A comparison of intradimensional and extradimensional shift learning in pigeons

In each of three experiments pigeons were trained on a simultaneous discrimination between stimuli that differed in both colour and orientation. For half the birds the colour dimension was relevant and for half orientation was relevant (i.e., differences along that dimension were correlated with reward and nonreward). All birds were then shifted to a second discrimination between new colours and orientations. For half this constituted an intradimensional shift in that the previously relevant dimension remained relevant; for the remainder the previously irrelevant dimension was made relevant (an extradimensional shift). Contrary to the predictions of attentional theory, the two types of shift were learned with equal ease.     

Short-term incidental memory for irrelevant cues

A new analysis of previously published studies of delayed matching-to-sample (DMTS) water-escape and the results of a new food-reinforced discrimination study are presented. In both cases, male Sprague-Dawley rats demonstrated short-term incidental memory for irrelevant cues in the context of two-alternative forced-choice problems that required learning about relevant cues. In the DMTS experiments, relevant and irrelevant cues were place or brightness. In the discrimination experiment, the relevant cues were place, brightness or a visual-tactile maze insert. In all experiments, after the rats attained high-level performance, consistently making choices with respect to the relevant stimuli, response latencies to the correct relevant cue were shorter when the irrelevant cue value(s) was the same as on the immediately preceding trial. These latency differences are interpreted as indicating that the rats demonstrated short-term incidental memory for the irrelevant cues. This mnemonic phenomenon resembles priming, an implicit form of memory.     

Risk conferring genes in multiple sclerosis

Multiple sclerosis (MS) is characterized by inflammation, axonal and oligodendrocyte pathology and progressive neurological disability. Epidemiologic data indicate that MS may be caused by interplay of genetic and environmental factors. Large samples collected in cooperative efforts and new technologies such as high throughput single nucleotide polymorphism (SNP) genotyping allowed recently to discover non-HLA genes associated with MS susceptibility that are mostly involved in the immune response. In addition, several studies indicate an effect of genetic variations on disease onset, progression and response to therapy. However, the polymorphisms discovered so far explain the genetic variation in MS only in part and are mostly common variants that have only low impact on MS susceptibility. Functional studies are required to validate the importance of the newly identified SNPs. Taking into account the interplay of genetic and environmental factors a combination of genome wide genotyping including HLA-typing and genome wide expression profiling as well as a collection on relevant or putatively relevant environmental factors in patients well characterized clinically and by MRI is a promising way to identify new disease relevant biomarkers.     

Cholera- and anthrax-like toxins are among several new ADP-ribosyltransferases

Chelt, a cholera-like toxin from Vibrio cholerae, and Certhrax, an anthrax-like toxin from Bacillus cereus, are among six new bacterial protein toxins we identified and characterized using in silico and cell-based techniques. We also uncovered medically relevant toxins from Mycobacterium avium and Enterococcus faecalis. We found agriculturally relevant toxins in Photorhabdus luminescens and Vibrio splendidus. These toxins belong to the ADP-ribosyltransferase family that has conserved structure despite low sequence identity. Therefore, our search for new toxins combined fold recognition with rules for filtering sequences--including a primary sequence pattern--to reduce reliance on sequence identity and identify toxins using structure. We used computers to build models and analyzed each new toxin to understand features including: structure, secretion, cell entry, activation, NAD+ substrate binding, intracellular target binding and the reaction mechanism. We confirmed activity using a yeast growth test. In this era where an expanding protein structure library complements abundant protein sequence data--and we need high-throughput validation--our approach provides insight into the newest toxin ADP-ribosyltransferases.     

Preoperative electrocardiography: its cost-effectiveness in detecting abnormalities when a previous tracing exists.

In 812 patients who underwent routine preoperative electrocardiography a mean of 24.6 months after undergoing electrocardiography at the same institution, the frequency of new abnormalities was estimated to evaluate the cost-effectiveness of this procedure prior to an operation. New abnormalities were judged to be either relevant or irrelevant to the assessment of operative risk, depending upon their previously demonstrated correlation with operative and postoperative morbidity and mortality. Since new abnormalities, especially new relevant abnormalities, were found to be relatively infrequent, the cost-effectiveness of routine preoperative electrocardiography was considered to be low. The evidence suggested that when a previous tracing exists preoperative electrocardiography is most clearly indicated for patients who are 60 years of age or older or whose previous tracing exhibited abnormalities. However, further research is required to develop more sensitive and specific protocols, and to evaluate the role of repeat electrocardiography in clinical decision-making.     

Using mouse forward genetics to define novel target space

Rapid advances in genomics technologies have identified a wealth of new therapeutic targets, but typically these targets are weakly validated with only circumstantial evidence to link them to human disease. The next challenge is testing gene-to-disease connections in a relevant animal model, a time-consuming and uncertain process using conventional reverse-genetic approaches such as knockout and transgenic mice. By contrast, forward genetics proceeds by measuring a physiological process that is relevant to disease, then identifying the gene products that impinge on this process. This ‘phenotype-first’ approach solves the bottleneck of target validation by using clinically relevant assays in a mammalian whole-animal system as a discovery platform. As an unbiased approach to gene discovery and validation, forward genetics will identify novel drug targets and increase the success rate of drug development.     

FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks

The characterization of the interacting behaviors of complex biological systems is a primary objective in protein–protein network analysis and computational biology. In this paper we present FunMod, an innovative Cytoscape version 2.8 plugin that is able to mine undirected protein–protein networks and to infer sub-networks of interacting proteins intimately correlated with relevant biological pathways. This plugin may enable the discovery of new pathways involved in diseases. In order to describe the role of each protein within the relevant biological pathways, FunMod computes and scores three topological features of the identified sub-networks. By integrating the results from biological pathway clustering and topological network analysis, FunMod proved to be useful for the data interpretation and the generation of new hypotheses in two case studies.     

Unsupervised feature selection via two-way ordering in gene expression analysis

MOTIVATION: Selection of genes most relevant and informative for certain phenotypes is an important aspect in gene expression analysis. Most current methods select genes based on known phenotype information. However, certain set of genes may correspond to new phenotypes which are yet unknown, and it is important to develop novel effective selection methods for their discovery without using any prior phenotype information. RESULTS: We propose and study a new method to select relevant genes based on their similarity information only. The method relies on a mechanism for discarding irrelevant genes. A two-way ordering of gene expression data can force irrelevant genes towards the middle in the ordering and thus can be discarded. Mechanisms based on variance and principal component analysis are also studied. When applied to expression profiles of colon cancer and leukemia, the unsupervised method outperforms the baseline algorithm that simply uses all genes, and it also selects relevant genes close to those selected using supervised methods. SUPPLEMENT: More results and software are online: http://www.nersc.gov/~cding/2way.     

The human genome project: Towards an analysis of the empirical,ethical, and conceptual issues involved

In this paper I claim that the goal of mapping and sequencing the human genome is not wholly new, but rather is an extension of an older project to map genes, a central aim of genetics since its birth. Thus, the discussion about the value of the HGP should not be posed in global terms of acceptance or rejection, but in terms of how it should be developed. The first section of this paper presents a brief history of the project. The second section distinguishes among four kinds of issues relevant to an evaluation of the HGP: those economic and organizational issues related to the feasibility of the project; the ethical questions arising in the development of the project and the application of the data gathered; the empirical issues relevant to the scientific value of the project; and conceptual issues like reductionism and determinism relevant to understand the nature and scope of the project. In a third section, I analyze in detail whether the HGP and, more generally, molecular biology is reductionistic.     

The Biology of Invasions: The Genetic Adaptation Paradox

One of the most relevant topics in the biology of invasion concerns the genetic changes that occur subsequent to a species invasion, an issue of particular focus among conservation biologists. Colonizing a novel environment presents a genetic challenge to invading species because such species surely have not experienced the selective pressures presented by the environment. Here we ask, by what mechanisms and processes do alien species genetically naïve to their new environment, become successful invaders? We attempt to resolve this paradox by considering the interplay between an invader’s ability to modify its new environment, and genetic modifications imposed by the new environment. We postulate that epigenetic adaptations, and adaptive mutations are likely play a role in enhancing invasion success.     

Predicting protein functions from PPI networks using functional aggregation

Predicting protein functions computationally from massive protein-protein interaction (PPI) data generated by high-throughput technology is one of the challenges and fundamental problems in the post-genomic era. Although there have been many approaches developed for computationally predicting protein functions, the mutual correlations among proteins in terms of protein functions have not been thoroughly investigated and incorporated into existing prediction methods, especially in voting based prediction methods. In this paper, we propose an innovative method to predict protein functions from PPI data by aggregating the functional correlations among relevant proteins using the Choquet-Integral in fuzzy theory. This functional aggregation measures the real impact of each relevant protein function on the final prediction results, and reduces the impact of repeated functional information on the prediction. Accordingly, a new protein similarity and a new iterative prediction algorithm are proposed in this paper. The experimental evaluations on real PPI datasets demonstrate the effectiveness of our method.     

Targeting Rab GTPases to distinct membrane compartments

Rab GTPases are key to membrane-trafficking events in eukaryotic cells, and human cells contain more than 60 Rab proteins that are localized to distinct compartments. The recent determination of the structure of a monoprenylated Rab GTPase bound to GDP-dissociation inhibitor provides new molecular details that are relevant to models of Rab delivery. The further discovery of an integral membrane protein that can dissociate prenylated Rab proteins from GDP-dissociation inhibitor gives new insights into the mechanisms of Rab localization.     

New methods for finding common insertion sites and co-occurring common insertion sites in transposon- and virus-based genetic screens

Insertional mutagenesis screens in mice are used to identify individual genes that drive tumor formation. In these screens, candidate cancer genes are identified if their genomic location is proximal to a common insertion site (CIS) defined by high rates of transposon or retroviral insertions in a given genomic window. In this article, we describe a new method for defining CISs based on a Poisson distribution, the Poisson Regression Insertion Model, and show that this new method is an improvement over previously described methods. We also describe a modification of the method that can identify pairs and higher orders of co-occurring common insertion sites. We apply these methods to two data sets, one generated in a transposon-based screen for gastrointestinal tract cancer genes and another based on the set of retroviral insertions in the Retroviral Tagged Cancer Gene Database. We show that the new methods identify more relevant candidate genes and candidate gene pairs than found using previous methods. Identification of the biologically relevant set of mutations that occur in a single cell and cause tumor progression will aid in the rational design of single and combinatorial therapies in the upcoming age of personalized cancer therapy.     

Dose finding - a challenge in statistics

A good understanding and characterization of the dose response relationship of any new compound is an important and ubiquitous problem in many areas of scientific investigation. This is especially true in the context of pharmaceutical drug development, where it is mandatory to launch safe drugs which demonstrate a clinically relevant effect. Selecting a dose too high may result in unacceptable safety problems, while selecting a dose too low may lead to ineffective drugs. Dose finding studies thus play a key role in any drug development program and are often the gate-keeper for large confirmatory studies. In this overview paper we focus on definitive and confirmatory dose finding studies in Phase II or III, reviewing relevant statistical design and analysis methods. In particular, we describe multiple comparison procedures, modeling approaches, and hybrid methods combining the advantages of both. An outlook to adaptive dose finding methods is also given. We use a real data example to illustrate the methods, together with a brief overview of relevant software.     

Flow cytometry in radiation research: past, present and future

Flow cytometry is an invaluable technique in research and clinical laboratories. The technique has been applied extensively to many areas of radiation research at both the experimental and clinical level. In the past few years, there has been a significant increase in the capabilities of modern flow cytometers to undertake multicolor analysis in a user-friendly manner. The developments in cytometric technology are being matched by the rapid development of new reagents, new fluorochromes and new platforms such as bead arrays. These developments are facilitating many new applications in both basic and clinical research that have relevance for many fields of biology, including radiation research. This review provides a historical overview of the application of flow cytometry to radiobiology and an update on how technology and reagents have changed and cites examples of new applications relevant to radiation researchers. In addition, some entirely new flow instrumentation is currently under development that has significant potential for applications in radiation research.     

On the validity of the steady state assumption of enzyme kinetics

By estimating relevant time scales, a simple new condition can be found that ensures the validity of the steady state assumption for a standard enzyme-substrate reaction. The generality of the approach is demonstrated by applying it to the determination of validity criteria for the steady state assumption applied to an enzyme-substrate-inhibitor system.     

Strategies for the implementation of new shift systems

Implementation barriers may be caused by deficiencies in the knowledge, skills, motivation, or support of those involved in the process of implementation of a new shift system. There is no 'one and only' way of planning and implementing a new shift system. However, if the following factors of success are taken into consideration there is a better chance that workers will accept a new shift system: worker participation, information, communication, training, promoter commitment, professional project management, tailor-made solutions and an adequate organizational framework. These factors are particularly relevant in addressing barriers to the implementation of new shift systems. The most important measures to cope with resistance to change of shift systems are: worker participation, information, communication, training, promoter commitment, professional project management, tailor-made solutions and an adequate organizational framework.