How ciliates manipulate their own DNA – A splendid example of natural computing

DNA computing is a novel and vivid researcharea which is genuinely interdisciplinary –computer scientists and molecular scientistscollaborate to investigate the use of DNAmolecules for the purpose of computing. DNAcomputing in vivo is the investigation ofcomputations taking place naturally in a livingcell, with the goal of understandingcomputational properties of DNA molecules intheir native environment. Gene assembly inciliates (single cell organisms) is perhaps themost involved process of DNA manipulation yetknown in living organisms. The computationalnature of this process has attracted muchattention in recent years. The resultsobtained so far demonstrate that this processof gene assembly is a splendid example ofcomputing taking place in nature, i.e., NaturalComputing. Indeed, DNA computing in vivomay be far more widespread in nature than wecurrently recognize. This paper is a tutorialon (computational nature of the) gene assemblyin ciliates, which is intended for a broadaudience of researchers interested in NaturalComputing. In particular, no knowledge ofmolecular biology is assumed on the part of themotivated reader.     

Natural occurrence of scirpentriol in cereals infected by Fusarium species.

Wheat, barley and oat grain samples naturally contaminated with Fusarium spp. were analysed for the presence of scirpentriol (STO). This toxin was detected in 1, 37 and 8% of 248 wheat, 32 barley and 99 oat grain samples, respectively, and the maximum concentration was 83 microg x kg(-1). Samples of wheat and oat grain with visible scab symptoms were also analysed, and STO (mean level 255 microg x kg(-1)) was detected only in oat samples infected with F. sporotrichioides and F. poae as the dominant species. We analysed 15 barley samples that were subdivided based on seed size into fractions of <2.5 and > 2.5 mm in diameter. The smaller kernels contained an average 94% of the STO in the samples (in kernel fraction > 2.5 mm 28 microg x kg(-1), <2.5 mm 297 microg x kg(-1)). In oats, STO levels were highest in the chaff, lower in the stalk's apical internode and lowest in the grain.     

Egotism versus generalization-of-uncontrollability explanations of helplessness: Reply to Snyder and Frankel (1989).

M. L. Snyder and A. Frankel (see record 1990-09504-001) argue that our experiments (M. Kofta and G. S?dek; see record 1989-24900-001) were inadequate for testing the egotism theory of helplessness because they did not directly address the role of threat to self-esteem, the process held responsible for helplessness deficits by this theory. We reply that failure experience—the chief manipulation in these experiments—is critical for arousing threat to self-esteem. Therefore, our findings—that (a) noncontingency, not ego-threatening failure, is specifically responsible for helplessness deficits, and (b) availability of excuse for failure in the test phase augments performance deficits instead of mitigating them—call into question the validity of the egotism explanation of helplessness. We conclude that by and large, our study lends support to the original learned helplessness theory of Seligman and his associates. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The investigation of aggregate grain size effect on fracture toughness of ordinary concrete structures

The material under investigation was ordinary conerete of B 20 class, different in the sizes of coarse aggregate and water-cement ratio of the same value w/c=0.55. It was found during the tests that there were two kinds of sample cracking mechanisms. Some samples cracked at the moment of the initiation of slit (when P _Q=P _max); in others the decohesion force P _max exceeded P _Q, which was identified as a minor deflection or relative extremum of the curve. The frequency of the second type of cracking increased with the growing size of coarse aggregate grains. Together with the growth of the grain size, the angle of curve inclination also became smaller. This phenomenon can be explained by the fact that, in the process of decohesion, the aggregate grains are relocated and the system of contact between them changes, so the K _Hc depends on coarse aggregate.     

Repeated failure: A source of helplessness or a factor irrelevant to its emergence?

Tested the validity of the egotism model of human helplessness (HE). In contrast to the original theoretical approach of M. E. P. Seligman (1975) and his associates, which points to response–outcome noncontingency as the main source of HE, the egotism alternative proposes that repeated failure itself is the critical determinant of HE symptoms. Repeated failure threatens the self-esteem of the S, who supposedly engages in a least-effort strategy during the test phase of a typical learned HE study, which results in performance impairment. To examine the egotism explanation, we gave Ss noncontingent-feedback training with or without repeated failure on 5 consecutive discrimination problems. In 2 experiments, noncontingent-feedback preexposure produced HE deficits in performance on avoidance learning, whereas repeated failure appeared irrelevant to HE. This and our other findings from research are inconsistent with the egotism explanation and support instead Seligman's original proposal, in which HE is attributed to prolonged experience with noncontingency. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Equivalency of Lightning Return-Stroke Models Employing Lumped and Distributed Current Sources

We show that any engineering return-stroke model can be expressed, using an appropriate continuity equation, in terms of either lumped or distributed current sources with the resultant longitudinal-current distribution along the channel being the same. This property can be viewed as the duality of engineering models. The conversion alters the actual-corona current (if any) of the model. For lumped-source (LS) models the actual-corona current is unipolar and directed radially out of the channel core, while for distributed-source (DS) models it is unipolar and directed into the channel core. For LS models converted to DS models and for the Diendorfer-Uman (DU) model converted to the equivalent LS model, the corona current is the sum of the negated actual-corona current (if any) and a fictitious-corona current, the latter being bipolar. For the transmission-line (TL) model (no longitudinal current attenuation with height) expressed in terms of DSs, there is only a fictitious bipolar corona current component. Conversion of the traveling-current source (TCS) and Bruce-Golde (BG) models to equivalent LS models involves replacement of the actual, unipolar corona current with a fictitious one, the latter current being bipolar near the channel base and unipolar at higher altitudes     

Scaling J2EE™ application servers with the Multi‐tasking Virtual Machine

The Java? 2 Platform, Enterprise Edition (J2EE?), is established as the standard platform for hosting enterprise applications written in the Java programming language. Similar to an operating system, a J2EE server can host multiple applications, but this is problematic due to limitations on scalability, weak inter‐application isolation and inadequate resource management facilities in the underlying Java platform. These limitations lead to a proliferation of server instances with a consequent dramatic increase in the total memory footprint and more complex system administration. The Multi‐tasking Virtual Machine (MVM) solves this problem by providing an efficient and scalable implementation of the isolate API for multiple, isolated tasks, enabling the co‐location of multiple server instances in a single MVM process. Isolates also enable the restructuring of a J2EE server implementation as a collection of isolated components, offering increased flexibility and reliability. The resulting system is a step towards a complete and scalable operating environment for enterprise applications. Copyright © 2006 John Wiley & Sons, Ltd.     

A Tool for Prioritizing DAGMan Jobs and its Evaluation

It is often difficult to perform efficiently a collection of jobs with complex job dependencies due to temporal unpredictability of the Grid. One way to mitigate the unpredictability is to schedule job execution in a manner that constantly maximizes the number of jobs that can be sent to workers. A recently developed scheduling theory provides a basis to meet that optimization goal. Intuitively, when the number of such jobs is always large, high parallelism can be maintained, even if the number of workers changes over time in an unpredictable manner. In this paper we present the design, implementation, and evaluation of a practical scheduling tool inspired by the theory. Given a DAGMan input file with interdependent jobs, the tool prioritizes the jobs. The resulting schedule significantly outperforms currently used schedules under a wide range of system parameters, as shown by simulation studies. For example, a scientific data analysis application, AIRSN, was executed at least 13% faster with 95% confidence. An implementation of the tool was integrated with the Condor high-throughput computing system. The research of G. Malewicz was supported in part by NSF Grant ITR-800864. The research of I. Foster and M. Wilde was supported in part by the NSF GriPhyN project and by the Mathematical, Information, and Computational Sciences Division subprogram of the Office of Advanced Scientific Computing Research, U.S. Department of Energy, under Contract W-31-109-Eng-38. The research of A.L. Rosenberg was supported in part by NSF Grant CCF-0342417.