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Propagation of Systemic Risk in Interbank Networks [article]

Vanessa Hoffmann de Quadros, Juan Carlos González-Avella, José Roberto Iglesias
2014 arXiv   pre-print
This work explores the characteristics of financial contagion in networks whose links distributions approaches a power law, using a model that defines banks balance sheets from information of network connectivity. By varying the parameters for the creation of the network, several interbank networks are built, in which the concentrations of debts and credits are obtained from links distributions during the creation networks process. Three main types of interbank network are analyzed for their
more » ... ilience to contagion: i) concentration of debts is greater than concentration of credits, ii) concentration of credits is greater than concentration of debts and iii) concentrations of debts and credits are similar. We also tested the effect of a variation in connectivity in conjunction with variation in concentration of links. The results suggest that more connected networks with high concentration of credits (featuring nodes that are large creditors of the system) present greater resilience to contagion when compared with the others networks analyzed. Evaluating some topological indices of systemic risk suggested by the literature we have verified the ability of these indices to explain the impact on the system caused by the failure of a node. There is a clear positive correlation between the topological indices and the magnitude of losses in the case of networks with high concentration of debts. This correlation is smaller for more resilient networks.
arXiv:1410.2549v1 fatcat:y5zsrh4s4ve3xj754aqyn6r2va

As estratégias da microempresa varejista e seus estágios de informatização

Roberto Antônio Hoffmann, Valmir Emil Hoffmann, Everton Luis Pellizzaro De Lorenzi Cancellier
2009 RAM. Revista de Administração Mackenzie  
doi:10.1590/s1678-69712009000200006 fatcat:smaggz3lvbgbhnlewhlridg2li

Training the 21st Century Immunologist

Roberto Spreafico, Simon Mitchell, Alexander Hoffmann
2015 Trends in immunology  
All rights reserved. Corresponding author: Hoffmann, A. ( 1 All authors contributed equally. Scientific Life 1471-4906/ ß 2015  ... 
doi:10.1016/ pmid:25911462 fatcat:ktxactimjbcu3hjqouens3pniu

Biorrelaciones entre los musgos y su acarofauna en México

Anita Hoffmann y Roberto Riverón
1992 Bryophyte Diversity and Evolution  
Tropical Bryology 6: [105] [106] [107] [108] [109] [110] 1992 Biorrelaciones entre los musgos y su acarofauna en México Anita Hoffmann y Roberto Riverón Facultad de Ciencias, UNAM, 04510 México, D.F  ... 
doi:10.11646/bde.6.1.12 fatcat:boibjwazinhdxevehieilbgcvm

Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations

Christian Hoffmann, Alessia Centi, Roberto Menichetti, Tristan Bereau
2020 Scientific Data  
The permeation of small-molecule drugs across a phospholipid membrane bears much interest both in the pharmaceutical sciences and in physical chemistry. Connecting the chemistry of the drug and the lipids to the resulting thermodynamic properties remains of immediate importance. Here we report molecular dynamics (MD) simulation trajectories using the coarse-grained (CG) Martini force field. A wide, representative coverage of chemistry is provided: across solutes-exhaustively enumerating all 105
more » ... CG dimers-and across six phospholipids. For each combination, umbrella-sampling simulations provide detailed structural information of the solute at all depths from the bilayer midplane to bulk water, allowing a precise reconstruction of the potential of mean force. Overall, the present database contains trajectories from 15,120 MD simulations. This database may serve the further identification of structure-property relationships between compound chemistry and drug permeability.
doi:10.1038/s41597-020-0391-0 pmid:32054852 pmcid:PMC7018832 fatcat:ottf4v4n3zfnjacc6iibheztpq

Advances in radiatively driven wind models

Joachim Puls, Tamara Repolust, Tadziu L. Hoffmann, Alexander Jokuthy, Roberto O.J. Venero
2003 Symposium - International astronomical union  
We report on a re-analysis of the Galactic O-type star sample presented by Pulset al.(1996) by means of non-LTE model atmospheres including line-blocking and line-blanketing. In particular, we concentrate on the question concerning the dependence of the wind-momentum luminosity relation (WLR) on luminosity class. Owing to the line-blanketing, the derived effective temperatures become significantly lower when compared to previous results, whereas the so-called 'modified wind-momentum rates'
more » ... n roughly at their former values. Therefore, we obtain a new WLR for O-type stars. By comparing these 'observational' results with new theoretical predictions and simulations, we conclude that the Hα forming region for objects with Hα in emission might be considerably clumped and thus a larger mass-loss rate than actually present is mimicked. We suggest that the previously found dependence of the WLR on luminosity class is an artefact.
doi:10.1017/s0074180900211650 fatcat:r2gpze7ehbepvg26mrzdvcwcgy

NFκB dynamics determine stimulus-responsive epigenomic reprogramming in macrophages [article]

Quen J Cheng, Sho Ohta, Katherine M Sheu, Roberto Spreafico, Adewunmi Adelaja, Brooks Taylor, Alexander Hoffmann
2020 bioRxiv   pre-print
The epigenome defines the cell type, but also shows plasticity that enables cells to tune their gene expression potential to the context of extracellular cues. This is evident in immune sentinel cells such as macrophages, which can respond to pathogens and cytokines with phenotypic shifts that are driven by epigenomic reprogramming. Recent studies indicate that this reprogramming arises from the activity of transcription factors such as nuclear factor kappa-light-chain-enhancer of activated B
more » ... lls (NFκB), which binds not only to available enhancers but may produce de novo enhancers in previously silent areas of the genome. Here, we show that NFκB reprograms the macrophage epigenome in a stimulus-specific manner, in response only to a subset of pathogen-derived stimuli. The basis for these surprising differences lies in the stimulus-specific temporal dynamics of NFκB activity. Testing predictions of a mathematical model of nucleosome interactions, we demonstrate through live cell imaging and genetic perturbations that NFκB promotes open chromatin and formation of de novo enhancers most strongly when its activity is non-oscillatory. These de novo enhancers result in the activation of additional response genes. Our study demonstrates that the temporal dynamics of NFκB activity, which encode ligand identity, can be decoded by the epigenome through de novo enhancer formation. We propose a mechanistic paradigm in which the temporal dynamics of transcription factors are a key determinant of their capacity to control epigenomic reprogramming, thus enabling the formation of stimulus-specific memory in innate immune sentinel cells.
doi:10.1101/2020.02.18.954602 fatcat:crf5eioz2faoxl7og2i7depefa

NaV1.7 and pain

Tal Hoffmann, Ohad Sharon, Jürgen Wittmann, Richard W. Carr, Alina Vyshnevska, Roberto De, Mohammed A. Nassar, Peter W. Reeh, Christian Weidner
2017 Pain  
The sodium channel NaV1.7 contributes to action potential (AP) generation and propagation. Loss-of-function mutations in patients lead to congenital indifference to pain, though it remains unclear where on the way from sensory terminals to central nervous system the signalling is disrupted. We confirm that conditional deletion of NaV1.7 in advillin-expressing sensory neurons leads to impaired heat and mechanical nociception in behavioural tests. With single-fiber recordings from isolated skin,
more » ... e found (1) a significantly lower prevalence of heat responsiveness to normally mechanosensitive C-fibers, although (2) the rare heat responses seemed quite vigorous, and (3) heat-induced calcitonin gene-related peptide release was normal. In biophysical respects, although electrical excitability, rheobase, and chronaxy were normal, (4) axonal conduction velocity was 20% slower than in congenic wild-type mice (5) and when challenged with double pulses (<100 milliseconds interval), the second AP showed more pronounced latency increase (6). On prolonged electrical stimulation at 2 Hz, (7) activity-dependent slowing of nerve fiber conduction was markedly less, and (8) was less likely to result in conduction failure of the mutant single fibers. Finally, recording of compound APs from the whole saphenous nerve confirmed slower conduction and less activity-dependent slowing as well as the functional absence of a large subpopulation of C-fibers (9) in conditional NaV1.7 knockouts. In conclusion, the clear deficits in somatic primary afferent functions shown in our study may be complemented by previously reported synaptic dysfunction and opioidergic inhibition, together accounting for the complete insensitivity to pain in the human mutants lacking NaV1.7.
doi:10.1097/j.pain.0000000000001119 pmid:29194125 fatcat:54da5ulgy5edrfyifijt5wbk3i

HTPheno: An image analysis pipeline for high-throughput plant phenotyping

Anja Hartmann, Tobias Czauderna, Roberto Hoffmann, Nils Stein, Falk Schreiber
2011 BMC Bioinformatics  
In the last few years high-throughput analysis methods have become state-of-the-art in the life sciences. One of the latest developments is automated greenhouse systems for high-throughput plant phenotyping. Such systems allow the non-destructive screening of plants over a period of time by means of image acquisition techniques. During such screening different images of each plant are recorded and must be analysed by applying sophisticated image analysis algorithms. Results: This paper presents
more » ... an image analysis pipeline (HTPheno) for high-throughput plant phenotyping. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening. HTPheno is applied to analyse two barley cultivars. Conclusions: HTPheno, an open source image analysis pipeline, supplies a flexible and adaptable ImageJ plugin which can be used for automated image analysis in high-throughput plant phenotyping and therefore to derive new biological insights, such as determination of fitness.
doi:10.1186/1471-2105-12-148 pmid:21569390 pmcid:PMC3113939 fatcat:tpeurxtj3veuth6yd4ljvyl5ji

Synapsin Condensates Recruit alpha-Synuclein

Christian Hoffmann, Roberto Sansevrino, Giuseppe Morabito, Chinyere Logan, R. Martin Vabulas, Ayse Ulusoy, Marcelo Ganzella, Dragomir Milovanovic
2021 Journal of Molecular Biology  
Christian Hoffmann : Hoffmann Conceptualization, Methodology, Investigation, Validation, Writingoriginal draft, Writing -review & editing.  ...  Roberto Sansevrino: Conceptualization, Methodology, Investigation, Validation, Writing -original draft, Writing -review & editing.  ... 
doi:10.1016/j.jmb.2021.166961 pmid:33774037 fatcat:qibpth3g6vcrhh44xt7pbwpwni

Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms

Christine S. Cheng, Marcelo S. Behar, Gajendra W. Suryawanshi, Kristyn E. Feldman, Roberto Spreafico, Alexander Hoffmann
2017 Cell Systems  
Requests should be made directly to Alexander Hoffmann at or by mail at Institute for Quantitative and Computational Biosciences, University of California Los Angeles, 611 S Charles  ...  polyinosine-polycytidylic acid (Poly (I:C Biochemical assays: Western blotting analysis and EMSAs were conducted with standard methods as described previously for fibroblasts (Basak et al., 2007; Hoffmann  ... 
doi:10.1016/j.cels.2017.01.012 pmid:28237795 pmcid:PMC5434763 fatcat:g3luu3ecwrappahx2b4dfyslmu

Methods and rates of poultry litter fertilization for corn silage in organic system

Renato Yagi, José Lino Martinez, Clóvis Roberto Hoffmann
2019 Acta Scientiarum: Agronomy  
The creation of proper soil fertility is fundamental to the agroecological transition phase and guarantees the sustainability of organic agribusiness. In a randomized complete block design with a 3 x 2 factorial scheme with 1 additional treatment (control, without organic fertilizer), we tested three poultry litter rates (7, 14, and 21 Mg ha-1) at sowing or splitting between sowing (30%) and side-dressing (70%) for two summer corn whole-plant silage crops and for the soil chemical attributes.
more » ... e splitting of the poultry litter rate during the rainy season preserves the soil K content, prevents the accumulation of soil P and increases the efficiency of the increasing yields of the organic whole-plant corn silage crop. The reapplication of pre-sowing poultry litter can lead to an accumulation of P and Ca in the soil but favors fresh matter and cob dry matter yields in the dry season. The splitting of the poultry litter rate for whole-plant corn silage can guarantee technical and environmental sustainability in rainy years, but on the other hand, the reapplication of this organic fertilizer only at pre-sowing can increase the fresh matter yield and protein quality of organic whole-plant corn silage cultivated in an Inceptisol in the dry season.
doi:10.4025/actasciagron.v42i1.42951 fatcat:r43avkqyjvh4lfia4jcu7me4lu

Condições de trabalho e saúde de motoristas de transporte coletivo urbano

Márcia Battiston, Roberto Moraes Cruz, Maria Helena Hoffmann
2006 Estudos de Psicologia (Natal)  
Hoffmann (2000) afirma que estas pressões têm origens externas e internas.  ... 
doi:10.1590/s1413-294x2006000300011 fatcat:5lell4wgnbdmvootq6oa333eua

Crystal Structures of S100A6 in the Ca2+-Free and Ca2+-Bound States

Ludovic R. Otterbein, Jolanta Kordowska, Carlos Witte-Hoffmann, C.-L.Albert Wang, Roberto Dominguez
2002 Structure  
manner. Most S100 genes appear clustered within human chromosome 1q21 [11], a region that is often altered in transformed cells, consistent with a role in tumor progression [6]. The expression of the S100A6 gene, in particular, is increased in leukemia cells [12] and during the G1 phase of the cell cycle [13], implying a role in cell cycle progression (thus, S100A6 is also known as calcyclin). Experiments at the protein level show that S100A6 is overexpressed in numerous human cancer Summary
more » ... ls [14-16]. It has also been reported that S100A6 may be involved in reversing the inhibition exerted by S100A6 is a member of the S100 family of Ca 2؉ binding caldesmon on smooth muscle contraction [17]. Binding proteins, which have come to play an important role of S100A6 to the regulatory domain of annexin XI, a in the diagnosis of cancer due to their overexpression Ca 2ϩ -dependent phospholipid binding protein, has been in various tumor cells. We have determined the crystal connected with a potential role in cell proliferation and structures of human S100A6 in the Ca 2؉ -free and Ca 2؉differentiation [18]. bound states to resolutions of 1.15 Å and 1.44 Å , re-Three-dimensional structures of S100 proteins in the spectively. Ca 2؉ binding is responsible for a dramatic Ca 2ϩ -bound form have been determined by X-ray cryschange in the global shape and charge distribution tallography [7, 19-22] and NMR spectroscopy [23-25]. of the S100A6 dimer, leading to the exposure of two Recently, three structures of S100 proteins bound to symmetrically positioned target binding sites. The retarget peptides have been also reported: S100A10sults are consistent with S100A6, and most likely other annexin II [8], S100A11-annexin I [9], and S100B-p53 S100 proteins, functioning as Ca 2؉ sensors in a way regulatory peptide [26] . Contrary to what might be exanalogous to the prototypical sensors calmodulin and pected, the binding site and orientation for the two troponin C. The structures have important implications annexin peptides is different from that of the p53 pepfor our understanding of target binding and cooperatide. Thus, interpretation of the current structural data tivity of Ca 2؉ binding in the S100 family. would suggest that target binding by different S100 proteins involves different sites. Introduction Three NMR structures of S100 proteins, corresponding to the Ca 2ϩ -free (or apo) state, are also available In higher eukaryotes, an extensive repertoire of Ca 2ϩ [27] [28] [29] . However, there is disagreement concerning binding proteins translate transient increases in intracelthese Ca 2ϩ -free structures [24, 30, 31]. For example, the lular Ca 2ϩ levels into a multitude of cellular processes structures of Ca 2ϩ -free and Ca 2ϩ -bound rabbit S100A6 [1]. The vast majority of these proteins bind Ca 2ϩ through are very similar, leading the authors to question the role helix-loop-helix structures that usually exist in pairs and of S100 proteins as Ca 2ϩ sensors [23, 29]. In contrast, are referred to as EF-hand motifs [2, 3]. While several the structures of Ca 2ϩ -free and Ca 2ϩ -bound rat S100B, EF-hand proteins, including calmodulin and troponin C, which is similar in sequence to S100A6, reveal a major work as Ca 2ϩ sensors, undergoing structural changes conformational change of helix III upon Ca 2ϩ binding that expose target binding sites upon Ca 2ϩ binding, oth-[24, 28]. A higher resolution update of the structure of ers, such as calbindin D 9k , exhibit little structural change Ca 2ϩ -free rabbit S100A6 appears to confirm the exisand are thought to work as Ca 2ϩ buffers [4]. tence of significant differences between the structures Most S100 proteins form dimers in solution. Each subof S100A6 and S100B [31]. Groves et al. [30] have sugunit is a 10-12 kDa acidic molecule with two EF-hand gested that these discrepancies might arise from model-Ca 2ϩ binding domains. While the C-terminal EF-hand ing errors due to insufficient structural constraints. displays a canonical 12 amino acid, parvalbumin-like We describe here the X-ray crystal structures of E. Ca 2ϩ binding loop, the N-terminal EF-hand, which is coli-expressed human S100A6 in the Ca 2ϩ -free and usually referred to as the S100-hand, encompasses 14 Ca 2ϩ -bound states to resolutions of 1.15 Å and 1.44 Å , amino acids and has a lower affinity for Ca 2ϩ [5, 6]. respectively. In both states, S100A6 forms dimers stabi-Observed deviations from this common description are lized by hydrophobic interactions between helices I and the facts that (1) some S100 proteins have lost their IV of each monomer. Ca 2ϩ binding is responsible for an ability to bind either one or both of the Ca 2ϩ ions while ‫68ف‬Њ reorientation of helix III and marked changes in still adopting a Ca 2ϩ -bound-like conformation [7-9]; (2) the positioning and structure of helix II, the linker loop there is at least one monomeric member in the family, between helices II and III, and the C-terminal end of calbindin D 9k [10]; and (3) some S100 proteins form hethelix IV. The combination of these structural differences erodimers [5]. results in a dramatic change in the global shape and In contrast to calmodulin, which is ubiquitously excharge distribution of the S100A6 dimer, leading to the pressed, S100 proteins are expressed in a cell-specific Key words: S100A6; calcyclin; Ca 2ϩ binding; Ca 2ϩ sensor; X-ray; Ca 2ϩ -free structure; Ca 2ϩ -bound structure 1 Correspondence:
doi:10.1016/s0969-2126(02)00740-2 pmid:11937060 fatcat:obvzqng2ebcdvo3lxad4m5rxhy

Controlled exploration of chemical space by machine learning of coarse-grained representations [article]

Christian Hoffmann, Roberto Menichetti, Kiran H. Kanekal, Tristan Bereau
2019 arXiv   pre-print
The size of chemical compound space is too large to be probed exhaustively. This leads high-throughput protocols to drastically subsample and results in sparse and non-uniform datasets. Rather than arbitrarily selecting compounds, we systematically explore chemical space according to the target property of interest. We first perform importance sampling by introducing a Markov chain Monte Carlo scheme across compounds. We then train an ML model on the sampled data to expand the region of
more » ... space probed. Our boosting procedure enhances the number of compounds by a factor 2 to 10, enabled by the ML model's coarse-grained representation, which both simplifies the structure-property relationship and reduces the size of chemical space. The ML model correctly recovers linear relationships between transfer free energies. These linear relationships correspond to features that are global to the dataset, marking the region of chemical space up to which predictions are reliable---a more robust alternative to the predictive variance. Bridging coarse-grained simulations with ML gives rise to an unprecedented database of drug-membrane insertion free energies for 1.3 million compounds.
arXiv:1905.01897v1 fatcat:2tyfrtrtifgufejlphvswwvp2e
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