On finite-size effects in computer simulations using the Ewald potential

We discuss the origin and relevance for computer simulations of a strong finite-size effect that appears when using the Ewald summation formula. It can be understood as arising from a volume-dependent shift of the potential in a finite, periodic box relative to the infinite volume limit. This shift is due to the fact that the ``zero of energy'' for a periodic system cannot be defined by letting the interacting particles be separated by an infinite distance; the correct definition corresponds to setting its \bbox k=\bbox 0 Fourier mode to zero. The implications of this effect for computer simulations are discussed.Comment: Submitted to Journal of Chemical Physic

Imidazolinone-tolerant rice: weed control, crop response, and environmental impact

Field and greenhouse research was conducted from 1999 to 2003 to evaluate weed control in imidazolinone-tolerant (IT) rice (Oryza sativa L.) under various tillage and planting systems, tolerance of IT rice cultivars to imazethapyr rate and application timing, and the impact of IT technology and tillage systems on solids runoff in rice drainage water. In both conventional and reduced tillage systems imazethapyr applied preemergence and postemergence at 70 g ai/ha controlled red rice (Oryza sativa L.), barnyardgrass [Echinochloa crus-galli (L.) Beauv.], Amazon sprangletop [Leptochloa panicoides (Presl) Hitchc.], and rice flatsedge (Cyperus iria L.) 87 to 99%. Indian jointvetch (Aeschynomene indica L.) control with sequential applications of imazethapyr was as high as 70% in water-seeded rice but no more than 54% in drill-seeded rice. With sequential applications of imazethapyr at 70 g/ha, rice yield was 63% greater when water-seeded compared with drill-seeded. Imazethapyr applied to one- to two-leaf or three- to four-leaf rice at 70, 140, and 280 g/ha was more injurious to the IT rice cultivar �CL 161� than to �CL 121�. Shoot:root ratio for CL 161 was not affected by imazethapyr application. For CL 121, shoot:root ratio following imazethapyr application was lower than that observed for CL 161 suggesting that CL 121 shoot fresh weight was inhibited more by imazethapyr than was root fresh weight. Based on shoot fresh weight two weeks after imazethapyr application at 70 g/ha, CL 161 was 1.8 times more tolerant than CL 121 and CL 161 was 2.9 times more tolerant than CL 121 with 280 g/ha imazethapyr. In the conventional tillage and water-seeded system where soil was worked under flooded conditions one day prior to drainage, off-site movement of solids in the initial discharge of irrigation water was 1250 kg/ha. This compares with no more than 80 kg/ha for the initial drainage in reduced tillage systems where rice was water-seeded or drill-seeded. Total off-site movement of solids from initial drainage through 12 weeks totaled 2,370 kg/ha for the conventional tillage system and loss of solids was reduced by as much as 79% where reduced tillage systems were used

Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

<p>Abstract</p> <p>Background</p> <p>The reaction of HIV protease to inhibitor therapy is characterized by the emergence of complex mutational patterns which confer drug resistance. The response of HIV protease to drugs often involves both primary mutations that directly inhibit the action of the drug, and a host of accessory resistance mutations that may occur far from the active site but may contribute to restoring the fitness or stability of the enzyme. Here we develop a probabilistic approach based on connected information that allows us to study residue, pair level and higher-order correlations within the same framework.</p> <p>Results</p> <p>We apply our methodology to a database of approximately 13,000 sequences which have been annotated by the treatment history of the patients from which the samples were obtained. We show that including pair interactions is essential for agreement with the mutational data, since neglect of these interactions results in order-of-magnitude errors in the probabilities of the simultaneous occurence of many mutations. The magnitude of these pair correlations changes dramatically between sequences obtained from patients that were or were not exposed to drugs. Higher-order effects make a contribution of as much as 10% for residues taken three at a time, but increase to more than twice that for 10 to 15-residue groups. The sequence data is insufficient to determine the higher-order effects for larger groups. We find that higher-order interactions have a significant effect on the predicted frequencies of sequences with large numbers of mutations. While relatively rare, such sequences are more prevalent after multi-drug therapy. The relative importance of these higher-order interactions increases with the number of drugs the patient had been exposed to.</p> <p>Conclusion</p> <p>Correlations are critical for the understanding of mutation patterns in HIV protease. Pair interactions have substantial qualitative effects, while higher-order interactions are individually smaller but may have a collective effect. Together they lead to correlations which could have an important impact on the dynamics of the evolution of cross-resistance, by allowing the virus to pass through otherwise unlikely mutational states. These findings also indicate that pairwise and possibly higher-order effects should be included in the models of protein evolution, instead of assuming that all residues mutate independently of one another.</p

Assessing the Future: Eportfolios at Johns Hopkins

The Eportfolio Task Force was charged by the Committee of Homewood Advisors to conduct a focused inquiry into the current and potential uses of electronic portfolios at johns Hopkins to assess their potential impact and facilitate their development on campus. The Task Force managed and evaluated six pilot eportfolio pilot projects and researched eportfolio implementations at other universities. The enclosed report summarizes these activities and describes the potential uses of eportfolios at johns Hopkins.Johns Hopkins Eportfolio Task Force; Center for Educational Resources; IT@J

Joint Modeling and Registration of Cell Populations in Cohorts of High-Dimensional Flow Cytometric Data

In systems biomedicine, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multi-variable network-level responses. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While computational methods can identify cell populations in individual samples, without the ability to automatically match them across samples, it is difficult to compare and characterize the populations in typical experiments, such as those responding to various stimulations or distinctive of particular patients or time-points, especially when there are many samples. Joint Clustering and Matching (JCM) is a multi-level framework for simultaneous modeling and registration of populations across a cohort. JCM models every population with a robust multivariate probability distribution. Simultaneously, JCM fits a random-effects model to construct an overall batch template -- used for registering populations across samples, and classifying new samples. By tackling systems-level variation, JCM supports practical biomedical applications involving large cohorts

International cooperation for Mars exploration and sample return

The National Research Council's Space Studies Board has previously recommended that the next major phase of Mars exploration for the United States involve detailed in situ investigations of the surface of Mars and the return to earth for laboratory analysis of selected Martian surface samples. More recently, the European space science community has expressed general interest in the concept of cooperative Mars exploration and sample return. The USSR has now announced plans for a program of Mars exploration incorporating international cooperation. If the opportunity becomes available to participate in Mars exploration, interest is likely to emerge on the part of a number of other countries, such as Japan and Canada. The Space Studies Board's Committee on Cooperative Mars Exploration and Sample Return was asked by the National Aeronautics and Space Administration (NASA) to examine and report on the question of how Mars sample return missions might best be structured for effective implementation by NASA along with international partners. The committee examined alternatives ranging from scientific missions in which the United States would take a substantial lead, with international participation playing only an ancillary role, to missions in which international cooperation would be a basic part of the approach, with the international partners taking on comparably large mission responsibilities. On the basis of scientific strategies developed earlier by the Space Studies Board, the committee considered the scientific and technical basis of such collaboration and the most mutually beneficial arrangements for constructing successful cooperative missions, particularly with the USSR

Impact of hands‐on care on infant sleep in the neonatal intensive care unit

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135460/1/ppul23513_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135460/2/ppul23513.pd