Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks

In recent years, in-silico literature-based mammalian protein-protein interaction network datasets have been developed. These datasets contain binary interactions extracted manually from legacy experimental biomedical research literature. Placing lists of genes or proteins identified as significantly changing in multivariate experiments, in the context of background knowledge about binary interactions, can be used to place these genes or proteins in the context of pathways and protein complexes.
Genes2Networks is a software system that integrates the content of ten mammalian literature-based interaction network datasets. Filtering to prune low-confidence interactions was implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from “seed” lists of human Entrez gene names. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. Genes2Networks is available at http://actin.pharm.mssm.edu/genes2networks.
Genes2Network is a powerful web-based software application tool that can help experimental biologists to interpret high-throughput experimental results used in genomics and proteomics studies where the output of these experiments is a list of significantly changing genes or proteins. The system can be used to find relationships between nodes from the seed list, and predict novel nodes that play a key role in a common function

Lag time for retinoblastoma in the UK revisited: a retrospective analysis

OBJECTIVES: To explore current delays in diagnosis of retinoblastoma (Rb) and effect on outcome with comparison to a study from the 1990s. SETTING: Primary, secondary, tertiary care: majority from South of England. PARTICIPANTS: A retrospective analysis of 93 new referrals of sporadic (non-familial) Rb to a specialist Rb unit in London, UK from January 2006 to February 2014. PRIMARY AND SECONDARY OUTCOMES: International Intraocular Retinoblastoma Classification, lag times including parental delay and healthcare professional delay, patients requiring enucleation and requirement of adjuvant chemotherapy postenucleation (high-risk Rb). RESULTS: During the study period, 29% presented via accident and emergency (A&E). The median referral time from symptom onset to visiting primary care (PC) was 28 days and PC to ophthalmologist 3 days (range 0-181 days). The median time from local ophthalmologist to the Rb Unit was 6 days (0-33). No significant correlation was found between delay and International Classification of Retinoblastoma grade (p>0.05) or between postenucleation adjuvant chemotherapy and enucleation groups (p>0.05). Less enucleations (60%) are being performed compared with the previous study (81%) (p=0.0015). CONCLUSIONS: Parents are attending A&E more compared with the 1990s and this may reflect the effect of public awareness campaigns. More eyes are being salvaged despite a similar number of children requiring adjuvant chemotherapy. High-risk Rb and Group E eyes do not correlate with increased lag time in the UK. Other determinants such as tumour biology may be more relevant

Mantra: an open method for object and movement tracking

Mantra is a free and open-source software package for object tracking. It is specifically designed to be used as a tool for response collection in psychological experiments and requires only a computer and a camera (a webcam is sufficient). Mantra is compatible with widely used software for creating psychological experiments. In Experiments 1 and 2, we validated the spatial and temporal precision of Mantra in realistic experimental settings. In Experiments 3 and 4, we validated the spatial precision and accuracy of Mantra more rigorously by tracking a computer controlled physical stimulus and stimuli presented on a computer screen

Lipoma of Guyon’s canal causing ulnar neuropathy

Lipoma is a benign soft tissue tumor which rarely causes neuropathy. In closed compartments such as Guyon’s canal, even small volume loss can lead to compression of nerve. Hence in such areas, even innocuous tumors such as lipomas can cause neuropathy and warrant surgery. We present one such case of ulnar neuropathy caused by lipoma of Guyon’s canal

Can We Really Prevent Suicide?

Every year, suicide is among the top 20 leading causes of death globally for all ages. Unfortunately, suicide is difficult to prevent, in large part because the prevalence of risk factors is high among the general population. In this review, clinical and psychological risk factors are examined and methods for suicide prevention are discussed. Prevention strategies found to be effective in suicide prevention include means restriction, responsible media coverage, and general public education, as well identification methods such as screening, gatekeeper training, and primary care physician education. Although the treatment for preventing suicide is difficult, follow-up that includes pharmacotherapy, psychotherapy, or both may be useful. However, prevention methods cannot be restricted to the individual. Community, social, and policy interventions will also be essentia

Cooperation, Norms, and Revolutions: A Unified Game-Theoretical Approach

Cooperation is of utmost importance to society as a whole, but is often challenged by individual self-interests. While game theory has studied this problem extensively, there is little work on interactions within and across groups with different preferences or beliefs. Yet, people from different social or cultural backgrounds often meet and interact. This can yield conflict, since behavior that is considered cooperative by one population might be perceived as non-cooperative from the viewpoint of another. To understand the dynamics and outcome of the competitive interactions within and between groups, we study game-dynamical replicator equations for multiple populations with incompatible interests and different power (be this due to different population sizes, material resources, social capital, or other factors). These equations allow us to address various important questions: For example, can cooperation in the prisoner's dilemma be promoted, when two interacting groups have different preferences? Under what conditions can costly punishment, or other mechanisms, foster the evolution of norms? When does cooperation fail, leading to antagonistic behavior, conflict, or even revolutions? And what incentives are needed to reach peaceful agreements between groups with conflicting interests? Our detailed quantitative analysis reveals a large variety of interesting results, which are relevant for society, law and economics, and have implications for the evolution of language and culture as well

Keep looking ahead? Re-direction of visual fixation does not always occur during an unpredictable obstacle avoidance task

Visual information about the environment, especially fixation of key objects such as obstacles, is critical for safe locomotion. However, in unpredictable situations where an obstacle suddenly appears it is not known whether central vision of the obstacle and/or landing area is required or if peripheral vision is sufficient. We examined whether there is a re-direction of visual fixation from an object fixated ahead to a suddenly appearing obstacle during treadmill walking. Furthermore, we investigated the temporal relationship between the onset of muscle activity to avoid the obstacle and saccadic eye and head movements to shift fixation. Eight females (mean SD; age = 24.8 2.3 years) participated in this experiment. There were two visual conditions: a central vision condition where participants fixated on two obstacles attached to a bridge on the treadmill and a peripheral vision condition where participants fixated an object two steps ahead. There were two obstacle release conditions: only an obstacle in front of the left foot was released or an obstacle in front of either foot could be released. Only trials when the obstacle was released in front of the left foot were analyzed such that the difference in the two obstacle conditions was whether there was a choice of which foot to step over the obstacle. Obstacles were released randomly in one of three phases during the step cycle corresponding to available response times between 219 and 462 ms. We monitored eye and head movements along with muscle activity and spatial foot parameters. Performance on the task was not different between vision conditions. The results indicated that saccades are rarely made (< 18% of trials) and, when present, are initiated ∼ 350 ms after muscle activity for limb elevation, often accompanied by a downward head movement, and always directed to the landing area. Therefore, peripheral vision of a suddenly appearing obstacle in the travel path is sufficient for successful obstacle avoidance during locomotion: visual fixation is generally not re-directed to either the obstacle or landing area

Stochastic accumulation of feature information in perception and memory

It is now well established that the time course of perceptual processing influences the first second or so of performance in a wide variety of cognitive tasks. Over the last20 years, there has been a shift from modeling the speed at which a display is processed, to modeling the speed at which different features of the display are perceived and formalizing how this perceptual information is used in decision making. The first of these models(Lamberts, 1995) was implemented to fit the time course of performance in a speeded perceptual categorization task and assumed a simple stochastic accumulation of feature information. Subsequently, similar approaches have been used to model performance in a range of cognitive tasks including identification, absolute identification, perceptual matching, recognition, visual search, and word processing, again assuming a simple stochastic accumulation of feature information from both the stimulus and representations held in memory. These models are typically fit to data from signal-to-respond experiments whereby the effects of stimulus exposure duration on performance are examined, but response times (RTs) and RT distributions have also been modeled. In this article, we review this approach and explore the insights it has provided about the interplay between perceptual processing, memory retrieval, and decision making in a variety of tasks. In so doing, we highlight how such approaches can continue to usefully contribute to our understanding of cognition