Information processing without brains--the power of intercellular regulators in plants.

Plants exhibit different developmental strategies than animals; these are characterized by a tight linkage between environmental conditions and development. As plants have neither specialized sensory organs nor a nervous system, intercellular regulators are essential for their development. Recently, major advances have been made in understanding how intercellular regulation is achieved in plants on a molecular level. Plants use a variety of molecules for intercellular regulation: hormones are used as systemic signals that are interpreted at the individual-cell level; receptor peptide-ligand systems regulate local homeostasis; moving transcriptional regulators act in a switch-like manner over small and large distances. Together, these mechanisms coherently coordinate developmental decisions with resource allocation and growth.

Predictions of the Pt(8)Ti phase in unexpected systems.

The binary A(8)B phase (prototype Pt(8)Ti) has been experimentally observed in 11 systems. A high-throughput search over all the binary transition intermetallics, however, reveals 59 occurrences of the A(8)B phase: Au(8)Zn(dagger), Cd(8)Sc(dagger), Cu(8)Ni(dagger), Cu(8)Zn(dagger), Hg(8)La, Ir(8)Os(dagger), Ir(8)Re, Ir(8)Ru(dagger), Ir(8)Tc, Ir(8)W(dagger), Nb(8)Os(dagger), Nb(8)Rh(dagger), Nb(8)Ru(dagger), Nb(8)Ta(dagger), Ni(8)Fe, Ni(8)Mo(dagger)*, Ni(8)Nb(dagger)*, Ni(8)Ta*, Ni(8)V*, Ni(8)W, Pd(8)Al(dagger), Pd(8)Fe, Pd(8)Hf, Pd(8)Mn, Pd(8)Mo*, Pd(8)Nb, Pd(8)Sc, Pd(8)Ta, Pd(8)Ti, Pd(8)V*, Pd(8)W*, Pd(8)Zn, Pd(8)Zr, Pt(8)Al(dagger), Pt(8)Cr*, Pt(8)Hf, Pt(8)Mn, Pt(8)Mo, Pt(8)Nb, Pt(8)Rh(dagger), Pt(8)Sc, Pt(8)Ta, Pt(8)Ti*, Pt(8)V*, Pt(8)W, Pt(8)Zr*, Rh(8)Mo, Rh(8)W, Ta(8)Pd, Ta(8)Pt, Ta(8)Rh, V(8)Cr(dagger), V(8)Fe(dagger), V(8)Ir(dagger), V(8)Ni(dagger), V(8)Pd, V(8)Pt, V(8)Rh, and V(8)Ru(dagger) ((dagger) = metastable, * = experimentally observed). This is surprising for the wealth of new occurrences that are predicted, especially in well-characterized systems (e.g., Cu-Zn). By verifying all experimental results while offering additional predictions, our study serves as a striking demonstration of the power of the high-throughput approach. The practicality of the method is demonstrated in the Rh-W system. A cluster-expansion-based Monte Carlo model reveals a relatively high order-disorder transition temperature.

Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.

The computational detection of regulatory elements in DNA is a difficult but important problem impacting our progress in understanding the complex nature of eukaryotic gene regulation. Attempts to utilize cross-species conservation for this task have been hampered both by evolutionary changes of functional sites and poor performance of general-purpose alignment programs when applied to non-coding sequence. We describe a new and flexible framework for modeling binding site evolution in multiple related genomes, based on phylogenetic pair hidden Markov models which explicitly model the gain and loss of binding sites along a phylogeny. We demonstrate the value of this framework for both the alignment of regulatory regions and the inference of precise binding-site locations within those regions. As the underlying formalism is a stochastic, generative model, it can also be used to simulate the evolution of regulatory elements. Our implementation is scalable in terms of numbers of species and sequence lengths and can produce alignments and binding-site predictions with accuracy rivaling or exceeding current systems that specialize in only alignment or only binding-site prediction. We demonstrate the validity and power of various model components on extensive simulations of realistic sequence data and apply a specific model to study Drosophila enhancers in as many as ten related genomes and in the presence of gain and loss of binding sites. Different models and modeling assumptions can be easily specified, thus providing an invaluable tool for the exploration of biological hypotheses that can drive improvements in our understanding of the mechanisms and evolution of gene regulation.

Information-theoretic analysis of a stimulated-Brillouin-scattering-based slow-light system.

We use an information-theoretic method developed by Neifeld and Lee [J. Opt. Soc. Am. A 25, C31 (2008)] to analyze the performance of a slow-light system. Slow-light is realized in this system via stimulated Brillouin scattering in a 2 km-long, room-temperature, highly nonlinear fiber pumped by a laser whose spectrum is tailored and broadened to 5 GHz. We compute the information throughput (IT), which quantifies the fraction of information transferred from the source to the receiver and the information delay (ID), which quantifies the delay of a data stream at which the information transfer is largest, for a range of experimental parameters. We also measure the eye-opening (EO) and signal-to-noise ratio (SNR) of the transmitted data stream and find that they scale in a similar fashion to the information-theoretic method. Our experimental findings are compared to a model of the slow-light system that accounts for all pertinent noise sources in the system as well as data-pulse distortion due to the filtering effect of the SBS process. The agreement between our observations and the predictions of our model is very good. Furthermore, we compare measurements of the IT for an optimal flattop gain profile and for a Gaussian-shaped gain profile. For a given pump-beam power, we find that the optimal profile gives a 36% larger ID and somewhat higher IT compared to the Gaussian profile. Specifically, the optimal (Gaussian) profile produces a fractional slow-light ID of 0.94 (0.69) and an IT of 0.86 (0.86) at a pump-beam power of 450 mW and a data rate of 2.5 Gbps. Thus, the optimal profile better utilizes the available pump-beam power, which is often a valuable resource in a system design.

Measurements of Epidural Space Depth Using Preexisting CT Scans Correlate with Loss of Resistance Depth during Thoracic Epidural Catheter Placement.

Background. Thoracic epidural catheters provide the best quality postoperative pain relief for major abdominal and thoracic surgical procedures, but placement is one of the most challenging procedures in the repertoire of an anesthesiologist. Most patients presenting for a procedure that would benefit from a thoracic epidural catheter have already had high resolution imaging that may be useful to assist placement of a catheter. Methods. This retrospective study used data from 168 patients to examine the association and predictive power of epidural-skin distance (ESD) on computed tomography (CT) to determine loss of resistance depth acquired during epidural placement. Additionally, the ability of anesthesiologists to measure this distance was compared to a radiologist, who specializes in spine imaging. Results. There was a strong association between CT measurement and loss of resistance depth (P < 0.0001); the presence of morbid obesity (BMI > 35) changed this relationship (P = 0.007). The ability of anesthesiologists to make CT measurements was similar to a gold standard radiologist (all individual ICCs > 0.9). Conclusions. Overall, this study supports the examination of a recent CT scan to aid in the placement of a thoracic epidural catheter. Making use of these scans may lead to faster epidural placements, fewer accidental dural punctures, and better epidural blockade.