bluuebunny/crossref_metadata_2025 huggingface dataset:
Symmetries and multiferroic properties of novel room-temperature magnetoelectrics: Lead iron tantalate – lead zirconate titanate (PFT/PZT)
Authors: Sanchez Dilsom A. , Ortega N. , Kumar Ashok , Roque-Malherbe R. , Polanco R. , Scott J. F. , Katiyar Ram S.
Published: December 2011

Mixing 60-70% lead zirconate titanate with 40-30% lead iron tantalate produces a single-phase, low-loss, room-temperature multiferroic with magnetoelectric coupling: (PbZr0.53Ti0.47O3) (1-x)- (PbFe0.5Ta0.5O3)x. The present study combines x-ray scattering, magnetic and polarization hysteresis in both phases, plus a second-order dielectric divergence (to epsilon = 6000 at 475 K for 0.4 PFT; to 4000 at 520 K for 0.3 PFT) for an unambiguous assignment as a C2v-C4v (Pmm2-P4mm) transition. The material exhibits square saturated magnetic hysteresis loops with 0.1 emu/g at 295 K and saturation polarization Pr = 25 μC/cm2, which actually increases (to 40 μC/cm2) in the high-T tetragonal phase, representing an exciting new room temperature oxide multiferroic to compete with BiFeO3. Additional transitions at high temperatures (cubic at T>1300 K) and low temperatures (rhombohedral or monoclinic at T<250 K) are found. These are the lowest-loss room-temperature multiferroics known, which is a great advantage for magnetoelectric devices.
Variation for kernel number and related traits in triticale (x Triticosecale Wittmack)
Authors: Motzo Rosella , Bassu Simona , Giunta Francesco
Published: December 2011

Assessing the existence and extent of genetic variation in kernel number per m2 (KNO) and in KNO-related traits is necessary both for overcoming sink limitations through breeding and in order to correctly model triticale grain yield. A set of 112 advanced breeding lines derived from various crosses between winter and spring hexaploid triticales was grown for 2 years in a field experiment to evaluate genetic variation and heritability for KNO, chaff weight per m2 at maturity (CHAFFW) and number of kernels per unit weight of chaff (K/CHAFF). Genetic correlations were also calculated between these traits and grain weight and yield. K/CHAFF (but not CHAFFW) exhibited a high level of genetic variation and a low contribution of the genotype by environment interaction component to the overall variance and was highly heritable. There was no detectable genetic correlation between K/CHAFF and CHAFFW; however, K/CHAFF was correlated with KNO (r = 0.66, P < 0.001). K/CHAFF fulfils the major requirements of an indirect screening trait for KNO and of a genetic coefficient in modelling.
Contribution of DNA-typing to bushmeat surveys: assessment of a roadside market in south-western Nigeria
Authors: Olayemi Ayodeji , Oyeyiola Akinlabi , Antunes Agostinho , Bonillo Céline , Cruaud Corinne , Gaubert Philippe
Published: December 2011

Context Following recent socioeconomic transformations in western and central Africa, the volume of bushmeat hunting, a traditional source of proteins and revenue for rural populations, has reached unsustainable levels. The morphological identification of species sold on bushmeat market stalls may be challenging because of the presence of cryptic taxa and smoked or processed carcasses. Aims To assess the contribution of DNA-typing to traditional bushmeat surveys. We conducted a case study at a roadside bushmeat market in Asejire, south-western Nigeria, to characterise the mammalian diversity and sketch out the dynamics of the bushmeat trade. Methods We generated a 402-bp Cytochrome b fragment using a ‘universal’ mitochondrial primer pair that successfully amplified across five mammalian orders, and used assignment procedures to assess the taxonomic identification of the traded species. We combined DNA-typing with morphological-based market surveys and questionnaires to half (n = 20) of the market stakeholders. Key results Our combined morphological–DNA-based survey revealed a total of 17 species, representing seven mammalian orders (Rodentia, Lagomorpha, Primates, Hyracoidea, Carnivora, Pholidota and Artiodactyla). DNA-typing allowed identifying the Walter’s duiker, a cryptic, newly described species from the Dahomey Gap, and diagnosing an unidentified primate as the white-throated monkey, Cercopithecus erythrogaster, a species of high conservation concern in Nigeria. K2P pairwise genetic distances among all species exceeded the 11% threshold, indicative of species-level distinction. The most hunted species were the Walter’s duiker and, to a lesser extent, the greater cane rat, Thryonomys swinderianus. Questionnaires to traders revealed that the Asejire roadside market was a straightforward trader–hunter system centralising off-takes from distant hunting sites. Conclusions We showed how mitochondrial DNA-typing combined with assignment procedures improved the characterisation of the mammalian diversity sold on bushmeat markets. The hunted mammalian community consisted of versatile, small- to medium-sized secondary forest species characteristic of the Dahomey Gap assemblage; their sustainable management is in doubt because of the lack of conservation and health awareness within the traders’ community. Implications Given the utility of mitochondrial DNA-typing in identifying species sold in bushmeat markets, we argue in favour of multi-entry investigations to reach a comprehensive characterisation of the bushmeat trade. The building of a web-accessible mtDNA database covering the spectrum of the species hunted for bushmeat would appear to be a valuable diagnostic tool that may help Nigeria and neighbouring countries to set up a rigorous monitoring of wildlife extirpation.
Prédicats et verbes supports d’occurrence météorologiques dans une perspective contrastive franco-polonaise
Authors: Kaliska Agnieszka K.
Published: December 2011

The common co-occurrence of words in a given context reflects both the extra-linguistic knowledge of a language user, and the specific intra-linguistic rules. We can say that lexicon and grammar are interpreters of the extra-linguistic reality. The purpose of our research is to consider, in French-Polish constrastive perspective, the relation between the pronoun and the meteorological verb (such as il and venter in Il vente) on the one hand and, on the other, the relation between the meteorological noun and the special kind of support verb named verbe d’occurrence on the Lexicon-Grammar ground (such as vent and mugir in Le vent mugit). We then raise the question of the particular status of meteorological nouns in the grammatical subject position and explain the non-predicative character of verbs in constructions such as Le vent mugit. In the end, we present a list of Polish and French examples containing meteorological support verbs or their stylistic and aspectual variants.
Noms prédicatifs, noms de résultat et noms concrets dans les constructions à verbe support
Authors: Radimský Jan
Published: December 2011

The paper aims to show that light verb constructions (LVC) are formed not only with predicative nouns, but also frequently with result nouns and some concrete nouns. We propose a quantitative verification of the hypothesis that in Czech, result nouns are at least as frequent in LVC as event nominalisations (“verbální substantiva”). The paper tries to explain reasons of this phenomenon and it shows the mechanism that allows concrete nouns to appear in LVC, not only in Czech, but also in French.
On a Class of Italian Frozen Sentences
Authors: Vietri Simonetta
Published: December 2011

This article describes the class of Italian frozen sentences that are defined by the relation N0 V (1C di N) = N0 V C1 a N2. These sentences are represented in a matrix table named CAN where each entry has ben analysed on the basis of distributional and transformational properties. This study has taken into account the complex net of relations among frozen sentences, sentences with support verbs, predicative nouns, compound words. The analysis of the class CAN has also shown the regularity of the syntactic behaviour of frozen sentences.
Seasonally Dynamic Diel Vertical Migrations of Mysis diluviana, Coregonine Fishes, and Siscowet Lake Trout in the Pelagia of Western Lake Superior
Authors: Ahrenstorff Tyler D. , Hrabik Thomas R. , Stockwell Jason D. , Yule Daniel L. , Sass Greg G.
Published: December 2011

Diel vertical migrations are common among many aquatic species and are often associated with changing light levels. The underlying mechanisms are generally attributed to optimizing foraging efficiency or growth rates and avoiding predation risk (μ). The objectives of this study were to (1) assess seasonal and interannual changes in vertical migration patterns of three trophic levels in the Lake Superior pelagic food web and (2) examine the mechanisms underlying the observed variability by using models of foraging, growth, and μ. Our results suggest that the opossum shrimp Mysis diluviana, kiyi Coregonus kiyi, and siscowet lake trout Salvelinus namaycush migrate concurrently during each season, but spring migrations are less extensive than summer and fall migrations. In comparison with M. diluviana, kiyis, and siscowets, the migrations by ciscoes C. artedi were not as deep in the water column during the day, regardless of season. Foraging potential and μ probably drive the movement patterns of M. diluviana, while our modeling results indicate that movements by kiyis and ciscoes are related to foraging opportunity and growth potential and receive a lesser influence from μ. The siscowet is an abundant apex predator in the pelagia of Lake Superior and probably undertakes vertical migrations in the water column to optimize foraging efficiency and growth. The concurrent vertical movement patterns of most species are likely to facilitate nutrient transport in this exceedingly oligotrophic ecosystem, and they demonstrate strong linkages between predators and prey. Fishery management strategies should use an ecosystem approach and should consider how altering the densities of long‐lived top predators produces cascading effects on the nutrient cycling and energy flow in lower trophic levels.
Effect of Predators on Growth and Reproductive Investment in Bluegills: Comparison of Populations with Differing Size and Age of Maturation
Authors: Oplinger Randall W. , Wahl David H. , Nannini Michael A.
Published: December 2011

Growth rate and age of maturation are two important factors that control adult body size. Predators can also exert an influence on the size and age of maturation of their prey. We compared the growth, timing of maturation, and investment in gonad development of bluegills Lepomis macrochirus in ponds with and without largemouth bass Micropterus salmoides predators. In addition, we compared the response between bluegills from stunted (small size and early age of maturation) and nonstunted (larger size and later age of maturation) populations to determine whether predation could explain the occurrence of stunted body size in bluegills. For both males and females, we found that bluegills grew faster but matured at the same rate in the presence of predators. The investment in gonad development (measured by the gonadosomatic index) did not differ between individuals raised with predators and those raised without. Regardless of predator treatment, fish from the nonstunted population grew more than those from the stunted population and invested less energy in gonad development. The interaction between population source and predator presence was not significant, suggesting that the observed predator responses did not differ between bluegills from the stunted and nonstunted populations. These results support the hypothesis that predators have a strong influence on the life history of the bluegill. Bluegills grew more in the presence of predators, but this did not result in a corresponding reduction in the investment in reproduction.
Thoughts on the Manchester Manifesto
Authors: Church George
Published: December 2011

George Church is a professor at Harvard University and founder of the personal genome project. He has patents in the fields of genome reading and writing, automation and instrumentation, and advocates open source and transparency; for example, by developing the open access next generation sequencing platform (Polonator.org) and the open access human genome plus trait dataset (PersonalGenomes.org).
Patents, practical ethics and scientists
Authors: Drahos Peter
Published: December 2011

Peter Drahos is a Professor in the Regulatory Institutions Network, College of Asia Pacific, Australian National University and holds a Chair in Intellectual Property in the Centre for Commercial Law Studies, Queen Mary, London University.
Effects of short‐term lifestyle activity modification on adiponectin mRNA expression and plasma concentrations
Authors: Moghadasi Mehrzad , Mohebbi Hamid , Rahmani‐Nia Farhad , Hassan‐Nia Sadegh , Noroozi Hamid
Published: December 2011

Adiponectin mRNA and plasma concentrations were reduced in obesity. Exercise training may reduce the adipose tissue (AT), although it is not well known, whether exercise – induced change in AT, increases adiponectin mRNA expression and plasma concentrations or not. Therefore, the purpose of this study was to examine the effects of short‐term lifestyle activity modification (LAM) on adiponectin mRNA and plasma concentrations. Sixteen obese and overweight middle‐aged men (age, 35–50 years) with type 2 diabetes participated in this study. The subjects were randomly assigned to LAM group (n=8) or control group (n=8). The subjects in LAM group walked two miles in 30 min on a treadmill on 4 days per week for 12 weeks according to the guidelines of the Centers for Disease Control and Prevention and American College of Sports Medicine. The results showed that body mass, body mass index, central visceral adipose tissue and subcutaneous adipose tissue volume and hip and thigh subcutaneous adipose tissue (hip and thigh SAT) volume were decreased in the LAM group compared to the control group (P<0.05). Adiponectin mRNA in abdominal and gluteal subcutaneous AT were increased significantly in the LAM group compared to the control group (P<0.05), while plasma adiponectin concentrations, hs‐CRP and insulin resistance did not change significantly. In conclusion, adiponectin mRNA levels increase after 12 weeks of LAM; however, plasma adiponectin levels were not affected by this protocol in obese and overweight middle‐aged men with type 2 diabetes.
Motor performance and bodyweight of children and adolescents in Saarland – Status quo
Authors: Klein Markus , Fröhlich Michael , Emrich Eike
Published: December 2011

The motor performance of children and adolescents has been a subject of controversial discussion. As part of a pilot project, 839 schoolchildren from 14 different schools in Saarland were studied and their height, weight and sport motor performance were measured using the German motor performance test DMT 6‐18. The results show a slight increase in the number of overweight children compared to reference samples. However, these discrepancies are minor and cannot be judged to be practically relevant because of the weakness of the effects. The average motor test performances of the Saarland schoolchildren were above the average performance of the reference samples in almost all individual performances. There are also hardly any weaker performances in comparison to older studies. The current results for motor performance of Saarland children and adolescents do not, therefore, give any great reason for concern. Further evaluation steps will be needed to clarify the influences that might be associated with adverse characteristics for motor performance (socio‐economic status, living situation, leisure behaviour, school performance, etc.).
Response timing in the lunge and target change in elite versus medium‐level fencers
Authors: Gutierrez‐Davila Marcos , Rojas Francisco J. , Antonio Raquel , Navarro Enrique
Published: December 2011

The aim of the present work is to examine the differences between two groups of fencers with different levels of competition, elite and medium level. The timing parameters of the response reaction have been compared together with the kinetic variables which determine the sequence of segmented participation used during the lunge with a change in target during movement. A total of 30 male sword fencers participated, 13 elite and 17 medium level. Two force platforms recorded the horizontal component of the force and the start of the movement. One system filmed the movement in 3D, recording the spatial positions of 11 markers, while another system projected a mobile target over a screen. For synchronisation, an electronic signal enabled all the systems to be started simultaneously. Among the timing parameters of the reaction response, the choice reaction time (CRT) to the target change during the lunge was measured. The results revealed differences between the groups regarding the flight time, horizontal velocity at the end of the acceleration phase, and the length of the lunge, these being higher for the elite group, as well as other variables related to the temporal sequence of movement. No significant differences have been found in the simple reaction time or in CRT. According to the literature, the CRT appears to improve with sports practice, although this factor did not differentiate the elite from medium‐level fencers. The coordination of fencing movements, that is, the right technique, constitutes a factor that differentiates elite fencers from medium‐level ones.
Effect of skill level on cardiorespiratory and metabolic responses during Tai Chi training
Authors: Xiong Kai‐Yu , He Hui , Ni Guo‐Xin
Published: December 2011

Nowadays, Tai chi chuan (TCC) is practiced by millions worldwide with a range of skill levels. However, the effect of skill level on physiological response to TCC performance has yet to be clarified. In this study, physiological parameters during practicing simplified 24‐form TCC were investigated and compared in 10 young high‐level (HL) male TCC athletes and 10 ordinary‐level (OL) male TCC practitioners with similar age and body size. Significantly higher energy expenditure, heart rate, oxygen uptake and tidal volume were found in HL group than OL group during TCC performance. The respiratory frequency and exhalation time were similar between the two groups during practicing TC; however, significantly less inhalation time was found in HL group (1.02±0.2 s) than OL group (1.12±0.28 s). Our results suggested that skill level may have considerable impact on metabolic and cardiorespiratory responses to TCC performance. TCC practitioners with different skill levels may practice TCC in different ways, which was supposed to lead to distinguishable response between the two groups.
Differences in energy expenditure between high‐ and low‐volume training
Authors: Drenowatz Clemens , Eisenmann Joey C. , Pivarnik James M. , Pfeiffer Karin A. , Carlson Joseph J.
Published: December 2011

Several studies have examined energy expenditure in various sports but there is a lack of research on the contribution of exercise and habitual activity during different training periods. This study examined changes in total daily energy expenditure (TDEE) and its components during high‐ and low‐volume training periods. Further, changes in time spent in sedentary, light, moderate and vigorous activity in response to different training volumes were explored. Energy expenditure was measured in 15 male endurance athletes during 2 non‐consecutive weeks – 1 week of high volume (>13 hours) training and another week of low volume (<7 hours) training. The SenseWear Pro 3 Armband, individual heart‐rate‐oxygen consumption regression and indirect calorimetry was used to measure non‐exercise activity thermogensis (NEAT), exercise energy expenditure (EEE) and resting metabolic rate, respectively. Time spent at different intensities was assessed using previously established MET cutpoints. TDEE as well as EEE increased significantly with higher training volume, while no difference in NEAT occurred. Further, significantly less time was spent in sedentary activities during the high‐volume week. These results suggest that highly trained athletes do not compensate for increased training volume and reduce sedentary activities to allow for more training time.
Acute caffeine ingestion enhances strength performance and reduces perceived exertion and muscle pain perception during resistance exercise
Authors: Duncan Michael J. , Stanley Michelle , Parkhouse Natalie , Cook Kathryn , Smith Mike
Published: December 2011

The efficacy of caffeine ingestion in enhancing aerobic performance is well established. However, despite suggestions that caffeine may enhance resistance exercise performance, research is equivocal on the effect of acute caffeine ingestion on resistance exercise performance. It has also been suggested that dampened perception of perceived exertion and pain perception might be an explanation for any possible enhancement of resistance exercise performance due to caffeine ingestion. Therefore, the aim of this study was to examine the acute effect of caffeine ingestion on repetitions to failure, rating of perceived exertion (RPE) and muscle pain perception during resistance exercise to failure. Eleven resistance trained individuals (9 males, 2 females, mean age±SD=26.4±6.4 years), took part in this double‐blind, randomised cross‐over experimental study whereby they ingested a caffeinated (5 mg kg−1) or placebo solution 60 minutes before completing a bout of resistance exercise. Experimental conditions were separated by at least 48 hours. Resistance exercise sessions consisted of bench press, deadlift, prone row and back squat exercise to failure at an intensity of 60% 1 repetition maximum. Results indicated that participants completed significantly greater repetitions to failure, irrespective of exercise, in the presence of caffeine (p=0.0001). Mean±S.D of repetitions to failure was 19.6±3.7 and 18.5±4.1 in caffeine and placebo conditions, respectively. There were no differences in peak heart rate or peak blood lactate values across conditions (both p >0.05). RPE was significantly lower in the caffeine compared to the placebo condition (p=0.03) and was significantly higher during lower body exercises compared to upper body exercises irrespective of substance ingested (p=0.0001). For muscle pain perception, a significant condition by exercise interaction (p=0.027) revealed that muscle pain perception was lower in the caffeine condition, irrespective of exercise. With caffeine, pain perception was significantly higher in the deadlift and back squat compared to the bench press. However, with placebo, pain perception was significantly higher for the deadlift and back squat compared to the prone row only. Therefore, acute caffeine ingestion not only enhances resistance exercise performance to failure but also reduces perception of exertion and muscle pain.
There goes the neighbourhood: Contextual control over the breadth of lexical activation when reading aloud
Authors: Reynolds Michael G. , Besner Derek
Published: December 2011

There are currently two computational accounts of how the time to read pseudohomophones (like BRANE) and their nonword controls (like FRANE) varies with changes in context. In Reynolds and Besner's (2005) account, readers vary the breadth of lexical activation in response to changes in context. A competing account proposed by Kwantes and Marmurek (2007) and independently by Perry, Ziegler, and Zorzi (2007) has readers varying their response criterion in response to changes in context. The present work adjudicates between these two accounts by examining how the effect of neighbourhood density changes as a function of list context when reading pseudohomophones aloud. The results of an experiment and simulations from a leading computational model support the lexical breadth account, but are inconsistent with the response criterion account.
The Interruptive Effect of Pain on Attention
Authors: Moore David J. , Keogh Edmund , Eccleston Christopher
Published: December 2011

Pain is known to disrupt attentional performance in both healthy adults and patients with chronic pain. Exactly which aspects of attentional function are affected are, however, still to be determined. The primary aim of this investigation was to systematically examine the effects of experimentally induced pain on a range of attentional performance tasks. Following a review of tests of attentional disruption, seven best candidate tasks were selected and examined across seven experiments. The tasks were: continuous performance, flanker, endogenous precueing, n-back, inhibition, attentional switching, and divided attention. Healthy adult participants performed each of these tasks under three different conditions: a painful heat sensation, a warm heat sensation, and a nonheat control. Pain differentially affected attentional performance across these tasks; pain-related attentional impairment was found on the n-back, attentional switching, and divided attention tasks, but not on the other tasks. This finding suggests that the aspects of attention most affected by pain are those essential for the completion of complex tasks that require the processing of multiple cues and control over attentional deployment. These results are discussed in the context of an emerging view of pain as a demand for executive control and the development of measures that could be used to examine attentional disruption in the context of pain.
Individual variation and population dynamics: lessons from a simple system
Authors: Benton T. G.
Published: December 2011

The mapping of environment, through variation in individuals' life histories, to dynamics can be complex and often poorly known. Consequently, it is not clear how important it is dynamically. To explore this, I incorporated lessons from an empirical system, a soil mite, into an individual-based model. Individuals compete for resource and allocate this according to eight ‘genetic’ rules that specify investment in growth or reserves (which influences survival or fecundity), size at maturation and reproductive allocation. Density dependence, therefore, emerges from competition for food, limiting individual's growth and fecundity. We use this model to examine the role that genetic and phenotypically plastic variation plays in dynamics, by fixing phenotypes, by allowing phenotypes to vary plastically and by creating genetic variation between individuals. Variation, and how it arises, influences short- and long-run dynamics in a way comparable in magnitude with halving food supply. In particular, by switching variation on and off, it is possible to identify a range of processes necessary to capture the dynamics of the ‘full model’. Exercises like this can help identify key processes and parameters, but a concerted effort is needed across many different systems to search for shared understanding of both process and modelling.
Modelling ecological systems in a changing world
Authors: Evans Matthew R.
Published: December 2011

The world is changing at an unprecedented rate. In such a situation, we need to understand the nature of the change and to make predictions about the way in which it might affect systems of interest; often we may also wish to understand what might be done to mitigate the predicted effects. In ecology, we usually make such predictions (or forecasts) by making use of mathematical models that describe the system and projecting them into the future, under changed conditions. Approaches emphasizing the desirability of simple models with analytical tractability and those that use assumed causal relationships derived statistically from data currently dominate ecological modelling. Although such models are excellent at describing the way in which a system has behaved, they are poor at predicting its future state, especially in novel conditions. In order to address questions about the impact of environmental change, and to understand what, if any, action might be taken to ameliorate it, ecologists need to develop the ability to project models into novel, future conditions. This will require the development of models based on understanding the processes that result in a system behaving the way it does, rather than relying on a description of the system, as a whole, remaining valid indefinitely.
Biodiversity in the context of ecosystem services: the applied need for systems approaches
Authors: Norris Ken
Published: December 2011

Recent evidence strongly suggests that biodiversity loss and ecosystem degradation continue. How might a systems approach to ecology help us better understand and address these issues? Systems approaches play a very limited role in the science that underpins traditional biodiversity conservation, but could provide important insights into mechanisms that affect population growth. This potential is illustrated using data from a critically endangered bird population. Although species-specific insights have practical value, the main applied challenge for a systems approach is to help improve our understanding of the role of biodiversity in the context of ecosystem services (ES) and the associated values and benefits people derive from these services. This has profound implications for the way we conceptualize and address ecological problems. Instead of focusing directly on biodiversity, the important response variables become measures of values and benefits, ES or ecosystem processes. We then need to understand the sensitivity of these variables to biodiversity change relative to other abiotic or anthropogenic factors, which includes exploring the role of variability at different levels of biological organization. These issues are discussed using the recent UK National Ecosystems Assessment as a framework.
Positive feedback and alternative stable states in inbreeding, cooperation, sex roles and other evolutionary processes
Authors: Lehtonen Jussi , Kokko Hanna
Published: December 2011

A large proportion of studies in systems science focus on processes involving a mixture of positive and negative feedbacks, which are also common themes in evolutionary ecology. Examples of negative feedback are density dependence (population regulation) and frequency-dependent selection (polymorphisms). Positive feedback, in turn, plays a role in Fisherian ‘runaway’ sexual selection, the evolution of cooperation, selfing and inbreeding tolerance under purging of deleterious alleles, and the evolution of sex differences in parental care. All these examples feature self-reinforcing processes where the increase in the value of a trait selects for further increases, sometimes via a coevolutionary feedback loop with another trait. Positive feedback often leads to alternative stable states (evolutionary endpoints), making the interpretation of evolutionary predictions challenging. Here, we discuss conceptual issues such as the relationship between self-reinforcing selection and disruptive selection. We also present an extension of a previous model on parental care, focusing on the relationship between the operational sex ratio and sexual selection, and the influence of this relationship on the evolution of biparental or uniparental care.
Bioinformatics tools in predictive ecology: applications to fisheries
Authors: Tucker Allan , Duplisea Daniel
Published: December 2011

There has been a huge effort in the advancement of analytical techniques for molecular biological data over the past decade. This has led to many novel algorithms that are specialized to deal with data associated with biological phenomena, such as gene expression and protein interactions. In contrast, ecological data analysis has remained focused to some degree on off-the-shelf statistical techniques though this is starting to change with the adoption of state-of-the-art methods, where few assumptions can be made about the data and a more explorative approach is required, for example, through the use of Bayesian networks. In this paper, some novel bioinformatics tools for microarray data are discussed along with their ‘crossover potential’ with an application to fisheries data. In particular, a focus is made on the development of models that identify functionally equivalent species in different fish communities with the aim of predicting functional collapse.
The philosophy of modelling or does the philosophy of biology have
any
use?
Authors: Orzack Steven Hecht
Published: December 2011

Biologists in search of answers to real-world issues such as the ecological consequences of global warming, the design of species' conservation plans, understanding landscape dynamics and understanding gene expression make decisions constantly that are based on a ‘philosophical’ stance as to how to create and test explanations of an observed phenomenon. For better or for worse, some kind of philosophy is an integral part of the doing of biology. Given this, it is more important than ever to undertake a practical assessment of what philosophy does mean and should mean to biologists. Here, I address three questions: should biologists pay any attention to ‘philosophy’; should biologists pay any attention to ‘philosophy of biology’; and should biologists pay any attention to the philosophy of biology literature on modelling? I describe why the last question is easily answered affirmatively, with the proviso that the practical benefits to be gained by biologists from this literature will be directly proportional to the extent to which biologists understand ‘philosophy’ to be a part of biology, not apart from biology.
Hydrogen-bonded assembly in six closely related pyrazolo[3,4-b]pyridine derivatives; a simple chain, three types of chains of rings and a complex sheet structure
Authors: Quiroga Jairo , Díaz Yurina , Cobo Justo , Glidewell Christopher
Published: December 2011

Six closely related pyrazolo[3,4-b]pyridine derivatives, namely 6-chloro-3-methyl-1,4-diphenylpyrazolo[3,4-b]pyridine-5-carbaldehyde, C20H14ClN3O, (I), 6-chloro-3-methyl-4-(4-methylphenyl)-1-phenylpyrazolo[3,4-b]pyridine-5-carbaldehyde, C21H16ClN3O, (II), 6-chloro-4-(4-chlorophenyl)-3-methyl-1-phenylpyrazolo[3,4-b]pyridine-5-carbaldehyde, C20H13Cl2N3O, (III), 4-(4-bromophenyl)-6-chloro-3-methyl-1-phenylpyrazolo[3,4-b]pyridine-5-carbaldehyde, C20H13BrClN3O, (IV), 6-chloro-4-(4-methoxyphenyl)-3-methyl-1-phenylpyrazolo[3,4-b]pyridine-5-carbaldehyde, C21H16ClN3O2, (V), and 6-chloro-3-methyl-4-(4-nitrophenyl)-1-phenylpyrazolo[3,4-b]pyridine-5-carbaldehyde, C20H13ClN4O3, (VI), which differ only in the identity of a single small substituent on one of the aryl rings, crystallize in four different space groups spanning three crystal systems. The molecules of (I) are linked into a chain of rings by a combination of C—H...N and C—H...π(arene) hydrogen bonds; those of (II), (IV) and (V), which all crystallize in the space groupP\overline{1}, are each linked by two independent C—H...O hydrogen bonds to form chains of edge-fused rings running in different directions through the three unit cells; the molecules of (III) are linked into complex sheets by a combination of two C—H...O hydrogen bonds and one C—H...π(arene) hydrogen bond; finally, the molecules of (VI) are linked by a single C—H...O hydrogen bond to form a simple chain.
Benz[cd]indol-2(1H)-one at 298 and 100 K
Authors: Khan Saeed I. , Knobler Carolyn B. , Maverick Emily F.
Published: December 2011

Weakly diffracting crystals of benz[cd]indol-2(1H)-one (naphtholactam), C11H7NO, were unsuitable for data collection by early photographic methods. However, a diffractometer data set collected at room temperature in 1989 was solved and refined. The peak scans were broad, and the results indicated disorder or a satellite crystal. Recent data collection (on another crystal from the same sample) with an area detector at 100 K revealed the same disorder, and made it possible to refine two different, more complete, disorder models. Both models assume an occasional 180° rotation of the nearly planar centrosymmetriccis-lactam dimer. The refinements differ, especially in the anisotropic displacement parameters for the –C(=O)—NH– portion of the molecule. Both models at 100 K give a C—N (`amide') bond distance of 1.38 Å, about 0.04 Å longer than the average distance in saturated γ-lactams in the Cambridge Structural Database. Cohesive packing interactions between molecules include opposing-dipole dimers; the packing may explain the 10:1 ratio favoring the major-occupancy molecule.
Establishing Proactive Auditor Responsibilities in Relation to Fraud: The Role of the Courts and Professional Bodies in Denmark
Authors: Holm Claus , Langsted Lars Bo , Seehausen Jesper
Published: December 2011

Over the years, there has been considerable discussion about the extent and exact nature of the responsibilities of the auditor to detect fraud. The purpose of our study is to examine how the courts and professional bodies in a principle‐based legal system respond to the change in the audit promulgations introducing proactive responsibilities in relation to fraud. We observe the outcome of actual fraud cases in which the court system and professional bodies in Denmark establish the responsibilities of auditors. The data set includes all publicized cases in the period 1996–2006. We find that the Danish audit profession has adopted the new proactive responsibilities identified by the standard setters, whilst the courts and the professional bodies seem to see ‘the changes’ as mere clarifications of existing responsibilities. The proactive responsibilities are not further accelerated by prescriptive court rulings.
A molecular linkage map for Drosophila mediopunctata confirms synteny with Drosophila melanogaster and suggests a region that controls the variation in the number of abdominal spots
Authors: Laborda P. R. , Gazaffi R. , Garcia A. A. F. , de Souza A. P.
Published: December 2011

The classic approach to gene discovery relies on the construction of linkage maps. We report the first molecular‐based linkage map for Drosophila mediopunctata, a neotropical species of the tripunctata group. Eight hundred F2 individuals were genotyped at 49 microsatellite loci, resulting in a map that is ≈450 centimorgans long. Five linkage groups were detected, and the species' chromosomes were identified through cross‐references to BLASTn searches and Müller elements. Strong synteny was observed when compared with the Drosophila melanogaster chromosome arms, but little conservation in the gene order was seen. The incorporation of morphological data corresponding to the number of central abdominal spots on the map was consistent with the expected location of a genomic region responsible for the phenotype on the second chromosome.
A vision for a biomedical cloud
Authors: Grossman R. L. , White K. P.
Published: December 2011

Grossman RL, White KP (Institute for Genomics and Systems Biology; The University of Chicago, Chicago) A vision for a biomedical cloud (Key Symposium). J Intern Med 2012; 271: 122–130.

We present a vision for a Biomedical Cloud that draws on progress in the fields of Genomics, Systems Biology and biomedical data mining. The successful fusion of these areas will combine the use of biomarkers, genetic variants, and environmental variables to build predictive models that will drastically increase the specificity and timeliness of diagnosis for a wide range of common diseases, whilst delivering accurate predictions about the efficacy of treatment options. However, the amount of data being generated by each of these fields is staggering, as is the task of managing and analysing it. Adequate computing infrastructure needs to be developed to assemble, manage and mine the enormous and rapidly growing corpus of ‘omics’ data along with clinical information. We have now arrived at an intersection point between genome technology, cloud computing and biological data mining. This intersection point provides a launch pad for developing a globally applicable cloud computing platform capable of supporting a new paradigm of data intensive, cloud‐enabled predictive medicine.
Predictive mathematical models of cancer signalling pathways
Authors: Bachmann J. , Raue A. , Schilling M. , Becker V. , Timmer J. , Klingmüller U.
Published: December 2011

Abstract.  Bachmann J, Raue A, Schilling M, Becker V, Timmer J, Klingmüller U (German Cancer Research Center, Heidelberg; BIOSS Centre for Biological Signalling Studies, Freiburg; and University of Freiburg, Freiburg; Germany). Predictive mathematical models of cancer signalling pathways (Key Symposium). J Intern Med 2012; 271:155–165.

Complex intracellular signalling networks integrate extracellular signals and convert them into cellular responses. In cancer cells, the tightly regulated and fine‐tuned dynamics of information processing in signalling networks is altered, leading to uncontrolled cell proliferation, survival and migration. Systems biology combines mathematical modelling with comprehensive, quantitative, time‐resolved data and is most advanced in addressing dynamic properties of intracellular signalling networks. Here, we introduce different modelling approaches and their application to medical systems biology, focusing on the identifiability of parameters in ordinary differential equation models and their importance in network modelling to predict cellular decisions. Two related examples are given, which include processing of ligand‐encoded information and dual feedback regulation in erythropoietin (Epo) receptor signalling. Finally, we review the current understanding of how systems biology could foster the development of new treatment strategies in the context of lung cancer and anaemia.
Systems medicine and metabolic modelling
Authors: Mardinoglu A. , Nielsen J.
Published: December 2011

Mardinoglu A, Nielsen J (University of Technology, Gothenburg, Sweden). Systems medicine and metabolic modelling (Key Symposium). J Intern Med 2012; 271:142–154.

Several complex diseases are caused by the malfunction of human metabolism, and deciphering the underlying molecular mechanisms can elucidate their aetiology. Systems biology is an integrative approach combining experimental and computational biology to identify and describe the molecular mechanisms of complex biological systems. Systems medicine has the potential to elucidate the onset and progression of complex metabolic diseases through the use of computational approaches. Advances in biotechnology have resulted in the provision of high‐throughput data, which provide information about different metabolic processes. The systems medicine approach can utilize such data to reconstruct genome‐scale metabolic models that can be used to study the function of specific enzymes and pathways in the context of the complete metabolic network. In this review, we outline the importance of genome‐scale models in systems medicine and discuss how they may contribute towards the development of personalized medicine.
Using the reconstructed genome‐scale human metabolic network to study physiology and pathology
Authors: Bordbar A. , Palsson B. O.
Published: December 2011

Abstract.  Bordbar A, Palsson BO (University of California San Diego, La Jolla, CA, USA). Using the reconstructed genome‐scale human metabolic network to study physiology and pathology (Key Symposium). J Intern Med 2012; 271: 131–141.

Metabolism plays a key role in many major human diseases. Generation of high‐throughput omics data has ushered in a new era of systems biology. Genome‐scale metabolic network reconstructions provide a platform to interpret omics data in a biochemically meaningful manner. The release of the global human metabolic network, Recon 1, in 2007 has enabled new systems biology approaches to study human physiology, pathology and pharmacology. There are currently more than 20 publications that utilize Recon 1, including studies of cancer, diabetes, host–pathogen interactions, heritable metabolic disorders and off‐target drug binding effects. In this mini‐review, we focus on the reconstruction of the global human metabolic network and four classes of its application. We show that computational simulations for numerous pathologies have yielded clinically relevant results, many corroborated by existing or newly generated experimental data.
Systems cancer medicine: towards realization of predictive, preventive, personalized and participatory (P4) medicine
Authors: Tian Q. , Price N. D. , Hood L.
Published: December 2011

Abstract.  Tian Q, Price ND, Hood L (Institute for Systems Biology, Seattle, WA, USA). Systems cancer medicine: towards realization of predictive, preventive, personalized and participatory (P4) medicine (Key Symposium). J Intern Med 2012; 271: 111–121.

A grand challenge impeding optimal treatment outcomes for patients with cancer arises from the complex nature of the disease: the cellular heterogeneity, the myriad of dysfunctional molecular and genetic networks as results of genetic (somatic) and environmental perturbations. Systems biology, with its holistic approach to understanding fundamental principles in biology, and the empowering technologies in genomics, proteomics, single‐cell analysis, microfluidics and computational strategies, enables a comprehensive approach to medicine, which strives to unveil the pathogenic mechanisms of diseases, identify disease biomarkers and begin thinking about new strategies for drug target discovery. The integration of multidimensional high‐throughput ‘omics’ measurements from tumour tissues and corresponding blood specimens, together with new systems strategies for diagnostics, enables the identification of cancer biomarkers that will enable presymptomatic diagnosis, stratification of disease, assessment of disease progression, evaluation of patient response to therapy and the identification of reoccurrences. Whilst some aspects of systems medicine are being adopted in clinical oncology practice through companion molecular diagnostics for personalized therapy, the mounting influx of global quantitative data from both wellness and diseases is shaping up a transformational paradigm in medicine we termed ‘predictive’, ‘preventive’, ‘personalized’, and ‘participatory’ (P4) medicine, which requires new strategies, both scientific and organizational, to enable bringing this revolution in medicine to patients and to the healthcare system. P4 medicine will have a profound impact on society – transforming the healthcare system, turning around the ever escalating costs of healthcare, digitizing the practice of medicine and creating enormous economic opportunities for those organizations and nations that embrace this revolution.
Verification of the influence of the arrangement of implants on the load distribution (a well‐known figure by Rangert)
Authors: SATO Y. , UCHIDA K. , OKUYAMA T. , KITAGAWA N.
Published: December 2011

Summary  The purpose of this study is to evaluate the effects of the number and the placement of implants on load distribution for multiple implants with three‐dimensional geometric analysis, and to verify the well‐known conceptual figure by Rangert. Three teeth missing in left mandibular region was geometrically modelled in clinically simulated situation. Two implants placement as ‘control’, ‘cantilever’, ‘three‐implants’ and ‘offset placements’ were analyzed with geometric analysis. The cantilever received 180–182% load of control, that is, almost same to the result by Rangert (200%). Three implants received 59–65% load of control, that is, almost same to the result by Rangert (67%). Offset arrangement received 59–65% load of control, that is, larger than the result by Rangert (40%). It was concluded that the influence of the arrangement of implants on the load distribution presented in the conceptual figure by (Rangert BR, Sullivan RM & Jemt TM, J Oral Maxillofac Implants. 1997;12:360) was verified except for the effects of the offset arrangement.