Acclimation of photosynthesis to supersaturated CO2 in aquatic plant bicarbonate users

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A brief history and popularity of methods and tools used to estimate micro‐evolutionary forces

Population genetics is a field of research that predates the current generations of sequencing technology. Those approaches, that were established before massively parallel sequencing methods, have been adapted to these new marker systems (in some cases involving the development of new methods) that allow genome‐wide estimates of the four major micro‐evolutionary forces—mutation, gene flow, genetic drift, and selection. Nevertheless, classic population genetic markers are still commonly used and a plethora of analysis methods and programs is available for these and high‐throughput sequencing (HTS) data. These methods employ various and diverse theoretical and statistical frameworks, to varying degrees of success, to estimate similar evolutionary parameters making it difficult to get a concise overview across the available approaches. Presently, reviews on this topic generally focus on a particular class of methods to estimate one or two evolutionary parameters. Here, we provide a brief history of methods and a comprehensive list of available programs for estimating micro‐evolutionary forces. We furthermore analyzed their usage within the research community based on popularity (citation bias) and discuss the implications of this bias for the software community. We found that a few programs received the majority of citations, with program success being independent of both the parameters estimated and the computing platform. The only deviation from a model of exponential growth in the number of citations was found for the presence of a graphical user interface (GUI). Interestingly, no relationship was found for the impact factor of the journals, when the tools were published, suggesting accessibility might be more important than visibility.     

Photosynthetic carbon sources in somepotamogeton species

The ability of somePotamogeton species to use bicarbonate for photosynthesis was assayed by means of relative net photosynthetic rates in alkaline (bicarbonate) and acid (free CO₂) solutions with an equivalent amount of inorganic carbon. The results showedPotamogeton crispus, P. oxyphyllus, P. maackianus, P. perfoliatus, P. malaianus and the submerged leaves ofP. distinctus to be able to use bicarbonate ions for photosynthesis. To the contrary, the submerged leaves ofP. fryeri, which is an inhabitant of soft and acid waters, and the floating leaves ofP. distinctus were proven to be ‘non-users’ of bicarbonate ions. Furthermore, the relative photosynthetic rates were determined using natural waters with various carbon conditions. The dependence of photosynthetic performance on the free CO₂, pH and alkalinity of the waters is discussed in relation to carbon metabolism. Further it is suggested that the carbon conditions are ecologically significant in relation to the productivity and success of macrophyte species in natural habitats.     

Are psychiatrists an endangered species? Observations on internal and external challenges to the profession

Based on recently voiced concerns about a crisis in psychiatry, six challenges to our profession are identified and discussed. As we approach the revisions of ICD-10 and DSM-IV, the validity of psychiatry’s diagnostic definitions and classification systems is increasingly questioned also from inside psychiatry. In addition, confidence in the results of therapeutic intervention studies is waning. A further challenge is the existence of de facto subgroups with opposing ideologies, a situation which is responsible for an unclear role profile of the psychiatrist. Challenges from outside include mounting patient and carer criticism, intrusion of other professions into psychiatry’s traditional field of competence, and psychiatry’s low status within medicine and in society in general. Studies suggest that the decline of the recruitment into psychiatry, as it is observed in many countries, might be related to problems arising from these challenges. It is unclear whether psychiatry will survive as a unitary medical discipline or whether those segments which are more rewarding, both financially and in status, will break away, leaving the unattractive tasks to carry out by what remains of psychiatry. The demise of the generalist and the rise of the specialist in modern society may contribute to this development. Attempts are underway by professional bodies to define the profile of a “general psychiatrist”. Such discussions should be complemented by an analysis of the incentives which contribute to the centrifugal tendencies in psychiatry.     

The needs of primary care mental health service users: a Q-sort study

Background Within scientific and policy literature, the broader needs and preferences of the service user are usually described as being relatively homogenous for any particular condition. Additionally, despite common adult mental health problems being a huge burden to primary care services, there has been little research into the client's perspective of their needs regarding such difficulties. The aim of this research was thus to uncover the issues and preferences for this sample.Method The attitudes of 28 service users were explored through use of a Q-methodology approach. This procedure involves statistical analysis of the order that participants rank pertinent statements associated with the area of study.Results Five independent factors (clusters of preferences) were identified. These differed over issues associated with: relationships with service providers, access/barriers associated with services, information provision, stigma, choices associated with therapy and the care pathway, medication and complementary approaches, as well as social support.Discussion The study suggests that differing individual needs exist within diagnostic categories which, unless considered, may impede service engagement. Issues associated with the implications for service delivery for these differing clusters of perceived needs and viewpoints are outlined.     

Performance Analysis of a Myrinet-Based Cluster

In recent years, there has been a growing interest in the cluster system as an accepted form of supercomputing, due to its high performance at an affordable cost. This paper attempts to elaborate performance analysis of Myrinet-based cluster. The communication performance and effect of background load on parallel applications were analyzed. For point-to-point communication, it was found that an extension to the Hockney's model was required to estimate the performance. The proposed model suggested that there should be two ranges to be used for the performance metrics to cope with the cache effect. Moreover, based on the extension of the point-to-point communication model, the Xu and Hwang's model for collective communication performance was also extended. Results showed that our models can make better estimation of the communication performance than the previous models. Finally, the interference of other user processes to the cluster system is evaluated by using synthetic background load generation programs.     

A benchmark testing ground for integrating homology modeling and protein docking

Protein docking procedures carry out the task of predicting the structure of a protein–protein complex starting from the known structures of the individual protein components. More often than not, however, the structure of one or both components is not known, but can be derived by homology modeling on the basis of known structures of related proteins deposited in the Protein Data Bank (PDB). Thus, the problem is to develop methods that optimally integrate homology modeling and docking with the goal of predicting the structure of a complex directly from the amino acid sequences of its component proteins. One possibility is to use the best available homology modeling and docking methods. However, the models built for the individual subunits often differ to a significant degree from the bound conformation in the complex, often much more so than the differences observed between free and bound structures of the same protein, and therefore additional conformational adjustments, both at the backbone and side chain levels need to be modeled to achieve an accurate docking prediction. In particular, even homology models of overall good accuracy frequently include localized errors that unfavorably impact docking results. The predicted reliability of the different regions in the model can also serve as a useful input for the docking calculations. Here we present a benchmark dataset that should help to explore and solve combined modeling and docking problems. This dataset comprises a subset of the experimentally solved ‘target’ complexes from the widely used Docking Benchmark from the Weng Lab (excluding antibody–antigen complexes). This subset is extended to include the structures from the PDB related to those of the individual components of each complex, and hence represent potential templates for investigating and benchmarking integrated homology modeling and docking approaches. Template sets can be dynamically customized by specifying ranges in sequence similarity and in PDB release dates, or using other filtering options, such as excluding sets of specific structures from the template list. Multiple sequence alignments, as well as structural alignments of the templates to their corresponding subunits in the target are also provided. The resource is accessible online or can be downloaded at http://cluspro.org/benchmark , and is updated on a weekly basis in synchrony with new PDB releases. Proteins 2016; 85:10–16. © 2016 Wiley Periodicals, Inc.     

Swiss-Prot: juggling between evolution and stability

We describe some of the aspects of Swiss-Prot that make it unique, explain what are the developments we believe to be necessary for the database to continue to play its role as a focal point of protein knowledge, and provide advice pertinent to the development of high-quality knowledge resources on one aspect or the other of the life sciences.     

shinyChromosome:An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes

Non-circular plots of whole genomes are natural representations of genomic data aligned along all chromosomes.Currently,there is no specialized graphical user interface(GUI) designed to produce non-circular whole genome diagrams,and the use of existing tools requires considerable coding effort from users.Moreover,such tools also require improvement,including the addition of new functionalities.To address these issues,we developed a new R/Shiny application,named shiny Chromosome,as a GUI for the interactive creation of non-circular whole genome diagrams.shiny Chromosome can be easily installed on personal computers for own use as well as on local or public servers for community use.Publication-quality images can be readily generated and annotated from user input using diverse widgets.shiny Chromosome is deployed at http://150.109.59.144:3838/shiny Chromosome/,http://shiny Chromosome.ncpgr.cn,and https://yimingyu.shinyapps.io/shiny Chromosome for online use.The source code and manual of shiny Chromosome are freely available at https://github.com/venyao/shiny Chromosome.