Shock persistence in a dual economy model of India

This article examines shock persistence in agricultural and industrial output in India. Drawing on the dual economy literature, the linkages between the sectors through the terms of trade are emphasised. However different dual economy models make differing assumptions regarding the categorisation of variables as being either endogenous or exogenous and this distinction is crucial in explaining the pattern of shock persistence. Using annual data for 1955-95, our results show that shocks to both output series are permanent while those to the terms of trade are transient.

The Origins of Lactase Persistence in Europe

Lactase persistence (LP) is common among people of European ancestry, but with the exception of some African, Middle Eastern and southern Asian groups, is rare or absent elsewhere in the world. Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans (-13,910 C/T) indicates that the derived allele is recent in origin and has been subject to strong positive selection. Furthermore, ancient DNA work has shown that the -13,910*T (derived) allele was very rare or absent in early Neolithic central Europeans. It is unlikely that LP would provide a selective advantage without a supply of fresh milk, and this has lead to a gene-culture coevolutionary model where lactase persistence is only favoured in cultures practicing dairying, and dairying is more favoured in lactase persistent populations. We have developed a flexible demic computer simulation model to explore the spread of lactase persistence, dairying, other subsistence practices and unlinked genetic markers in Europe and western Asia's geographic space. Using data on -13,910*T allele frequency and farming arrival dates across Europe, and approximate Bayesian computation to estimate parameters of interest, we infer that the -13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly in association with the dissemination of the Neolithic Linearbandkeramik culture over Central Europe. Furthermore, our results suggest that natural selection favouring a lactase persistence allele was not higher in northern latitudes through an increased requirement for dietary vitamin D. Our results provide a coherent and spatially explicit picture of the coevolution of lactase persistence and dairying in Europe.

Legumes regulate Rhizobium bacteroid development and persistence by the supply of branched-chain amino acids

One of the largest contributions to biologically available nitrogen comes from the reduction of N-2 to ammonia by rhizobia in symbiosis with legumes. Plants supply dicarboxylic acids as a carbon source to bacteroids, and in return they receive ammonia. However, metabolic exchange must be more complex, because effective N-2 fixation by Rhizobium leguminosarum bv viciae bacteroids requires either one of two broad-specificity amino acid ABC transporters (Aap and Bra). It was proposed that amino acids cycle between plant and bacteroids, but the model was unconstrained because of the broad solute specificity of Aap and Bra. Here, we constrain the specificity of Bra and ectopically express heterologous transporters to demonstrate that branched-chain amino acid (LIV) transport is essential for effective N-2 fixation. This dependence of bacteroids on the plant for LIV is not due to their known down-regulation of glutamate synthesis, because ectopic expression of glutamate dehydrogenase did not rescue effective N-2 fixation. Instead, the effect is specific to LIV and is accompanied by a major reduction in transcription and activity of LIV biosynthetic enzymes. Bacteroids become symbiotic auxotrophs for LIV and depend on the plant for their supply. Bacteroids with aap bra null mutations are reduced in number, smaller, and have a lower DNA content than wild type. Plants control LIV supply to bacteroids, regulating their development and persistence. This makes it a critical control point for regulation of symbiosis. MICROBIOLOGY

API-CALC 1.0: a computer program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives

Individual identification via DNA profiling is important in molecular ecology, particularly in the case of noninvasive sampling. A key quantity in determining the number of loci required is the probability of identity (PIave), the probability of observing two copies of any profile in the population. Previously this has been calculated assuming no inbreeding or population structure. Here we introduce formulae that account for these factors, whilst also accounting for relatedness structure in the population. These formulae are implemented in API-CALC 1.0, which calculates PIave for either a specified value, or a range of values, for F-IS and F-ST.

The roles of persistence and perseveration in psychopathology

Two constructs were hypothesized to be of importance in psychological disorders: persistence (the ability to keep going to reach a goal, even when the task is difficult or drawn out) and perseveration (the tendency to continue a behavior, even when it ceases to be effective or rewarding). These are contrasted with perfectionism (having high standards for oneself or others). A measure was developed to address these constructs (the Persistence, Perseveration and Perfectionism Questionnaire; PPPQ). The PPPQ was administered to 325 nonclinical participants, alongside a measure of psychological disturbance. Factor analysis resulted in a 22-item version of the measure, consisting of subscales with good psychometric properties corresponding to the 3 theoretical constructs. Persistence was associated with lower levels of psychopathology, whereas perseveration was associated with higher levels of psychopathology. Perfectionism was weakly associated with psychopathology. Further work is needed to develop these constructs with clinical groups, but the findings support the hypothesis that persistence is an adaptive construct whereas perseveration is maladaptive.

Parallel and distributed computing with Java

The Java language first came to public attention in 1995. Within a year, it was being speculated that Java may be a good language for parallel and distributed computing. Its core features, including being objected oriented and platform independence, as well as having built-in network support and threads, has encouraged this view. Today, Java is being used in almost every type of computer-based system, ranging from sensor networks to high performance computing platforms, and from enterprise applications through to complex research-based.simulations. In this paper the key features that make Java a good language for parallel and distributed computing are first discussed. Two Java-based middleware systems, namely MPJ Express, an MPI-like Java messaging system, and Tycho, a wide-area asynchronous messaging framework with an integrated virtual registry are then discussed. The paper concludes by highlighting the advantages of using Java as middleware to support distributed applications.

MPJ express meets gadget: towards a java code for cosmological simulations

Gadget-2 is a massively parallel structure formation code for cosmological simulations. In this paper, we present a Java version of Gadget-2. We evaluated the performance of the Java version by running colliding galaxies simulation and found that it can achieve around 70% of C Gadget-2's performance.

A buffering layer to support derived types and proprietary networks for Java HPC

MPJ Express is our implementation of MPI-like bindings for Java. In this paper we discuss our intermediate buffering layer that makes use of the so-called direct byte buffers introduced in the Java New I/O package. The purpose of this layer is to support the implementation of derived datatypes. MPJ Express is the first Java messaging library that implements this feature using pure Java. In addition, this buffering layer allows efficient implementation of communication devices based on proprietary networks such as Myrinet. In this paper we evaluate the performance of our buffering layer and demonstrate the usefulness of direct byte buffers. Also, we evaluate the performance of MPJ Express against other messaging systems using Myrinet and show that our buffering layer has made it possible to avoid the overheads suffered by other Java systems such as mpiJava that relies on the Java Native Interface.

A buffering layer to support derived types and proprietary networks for Java HPC

MPJ Express is our implementation of MPI-like bindings for Java. In this paper we discuss our intermediate buffering layer that makes use of the so-called direct byte buffers introduced in the Java New I/O package. The purpose of this layer is to support the implementation of derived datatypes. MPJ Express is the first Java messaging library that implements this feature using pure Java. In addition, this buffering layer allows efficient implementation of communication devices based on proprietary networks such as Myrinet. In this paper we evaluate the performance of our buffering layer and demonstrate the usefulness of direct byte buffers. Also, we evaluate the performance of MPJ Express against other messaging systems using Myrinet and show that our buffering layer has made it possible to avoid the overheads suffered by other Java systems such as mpiJava that relies on the Java Native Interface.

Nested parallelism for multi-core HPC systems using Java

Since its introduction in 1993, the Message Passing Interface (MPI) has become a de facto standard for writing High Performance Computing (HPC) applications on clusters and Massively Parallel Processors (MPPs). The recent emergence of multi-core processor systems presents a new challenge for established parallel programming paradigms, including those based on MPI. This paper presents a new Java messaging system called MPJ Express. Using this system, we exploit multiple levels of parallelism - messaging and threading - to improve application performance on multi-core processors. We refer to our approach as nested parallelism. This MPI-like Java library can support nested parallelism by using Java or Java OpenMP (JOMP) threads within an MPJ Express process. Practicality of this approach is assessed by porting to Java a massively parallel structure formation code from Cosmology called Gadget-2. We introduce nested parallelism in the Java version of the simulation code and report good speed-ups. To the best of our knowledge it is the first time this kind of hybrid parallelism is demonstrated in a high performance Java application. (C) 2009 Elsevier Inc. All rights reserved.

A comparative study of Java and C performance in two large-scale parallel applications

In the 1990s the Message Passing Interface Forum defined MPI bindings for Fortran, C, and C++. With the success of MPI these relatively conservative languages have continued to dominate in the parallel computing community. There are compelling arguments in favour of more modern languages like Java. These include portability, better runtime error checking, modularity, and multi-threading. But these arguments have not converted many HPC programmers, perhaps due to the scarcity of full-scale scientific Java codes, and the lack of evidence for performance competitive with C or Fortran. This paper tries to redress this situation by porting two scientific applications to Java. Both of these applications are parallelized using our thread-safe Java messaging system—MPJ Express. The first application is the Gadget-2 code, which is a massively parallel structure formation code for cosmological simulations. The second application uses the finite-domain time-difference method for simulations in the area of computational electromagnetics. We evaluate and compare the performance of the Java and C versions of these two scientific applications, and demonstrate that the Java codes can achieve performance comparable with legacy applications written in conventional HPC languages. Copyright © 2009 John Wiley & Sons, Ltd.

Experimental comparison of the comprehensibility of a Z specification and its implementation in Java

Comprehensibility is often raised as a problem with formal notations, yet formal methods practitioners dispute this. In a survey, one interviewee said 'formal specifications are no more difficult to understand than code'. Measurement of comprehension is necessarily comparative and a useful comparison for a specification is against its implementation. Practitioners have an intuitive feel for the comprehension of code. A quantified comparison will transfer this feeling to formal specifications. We performed an experiment to compare the comprehension of a Z specification with that of its implementation in Java. The results indicate there is little difference in comprehensibility between the two. (C) 2004 Elsevier B.V. All rights reserved.

Resource availability and the persistence of seed-eating bird populations in agricultural landscapes – a mechanistic modelling approach

1. Reductions in resource availability, associated with land-use change and agricultural intensification in the UK and Europe, have been linked with the widespread decline of many farmland bird species over recent decades. However, the underlying ecological processes which link resource availability and population trends are poorly understood. 2. We construct a spatial depletion model to investigate the relationship between the population persistence of granivorous birds within the agricultural landscape and the temporal dynamics of stubble field availability, an important source of winter food for many of those species. 3. The model is capable of accurately predicting the distribution of a given number of finches and buntings amongst patches of different stubble types in an agricultural landscape over the course of a winter and assessing the relative value of different landscapes in terms of resource availability. 4. Sensitivity analyses showed that the model is relatively robust to estimates of energetic requirements, search efficiency and handling time but that daily seed survival estimates have a strong influence on model fit. Understanding resource dynamics in agricultural landscapes is highlighted as a key area for further research. 5. There was a positive relationship between the predicted number of bird days supported by a landscape over-winter and the breeding population trend for yellowhammer Emberiza citrinella, a species for which survival has been identified as the primary driver of population dynamics, but not for linnet Carduelis cannabina, a species for which productivity has been identified as the primary driver of population dynamics. 6. Synthesis and applications. We believe this model can be used to guide the effective delivery of over-winter food resources under agri-environment schemes and to assess the impacts on granivorous birds of changing resource availability associated with novel changes in land use. This could be very important in the future as farming adapts to an increasingly dynamic trading environment, in which demands for increased agricultural production must be reconciled with objectives for environmental protection, including biodiversity conservation.