Their paucity, combined with their molecular, anatomical, and physiological diversity, has made it difficult to even establish a consensual nomenclature. However, recent technological advances in microscopy and mouse genetics have fostered a renewed interest in neocortical interneurons by putting them within “visible” reach of experimenters. The anatomically well-defined whisker-to-barrel pathway of the rodent is particularly amenable to studies attempting to link cortical circuit dynamics to behavior. To each whisker corresponds a discrete cortical unit equivalent to a single column, specialized in the encoding and processing of the sensory information it receives. In this review, we will focus on the functional role that each subtype of supragranular GABAergic neuron embedded within such a single neocortical unit may play in shaping the dynamics of the local circuit during somatosensory integration.Although the neocortex forms a distributed system comprised of several functional areas, its vertical columnar organization is largely conserved across areas and species, suggesting the existence of a canonical neocortical microcircuit. In order to elucidate the principles governing the organization of such a cortical diagram, a detailed understanding of the dynamics binding different types of cortical neurons into a coherent algorithm is essential. Within this complex circuitry, GABAergic interneurons, while forming approximately only 15–20% of all cortical neurons, appear critical in maintaining a dynamic balance between excitation and inhibition. Despite their importance, cortical GABAergic neurons have not been extensively studied  When the whisker of a rodent contacts an object, the ensuing deflection is encoded into action potential output of sensory neurons located in the infraorbital branch of the trigeminal nerve. These neuronal signals eventually reach the primary somatosensory cortex, where the information they contain is thought to be integrated and processed [reviewed in Petersen ]. While 2+ spikes that efficiently propagate to the soma and initiate action potential firing  to have a significant impact on action potential generation. However, coincident and temporally precise sequences of dendritic inputs may generate local CaThe diversity of cortical GABAergic neurons extends beyond targeted domains of principal cells, and it is now widely accepted that molecular and physiological properties also contribute to this remarkable heterogeneity  inhibitory neurons. Non-FS GABAergic neurons, which form the majority of cortical interneurons, may therefore often be mistaken for pyramidal neurons without proper identification. Analytical tools such as cross-correlation of spike dynamics provide increasingly better resolution, but errors in properly assigning single-unit recordings to a particular cellular type are still unavoidable  allows cellular imaging several hundred microns deep in living animal tissue  is a cation channel which, upon blue light stimulation, leads to rapid depolarization of the neuronal membrane potential and reliable action potential firing. On the other hand, halorhodospin (NpHR) is a chloride pump that is activated upon yellow light illumination, leading to rapid hyperpolarization of the neuronal membrane potential and suppression of action potential firing. Co-expressed with conditional AAV expression vectors carrying transgene cassettes that are activated only in the presence of Cre, these opsins can be targeted for expression in specific cell types using a variety of commercially-available Cre-driver mice lines  and six of which in layer 2/3 (L2/3). Because of their intrinsic connectivity patterns, chemical marker content, anatomical features and passive electrophysiological properties, these eight different types of cells may form functionally-relevant clusters of inhibitory sources within local microcircuits. GABAergic cells of a particular subtype most often form electrical synapses or gap junctions between themselves, a property that may promote synchronization of action potential discharges [reviewed in Hestrin and Galarreta ]. Cell-tin vivo, while the behaviorally-dependent neuronal activity of others still remains to be determined. Here, we provide a framework for engaging the research community into probing still deeper into this fascinating family of cortical neurons.Some of the following neuronal classes have already been studied in vivo powerfully modulates sensory responses in L2/3 PC  of the cortex extends roughly 10% of the way down at the level of mouse somatosensory cortex. Almost all neurons located within its boundaries are believed to be GABAergic in the mature cortex  form one of two major subtypes of GABAergic neurons identified in the outermost layer of barrel cortex. Genetically, they are characterized by the expression of neuronal nitric oxide synthase (nNOS) . The level of spike frequency adapation during high current injections was found to be non-accommodating in the juvenile rat   can respond to principal whisker deflection with short latencies, indicating that they may receive direct thalamocortical afferents  in addition to alpha-actinin-2 (Aac) which is also present in L1 NGFCs , but can also co-express a variety of other neuropeptides including NPY, VIP, and cholecystokinin (CCK) Druga, .In vivo, the spontaneous firing rate of BC neurons was found to be the highest amongst all L2/3 cell types despite their low input resistance and high rheobase , serotonin 3a receptors (5HT3AR), making them the most genetically diverse subtype of supragranular cortical GABAergic neuronal classes ” has been identified in juvenile mouse neocortex In this review, we have focused on the potential functional role played eight of the numerous cellular subtypes encountered within the family of cortical GABAergic supragranular neurons. While we assigned one possible circuit role to each of these, it is probable that any particular GABAergic subtype we described conveys several key functional properties to the cortical network in a state-dependent manner. In order to better understand how each subtype is integrated into the local circuit dynamics, it will be essential to monitor their activity during different behaviors. The whisker of a rodent may be passively deflected, or a rodent may engage in active whisking behavior leading to large and rapid cycles of whisker protractions and retractions interrupted when a nearby obstacle is encountered. Preliminary results suggest that GABAergic neurons are differentially activated during such behavioral events (Gentet et al., While most cortical GABAergic cells are interneurons with restricted local axonal arborizations, their recruitment may involve presynaptic neurons from many parts of the brain. Ascending pathways from the brainstem are particularly prone to such cell-type specific neuromodulation. Behaviorally-relevant fast synaptic excitation of specific cortical GABAergic subtypes through the activation of inotropic 5HT3AR receptors may be controlled by cortically-projecting serotonergic neurons in the dorsal raphe (Bang et al., Recently, the recruitment of cortical GABAergic neurons has been established in the cortico-cortical crossmodal synaptic inhibition of L2/3 PC in mouse primary sensory cortices (Iurilli et al., We live an exciting time in the field of cortical GABAergic neuron research. More powerful and specific transgenic mice models are bound to emerge in the next few years, offering researchers opportunities to probe with ever greater details the array of complex functions subserved by this essential neuronal family. In the future, we should endeavor to perform more systematic studies of the response properties of identified GABAergic neurons to help us uncover the temporal sequence of synaptic events leading to the efficient sensory integration of somatosensory information within a single barrel column. This basic framework for sensory processing may subsequently serve in the formulation of rules governing a putative canonical neocortical circuit [reviewed in Douglas and Martin ] that maThe author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


To assess and manage pain in children and adolescents with mild to moderate intellectual disability, healthcare providers need access to updated tools and current knowledge. Recent studies show that these children can verbally express pain and use self-assessment tools accurately. Moreover, they know pain coping strategies. Finally, they show mental imaging skills and are able to recall autobiographical memories. These new data suggest that such children and adolescents could be candidates to for hypno-analgesia protocols and behavioral relaxation. People with intellectual disabilities are now recognized as a population at risk for unmanaged pain , after bAppropriate management of pain requires appropriate assessment. Caregivers need access to reliable and scientifically validated scales as well as updated knowledge about pain in this population.Research has been slow to develop specific assessment tools, for a review, see , 8. Now a priori from assessment practices.Pain is a highly subjective phenomenon, self-report is appropriate in many clinical settings and it is fast and easy to use. Nevertheless in children with developmental or intellectual disabilities, self-assessment seems systematically excluded The first study about pain self-assessment abilities in children with intellectual disabilities included 47 children with various levels of disability and 111 children without any disability, all with planned surgery , or emotional regulation control (distraction). These strategies reduce the anxiety caused by pain when the event is uncontrollable . But if Healthcare providers still seem to have prejudices about the relevance and efficacy of pain treatments in people with intellectual disabilities . Even whThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


To what extent are sensory responses in the brain compatible with first-order principles? The efficient coding hypothesis projects that neurons use as few spikes as possible to faithfully represent natural stimuli. However, many sparsely firing neurons in higher brain areas seem to violate this hypothesis in that they respond more to familiar stimuli than to nonfamiliar stimuli. We reconcile this discrepancy by showing that efficient sensory responses give rise to stimulus selectivity that depends on the stimulus-independent firing threshold and the balance between excitatory and inhibitory inputs. We construct a cost function that enforces minimal firing rates in model neurons by linearly punishing suprathreshold synaptic currents. By contrast, subthreshold currents are punished quadratically, which allows us to optimally reconstruct sensory inputs from elicited responses. We train synaptic currents on many renditions of a particular bird's own song (BOS) and few renditions of conspecific birds' songs (CONs). During training, model neurons develop a response selectivity with complex dependence on the firing threshold. At low thresholds, they fire densely and prefer CON and the reverse BOS (REV) over BOS. However, at high thresholds or when hyperpolarized, they fire sparsely and prefer BOS over REV and over CON. Based on this selectivity reversal, our model suggests that preference for a highly familiar stimulus corresponds to a high-threshold or strong-inhibition regime of an efficient coding strategy. Our findings apply to songbird mirror neurons, and in general, they suggest that the brain may be endowed with simple mechanisms to rapidly change selectivity of neural responses to focus sensory processing on either familiar or nonfamiliar stimuli. In summary, we find support for the efficient coding hypothesis and provide new insights into the interplay between the sparsity and selectivity of neural responses. Brains of higher vertebrates analyze the sensory world in hierarchical networks. In lower sensory brain areas, neurons tend to respond to generic stimulus features, whereas in higher areas they typically respond to only very small subsets of natural stimuli Feature tuning in sensory neurons can be explained by a neuronal strategy to efficiently encode natural stimulus ensembles, such as e.g. in simple cells of primary visual cortex or in auditory cells of the cochlear ganglion The rationale of our work is that the firing sparsity of cells is governed by slow developmental mechanisms that construct efficient representations of natural stimulus statistics and by faster mechanisms influenced by the recent stimulus history and the state of the animal and its environment. In many cells, excitatory and inhibitory currents are balanced in proximity of the firing threshold, though currents can be dominated by inhibition, as for example in some sparsely firing neurons In our model, we reflect the asymmetry imposed by the firing threshold (supra- versus sub-threshold responses) by an asymmetric cost on sub- and suprathreshold synaptic currents. We train neurons using a particular firing threshold and thereafter we explore the consequences of shifts in the excitatory/inhibitory balance by evaluating neural responses for an entire range of firing thresholds.Our model is applicable to sensory systems in general but presented as a model of the auditory forebrain pathway of songbirds. This pathway extends over the nucleus ovoidalis to field L, and from there up to HVC We model the auditory pathway as a feedforward network that receives (indirect) auditory input from the cochlea in the form of spectro-temporal sound patterns. These patterns are mean-subtracted, multiplied by synaptic weights, and summed, to result in the total synaptic current impinging onto neurons. Given this linear model we interpret the set of synaptic weights onto a neuron as its spectro-temporal receptive field (STRF). We devised an algorithm that optimizes synaptic weights for their propensity to decorrelate (whiten) and sparsify synaptic inputs: First, we whitened cochlear inputs using a projection matrix This model guarantees zero mean synaptic current and minimal variance (see Equation 8). Intuitively, to minimize the cost, frequent cochlear input patterns must elicit weak subthreshold currents . By contrast, rare cochlear input patterns must elicit strong suprathreshold currents . We defined firing rates to be equal to suprathreshold synaptic currents, meaning that the linear cost of suprathreshold currents is in effect a cost on the average population firing rate. In the After training, neurons displayed a large diversity of STRFs. Typically, STRFs were patchy and had multiple adjacent inhibitory and excitatory spectral/temporal subfields. In many neurons, STRFs were regularly arranged into horizontal or vertical stripes , similarModel STRFs had excitatory and inhibitory subfields that together covered the entire spectro-temporal window of the STRF. Typically STRFs in field L are of considerably lower density in that they mostly possess only two or three subfields instead of more than six. We therefore explored whether STRFs in our model would be of lower density when we added a third term to the cost function, a term corresponding to a linear cost on absolute synaptic weights. We found indeed low-density STRFs if the parameter We explored the correspondence between STRFs and the stimulus features to which neurons responded most. In most cells, presentation of different BOS versions elicited reliable responses to specific song notes, Some neurons were not just tuned to a particular syllable within the motif, but had even more specific tuning to particular subsets of that syllable. Finches often produce harmonic stack syllables and can subtly vary the pitch of these syllables in a well-controlled and goal-directed manner STRFs are optimal models of the linear part of neural responses. Can we recover the STRFs found by our algorithm in simulated neural responses which contain a threshold nonlinearity? To this end, we estimated STRFs from nonlinear responses to birdsong stimuli for a range of firing thresholds  regions  than the regions . We founThe distribution of total synaptic currents over all neurons and over all training stimuli was highly asymmetric and contained many positive but few negative outliers,  and REV . Hence, We also explored the influence of other model parameters such as We computed firing rates in model neurons by thresholding total synaptic currents. A recent analysis of sparsely firing cells in primary auditory cortex of unanesthetized rats has revealed that both background and stimulus-evoked firing rates are well fit by log-normal distributions Training the network increased the independence of neural responses. If responses were perfectly independent among neurons, the size distribution of coactive neurons would be binomial (the size distribution is the probability that a given number of neurons fire synchronously). The sole parameter of this binomial model is the single-neuron firing density that we estimated in terms of the fraction of suprathreshold events observed in the entire neuron population and for all training stimuli. In comparison to this binomial model, the observed size distribution elicited by whitened cochlear inputs was substantially wider, illustrating strong firing dependencies. The sparseness transformation significantly narrowed the observed size distribution towards the binomial case, Our network allowed us to decode firing rates and reconstruct the spectro-temporal sound patterns that elicited them, using the pseudo-inverse of the sparseness transformation  see . We evalIn all cases, reconstruction errors increased with increasing firing threshold in a monotonic manner, Moreover, for a given threshold, reconstruction errors tended to be larger for the BOS played back in reverse (REV) than for BOS or CON, illustrating that reconstructions were optimized for stimulus ensembles experienced during training but not for novel ensembles. In the As illustrated in We explored the response selectivity of model neurons using the psychophysical We found a wide range of selectivity behaviors. Many neurons responded more strongly to CON than to BOS, but this CON preference often reversed to BOS preference at high firing thresholds, Our training set contained many versions of two different CONs. For BOS-CON selectivity reversal it did not matter whether selectivity was tested on three novel CONS as in For any given threshold We tested the dependence of BOS selectivity on the temporal summation window and found that our results did not depend critically on STRF width. Model STRFs were 50 ms wide. For 100-ms wide STRFs, BOS-CON and BOS-REV selectivities reversed at around We also tested the effect of neuron number on We assessed whether our model neurons preferred CON over artificial stimuli, as has been reported in field L The key element in our model seemed to be the positive tail of synaptic currents. Because this tail has a non-Gaussian shape, our model can be seen as part of a broader class of independent-component analysis (ICA) algorithms that extract maximally non-Gaussian components from data To account for the layered architecture of the auditory pathway, we also explored a two-layer network, in which the second layer was trained on thresholded first-layer outputs. In simulations, first-layer outputs were first summed over consecutive time bins (to extend receptive field widths in the second layer) and were then subjected to whitening and sparseness transformations  inputs into independent outputs . In most ICA algorithms, independence of outputs is enforced by a symmetric cost such as kurtosis or entropy In our model, the prominence of BOS in the training set and the shape of our cost function conjunctively forced neurons to display minimal suprathreshold synaptic currents to BOS (on average). These minimal responses explain why neurons preferred CON over BOS at moderately low firing thresholds, very much like field-L neurons do. At higher thresholds, neurons responded to specific BOS features more than to other features. In the high-threshold regime, model neurons were BOS selective, and during BOS presentation they fired sparsely and were hyperpolarized on average, all very much like HVC mirror neurons that project to Area X , undesirable signals encountered in the training set can be conveniently suppressed. For example, by excluding the five neurons that encoded high-frequency noise (e.g. Neuron 106), BOS could be efficiently cleaned from that noise see  and S2. Our algorithm offers a powerful method for bioacoustic signal analysis. The diversity of STRFs in our model is well matched with the behavioral richness of birdsong. Stereotyped syllables can be readily detected because they are represented essentially by a single STRF, whereas more variable syllables such as harmonic stacks may be associated with multiple STRFs as in Our study is not the first to examine sparse coding of birdsong. Greene et al. applied a popular sparse coding algorithm to compute optimal linear kernels on large numbers of birdsong spectrograms Our findings may have relevance for the encoding of sensory modalities other than audition, including olfaction. In mammals, strong odorant-selective responses arise immediately downstream of primary sensory inputs Our model can reproduce the selectivity reversal seen in Regarding shifts in excitatory/inhibitory balance, our model predicts that the effect on response selectivity depends on how balance shifts affect firing rates. For example, if increased inhibition leads to decreased firing rates, our model predicts increased response selectivity . In general, manipulations of excitation or inhibition within a network can lead to highly non-trivial reactions, e.g. disruption of local inhibition onto a cell can lead to lower baseline firing rate and to significant changes in firing patterns. For example, in Rosen and Mooney As a model of HVC responses, our findings suggests that vocal-auditory mirrored activity in HVC has a sensory origin  we run a few simulations with an additional term in the cost function, corresponding to a linear cost on absolute synaptic weights, density  in closeWe examined the question whether estimated STRFs using reverse correlation depend strongly on the firing threshold and whether they resemble the STRFs encoded in the synaptic weights. For various thresholds The first term of the cost function in Equation 6 imposes a linear cost on suprathreshold synaptic currents. Because suprathreshold synaptic currents are equivalent to instantaneous firing rates at zero noise, the first term enforces firing sparseness across the population (for the training threshold). The second term imposes a quadratic cost on subthreshold synaptic currents, which is equivalent to minimizing an error bound on decoded cochlear inputs. To see this, consider the following estimate The decoding error associated with the decoding The key insight is that for the training threshold Note that the decoding scheme defined in Equation 12 may not be globally optimal, but was motivated by our assumption that only suprathreshold events carry meaningful information. Also, a benefit of this decoding scheme is its asymptotic robustness (for a threshold of minus infinity the decoding error vanishes).Our algorithm minimizes an approximation of the reconstruction error, but not the reconstruction error itself. Exploratively, we have adapted the algorithm to directly minimize the reconstruction error (defined in Equations 13) for a given threshold From the decoded whitened inputs trograms  using thThe constraint in Equation 8 was naturally enforced by our choice of parameterization of the inverse:Starting with the identity matrix Note that we also formulated an overcomplete version of our algorithm, in which there are more neurons than principal components (the matrix Our training data consisted of 46 sound files of average duration 1.7 s. Thirty-four of these files contained different renditions of a zebra finch song (BOS), twelve files contained conspecific songs (CON) from two independently raised adult zebra finches in our colony (six files each). Our results did not depend sensitively on these file numbers and which song was chosen as the BOS, as long as there was an overall predominance of BOS.To train the synaptic weight matrices, we used a randomized batch learning scheme. First we computed the whitened cochlear inputs based on the matrix In separate simulations we also included in the training set various numbers of files with cage noises such as wing flaps, subsongs and other natural sounds; results did not qualitatively change with the inclusion of these files.We measured the selectivity of neural responses using the psychophysical To evaluate the Audio S1Original Recording of a zebra finch song.(WAV)Click here for additional data file.Audio S2Reconstruction of the song in (WAV)Click here for additional data file.


Motivated behavior exhibits properties that change with experience and partially dissociate among a number of brain structures. Here, we review evidence from rodent experiments demonstrating that multiple brain systems acquire information in parallel and either cooperate or compete for behavioral control. We propose a conceptual model of systems interaction wherein a ventral emotional memory network involving ventral striatum (VS), amygdala, ventral hippocampus, and ventromedial prefrontal cortex triages behavioral responding to stimuli according to their associated affective outcomes. This system engages autonomic and postural responding  in accordance with associated stimulus valence , but does not engage particular operant responses. Rather, this emotional system suppresses or invigorates actions that are selected through competition between goal-directed control involving dorsomedial striatum (DMS) and habitual control involving dorsolateral striatum (DLS). The hippocampus provides contextual specificity to the emotional system, and provides an information rich input to the goal-directed system for navigation and discriminations involving ambiguous contexts, complex sensory configurations, or temporal ordering. The rapid acquisition and high capacity for episodic associations in the emotional system may unburden the more complex goal-directed system and reduce interference in the habit system from processing contingencies of neutral stimuli. Interactions among these systems likely involve inhibitory mechanisms and neuromodulation in the striatum to form a dominant response strategy. Innate traits, training methods, and task demands contribute to the nature of these interactions, which can include incidental learning in non-dominant systems. Addition of these features to reinforcement learning models of decision-making may better align theoretical predictions with behavioral and neural correlates in animals. Natural environments pose numerous challenges to animals seeking to survive and reproduce. Advantage is gained by adapting behavior so as to exploit new opportunities and avoid hazards. The study of these adaptations has enjoyed a rich and active history. Pioneering animal learning psychologists of the mid-twentieth century were divided among those who viewed behavior as the learning of stimulus–response habit associations driven by reinforcement  habits involving dorsolateral striatum (DLS) and (ii) goal-directed control involving dorsomedial striatum (DMS), they also form (iii) an emotional memory system involving the ventral striatum (VS) and its limbic inputs that exerts an important influence on behavior Figure . This emResearch on the functional significance of the amygdala has consistently implicated this brain structure in emotional learning and memory  associations can be used as conditioned reinforcers for learning instrumental responses in the absence of primary rewards  when animals are moved among different testing environments  a dorsolateral “motor” sector involved in skilled movements and habits, (2) a dorsomedial “cognitive” sector involved in allocentric navigation and flexible responding for strategic acquisition of goals, and (3) a ventral “limbic” sector incorporating the core and shell of the nucleus accumbens in the VS that are involved in approach behaviors, arousal, extinction, and response vigor. We first briefly review key literature on the function of each sector before turning to their interaction with each other and other cortico-limbic structures.The rodent DLS appears to primarily bring reinforcement-related operant movements under specific stimulus and temporal control as a result of repeated reinforced stimulus-response (S-R) experiences, which can eventually form habits  of a compound stimulus, but are impaired when they have to switch dimensions for proper discrimination  learning . CPP is an appetitive classical conditioning paradigm that uses distal spatial cues as the conditioned stimuli. Acquisition of this task normally involves a synergistic interaction between the amygdala, hippocampus, and VS  in one room, and learn operant responding for food in another room. Animals drastically reduce responding when the Pavlovian cue is presented during the operant task, likely owing to a fearful state that suppresses instrumental responding  strategy later in training  and within-session spatial information (what arms have been previously visited) requires both intact DLS and hippocampus  and response (turn) that is repeatedly reinforced in a particular context “A” (room). Responses to a CS-  are not reinforced. The effects of reversal learning among these stimuli in context A or a different context B show that reversal is slower in context A, in which the original training occurred  approach behaviors needed to engage in operant responding and (ii) the vigor of responding , rather than selecting specific operant responses. We propose that the emotional memory network formed by VS, amygdala, ventral hippocampus, prefrontal cortex, and dopamine input can be conceptualized as triaging responses to stimuli based on their associated affective value in a context. When stimuli are associated with aversive outcomes, this system engages freezing and autonomic responses  via brainstem targets dissociated from habit or goal directed systems. For stimuli with positive valence, we propose the following simple model Figure . Early iDopamine in the striatum is critical for learning and executing actions  and sensory-sensory (hippocampus) associations may provide a solution for the problem of learning to thrive in large environments that present many unproductive stimuli and permit many inconsequential actions, which is computationally difficult to solve (Sutton and Barto, Learning and memory systems involved in behavioral control appear to function in parallel, even when they are not part of the dominant response strategy. However, these non-dominant associations may become relevant when adapting to changing environmental contingencies. For reversal learning of a habit, suppression of both the dominant response and latent/conditioned inhibition to previously-irrelevant stimuli must accompany formation of new associations between stimuli, responses, and values. Dysfunction of any of these processes will retard reversals. Thus, a multiple-systems-level conceptualization may help drive new insight to decision-making processes in the brain, particularly regarding the role of emotional memories and the control of habitual responding, and may come to illuminate the processes underlying many examples of inflexible or irrational human behavior involving emotion (Ditto et al., The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Microsatellite instability (MSI) is characterized by the expansion or contraction of DNA repeat tracts as a consequence of DNA mismatch repair deficiency (MMRD). Accurate detection of MSI in cancer cells is important since MSI is associated with several cancer subtypes and can help inform therapeutic decisions. Although experimental assays have been developed to detect MSI, they typically depend on a small number of known microsatellite loci or mismatch repair genes and have limited reliability. Here, we report a novel genome-wide approach for MSI detection based on the global detection of insertions and deletions (indels) in microsatellites found in expressed genes. Our large-scale analyses of 20 cancer cell lines and 123 normal individuals revealed striking indel features associated with MSI: there is a significant increase of short microsatellite deletions in MSI samples compared to microsatellite stable (MSS) ones, suggesting a mechanistic bias of repair efficiency between insertions and deletions in normal human cells. By incorporating this observation into our MSI scoring metric, we show that our approach can correctly distinguish between MSI and MSS cancer cell lines. Moreover, when we applied this approach to primal tumor samples, our metric is also well consistent with diagnosed MSI status. Thus, our study offers new insight into DNA mismatch repair system, and also provides a novel MSI diagnosis method for clinical oncology with better reliability. In normal cells, mismatch repair (MMR) system provides a highly efficient mechanism for correcting errors that occur during DNA replication. When impaired, e.g. through inactivation of human mismatch repair genes such as MLH1, MSH2 and MSH3, mismatch repair deficiency leads to uncorrected insertions/deletions (indels), particularly in microsatellites where a short sequence unit (one to six nucleotides long) is repeated multiple times Microsatellite instability (MSI) refers to the genetically aberrant condition in which microsatellite alleles in genome gain or lose repeat units at much higher frequency than in normal cells. The normal condition is often referred to as microsatellite stable, or MSS. Widespread MSI usually indicates mismatch repair deficiency (MMRD), which can cause accumulation of mutations in cancer-related genes and lead to carcinogenesis and tumor progression. Accordingly, MSI is frequently observed in several types of cancers, most notably in colon cancer Currently, several assays exist for the detection of MSI, including those looking for mutations in MMR genes, measuring their expression, or looking for unit number alterations in a set of microsatellites frequently affected by MSI Many other factors can negatively affect the accuracy of available MSI detection techniques. Methods that use loss of expression or mutation of known MMR genes may be hampered by the complexity of the MMR system, which consists of multiple genes and possibly other uncharacterized ones. The low sensitivity of unit number based approaches may be explained by the random nature of MSI: MMRD may affect different sets of microsatellites in different individuals. That may explain why the limited sets of markers used in current MSI detection assays sometimes give false negatives.To overcome such limitations, we developed a novel method that improves the sensitivity of MSI detection by incorporating all detectable microsatellites across the genome characterized by next-generation sequencing. We chose to base our analysis on RNA-Seq, as it is a relatively mature next-generation sequencing technique and has already been widely performed for various applications. Although short-read sequences pose challenges for mapping and characterizing microsatellites, we have overcome these issues and demonstrated the reliability of our genome-wide scanning approach for MSI detection. In addition to basing detection on a vastly increased number of microsatellite indels in MSI cells, our approach exploits a phenomenon so far only reported in yeast but that we observed in human cells in this study: indel length distributions in MSI and MSS samples are significantly different In this study, we used RNA-seq datasets for 20 different cancer cell lines in order to investigate MSI frequencies in different cancer types. All cancer cell line datasets were obtained from published studies, and the MSI status of many of these cell lines has already been reported . We first extracted microsatellites in all human RefSeq transcripts using Tandem Repeats Finder (TRF) We evaluated several MSI measures based on the number of indels and microsatellites determined by our analysis pipeline. These measures included the proportion of microsatellite insertions over all insertions (denoted as PI), and the proportion of microsatellite deletions over all deletions  in cancer cell lines from the RNA-seq data. We used Cufflinks We first sought to identify indels within the RNA-seq samples used in this study . After short-read alignment using BWA, we used DINDEL to call indels in our 20 cancer cell lines and 123 HapMap RNA-seq datasets. From the DINDEL outputs, we filtered out indels listed in Single Nucleotide Polymorphism database  Next, we sought to determine the frequency with which microsatellite sequences are altered by indels in each RNA-seq sample. A total of 505,657 microsatellites were found in 32,199 Refseq transcript sequences using TRF. We then determined the number of microsatellites altered by at least one indel in each RNA-seq sample. This quantity ranges from 54 to 482 in HapMap samples, and from 77 to 1454 in cancer cell lines. In all following analyses, we only study indels within microsatellites. In each sample, we then determined the proportion of microsatellites altered by indels located in 5′ UTR, coding sequence, 3′ UTR or non-coding RNAs, and determined whether these proportions are significantly different between MSI and HapMap samples and between MSS and HapMap samples. We observed a significant increase in the proportion of indels in MSI samples’ coding sequences , and the proportion of microsatellite deletions over all deletions  for detecting microsatellite instability using transcriptome sequencing data. Unlike other approaches that are limited to querying a small number of genes or microsatellite regions, our method integrates indel data from a large number of expressed microsatellites. Our approach does not depend on germline DNA and is therefore equally applicable to cancer cell lines and primary samples. We have shown that our approach is more accurate than approaches based on the detection of point mutation or expression changes in mismatch repair genes. Another advantage of our approach is that the MSI-seq index provides a continuous measure of MSI. In previous studies, MSI was often treated as an all-or-nothing event. Traditional assays could only tell whether a sample is MSI or MSS. However, in biologically relevant cases, the MSI status of samples are likely to span a continuous spectrum, and the extent of MSI may have therapeutic implications. Therefore, the MSI-seq index (PI/PD ratio) used in this study may be a promising candidate for quantifying the relative MSI degree of a sample.During the course of our investigations regarding indels in cancer cell lines, we have made a number of interesting observations. We have found that short deletions in microsatellite regions, especially 1 bp deletions, are consistently highly over-represented in MSI cancer cell lines compared to MSS cancer cell lines and immortalized but non-malignant HapMap samples. On the other hand, we did not find any consistent increase in longer deletions or insertions in MSI samples. A similar observation has been made in yeast Another observation is that that there are more microsatellite indels in coding regions in cancer cells and especially in MSI-positive cancer cells. This discovery is surprising since a substantial fraction of these indels are expected to cause internal frameshifts, non-sense mediated decay and therefore gene inactivation. Our results on the other hand suggest that cancer cells with increased coding microsatellite indels might be positively selected and therefore that coding microsatellite indels could contribute to the tumor phenotypes. Alternatively, these indels might generate functional diversity that allows rapid adaptation of the tumor cells to changing environments, perhaps similar to what has been observed in yeast Our method is based on transcriptome sequencing, which has some limitations when used for MSI characterization. For instance, it will miss altered microsatellites located in regulatory sequences, which may also play important roles in oncogenesis. Moreover, as indel detection requires adequate read coverage, it may be difficult to detect microsatellite indels in transcripts with low abundances. Despite above disadvantages, inspection of expressed transcripts still provides significant information about MMRD. As RNA-seq experiments are widely performed and the price for sequencing cancer samples is rapidly decreasing, in the future RNA-seq based diagnosis method will become cost effective for clinical applications. Moreover, one single RNA-Seq assay is able to provide accurate MSI diagnosis along with rich information about the many other aspects of tumor, including functional mutations, gene expression profiles, active pathways and gene fusions, etc, making specialized PCR assays for MSI unnecessary.In conclusion, our method is the first to enable genome-wide characterization of MMRD status in human cell through the integration of high-throughput sequencing data. Consistent with previous findings, we have observed a significant increase of short deletions in MSI cells compared to MSS ones. Based on this observation, we showed that the PI/PD ratio  can be used to quantify MSI status in both cancer cell lines and primal tumor samples from patients, and has multiple advantages over traditional assays. Therefore, our method has the potential of serving as a novel diagnosis tool of genomic instability for different cancer samples.


Hyperglycemia, in both diabetic and nondiabetic patients, has a significant negative impact on the morbidity and mortality of patients presenting with an acute myocardial infarction (AMI). Contemporary evidence indicates that persistent hyperglycemia after initial hospital admission continues to exert negative effects on AMI patients. There have been a number of studies demonstrating the benefit of tight glucose control in patients presenting with AMI, but a lack of convincing clinical data has led to loose guidelines and poor implementation of glucose targets for this group of patients. The CREATE-ECLA study, which hypothesized that a fixed high dose of glucose, insulin, and potassium (GIK) would change myocardial substrate utilization from free fatty acids to glucose and therefore protect ischemic myocardium, failed to demonstrate improved clinical outcomes in AMI patients. Studies that specifically investigated intensive insulin therapy, including DIGAMI-2 and HI-5, also failed to improve clinical outcomes such as mortality. There are a number of reasons that these trials may have fallen short, including the inability to reach glucose targets and inadequate power. There is now a need for a large placebo-controlled randomized trial with an adequate sample size and adherence to glucose targets in order to establish the benefit of treating hyperglycemia in patients presenting with AMI. Major advances in cardiovascular disease, and specifically the treatment of acute coronary syndrome (ACS), have had a significant impact on the morbidity and mortality of patients with acute myocardial infarctions (AMI). Despite these advances, diabetes continues to put patients with and without a prior history of myocardial infarction at significant cardiovascular risk .  The prIt has been well documented that with adequate glycemic control, cardiovascular outcomes improve in patients with both type 1 and type 2 diabetes . InteresThis raises the question: what are the effects of hyperglycemia, standard glycemic control, and intensive glycemic control in the setting of acute myocardial infarction and/or acute coronary syndrome? How do these effects differ in long-standing diabetic and nondiabetic populations? While there has been extensive study in the area of hyperglycemia and cardiovascular outcomes in AMI, there is no consensus regarding blood glucose targets and the benefits of treating hyperglycemia in this setting. This in turn is leading to poor control of blood glucose in the AMI setting, an area where further studies could yield significant improvement in cardiovascular outcomes.The prevalence of admission hyperglycemia (glucose levels of >140 mg/dL) in different epidemiological studies ranges from 51% to >58% of patients admitted with AMI . In patiIn addition to decreased contractility, pump failure, and arrhythmia, hyperglycemia in AMI may affect coronary perfusion prior to and following percutaneous coronary intervention (PCI). A 2005 observational analysis by Timmer and colleagues sought to determine how hyperglycemia affected coronary perfusion prior to revascularization in ST-segment elevation myocardial infarction (STEMI) . In 460 Another interesting aspect of the prognostic value of hyperglycemia in AMI is the differences observed in nondiabetic and diabetic patients. In their 2011 study, Lazerri and colleagues observed that in a cohort of STEMI patients undergoing mechanical revascularization, in-hospital peak glycemia was an independent predictor for early death in patients without previously known diabetes, but not in diabetic STEMI patients. At followup, in hospital peak glycemia was able to affect long-term survival in both diabetic and nondiabetic patients. This data underscores the clinical importance of the prognostic role of in-hospital glucose values and strongly suggests that different glucose targets and thresholds may be pursued in diabetic and nondiabetic STEMI patients . Controlling hyperglycemia during AMI admissions has been the target of a great deal of basic and clinical research, with results primarily trending toward a benefit. The optimal “glucose target” has been elusive, and contemporary guidelines reflect this , 21.  A Although this data looks promising, previous large prospective studies of insulin in AMI have resulted in varying levels of benefit. Many of these studies involved infusion of a fixed high dose of glucose, insulin, and potassium (GIK) to change myocardial substrate utilization from free fatty acids to glucose. It was hypothesized that this, in turn, would protect the ischemic myocardium , 25. In Apart from GIK regimens, there have been other studies that have infused insulin in hyperglycemic patients with AMI with the intent to reduce glucose, including the DIGAMI, DIGAMI-2 and HI-5 trial. While the DIGAMI study was able to demonstrate a decrease in both mortality and mean 24-hour blood glucose levels, the DIGAMI-2 and HI-5 studies showed no such significant decrease  27–29].–29.27–29The benefit of insulin infusion in patients with hyperglycemia in ACS has yet to be demonstrated convincingly in a large prospective clinical trial. While there is significant evidence that admission and postadmission hyperglycemia is associated with increased mortality and morbidity in AMI, there is no consensus regarding the targets and the benefits of treating hyperglycemia in this setting. This is illustrated by the 2009 ACC/AHA focused update on STEMI, which makes a rather weak recommendation  for the If the lowering of glucose levels with insulin infusion can demonstrate a reduction in adverse cardiac outcomes over and above the benefits provided by reperfusion therapy, it would be a significant improvement in the management of ACS in the reperfusion era. Indeed, this was reflected in a 2008 AHA statement on hyperglycemia in ACS, where the guidelines emphasized the need for a large prospective randomized study examining this issue. Specifically, it recommends randomized multicenter trials which should include hyperglycemic patients both with and without preexisting diabetes (suggested definition is plasma glucose >140 mg/dL at admission), should use safe and effective protocols for glucose control, and should afford sufficient statistical power to assess mortality as a primary outcome . While significant advances have been made in the treatment and prevention of cardiovascular disease, hyperglycemia in the setting of acute myocardial infarction remains an area where aggressive therapy could lead to a significant improvement in outcomes. Current guidelines stipulate a blood glucose goal of 180 mg/dL with the use of an insulin-based regimen in the setting of AMI; however, a more aggressive target has not been universally recommended primarily due to lack of convincing evidence. While observational and small prospective studies, as well as experimental data, have demonstrated a benefit in driving down a glucose target using insulin infusion , a rando


The FDA in its 2004 Critical Path Initiative document highlighted an alarming decline in the number of innovative medicinal products being submitted for approval2i) makes the study more efficient , (ii) increases likelihood of success of study objective, and (iii) yields improved understanding of treatment effect An adaptive design is defined as a clinical trial design that uses accumulating data to decide on how to modify aspects of the study as it continues, without undermining the validity and integrity of the trialad-hoc rescue measure for poor planning5It needs to be emphasized that the use of adaptive design in a particular trial needs to be supported by a sound rationale. Such rationale might include treating trial patients as effectively and/or ethically as possible, minimizing overall drug development cost and making development process more efficient. This ensures that the most appropriate  means have been utilized in seeking answer to the research question. Adaptations are thus meant as a design feature to enhance trial efficiency and not as an ad-hoc adaptation) imply changes that could not be envisioned at the beginning, but their need became apparent as trial continues. Retrospective adaptations generally imply changes in statistical analysis plan made prior to database lock or un-blindinge.g., response adaptive randomization); sampling rule defines how many subjects will be sampled in the next stage ; stopping rule defines when to stop the trial ; decision rule defines decisions pertaining to design change, not covered by the other three rules 9Although the enthusiasm surrounding adaptive designs is relatively a recent phenomenon, concept-wise, the origin of adaptive designs can be traced back to 1970s when adaptive randomization and sequential trial designs were introducedExamples of some commonly used adaptive designs include: (1) Adaptive randomization design wherein starting with equal number of subjects in each study arm, modification of randomization scheme is made based on treatment response and more patients are randomized to the arm showing better response, (2) Group sequential design that allows premature stopping of a trial based on efficacy / safety / futility, (3) Sample-size re-estimation that allows adjustment of sample size based on updated variance estimation at an interim look, (4) Drop-the-loser design which is a two-stage design mostly employed in phase II clinical development and allows dropping inferior treatment arm at the end of first stage and taking only the superior arm to the second stage, (5) Adaptive seamless phase II-III design having a learning stage (phase II) and a confirmatory stage (phase III) and the transition from phase II to phase III occurs without any gap, saving considerable time and using fewer number of subjects, (6) Adaptive dose finding design that is often used in early clinical development to identify the minimum effective dose and/or maximum tolerated dose, (7) Biomarker adaptive design that allows for adaptations based on response of biomarkers such as genomic markers, 8) Adaptive treatment switching design that allows switching of a patient’s treatment from an initial treatment to some alternative treatment, based on evidence of lack of efficacy or safety concerns of the initial treatment, (9) Adaptive hypothesis design that allows changes in hypothesis from superiority to non-inferiority before database lock or un-blinding, and (10) Multiple adaptive design which is a combination of any of the above designs AdaptiveDespite their well-perceived advantages, the adaptive trials are complex to design, require more upfront planning, and are often met with statistical, procedural, logistic and regulatory challenges. Too many adaptations in the inclusion-exclusion criteria might result in incorporation of a totally different population, compared to what was originally planned. The major statistical concern arising out of too many such adaptations is that they tend to introduce operational bias and the overall type I error rate  might not be controlled4588The crux of successful adaptation lies in preserving validity, integrity and quality of the trial, despite making changes based on interim analyses. To this end, it is imperative that all company staff involved in the conduct of trial remain blind to the results of interim analysis, so as to avoid any operational bias. Thus, setting up an Independent Data Monitoring Committee (IDMC) with responsibility to monitor accruing efficacy - safety data and recommend appropriate modifications is crucial for adaptive trials. The operation of such IDMC in adaptive trial is often challenging, as compared to its operation in a conventional trial. For example, sponsor perspectives might often be relevant to take the best decision regarding the trial. However, the extent of sponsor involvement in decision making process of IDMC needs fine tuning to ensure that independence of the IDMC is preserved6Procedural and logistic issues are another major challenge in implementation of adaptive trials56ad-hoc changes to rescue a poorly planned study), regulators across the world often scrutinize adaptive designs much more closely. It is thus wise to enter into a discussion with the regulators early in the planning stage of adaptive studies, in order to understand what level of adaptation is acceptable and the overall regulatory expectations. Such expectations might include allowing only prospective adaptations for pivotal trials supporting product registration; clearly defined statistical methods to control type I error rate; written SOPs for adaptive design decisions; robust documentation practice; submission of trial simulation report and IDMC charter for regulatory review68Given that adaptive trials are liable to misuse (for example, To conclude, adaptive designs are not necessarily better than conventional designs in all trial settings. The merit of adaptive design over conventional design is to be judged on a case-by-case basis, looking at the overall clinical development plan. An adaptive design should be resorted to only when one is convinced of its merits over a conventional design. Further, implementation of adaptive trials is often fraught with challenges. Also, many areas of adaptive design still remain controversial and some regulatory agencies are still skeptical about acceptance of such designs. This explains why despite their attractiveness in terms of cost-efficiency and flexibility, adaptive designs are still in their infancy worldwide. Thus, while taking proactive measures towards implementation of adaptive designs regulators such as FDA are also leaving the industry with a word of caution: to allow time to build a better knowledge – base and understanding of adaptive designs before moving forward with their implementation


Globally, fisheries are challenged by the combined impacts of overfishing, degradation of ecosystems and impacts of climate change, while fisheries livelihoods are further pressured by conservation policy imperatives. Fishers' adaptive responses to these pressures, such as exiting from a fishery to pursue alternative livelihoods, determine their own vulnerability, as well as the potential for reducing fishing effort and sustaining fisheries. The willingness and ability to make particular adaptations in response to change, such as exiting from a declining fishery, is influenced by economic, cultural and institutional factors operating at scales from individual fishers to national economies. Previous studies of exit from fisheries at single or few sites, offer limited insight into the relative importance of individual and larger-scale social and economic factors. We asked 599 fishers how they would respond to hypothetical scenarios of catch declines in 28 sites in five western Indian Ocean countries. We investigated how socioeconomic variables at the individual-, household- and site-scale affected whether they would exit fisheries. Site-level factors had the greatest influence on readiness to exit, but these relationships were contrary to common predictions. Specifically, higher levels of infrastructure development and economic vitality - expected to promote exit from fisheries - were associated with less readiness to exit. This may be due to site level histories of exit from fisheries, greater specialisation of fishing households, or higher rewards from fishing in more economically developed sites due to technology, market access, catch value and government subsidies. At the individual and household scale, fishers from households with more livelihood activities, and fishers with lower catch value were more willing to exit. These results demonstrate empirically how adaptive responses to change are influenced by factors at multiple scales, and highlight the importance of understanding natural resource-based livelihoods in the context of the wider economy and society. Globally, many fisheries suffer from an excess of fishing effort endangering their long-term sustainability Models based on economic rationality predict that entry to and exit from fisheries are driven by the profitability of fishing Studies of fishery exit at multiple sites have found considerable variation in readiness to exit between villages and countries Environmental factors, such as lower stocks and catch rates may also explain differences in occupational mobility between sites While previous studies have identified a range of individual characteristics and economic factors that influence fishers' decisions to exit a fishery, this is the first to explicitly evaluate how readiness to exit small-scale fisheries is affected by factors operating at different scales. We ask which factors at which scale determine readiness to exit across a gradient of economic development in five western Indian Ocean (WIO) countries. This can help to identify appropriate points of intervention for policies that aim to reduce fishing effort or improve adaptive capacity within fishing communities. The research also contributes to the understanding of the complex and multi-scale nature of adaptive capacity, where non-asset based factors, particularly those concerned with identity, place and culture are increasingly recognized as important factors in decisions and adaptation We collected data on individual, household and community characteristics alongside readiness to exit in 28 coastal sites in Kenya, Tanzania, Seychelles, Mauritius, and Madagascar  in 2005.th household  was determined by dividing the total population by the sample size Sampling of households within sites was based on a systematic design, where a fraction of every iWe conducted household surveys with heads of household or an available adult household member from 1732 households, which included 599 fishers. The survey covered household demographics and livelihood activities, perceptions about resource conditions, any occupational changes experienced by the interviewee in the past five years and specific additional questions about fishing activities if the interviewee was a fisher. Fishers were asked to describe the magnitude of a ‘good’, ‘poor’ and ‘typical’ catch from a day's fishing. We used the typical-day figure to construct hypothetical scenarios involving a reduction of catch. Fishers were asked what they would do in response to a sustained decline in their normal catch of 10%, 20%, 30%, and 50% and responses were coded for each level according to whether fishers envisaged that they would keep fishing or exit the fishery.We obtained verbal consent from participants before conducting household surveys. During verbal consent, participants were informed about the survey, its purpose, and how the data would be utilized. Participant's names were not recorded. Written consent from participants was not obtained because of low literacy rates in many of our field sites, which meant that participants may not have fully understood what they signed. This project was administered by the Wildlife Conservation Society, which does not have an Institutional Review Board for research ethics regarding social science surveys.Previous literature identified a number of factors that may influence labour mobility in small-scale fisheries including individual factors, relationship to and perceptions of fishing, livelihoods, fishing characteristics, resource availability and socioeconomic context . We seleSurvey questions facilitated collection of demographic information on age, education and experience of other occupations. Wealth was evaluated by using a Material Style of Life (MSL) scale based on the presence or absence of various household possessions such as a TV, a toilet, radio, and the type of material the house was constructed from, factor analyzed using principal component analysis in SPSS We characterised each fisher according to their principal fishing gear used and recorded whether they had made a significant capital investment in the fishery, in terms of a boat or ‘capital intensive gear’ (e.g. large net) as judged according to the local fishery context in which they operated. We asked fishers why they started fishing and coded their responses into tradition, necessity, or free choice. We asked fishers about their perception of the condition of the fishery resource compared to five years previously, and coded responses into a binary variable indicating whether they perceived a decline. To account for different values of different species, catch rate was calculated as reported catch value in US$ adjusted for national purchasing price parity.We used the full sample of random household surveys – fishers and non-fishers - in each community to calculate the proportion of households involved in fisheries and the proportion of interviewees who had changed occupation within the previous five years and preferred their new occupation. The latter was designed to indicate whether the local economy was providing attractive alternative occupations that may affect the opportunity cost of labour.We developed an ‘infrastructure index’ for each site, as described in Biomass of reef fishes (kg/ha) on adjacent reefs was taken as an indicator of the condition of local fisheries resources. Reef fish biomass has been found to be a sensitive indicator of fishing pressure in the region Following visual assessment of responses to 10, 20, 30 and 50% declines, we focussed on the response to a 50% decline for detailed analysis as this provided approximately equal proportions of fishers who stated they would exit or remain fishing. We used three types of analysis to identify site, household, and individual-level factors predicting fishers' stated response to a 50% decline.a priori specified interaction terms in the model Firstly, we used classification trees to compare the predictive ability of factors at individual, household, and site level. Univariate tree models are an improvement on conventional linear and logistic regression methods where non-linear relationships and multiple interactions between predictor variables are likely, because they are non-linear and do not require the Secondly, we examined the relationship between readiness to exit and site-level variables. For this analysis, we used regression trees and bivariate plots to examine the community-scale variables that predicted the proportion of fishers opting to exit at each site.Thirdly, we assessed whether individual or household-level variables predicted variation in responses, beyond the variation explained by site. We fitted a generalised linear mixed model (GLMM) to assess the ability of these variables to predict individual stay or exit responses, with site a-priori set as a random intercept to account for inter-site variation. We assessed the full model for the significance of individual variables, and then ran a stepwise selection based on AIC to remove or add variables to find the most parsimonious model. The GLMM analysis was preceded by analysis of collinearity by calculating variance inflation factors Greater proportions of fishers responded that they would exit fisheries in response to higher levels of hypothetical decline . At 50% Classification-tree analysis identified the variable ‘site’ as having the greatest power to predict readiness to exit , which wGiven the importance of site for predicting willingness to exit, we examined how site-scale factors were related to the proportion of fishers at that site who would exit the fishery. Regression tree analysis resulted in splits according to the infrastructure index which separated low infrastructure sites (dominated by Madagascar) with high proportions of fishers exiting. A second split also used infrastructure, and split off a group of high infrastructure sites, dominated by Seychelles, with low proportions of fishers exiting . This neThe proportion of household surveys reporting a favourable change in occupation in the previous five years was weakly to moderately correlated with infrastructure (Spearman's Rho = 0.499), and also showed a significant negative linear relationship with proportion of fishers willing to exit  (p = 0.017) and typical daily catch value (p<0.001), were positively related to exit . This waAs with the literature, a wide range of economic and non-economic variables measured at different scales were related to readiness to exit fisheries. Although responses differed between countries, with high levels of readiness to exit in Madagascar and low levels in Seychelles, site-level differences were most prominent. Beyond the strong effect of site, we also found that household and individual characteristics also influenced fishers' willingness to exit. Individual fishers whose fellow householders had more occupations and whose catches were larger were less willing to exit.In agreement with previous work this study found that the readiness to exit a fishery varied significantly between sites The direction of relationships between site-scale variables and fishery exit were surprising and contrary to conventional understanding of fishery bioeconomics.The site-level variables are indicative of a broadly defined ‘economic development’. The infrastructure index indicates both material community development as well as the degree of connectedness to global and national economies. The proportion of households whose members had favourably changed jobs within the previous five years, and the proportion of households with fishing as a primary occupation are indicators of the nature of employment opportunities available in the local economy.Smith et al. We suggest three plausible and possibly complementary explanations for these results:Levels of economic development and diversification, indicated by the infrastructure index and occupational mobility variable may be associated with specialisation of livelihoods and professionalization of employment, including fisheries. In regions and countries with better infrastructure and more diversified economies, fisheries are more specialised and professionalised and less frequently part of multiple household livelihoods Fishers in more economically developed sites may be more committed due to the history of change in fisheries during the process of development. Fishers at developed sites have chosen fisheries in the context of other available occupations. In contrast, less economically developed sites with fewer opportunities have higher proportions of fishers, many of whom pursue a diverse livelihood strategy Markets, technology and government assistance facilitate and reward fishing more in economically developed sites. The value of the catch varied greatly between countries, being for example two orders of magnitude greater in Seychelles than Madagascar , despiteGovernment support may also influence fisheries behaviours more in developed locations through subsidies and infrastructure. For example in Seychelles, fishers are supported by government funded fuel subsidies and health insurance, while in Mauritius registered fishers receive a bad weather allowance, which compensates them when fishing activity is disrupted by unfavourable weather.A simplistic perspective in which poverty, lack of alternative occupations and overexploitation are mutually reinforcing see  predictsInterestingly, the unexpected direction of relationships between economic development and readiness to exit was apparent only at the largest scale. The negative relationship between readiness to exit and infrastructure across the region was not apparent within individual countries. Instead, the only significant within-country relationships between exit and infrastructure, in the Seychelles and Mauritius were positive. Consequently, the direction of the relationship may differ with the scale of analysis because of different processes operating at different scales. For example, the differences in infrastructure within a small island country may improve alternative livelihood options, while the larger differences observed across the region may be associated with structural differences in national economies and fisheries policy, leading to the large-scale negative relationship.The study also found that household–scale factors affected readiness to exit as reported in Kenya, where household occupational multiplicity was positively related to readiness to exit This suggests that adaptation of fishers to disturbances or fisheries declines, and reduction of fishing effort, may be facilitated by alternative livelihoods, even if they are not suitable to fishers themselves. This contrasts with the assertion concerning seaweed farming, often conducted by women, that extra household occupations may subsidise rather than reduce fishing activity Household wealth was found to positively affect the willingness to exit in Kenya Normal daily catch value was the strongest determining factor at the individual scale, and was negatively related to readiness to exit. This makes practical sense, as we asked about a catch decline proportional to stated normal catch. Fishers with higher value catches may have more scope to absorb declines. Different results may have been found by comparing responses to absolute as well as relative declines Several of the characteristics we looked at were poor predictors of readiness to exit. Individual-scale characteristics identified in other studies Climate change, globalisation and environmental degradation are leading to unprecedented levels of change and disturbance to social-ecological systems such as fisheries, and their associated livelihoods. Our study provided further evidence that adaptation is influenced by multiple scales that go beyond the assets and characteristics of individuals and include the social and economic environment enabling adaptation Fishers face an increasing variety of changing conditions related to overexploitation, climate change, globalization, and conservation of marine biodiversity. Understanding how fishers will respond to these ecosystem and institutional changes is critical to better managing fisheries and improving the livelihoods of those dependent on fisheries. Some conventional fisheries economic thinking was supported by this large-scale study, such as the greater occupational mobility of less-successful fishers, while some was refuted. In particular, the often-assumed positive relationship between economic development, and mobility of fishing labour was contradicted by our results. Our results highlight the strong context dependency in adaptive responses, requiring different recommendations and interventions in different contextual conditions.Figure S1Classification-tree analysis for the responses of 599 fishers to hypothetical declines including site-level variables, but not including the variable of ‘site’. Branches classifying fishers as ‘exit’ are on the right hand branches.(DOCX)Click here for additional data file.Figure S2Regression-tree analysis for proportion of fishers within a site opting to stop fishing in response to a halving of catch value.(DOCX)Click here for additional data file.Figure S3Relationships between the probability of a fisher stating they would exit from a hypothetical 50% decline in catch and the occupational multiplicity of their fellow householders, the value of their typical daily catch.(DOCX)Click here for additional data file.Table S1Factors considered in previous empirical studies of fisher mobility and whether they were found to be significant .(DOCX)Click here for additional data file.Table S2Communities surveyed and summary statistics for each. * Only targeted fisher surveys (no random household surveys) conducted in Stone Town or Mazizini.(DOCX)Click here for additional data file.Table S3Variables included in analysis and data summarised by country.(DOCX)Click here for additional data file.Table S4Results of GLMM regression with all individual or household variables.(DOCX)Click here for additional data file.