Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards...

With the availability of the Internet, virtual communities are proliferating at an unprecedented rate. Indepth understanding of virtual community dynamics can help us to address critical organizational and information systems issues such as communities-of-practice, virtual collaboration, and knowledge management. The biggest challenge in fostering a virtual community is the supply of knowledge ...

A species may overlap with a mosaic of species across its geographic range. Many types of species interaction cause selection on mating traits, but their role in generating within-species divergence has been neglected. The pattern of reproductive character displacement (RCD) has been classically attributed to reinforcement, a process driven by selection against hybridisation. Recent reinforceme...

sReceived 9 May 2004; accepted 28 March 2005; published online 26 May 2005d Simulations of He– He mixtures with negative separation ratios in two-dimensional containers with realistic boundary conditions and moderately large aspect ratio G are described. The system exhibits a large variety of states with complex time dependence including intermittent wave localization and chaotic “repeated tran...

Refractory celiac disease (RCD) is a rare but life-threatening complication of celiac disease (CD), and only 1 pediatric case has been reported. We report a case of a 14-year-old girl with CD presenting with persistent symptoms and positive tissue celiac-specific antibodies despite a gluten-free diet. Push enteroscopy showed jejunal scalloping and partial villous atrophy on histology. She was d...

Selection can facilitate diversification by inducing character displacement in mate choice traits that reduce the probability of maladaptive mating between lineages. Although reproductive character displacement (RCD) has been demonstrated in two-taxa case studies, the frequency of this process in nature is still debated. Moreover, studies have focused primarily on visual and acoustic traits, de...

Many applications call for learning causal models from relational data. We investigate Relational Causal Models (RCM) under relational counterparts of adjacency-faithfulness and orientation-faithfulness, yielding a simple approach to identifying a subset of relational d-separation queries needed for determining the structure of an RCM using d-separation against an unrolled DAG representation of...

Laminin-binding integrins (α3β1, α6β1, α6β4, α7β1) are almost always expressed together with tetraspanin CD151. In every coexpressing cell analyzed to date, CD151 makes a fundamental contribution to integrin-dependent motility, invasion, morphology, adhesion and/or signaling. However, there has been minimal mechanistic insight into how CD151 affects integrin functions. In MDA-MB-231 mammary cel...

A series of HIV integrase (HIV-1 IN) inhibitors were synthesized to evaluate the role of the metal-binding group (MBG) in this class of metalloenzyme inhibitors. A total of 21 different raltegravir-chelator derivative (RCD) compounds were prepared that differed only in the nature of the MBG. These IN strand-transfer inhibitors (INSTIs) were evaluated in vitro in cell-free enzyme activity assays...

A fertilization rate of 2 or 3 mg nitrogen (N) per week for 20 weeks yielded longleaf pine (Pinus palustris) seedlings grown inside a greenhouse that survived well and produced good root collar diameter (RCD) growth the first year after outplanting. Of a range of fertilization rates (0.5 to 4 mg N/week), the 2 mg rate yielded seedlings that did not require needle clipping during nursery product...