Peer assessment in large undergraduate classes: an evaluation of a procedure for marking laboratory reports and a review of related practices

This study provides evidence that peer marking can be a reliable tool for assessing laboratory reports in large cohorts. It was conducted over a 4-yr period with first-year undergraduates (～180 students/cohort) taking a mammalian physiology course, but the procedure adopted would be applicable to any other laboratory-based discipline. The process was found to be efficient in staff time, enabling a summative practical report to be marked in <1 h (<5% of the time that had previously been required for staff marking), facilitating rapid feedback to students on their performance. When samples of the peer-assessed reports were marked by a single member of staff, there was excellent correlation between peer and staff marks (r = 0.96-0.98), although peer-awarded marks exceeded staff marks by an average of 2.5-3.0%. The validity of peer marking was independent of both the sex of the marker and the staff score awarded to the marker for the same piece of work. Feedback from students was largely positive; they reported that the procedure adopted was effective in increasing their understanding of the underlying physiology and contributed to their understanding of best practice in presenting a laboratory report. Seventy percent of students agreed that it was acceptable for peer assessment to contribute a small (up to 5%) component of the overall mark for the course. The results are discussed in relation to other reports of peer marking, particularly when used to assess an academic product or process in a scientific discipline.     

Commissioning a national programme of research and development on the interface between primary and secondary care.

The first call for applications to the NHS research and development programme on the interface between primary and secondary care was advertised in February 1994. A total of 674 outline proposals were submitted and 54 (8%) secured funding. Projects have been commissioned in 16 of the 21 priority areas and around 6m pounds has been committed. Analysis shows that multidisciplinary applications are more likely to be funded and that the odds for a successful application are on average nearly doubled for each discipline represented up to five. A survey of applicants and peer reviewers found satisfaction with much of the commissioning process, but peer review and feedback were subject to criticism, particularly by unsuccessful applicants. The programme shows that it is possible to commission a large number of projects in an innovative area of research and development and has identified refinements that will further increase the efficiency and acceptability of the process.     

A model biological neural network: the cephalopod vestibular system

Artificial neural networks (ANNs) have become increasingly sophisticated and are widely used for the extraction of patterns or meaning from complicated or imprecise datasets. At the same time, our knowledge of the biological systems that inspired these ANNs has also progressed and a range of model systems are emerging where there is detailed information not only on the architecture and components of the system but also on their ontogeny, plasticity and the adaptive characteristics of their interconnections. We describe here a biological neural network contained in the cephalopod statocysts; the statocysts are analogous to the vertebrae vestibular system and provide the animal with sensory information on its orientation and movements in space. The statocyst network comprises only a small number of cells, made up of just three classes of neurons but, in combination with the large efferent innervation from the brain, forms an 'active' sense organs that uses feedback and feed-forward mechanisms to alter and dynamically modulate the activity within cells and how the various components are interconnected. The neurons are fully accessible to physiological investigation and the system provides an excellent model for describing the mechanisms underlying the operation of a sophisticated neural network.     

Ecosystem‐level effects of keystone species reintroduction: a literature review

The keystone species concept was introduced in 1969 in reference to top‐down regulation of communities by predators, but has expanded to include myriad species at different trophic levels. Keystone species play disproportionately large, important roles in their ecosystems, but human‐wildlife conflicts often drive population declines. Population declines have resulted in the necessity of keystone species reintroduction; however, studies of such reintroductions are rare. We conducted a literature review and found only 30 peer‐reviewed journal articles that assessed reintroduced populations of keystone species, and only 11 of these assessed ecosystem‐level effects following reintroduction. Nine of 11 publications assessing ecosystem‐level effects found evidence of resumption of keystone roles; however, these publications focus on a narrow range of species. We highlight the deficit of peer‐reviewed literature on keystone species reintroductions, and draw attention to the need for assessment of ecosystem‐level effects so that the presence, extent, and rate of ecosystem restoration driven by keystone species can be better understood.     

Functional imaging of proteases: recent advances in the design and application of substrate-based and activity-based probes

Proteases are enzymes that cleave peptide bonds in protein substrates. This process can be important for regulated turnover of a target protein but it can also produce protein fragments that then perform other functions. Because the last few decades of protease research have confirmed that proteolysis is an essential regulatory process in both normal physiology and in multiple disease-associated conditions, there has been an increasing interest in developing methods to image protease activity. Proteases are also considered to be one of the few 'druggable' classes of proteins and therefore a large number of small molecule based inhibitors of proteases have been reported. These compounds serve as a starting point for the design of probes that can be used to target active proteases for imaging applications. Currently, several classes of fluorescent probes have been developed to visualize protease activity in live cells and even whole organisms. The two primary classes of protease probes make use of either peptide/protein substrates or covalent inhibitors that produce a fluorescent signal when bound to an active protease target. This review outlines some of the most recent advances in the design of imaging probes for proteases. In particular, it highlights the strengths and weaknesses of both substrate-based and activity-based probes and their applications for imaging cysteine proteases that are important biomarkers for multiple human diseases.     

The evolution of the endowment effect

People often value an item more when they own it than when it is available for purchase, and consequently are relatively reluctant to trade. This is the “endowment effect”, which has been widely documented in human populations and also in some non-human species. This paper develops a simple model in which it is adaptive to have a bias against trade, potentially explaining the basis of the endowment effect. The bias against trade arises from the strategic nature of trade in a moderately competitive environment: the interest of a potential trading partner in making the exchange is evidence that the decision maker already has the more valuable object. The model predicts that an endowment effect is promoted by large uncertainty about the fitness value of items, and also by conditions in which there are on average small gains to be had from trade. Because the model employs a simple bounded rationality heuristic for trade, it explains how the endowment effect could arise in species that lack theory of mind and related strategic reasoning abilities. The model also suggests an explanation for why endowment effects are so rarely observed in biological markets that exist between species. Because the trading classes have very different fitness functions, there is negligible competition across those classes. Consequently, there are substantial mutual gains to trade, so our model predicts there is unlikely to be adaptive pressure for an endowment effect.     

Dynamic stability of steady states and static stabilization in unbranched metabolic pathways

The paper is concerned with the conditions of dynamic (asymptotic) stability of steady states in unbranched metabolic pathways. The stationary flux in such pathways is generally determined by the concentration of the end product due to the effector action of this product on the reactions proceeding in its synthetic pathway. The delay in feedback circuits causes violation of dynamic stability at large static stabilization factors. A method permitting analytic estimation of the critical stabilization factor is suggested. Sufficient and necessary conditions for asymptotic stability of the steady state in the general case of the pathway with a single feedback loop have been established. Mechanisms for maintenance of the steady state asymptotic stability at large static stabilization factors are studied. It has been shown that the range of dynamic stability can be widened greatly, if the pathway contains one or two reactions (but not more) of relatively small effective rate constants. Short strong negative feedback is also found to extend considerably the range of dynamic stability of the pathway. The feedback is more effective if it acts on the reaction with small effective rate constant.     

Climate-driven impacts of prey abundance on the population structure of a tropical aquatic predator

In the present study we explore how annual variation in climate (late wet-season rainfall) affects population demography in a gape-limited obligate piscivorous predator, the Arafura filesnake Acrochordus arafurae in the Australian tropics. These aquatic snakes display extreme sexual dimorphism, with body sizes and relative head sizes of females much larger than those of males. Two consecutive years with low rainfall during the late wet season reduced the abundance of small but not large sized fish. Although snake residual body mass (RBM, calculated from a general linear regression of ln-transformed mass to ln-SVL) decreased after the first year with low prey availability, it was not until the second year that reduced prey abundance caused a dramatic decline in filesnake survival, and hence in population numbers. Thus, our results suggest that most snakes survived the first year of reduced prey abundance, but a successive year with low prey availability proved fatal for many animals. However, the effects of prey scarcity on RBM and survival fell disproportionately on some size classes of snakes. Medium-sized animals (large males and intermediate-sized females) were affected more dramatically than were small or large snakes. We attribute the higher survival of small snakes to their lower energy needs compared to medium-sized individuals, and the higher survival of large snakes to the continued abundance of large prey (mainly large catfish). Two successive years with low abundance of smaller sized prey thus massively modified the size-structure of the filesnake population, virtually eliminating large males and intermediate-sized females. Our field data provide a clear demonstration of the ways in which stochastic variation in climatic conditions can have dramatic effects on predator population demography, mediated via effects on prey availability.     

Predator biomass determines the magnitude of non-consumptive effects (NCEs) in both laboratory and field environments

Predator body size often indicates predation risk, but its significance in non-consumptive effects (NCEs) and predator risk assessment has been largely understudied. Although studies often recognize that predator body size can cause differing cascading effects, few directly examine prey foraging behavior in response to individual predator sizes or investigate how predator size is discerned. These mechanisms are important since perception of the risk imposed by predators dictates behavioral responses to predators and subsequent NCEs. Here, we evaluate the role of predator body size and biomass on risk assessment and the magnitude of NCEs by investigating mud crab foraging behavior and oyster survival in response to differing biomasses of blue crab predators using both laboratory and field methods. Cues from high predator biomass treatments including large blue crab predators and multiple small blue crab predators decreased mud crab foraging and increased oyster survival, whereas mud crab foraging in response to a single small blue crab did not differ from controls. Mud crabs also increased refuge use in the presence of large and multiple small, but not single small, blue crab predators. Thus, both predator biomass and aggregation patterns may affect the expression of NCEs. Understanding the impact of predator biomass may therefore be necessary to successfully predict the role of NCEs in shaping community dynamics. Further, the results of our laboratory experiments were consistent with observed NCEs in the field, suggesting that data from mesocosm environments can provide insight into field situations where flow and turbulence levels are moderate.     

Small Modifications to Network Topology Can Induce Stochastic Bistable Spiking Dynamics in a Balanced Cortical Model

Directed random graph models frequently are used successfully in modeling the population dynamics of networks of cortical neurons connected by chemical synapses. Experimental results consistently reveal that neuronal network topology is complex, however, in the sense that it differs statistically from a random network, and differs for classes of neurons that are physiologically different. This suggests that complex network models whose subnetworks have distinct topological structure may be a useful, and more biologically realistic, alternative to random networks. Here we demonstrate that the balanced excitation and inhibition frequently observed in small cortical regions can transiently disappear in otherwise standard neuronal-scale models of fluctuation-driven dynamics, solely because the random network topology was replaced by a complex clustered one, whilst not changing the in-degree of any neurons. In this network, a small subset of cells whose inhibition comes only from outside their local cluster are the cause of bistable population dynamics, where different clusters of these cells irregularly switch back and forth from a sparsely firing state to a highly active state. Transitions to the highly active state occur when a cluster of these cells spikes sufficiently often to cause strong unbalanced positive feedback to each other. Transitions back to the sparsely firing state rely on occasional large fluctuations in the amount of non-local inhibition received. Neurons in the model are homogeneous in their intrinsic dynamics and in-degrees, but differ in the abundance of various directed feedback motifs in which they participate. Our findings suggest that (i) models and simulations should take into account complex structure that varies for neuron and synapse classes; (ii) differences in the dynamics of neurons with similar intrinsic properties may be caused by their membership in distinctive local networks; (iii) it is important to identify neurons that share physiological properties and location, but differ in their connectivity.     

A partial flip classroom exercise in a large introductory general biology course increases performance at multiple levels

Incorporation of active learning into large lecture classes is gaining popularity as a pedagogical method due to its known benefits in helping learning outcomes. A more recent active learning technique that has emerged is the flipped classroom. In this study, we investigated the effects of incorporating a ‘partial-flip’ into an introductory general biology course, where only a portion of the class time was spent in a flipped classroom format. This partial flip presented the classic biology experiment of Meselson and Stahl that discovered the mechanism of DNA replication. Performance on in-class formative assessments and subsequent summative assessments (eg out-of-class assignments and exams relating to this material) was compared between a class that had the partial flip and a control class that had a traditional lecture. The partial flip students scored higher on in-class formative questions, specific exam questions and final exam essay questions. We found that the partial flip had different effects in males versus females depending on the assessment. The partial flip manipulation appeared equally effective in aiding both below and above average students in formative assessments. Overall, this study shows that the partial flip classroom can be an effective technique to incorporate into existing courses and that it does provide some benefits compared to traditional lecture.     

Restricted movement by mottled sculpin (pisces: cottidae) in a southern Appalachian stream

1. We used direct observation and mark‐recapture techniques to quantify movements by mottled sculpins (Cottus bairdi) in a 1 km segment of Shope Fork in western North Carolina. Our objectives were to: (i) quantify the overall rate of sculpin movement, (ii) assess variation in movement among years, individuals, and sculpin size classes, (iii) relate movement to variation in stream flow and population size structure, and (iv) quantify relationships between movement and individual growth rates. 2. Movements were very restricted: median and mean movement distances for all sculpin size classes over a 45 day period were 1.3 and 4.4 m respectively. Nevertheless, there was a high degree of intrapopulation and temporal variation in sculpin movement. Movement of juveniles increased with discharge and with the density of large adults. Movement by small and large adults was not influenced by stream flow, but large adults where more mobile when their own density was high. Finally, there were differences in the growth rates of mobile and sedentary sculpins. Mobile juveniles grew faster than sedentary individuals under conditions of low flow and high density of large adults, whereas adults exhibited the opposite pattern. 3. Our results support the hypothesis that juvenile movement and growth is influenced by both intraspecific interactions with adults and stream flow. In contrast, adult movement appears to be influenced by competitive interactions among residents for suitable space. The relationship between movement and growth may provide a negative feedback mechanism regulating mottled sculpin populations in this system.     

Mechanisms of ventricular arrhythmias: a dynamical systems-based perspective

Defining the cellular electrophysiological mechanisms for ventricular tachyarrhythmias is difficult, given the wide array of potential mechanisms, ranging from abnormal automaticity to various types of reentry and kk activity. The degree of difficulty is increased further by the fact that any particular mechanism may be influenced by the evolving ionic and anatomic environments associated with many forms of heart disease. Consequently, static measures of a single electrophysiological characteristic are unlikely to be useful in establishing mechanisms. Rather, the dynamics of the electrophysiological triggers and substrates that predispose to arrhythmia development need to be considered. Moreover, the dynamics need to be considered in the context of a system, one that displays certain predictable behaviors, but also one that may contain seemingly stochastic elements. It also is essential to recognize that even the predictable behaviors of this complex nonlinear system are subject to small changes in the state of the system at any given time. Here we briefly review some of the short-, medium-, and long-term alterations of the electrophysiological substrate that accompany myocardial disease and their potential impact on the initiation and maintenance of ventricular arrhythmias. We also provide examples of cases in which small changes in the electrophysiological substrate can result in rather large differences in arrhythmia outcome. These results suggest that an interrogation of cardiac electrical dynamics is required to provide a meaningful assessment of the immediate risk for arrhythmia development and for evaluating the effects of putative antiarrhythmic interventions.     

Winner-take-all selection in a neural system with delayed feedback

We consider the effects of temporal delay in a neural feedback system with excitation and inhibition. The topology of our model system reflects the anatomy of the avian isthmic circuitry, a feedback structure found in all classes of vertebrates. We show that the system is capable of performing a 'winner-take-all' selection rule for certain combinations of excitatory and inhibitory feedback. In particular, we show that when the time delays are sufficiently large a system with local inhibition and global excitation can function as a 'winner-take-all' network and exhibit oscillatory dynamics. We demonstrate how the origin of the oscillations can be attributed to the finite delays through a linear stability analysis.     

Impact of problem-based learning in a large classroom setting: student perception and problem-solving skills

Problem-based learning (PBL) can be described as a learning environment where the problem drives the learning. This technique usually involves learning in small groups, which are supervised by tutors. It is becoming evident that PBL in a small-group setting has a robust positive effect on student learning and skills, including better problem-solving skills and an increase in overall motivation. However, very little research has been done on the educational benefits of PBL in a large classroom setting. Here, we describe a PBL approach (using tutorless groups) that was introduced as a supplement to standard didactic lectures in University of British Columbia Okanagan undergraduate biochemistry classes consisting of 45-85 students. PBL was chosen as an effective method to assist students in learning biochemical and physiological processes. By monitoring student attendance and using informal and formal surveys, we demonstrated that PBL has a significant positive impact on student motivation to attend and participate in the course work. Student responses indicated that PBL is superior to traditional lecture format with regard to the understanding of course content and retention of information. We also demonstrated that student problem-solving skills are significantly improved, but additional controlled studies are needed to determine how much PBL exercises contribute to this improvement. These preliminary data indicated several positive outcomes of using PBL in a large classroom setting, although further studies aimed at assessing student learning are needed to further justify implementation of this technique in courses delivered to large undergraduate classes.     

New gene selection method for classification of cancer subtypes considering within-class variation

In this work we propose a new method for finding gene subsets of microarray data that effectively discriminates subtypes of disease. We developed a new criterion for measuring the relevance of individual genes by using mean and standard deviation of distances from each sample to the class centroid in order to treat the well-known problem of gene selection, large within-class variation. Also this approach has the advantage that it is applicable not only to binary classification but also to multiple classification problems. We demonstrated the performance of the method by applying it to the publicly available microarray datasets, leukemia (two classes) and small round blue cell tumors (four classes). The proposed method provides a very small number of genes compared with the previous methods without loss of discriminating power and thus it can effectively facilitate further biological and clinical researches.     

Future of antibody purification

Antibody purification seems to be safely ensconced in a platform, now well-established by way of multiple commercialized antibody processes. However, natural evolution compels us to peer into the future. This is driven not only by a large, projected increase in the number of antibody therapies, but also by dramatic improvements in upstream productivity, and process economics. Although disruptive technologies have yet escaped downstream processes, evolution of the so-called platform is already evident in antibody processes in late-stage development. Here we perform a wide survey of technologies that are competing to be part of that platform, and provide our [inherently dangerous] assessment of those that have the most promise.