Ecological assembly rules in plant communities--approaches, patterns and prospects.

Understanding how communities of living organisms assemble has been a central question in ecology since the early days of the discipline. Disentangling the different processes involved in community assembly is not only interesting in itself but also crucial for an understanding of how communities will behave under future environmental scenarios. The traditional concept of assembly rules reflects the notion that species do not co-occur randomly but are restricted in their co-occurrence by interspecific competition. This concept can be redefined in a more general framework where the co-occurrence of species is a product of chance, historical patterns of speciation and migration, dispersal, abiotic environmental factors, and biotic interactions, with none of these processes being mutually exclusive. Here we present a survey and meta-analyses of 59 papers that compare observed patterns in plant communities with null models simulating random patterns of species assembly. According to the type of data under study and the different methods that are applied to detect community assembly, we distinguish four main types of approach in the published literature: species co-occurrence, niche limitation, guild proportionality and limiting similarity. Results from our meta-analyses suggest that non-random co-occurrence of plant species is not a widespread phenomenon. However, whether this finding reflects the individualistic nature of plant communities or is caused by methodological shortcomings associated with the studies considered cannot be discerned from the available metadata. We advocate that more thorough surveys be conducted using a set of standardized methods to test for the existence of assembly rules in data sets spanning larger biological and geographical scales than have been considered until now. We underpin this general advice with guidelines that should be considered in future assembly rules research. This will enable us to draw more accurate and general conclusions about the non-random aspect of assembly in plant communities.

Transformation rules form OntoProcED to OntoOKI

This file contains the transformtion rules in SWRL to translate formal specifications of two lower ontology levels (patterns and organization) to the upper level (implementation according to the OKI specification).

Social Cognition is not Reducible to Theory of Mind. When Children use Deontic Rules to Predict Others' Behaviors

The objective of this paper is to discuss whether children have a capacity for deonticreasoning that is irreducible to mentalizing. The results of two experiments point tothe existence of such non-mentalistic understanding and prediction of the behaviourof others. In Study 1, young children (3- and 4-year-olds) were told different versionsof classic false-belief tasks, some of which were modified by the introduction of a ruleor a regularity. When the task (a standard change of location task) included a rule, theperformance of 3-year-olds, who fail traditional false-belief tasks, significantly improved.In Study 2, 3-year-olds proved to be able to infer a rule from a social situation and touse it in order to predict the behaviour of a character involved in a modified versionof the false-belief task. These studies suggest that rules play a central role in the socialcognition of young children and that deontic reasoning might not necessarily involvemind reading.

Fine-Tuning Translation Kinetics Selection as the Driving Force of Codon Usage Bias in the Hepatitis A Virus Capsid

Hepatitis A virus (HAV), the prototype of genus Hepatovirus, has several unique biological characteristics that distinguish it from other members of the Picornaviridae family. Among these, the need for an intact eIF4G factor for the initiation of translation results in an inability to shut down host protein synthesis by a mechanism similar to that of other picornaviruses. Consequently, HAV must inefficiently compete for the cellular translational machinery and this may explain its poor growth in cell culture. In this context of virus/cell competition, HAV has strategically adopted a naturally highly deoptimized codon usage with respect to that of its cellular host. With the aim to optimize its codon usage the virus was adapted to propagate in cells with impaired protein synthesis, in order to make tRNA pools more available for the virus. A significant loss of fitness was the immediate response to the adaptation process that was, however, later on recovered and more associated to a re-deoptimization rather than to an optimization of the codon usage specifically in the capsid coding region. These results exclude translation selection and instead suggest fine-tuning translation kinetics selection as the underlying mechanism of the codon usage bias in this specific genome region. Additionally, the results provide clear evidence of the Red Queen dynamics of evolution since the virus has very much evolved to re-adapt its codon usage to the environmental cellular changing conditions in order to recover the original fitness.

Analysis of patient physical restraints usage in a Swiss emergency service

Introduction: Emergency services (ES) are often faced with agitated,confused or aggressive patients. Such situations may require physicalrestraint. The prevalence of these measures is poorly documented,concerning 1 to 10% of patients admitted in the ES. The indications forrestraint, the context and the related complications are poorly studied.The emergency service and the security service of our hospital havedocumented physical restraint for several years, using specific protocolsintegrated into the medical records. The study evaluated the magnitudeof the problem, the patient characteristics, and degree of adherence tothe restraint protocol.Methods: Retrospective study of physical restraint used on adultpatients in the ES in 2009. The study included analysis of medical anddemographic characteristics, indications justifying restraint and qualityof restraint documentation. Patients were identified from computerizedES and security service records. The data were supplemented byexamination of patients' medical records.Results: In 2009, according to the security service, 390 patients (1%)were physically restrained in the ES. The ES computerized systemidentified only 196 patients. Most patients were male (62%). The medianage was 40 years (15-98 years; P90 = 80 years). 63 % of the situationsoccurred between 18h00 and 6h00, and most frequently on Saturday(19%). Substance or alcohol abuse was present in 48.7% of cases andacute psychiatric crisis was mentioned in 16.7%. In most cases,restraint was motivated by extreme agitation or auto / hetero-aggressiveviolence. Most patients (68 %) were restrained with upper limb andabdominal restraints. More than three anatomic restraints werenecessary in 52 % of the patients. Intervention of security guards wasrequired in 77% of the cases. 61 restraint protocols (31 %) were missingand 57% of the records were incomplete. In many cases, the protocolsdid not include the signature of the physician (22%) or of the nurse(43.8%). Medical records analysis did not allow reliable estimation ofthe number of restraint-induced complications.Conclusions: Physical restraint is most often motivated by majoragitation and/or secondary to substance abuse. Caregivers regularlycall security guards for help. Restraint documentation is often missing orincomplete, requiring major improvement in education and prescription.

T cell receptor beta chain gene rearrangements and V beta gene usage in horse cytochrome c-specific T cell hybridomas.

Comparison of T cell receptor alpha and beta-chain genes in murine major histocompatibility complex (MHC) class I and class II-restricted T cell clones and hybridomas recognizing different antigens indicates that no simple correlation exists between the observed antigen/MHC specificity and the expression of certain alpha and beta-chain heterodimers. We have attempted to establish a possible correlation by analyzing T cell receptor beta chain gene rearrangements and V beta gene usage in five T cell hybridomas with identical antigen/MHC specificity and another hybridoma recognizing a different antigenic determinant in association with the same restriction molecule. We report here that in each of the five clones a uniquely rearranged beta chain gene is expressed in combination with at least two different V beta gene segments. The presence of the differently rearranged T cell receptor beta chain genes correlated with the finding of distinct fine specificity pattern of antigen recognition in each of the hybridomas. Interestingly, two hybridomas specific for different epitopes showed identical beta chain D-J rearrangements indicating that the differences might be encoded by the alpha chain gene or/and the V beta gene element.