Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities

An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more complex multi-species communities based on the assumption that microbes minimize adjustments of pairwise interactions in response to neighbor species. We termed this rule-based inference minimal interspecies interaction adjustment (MIIA). Our critical assessment of MIIA has produced reliable predictions of shifting interspecies interactions that are dependent on the functional role of neighbor organisms. We also show how MIIA has been applied to a microbial community composed of competing soil bacteria to elucidate a new finding that – in many cases – adding fewer competitors could impose more significant impact on binary interactions. The ability to predict membership-dependent community behavior is expected to help deepen our understanding of how microbiomes are organized in nature and how they may be designed and/or controlled in the future

Solstice: An Electronic Journal of Geography and Mathematics: Vol. 31, No. 2

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/163731/1/SolsticeVolumeXXXINumber2.pdfd0a18e86-7d9e-4669-812b-ead353cc4899b2c2c9fd-ee9d-4e83-89fe-dc520ef84368Description of SolsticeVolumeXXXINumber2.pdf : Solstice, Vol. XXXI, No. 2.SEL

Quick Start Guide to Soil Methods for Ecologists

Increasingly biologists and ecologists are becoming aware of the vital importance of soil to processes observed above ground and are incorporating soil analyses into their research. Because of the dynamic and heterogeneous nature of soil, proper incorporation of soil analysis into ecological studies requires knowledge and planning. Unfortunately, many ecologists may not be current (or trained at all) in soil science.We provide this review, based on our cumulative \u3e60 years of work in soil science,to help familiarize researchers with essential information to appropriately incorporate soil analyses into ecological studies. Specifically, we provide a brief introduction into soils and then discuss issues related to soil sterilization, choosing a soil for a greenhouse project, sampling soils, and soil analyses

Physiological Response to Salt (NaCl) Stress in Selected Cultivated Tetraploid Cottons

In the southwestern and western Cotton Belt of the U.S. soil salinity can reduce cotton productivity and quality. This study was conducted to determine the physiological responses of six genotypes including five Upland cotton (Gossypium hirsutum L.) cultivars and one Pima cotton line (G. barbadense L.) to NaCl under greenhouse conditions. Seeds were germinated and grown for 14 days prior to salt treatment (daily 100 ml of 200 mM NaCl) for 21 days. Compared with the control (daily 100 ml tap water), the NaCl treatment significantly reduced plant height, leaf area, fresh weight, and dry weight. The NaCl stress also significantly increased leaf chlorophyll content, but did not affect leaf fluorescence. Of the six genotypes, Pima 57-4 and SG 747 had the most growth reduction, and were most sensitive to NaCl; DP 33B, JinR 422 and Acala Phy 72 had the least growth reduction and were most NaCl tolerant. Although all the six genotypes under the salt treatment had significantly higher Na and Cl accumulation in leaves, SG 747 and Pima 57-4 accumulated more Na and Cl than DP 33B. Increases in leaf N, Zn, and Mn concentrations were also observed in the NaCl-treated plants. While leaf P, Ca, and S concentrations remained unchanged overall in the genotypes tested, leaf K, Mg, Fe, and Cu concentrations significantly decreased during salt stress. Reduction in plant height is a simple, easy, sensitive, non-destructive measurement to evaluate salt tolerance in cotton

Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities

An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more complex multi-species communities based on the assumption that microbes minimize adjustments of pairwise interactions in response to neighbor species. We termed this rule-based inference minimal interspecies interaction adjustment (MIIA). Our critical assessment of MIIA has produced reliable predictions of shifting interspecies interactions that are dependent on the functional role of neighbor organisms. We also show how MIIA has been applied to a microbial community composed of competing soil bacteria to elucidate a new finding that – in many cases – adding fewer competitors could impose more significant impact on binary interactions. The ability to predict membership-dependent community behavior is expected to help deepen our understanding of how microbiomes are organized in nature and how they may be designed and/or controlled in the future

Islam, Budaya dan komunikasi antarbudaya Islam di Indonesia

The occurrence of contacts between various ethnic groups in Indonesia, the different respond to socio-political conditions in Indonesia, the occurrence of Indonesian Islamic affiliations with various countries, gave diverse Islamic cultures with various roles and functions in the history of Indonesia's development since colonial period. to the existence, role and function of various existing Islamic cultural identities, conflict of identity cannot be avoided. This condition requires an intercultural communication with the principle of mutual understanding, mutual respect and mutual support, as in the concept of intercultural communication by Ting-Toomey (1999). Government support for one of the  Islamic cultures in Indonesia has triggered a conflict of triangles between the  government, Islamic culture mainstreams and Islamic culture streams. With the constructivism paradigm, this study interpreted social facts constructed based on subjective experience of informants. Qualitative data and analysis were obtained from twenty informants as sources of research in

Wasting Breath in Hamlet

This is the final version. Available on open access from Palgrave via the DOI in this recordThis chapter draws on instances of disordered breathing in Hamlet in order to examine the cultural signifcance of sighs in the early modern period, as well as in the context of current work in the feld of medical humanities. Tracing the medical history of sighing in ancient and early modern treatises of the passions, the chapter argues that sighs, in the text and the performance of the tragedy, exceed their conventional interpretation as symptoms of pain and disrupt meaning on the page and on stage. In the light of New Materialist theory, the air circulating in Hamlet is shown to dismantle narratives of representation, posing new questions for the future of medical humanities

Measurement of inclusive D*+- and associated dijet cross sections in photoproduction at HERA

Inclusive photoproduction of D*+- mesons has been measured for photon-proton centre-of-mass energies in the range 130 < W < 280 GeV and a photon virtuality Q^2 < 1 GeV^2. The data sample used corresponds to an integrated luminosity of 37 pb^-1. Total and differential cross sections as functions of the D* transverse momentum and pseudorapidity are presented in restricted kinematical regions and the data are compared with next-to-leading order (NLO) perturbative QCD calculations using the "massive charm" and "massless charm" schemes. The measured cross sections are generally above the NLO calculations, in particular in the forward (proton) direction. The large data sample also allows the study of dijet production associated with charm. A significant resolved as well as a direct photon component contribute to the cross section. Leading order QCD Monte Carlo calculations indicate that the resolved contribution arises from a significant charm component in the photon. A massive charm NLO parton level calculation yields lower cross sections compared to the measured results in a kinematic region where the resolved photon contribution is significant.Comment: 32 pages including 6 figure

Measurement of Jet Shapes in Photoproduction at HERA

The shape of jets produced in quasi-real photon-proton collisions at centre-of-mass energies in the range $134-277$ GeV has been measured using the hadronic energy flow. The measurement was done with the ZEUS detector at HERA. Jets are identified using a cone algorithm in the $\eta - \phi$ plane with a cone radius of one unit. Measured jet shapes both in inclusive jet and dijet production with transverse energies $E^{jet}_T>14$ GeV are presented. The jet shape broadens as the jet pseudorapidity ($\eta^{jet}$) increases and narrows as $E^{jet}_T$ increases. In dijet photoproduction, the jet shapes have been measured separately for samples dominated by resolved and by direct processes. Leading-logarithm parton-shower Monte Carlo calculations of resolved and direct processes describe well the measured jet shapes except for the inclusive production of jets with high $\eta^{jet}$ and low $E^{jet}_T$. The observed broadening of the jet shape as $\eta^{jet}$ increases is consistent with the predicted increase in the fraction of final state gluon jets.Comment: 29 pages including 9 figure