chain. We have generated a set of single-chain Fv fragments with specific binding capacity to the extracellular domain of the human IL-13Ralpha1 receptor. Bacteriophage clones displaying receptor-binding antibody domains were selected from both naive and synthetic libraries by repetitive panning on recombinant and cell surface-expressed recombinant IL-13Ralpha1. Their specific reactivity with native human IL-13Ralpha1 expressed on the surface of transfected cells was demonstrated by flow cytometry. One binder that specifically interfered with cell activation by IL-13 was extensively characterized. This scFv inhibited IL-13-driven gene transcription and cell proliferation in test cell lines, as well as IL-13-induced activation of primary human monocytes in a dose-dependent manner, with an IC(50) below 300 nM. This novel reagent thus constitutes a valuable tool for the further elucidation of IL-13 function in disease and offers potential therapeutic perspectives.

Grafting of thrombopoietin-mimetic peptides into cystine knot miniproteins yields high-affinity thrombopoietin antagonists and agonists.

Thrombopoietin is the primary regulator of platelet production. We exploited two naturally occurring miniproteins of the inhibitor cystine knot family as stable and rigid scaffolds for the incorporation of peptide sequences that have been shown to act as high-affinity thrombopoietin antagonists. Several miniproteins that antagonistically block thrombopoietin-mediated receptor activation were identified using a microscale reporter assay. Covalent miniprotein dimerization yielded potent bivalent c-Mpl receptor agonists with EC(50) values in the low nanomolar or picomolar range. One selected miniprotein-derived thrombopoietin agonist was almost as active as natural thrombopoietin with regard to stimulation of megakaryocyte colony formation from human bone marrow mononuclear cells, and elicited doubling of platelet counts in mice. Our data suggest that dimeric cystine knot miniproteins have considerable potential for the future development of small and stable receptor agonists. This approach may provide a promising strategy for pharmaceutical interference with other receptors activated by ligand-induced dimerization.

Blockade of interleukin-13-mediated cell activation by a novel inhibitory antibody to human IL-13 receptor alpha1.

Interleukin-13 (IL-13) is a cytokine with a crucial role in the development of allergic asthma. The IL-13 receptor shares the IL-4Ralpha subunit with the IL-4R system, but contains as a specific component the IL-13Ralpha1 chain. Blocking signal release by IL-13 without affecting IL-4 function is a potentially interesting therapeutical option for the treatment of asthma. Employing genetic immunization, we generated a set of novel monoclonal antibodies to the IL-13Ralpha1 receptor that proved very specific and efficient inhibitors of human IL-13 activity. Receptor binding antibodies were identified by their specific reactivity with both human monocytes and a murine pro-B cell line overexpressing human IL-13Ralpha1 by flow cytometry and cell ELISA. A luciferase reporter cell system based on STAT6-mediated promoter activation in murine Ba/F3 cells was employed to screen the antibodies for IL-13 antagonistic properties. Inhibitory antibody effects were quantified by interference with IL-13-dependent proliferation of TF-1 cells. The capability of blocking IL-13-driven responses of primary, inflammation-relevant cells was tested by Western blot analysis of STAT6 tyrosine phosphorylation and expression of 15-lipoxygenase in monocytes from fresh blood. The most potent inhibitory antibody identified, GM1E7, inhibited IL-13-driven gene activation and cell proliferation in immune cell lines with IC(50) values in the low nanomolar range. Both short-term (STAT6 activation) and long-term (15-LO induction) responses of primary human blood cells to IL-13 were almost entirely blocked, whereas IL-4 effects remained virtually unaffected. GM1E7 is superior to available agents interfering with IL-13 activity in terms of specificity and efficiency and offers potential novel therapeutic perspectives for the treatment of allergic asthma.

Expression of interleukin-13 receptor alpha 1-subunit on peripheral blood eosinophils is regulated by cytokines.

Interleukin-13 (IL-13) is critical for the development of allergic asthma and is involved in the activation of eosinophils within the airways. IL-13 exerts its activity on target cells via the dimeric IL-13 receptor (IL-13R), which comprises the IL-13 receptor alpha1-chain (IL-13Ralpha1) as a specific component. The aim of this study was to investigate the expression of the IL-13Ralpha1-chain on primary human eosinophilic granulocytes. Furthermore, it addresses the regulatory influence of cytokines on the level of surface abundance of this receptor subunit. Expression of IL-13- and IL-4-receptor subunits in purified primary human eosinophils was monitored at the messenger RNA level by reverse transcription polymerase chain reaction and at the protein level by flow cytometry. For the analysis of IL-13Ralpha1 surface expression, a new monoclonal antibody, which was generated using genetic immunization, was employed. Different cytokines with established activity on eosinophils were studied with regard to their influence on IL-13Ralpha1 in vitro by flow cytometry. Whereas IL-13 and IL-4 had inhibitory effects on IL-13Ralpha1 expression on eosinophils, interferon-gamma, tumour necrosis factor-alpha, and, to the largest extent, transforming growth factor-beta, enhanced the expression of this receptor subunit. A positive regulatory response evoked by transforming growth factor-beta and interferon-gamma does not prevent inhibitory effects caused by IL-13. These findings suggest a regulatory cytokine network influencing the reactivity of eosinophils to IL-13.

Bacteria displaying interleukin-4 mutants stimulate mammalian cells and reflect the biological activities of variant soluble cytokines.

We describe a novel procedure that allows the rapid determination of cytokine activity on cells that express their cognate receptor. The four-helix bundle cytokine interleukin-4 (IL-4) was inducibly expressed as a fusion with the E. coli outer-membrane protein intimin, such that IL-4 was presented on the surfaces of the bacteria. Expression and accessibility of the cytokine on the cell exteriors were monitored by Western blotting and fluorescence microscopy, making use of two epitopes flanking the IL-4 component of the fusion protein. To demonstrate the biological activity of the immobilized cytokine, a Ba/F3-derived cell line stably transfected with both the bipartite human IL-4 receptor and an IL-4-specific luciferase reporter gene construct was employed. Bacterial cells displaying interleukin-4 elicited a specific, dose-dependent response in the reporter cells. Two variants of IL-4 with previously characterized (partial) antagonistic properties were also expressed as membrane-bound fusion proteins and were tested for their activity in the immobilized state. In comparison with bacteria displaying wild-type IL-4, E. coli clones presenting variants IL-4 Y124G and Y124D showed diminished or abolished activity, respectively, on murine reporter cells. The relative signaling potencies of the immobilized IL-4 variants thus closely mirror the agonistic properties of the corresponding soluble cytokines. This approach should be generally applicable for the mutational analysis of numerous signal mediators that trigger cellular responses through dimerization of transmembrane receptors.