Time Development in the Early History of Social Networks: Link Stabilization,Group Dynamics,and Segregation

Studies of the time development of empirical networks usually investigate late stages where lasting connections have already stabilized. Empirical data on early network history are rare but needed for a better understanding of how social network topology develops in real life. Studying students who are beginning their studies at a university with no or few prior connections to each other offers a unique opportunity to investigate the formation and early development of link patterns and community structure in social networks. During a nine week introductory physics course, first year physics students were asked to identify those with whom they communicated about problem solving in physics during the preceding week. We use these students'' self reports to produce time dependent student interaction networks. We investigate these networks to elucidate possible effects of different student attributes in early network formation. Changes in the weekly number of links show that while roughly half of all links change from week to week, students also reestablish a growing number of links as they progress through their first weeks of study. Using the Infomap community detection algorithm, we show that the networks exhibit community structure, and we use non-network student attributes, such as gender and end-of-course grade to characterize communities during their formation. Specifically, we develop a segregation measure and show that students structure themselves according to gender and pre-organized sections (in which students engage in problem solving and laboratory work), but not according to end-of-coure grade. Alluvial diagrams of consecutive weeks'' communities show that while student movement between groups are erratic in the beginnning of their studies, they stabilize somewhat towards the end of the course. Taken together, the analyses imply that student interaction networks stabilize quickly and that students establish collaborations based on who is immediately available to them and on observable personal characteristics.     

The major allergen from birch tree pollen, Bet v 1, binds and permeabilizes membranes

The 159 residue Bet v 1 is the major allergen from birch tree pollen. Its natural function is unknown although it is capable of binding several types of physiologically relevant ligands in a centrally placed cavity in the protein structure. Here we use circular dichroism and fluorescence spectroscopy to show that Bet v 1 binds to DOPC and DOPG phospholipid vesicles in a pH-dependent manner. Binding is facilitated by low pH, negatively charged phospholipids, and high vesicle curvature, indicating that electrostatic interactions and vesicle surface defects are important parameters for binding. Binding is accompanied by major structural rearrangements, involving an increase in alpha-helical structure and a decrease in beta-structure. A bilayer structure per se is not a prerequisite for these rearrangements, since they also occur in the presence of the micelle-forming lysophospholipids lysoMPC and lysoMPG. Two major bound states (A and B) with distinct secondary structure compositions were identified, which predominate in the pH ranges approximately 9.5-6.5 and approximately 5-2.5, respectively. Despite the high content of secondary structure, the A- and B-states are partially unfolded as they unfold noncooperatively in CD thermal scans, in contrast to the native state. In addition, the B-state (but not the A-state) shows intermediate proteolysis-resistance and is able to induce complete leakage of calcein from the vesicles, indicating that this state is partially inserted into and significantly perturbs the bilayer structure. We conclude that Bet v 1 is a membrane binding protein, highlighting a possible biological function of this protein.     

Development of a simple proton nuclear magnetic resonance-based procedure to estimate the approximate distribution coefficient at physiological pH (log D7.4): Evaluation and comparison to existing practices

In drug discovery, lipophilicity is a key parameter for drug optimization. Lipophilicity determinations can be both work and time consuming, especially for non-UV active compounds. Herein, an improved and simple 1H NMR-based method is described to estimate the lipophilicity at physiological pH (log D_7.4) in 1-octanol and D₂O buffer. The method can be applied to both UV and non-UV active compounds. In addition, neither calibration curves nor internal/external standards are needed. We have demonstrated that log D_7.4 can be accurately measured using 1H NMR for compounds within the log D_7.4 interval between 0.7 and 3.3. The method was also compared to a previously described HPLC method.     

Modelling pink-footed goose (Anser brachyrhynchus) wintering distributions for the year 2050: potential effects of land-use change in Europe

Feeding on farmland by overwintering populations of pink-footed geese ( Anser brachyrhynchus ) conflicts with agricultural interests in Northern Europe. In order to forecast the potential future of this conflict, we used generalized linear models to relate the presence and absence of pink-footed geese to variables describing the contemporary landscape, and predicted their future distributions in relation to two land-use scenarios for the year 2050. One future scenario represented a global, economically orientated world (A1) and the other represented a regional, environmentally concerned world (B2). The probability of goose occurrence increased within cropland and grassland, and could be explained by their proximity to coast, elevation, and the degree of habitat closure. Predictions to future scenarios revealed noticeable shifts in the suitability of goose habitat evident at the local and regional scale in response to future shifts in land use. In particular, as grasslands and croplands give way to unsuitable land-use types (e.g. woody biofuel crops, increased urbanization, and forest) under both future scenarios, our models predicted a decrease in habitat suitability for geese. If coupled with continued goose population expansion, we expect that the agricultural conflict will intensify under the A1 and particularly the B2 scenarios.     

Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure

Background  

Efficient communication between distant sites within a protein is essential for cooperative biological response. Although often associated with large allosteric movements, more subtle changes in protein dynamics can also induce long-range correlations. However, an appropriate formalism that directly relates protein structural dynamics to information exchange between functional sites is still lacking.