Part of the development and maturation of the central nervous system (CNS) occurs through interactions with the environment. Through physical activities and interactions with the world, an animal receives considerable sensory information from various sources. These sources can be internally (proprioceptive) or externally (such as touch and pressure) generated senses. Ample evidence exists to demonstrate that the sensory information originating from large diameter afferents (Ia fibers) have an important role in inducing essential functional and morphological changes for the maturation of both the brain and the spinal cord. The Ia fibers transmit sensory information generated by muscle activity and movement. Such use or activity-dependent plastic changes occur throughout life and are one reason for the ability to acquire new skills and learn new movements. However, the extent and particularly the mechanisms of activity-dependent changes are markedly different between a developing nervous system and a mature nervous system. Understanding these mechanisms is an important step to develop strategies for regaining motor function after different injuries to the CNS. Plastic changes induced by activity occur both in the brain and spinal cord. This paper reviews the activity-dependent changes in the spinal cord neural circuits during both the developmental stages of the CNS and in adulthood. These activity-dependent changes occur ubiquitously in the CNS; connections between the brain and spinal neurons and connections between sensory neurons and motoneurons of the spinal cord also show extensive reorganization in response to movement and activity.Deprivation of sensory information during certain periods of an animal's life span causes substantial impairment in the normal development and function of the central nervous system (CNS). Hence, this period is referred to as a critical period. The pioneering works of Hubel and Wiesel –5, whichHowever, activity-dependent changes in the nervous system are not solely limited to the developing period but also exist throughout the life span for both the spinal cord  and the The purpose of this paper is to review and compare activity-dependent plasticity of spinal circuits during development and in adulthood, focusing on the fundamental differences in the mechanisms of spinal plasticity between development and adulthood. Understanding the underlying mechanisms involved in the activity-dependent induction of plasticity is potentially meaningful for modern treatments of a variety of movement disorders.A variety of mechanisms ranging from intrinsic cellular and morphological properties to genetic and epigenetic factors , 18 haveExperimental studies have found molecular correlates with activity, which are predominantly observed during maturation and the developmental progression of motoneurons. One of the well-studied molecules is a monoclonal antibody which recognizes a certain proteoglycan known as Cat-301 proteoglycan. Expression of Cat-301 substantially increases in association with movement , 27. Thiin vitro experimental setup, Fields and colleagues cultured the spinal motoneurons of 13-d mouse fetuses in a 3-chambered cell-culture system and electrically stimulated the sensory afferents of the motoneurons of one of the chambers. It was shown that the motoneurons which were subject to chronic stimulation developed stronger synaptic connections with the afferent fibers in terms of yielding larger excitatory postsynaptic potentials (EPSP) compared to the untreated chambers of the sensory afferents. Therefore, this experimental model suggested that an increase in sensory input to spinal motoneurons could increase the efficacy of this synaptic connection. These stimulation-induced changes in sensory afferent efficacy were suppressed by the application of the selective NMDAR antagonist APV [It is well known that sensory Ia fibers make both monosynaptic and oligosynaptic connections to alpha motoneurons in the ventral horn and comprise the reflex arc, using glutamine as the excitatory neurotransmitter. In the spinal cord, glutamine activates two major types of ionotropic receptors: NMDA and AMPA receptors. It was initially thought that these two types of glutamatergic ionotropic receptors have differential roles in synaptic transmission of the reflexes. Initial studies suggested that NMDA receptors were involved in the transmission of polysynaptic reflexes and AMPA receptors were involved in the transmission of the monosynaptic reflexes; however subsequent studies have shown this not to be the case . Rather,nist APV , suggestnist APV . In concInterestingly, NMDA receptors can be found throughout the spinal cord gray matter  at very early stages of development , but durThe induction of temporary or permanent plastic change is, logically, also contingent on descending drive. For example, severing the spinal cord during the developmental stages substantially reduces the expression of Cat-301 on the motoneuron soma in neonatal hamsters . At birt2+ into the cells. While it is understood that NMDA receptors mediate many activity-dependent changes during the early stages of spinal cord development, the exact mechanism by which NMDA receptors function to regulate development is unknown.Comparison of the findings regarding the activity-dependent role of NMDA receptors at the level of the spinal cord and the importance of cortical input to the spinal cord strongly suggests that both peripheral and descending inputs are required for activity-dependent plasticity in the spinal cord. It is shown that these activity dependent eliminations of synapses are at least partly mediated by NMDA receptor activation. Recent investigations  have shoUnlike the literature on the developing spinal cord, much of our understanding of activity-dependent plasticity of the mature spinal cord comes from human studies. The H-reflex is a well-recognized and accepted method for investigating the function of the spinal circuits during various movements. For eliciting an H-reflex, an electrical stimulus  is applied to a peripheral nerve . The larApplying this technique to any accessible mixed nerve will elicit the H-reflex in the corresponding muscles; however, this technique has been most widely used for examination of the soleus muscle due to the superficial location of its neural innervation. More importantly, the soleus is a crucial muscle for the control of posture and gait. Therefore, measuring the H-reflex in the soleus muscle is an appropriate model for studying the role that spinal circuits play in the control and modulation of a variety of bipedal movements. We would like to point out that the findings from this type of artificially induced reflex might be different than those of stretch reflexes. There are studies that show that modulations observed in the H-reflex are not present in the stretch reflex . It is aIn adult humans, monkeys, and rats learning new skills is accompanied by temporary or permanent changes in the spinal cord, and these changes have been extensively studied with the stretch reflex or the H-reflex.It is well accepted that there exists short-term task-dependent modulation of spinal reflexes, and this modulation does not immediately impose any structural or long-lasting functional change in spinal circuits. The prevailing notion is that synapse strength is altered in a task-specific manner. However, practicing the same task or stimulating the same pathway for an extended period of time  can result in long-term structural changes in spinal circuits. One example from the athletic area is the reflex regulation in dancers in whom the amplitude of the H-reflex is substantially lower than the normal population –53. PresTo examine the induction of such long-term change in the adult spinal cord, an operant conditioning model of spinal reflexes has routinely been used. In this model of learning, a spinal reflex (stretch or H-reflex) is elicited, and the resulting EMG response is recorded. The amplitude of the reflex is presented to the subject as a feedback. A reward is provided if the reflex response is modulated in one particular direction (increase or decrease) as determined by the examiner. This reward encourages the animal (or human) to purposefully direct its behavior toward the desired reflex response. Operant conditioning has been extensively used for documenting changes in the input-output relationship of both the spinal stretch and the H-reflex. This model has provided a powerful tool for the investigation of spinal circuits as well as any morphological alterations in the motoneurons associated with learning. It is now well established that both animals and humans can similarly increase or decrease the amplitude of the stretch or H-reflex . TypicalHow do these changes in the reflex pathway occur and how do they become permanent?For the efficacy of the synaptic transmission to change (either transiently or permanently), there are some mechanisms which act on the presynaptic terminals and some mechanisms which affect the postsynaptic terminal. Collectively, such presynaptic or postsynaptic alterations can increase or decrease the amplitude of EPSPs or inhibitory postsynaptic potentials (IPSPs). There is a variety of these mechanisms throughout the central nervous system which are involved in almost all activities of the CNS from learning and memory , habituaA receptors in the Ia terminals, chloride ions leave the presynaptic terminal and thereby cause the active zone to depolarize. It is suggested that this GABAergic mechanism shunts the EPSP through GABAA receptor activation, or directly affects the Ca2+ channels through GABAB receptors [2+, vesicle mobilization is impaired, decreasing the probability of neurotransmitter release from the afferent terminals [Frank and Fuortes (1957) were among the first to report that sensory inflow can indeed be suppressed without affecting the resting potential of the postsynaptic alpha motoneuron . Howevereceptors , 76. Witerminals , 77. It erminals , 78, 79 erminals , as wellerminals  and corterminals , 83. HowPresynaptic inhibition of Ia afferents is highly modifiable in response to postural changes  and motoHomonymous  as well There is evidence to show that peripheral and central drives merge to the same common PAD interneurons  and therTaken together, it can be argued that adjusting the amount of presynaptic inhibition through the interaction of central and peripheral inputs has an important role in the execution of voluntary movements. For these reasons, it is now difficult to differentiate between reflexive and voluntary movements . WhereasOn the other hand, presynaptic inhibition has been repetitively shown to be modifiable in response to motor practice and learning new skills. In the following sections, we briefly review some key studies which have demonstrated short-term and long-term adaptations of the spinal circuits.During normal movement execution, such as changes in posture , movemenIn operant-conditioning protocols, there seems to be a complex interaction of mechanisms involved in the induced plasticity including presynaptic modulation of the Ia terminals, specifically for the short-term adaptation phase . While oSuch types of training-induced plasticity have also been observed in more complex movements. In a novel locomotion study, subjects were trained to walk backward on a treadmill for several weeks. In untrained subjects a large amplitude H-reflex was observed during the midswing phase of walking. Training progressively reduced the amplitude of the reflex. However, these changes in the reflex amplitude were not related to leg muscle motor evoked potentials (MEPs). It was suggested that the plasticity induced in the H-reflex circuits was heavily dependent on the presynaptic control of the inflow of sensory information . It is iIn humans, it has been clearly established that long-term, repetitive activity produces changes in the reflex arc. For example, strength training has been shown to increase H-reflex amplitude; 14 weeks of muscle-specific heavy resistance training can increase the soleus H-reflex amplitude by 20% . ResearcAs another example, several studies have shown that the amplitude of the H-reflex is significantly reduced in trained dancers –53. The Taken together, these studies provide evidence that neural circuits can undergo long-lasting activity-induced plastic changes. However, these studies cannot unambiguously conclude that the plastic changes were induced solely in the spinal cord circuits. One possibility is that functional changes in these circuits are due to changes in descending drive rather than the spinal cord.To determine whether the long-term changes occur at the spinal or supraspinal levels, Wolpaw and his colleagues examined the effect of operant conditioning on the stretch or the H-reflex in monkeys and human subjects , 110. Woconsequences of a motor demand. Second, no functional tasks are involved during classical operant conditioning, which means that this type of conditioning may not be behaviorally relevant and these results do not translate to real-life situations.Acute changes in spinal pathways are believed to be triggered by descending inputs. However, changes in the descending input over a long period of time can produce permanent changes in the spinal cord which are regarded as spinal fixation. Animals with partial transection of the spinal cord with an intact corticospinal tract are still able to volitionally up- or downregulate the H-reflex in an operant conditioning protocol . HoweverDoes the spinal cord have the ability to acquire new motor skills without the need of the descending drive for this skill acquisition?pattern of sensory input (such as that generated by a specific task) may induce plastic changes in spinal circuits without the involvement of descending drive. In an excellent investigation, Meunier and colleagues [pattern of sensory inflow that produced the change in synaptic efficacy between the Ia afferents and the alpha motoneurons. Again, understanding this discrepancy is extremely important for the improvement of modern rehabilitation techniques for spinal cord injury patients.Spinalized cats are indeed able to develop functional tasks despite the permanent loss of descending input , 113. Sulleagues  examinedThe exact mechanism of long-term activity-dependent changes in spinal circuits is not yet well understood. In operant-conditioning experiments designed to modulate the reflexes, initially the induced changes (in terms of the modulation of the reflexes) are reversible and will be abolished if training is discontinued. However, by continuing the task, the changes in the amplitude of the reflexes become permanent. In contrast, in mature animals, the transection of the corticospinal tract before or during the learning phase prevents the induction of long-term plastic changes , 117. Hiin vitro and in vivo animal studies, blocking NMDA receptors in human subjects using Dextromethorphan interferes with the acquisition of motor memory but does not impair motor memory recall [Learning a new skill is accompanied by a novel combination of muscle activity patterns that are temporally and spatially timed. These novel biomechanical configurations produce new sensory information feedback to the nervous system. Timely coupling of the EPSPs with action potentials has been shown to alter synaptic efficacy . The bacy recall .The studies that have shown LTP in other areas of spinal cord have not investigated the mechanisms of LTP induction and maintenance, but it is unlikely that the role of NMDA receptors in LTP induction and maintenance is topographically distinct across spinal cord regions. A direct study between LTP and reflex regulation has not yet been reported however, it would be of value to examine the effect of NMDA receptor antagonists on the induction of H-reflex upregulation. If a behaving animal, treated with NMDA antagonist to the substantia gelatinosa, cannot upregulate the H-reflex, this might suggest the importance of the substantia gelatinosa on the memory capacity of the spinal cord for movement regulation. Such investigations on NMDA receptors might provide new advances for the restoration of spinal ability and motor control. Increasing the basic knowledge of activity-dependent plasticity throughout the life span of humans can substantially influence the treatment and rehabilitation methods used for various neurological conditions.Spinal circuits possess the ability for plastic changes to fulfill short- and long-term motor demands. These reversible changes in spinal circuits are typically accompanied by alterations in synaptic strength for acute adaptations, and by morphological and electrophysiological changes for long-term adaptations. Examining the modulation of spinal reflexes during different tasks has provided much of our understanding about activity-dependent plasticity in the spinal cord. During normal walking, for example, stretch reflexes are modulated differently compared with upright standing. The amplitude of the stretch reflex is not constant throughout the cycle of gait, and the phases of gait also affect the strength of the stretch reflex. Practicing a particular skill for extended periods of time can also affect the amplitude of the reflexes. Such changes in reflex gain have been shown to be associated with the degree of performance. For example, the ability of subjects to maintain a constant pedaling speed against varying the resistance during the bout of exercise was shown to be strongly correlated to the degree of H-reflex modulation . These f


Herpes Simplex Virus 1 and 2 causes several infections in humans including cold sores and encephalitis. Previous antiviral studies on herpes viruses have focussed on developing nucleoside analogues that can inhibit viral polymerase and terminate the replicating viral DNA. However, these drugs bear an intrinsic non-specificity as they can also inhibit cellular polymerase apart from the viral one. The present study is an attempt to elucidate the action mechanism of naturally occurring withaferin A in inhibiting viral DNA polymerase, thus providing an evidence for its development as a novel anti-herpetic drug.Withaferin A was found to bind very similarly to that of the previously reported 4-oxo-DHQ inhibitor. Withaferin A was observed binding to the residues Gln 617, Gln 618, Asn 815 and Tyr 818, all of which are crucial to the proper functioning of the polymerase. A comparison of the conformation obtained from docking and the molecular dynamics simulations shows that substantial changes in the binding conformations have occurred. These results indicate that the initial receptor-ligand interaction observed after docking can be limited due to the receptor rigid docking algorithm and that the conformations and interactions observed after simulation runs are more energetically favoured.de novo MD simulations for 10 ns performed allowed us to evaluate the dynamic behaviour of the system studied and corroborate the docking results, as well as identify key residues in the enzyme-inhibitor interactions. The present MD simulations support the hypothesis that withaferin A is a potential ligand to target/inhibit DNA polymerase of the Herpes simplex virus. Results of these studies will also guide the design of selective inhibitors of DNA POL with high specificity and potent activity in order to strengthen the therapeutic arsenal available today against the dangerous biological warfare agent represented by Herpes Simplex Virus.We have performed docking and molecular dynamics simulation studies to elucidate the binding mechanism of prospective herbal drug withaferin A onto the structure of DNA polymerase of Herpes simplex virus. Our docking simulations results give high binding affinity of the ligand to the receptor. Long  Herpesviridae family, which infect almost 85% of the world population  was obtained from the Protein Data Bank (PDB) [The crystal structure of HSV DNA polymerase [PDB: nk (PDB) . The strnk (PDB) . This stnk (PDB) . The strnk (PDB)  is shownnk (PDB) , was useSemi-flexible molecular docking of the HSV DNA polymerase along with ligand WA was implemented using AutoDock 4.0 . The genThe energy minimization and MD simulations of HSV POL and its complex with WA were carried out using AMBER package as fully described elsewhere by the authors .We performed docking of WA into X-Ray crystal structure of HSV POL. Using binding pocket analysis, a cavity around the active site/subsites of HSV POL was predicted where WA was found binding to the critical active site residues of HSV POL with a binding energy of -8.46 Kcal/mol. The ligand formed several H-bond interactions with the crucial residues of the polymerase Figure . Ring amSince molecular docking provides only a static view of the protein-ligand interactions, we performed molecular dynamics simulations on HSV POL in complex with WA to study the interactions in motion. The overall goal of these simulation steps was to account for protein flexibility and movement that however could not be achieved in the docking simulations alone. Figure n) for the Cα atoms were calculated using the following relation:To probe the dynamic flexibility changes in the protein, due to the inhibitor binding in its critical regions, B-factors  have shown broad anti-HSV activity ,36. This effects ,36. The  effects .The emergence of HSV resistance to antiviral drugs is also a major concern. Three basic mechanisms have been identified: altered thymidine kinase substrate specificity, absent or partial production of viral thymidine kinase and altered viral DNA polymerase . The mosBased on the results from WA-HSV POL complex, it appears that interactions with the residues Gln 617, Gln 618, Tyr 722, Asn 815 and Asp 888 of HSV POL are important for inhibitory activity of WA. A comparison between the conformation obtained from docking and that from molecular dynamics simulations show that substantial changes in binding conformations have occurred. These results indicate that the initial receptor-ligand interaction observed after docking can be limited due to the receptor rigid docking algorithm and that the conformations and interactions observed after simulation runs are more energetically favoured and should be better representations of derivative poses in receptor.de novo MD simulations for 10 ns performed allowed us to evaluate the dynamic behaviour of the system studied and corroborate the docking results, as well as identify key residues in the enzyme-inhibitor interactions. The present MD simulations support the hypothesis that WA is a prospective ligand that has potential to target/inhibit DNA polymerase of the Herpes simplex virus. Results of these studies will also guide the design of selective inhibitors of DNA POL with high specificity and potent activity in order to strengthen the therapeutic arsenal available today against the dangerous biological warfare agent represented by Herpes Simplex Virus.We have performed docking and molecular dynamics simulation studies to elucidate the binding mechanism of prospective herbal drug withaferin A onto the structure of DNA polymerase of Herpes simplex virus. Our docking simulations results give high binding affinity of the ligand to the receptor. Long AG, VSB and DS designed the methods and experimental setup. AG carried out the implementation of the various methods. AS and VA assisted AG in this process. AG and DS wrote the manuscript. All authors have read and approved the final manuscript.The authors declare that they have no competing interests


Publication bias is one of the major threats of validity in systematic reviews and meta-analyses. Previous empirical studies suggested that systematic reviews and meta-analyses have become more prevalent until 2010 and found evidence for compromised methodological rigor with a trend towards improvement. We aim to comprehensively summarize and update the evidence base on systematic reviews and meta-analyses of animal studies, their methodological quality and assessment of publication bias in particular.Systematic reviews and meta-analyses of pre-clinical studies, The objectives of this systematic review are as follows:•To investigate the epidemiology of published systematic reviews of animal studies until present.•To examine methodological features of systematic reviews and meta-analyses of animal studies with special attention to the assessment of publication bias.•To investigate the influence of systematic reviews of animal studies on clinical research by examining citations of the systematic reviews by clinical studies.in vivo animal experiments with the purpose of reviewing animal evidence to inform human health. We will exclude genome-wide association studies and animal experiments with the main purpose to learn more about fundamental biology, physical functioning or behavior.Eligible studies for this systematic review constitute systematic reviews and meta-analyses that summarize In addition to the inclusion of systematic reviews and meta-analyses identified by other empirical studies, we will systematically search Ovid Medline, Embase, ToxNet, and ScienceDirect from 2009 to January 2013 for further eligible studies without language restrictions.Two reviewers working independently will assess titles, abstracts, and full texts for eligibility and extract relevant data from included studies. Data reporting will involve a descriptive summary of meta-analyses and systematic reviews.Results are expected to be publicly available later in 2013 and may form the basis for recommendations to improve the quality of systematic reviews and meta-analyses of animal studies and their use with respect to clinical care. For instance, in the widely accepted Surviving Sepsis Guidelines recommendations regarding target arterial blood pressure for vasopressor use and positive end-expiratory pressure in the prevention of lung injury, draw on results from animal experiments [Pre-clinical research has its main purpose in enhancing our understanding of physiologic and pathologic processes. However, many pre-clinical studies, eriments . In addieriments .et al. found 86 using a more sensitive search strategy and a broader definition of laboratory animal experiments [et al. reported that SRs of pre-clinical studies are getting more common over time, doubling their number roughly every 3 years between 1997 and 2010 [Whenever a summary of the current evidence is needed for decision-making in clinical research, health-care policy, or clinical practice, systematic reviews (SRs) and, where appropriate, meta-analyses are most useful tools. SRs offer a structured and transparent way to comprehensively identify and evaluate the available evidence on a specific topic. Meta-analyses increase the precision and generalizability of effect estimates by quantitatively summarizing the results of individual studies included in an SR in order to provide a single best estimate with maximal statistical power . SRs anderiments ,5. HowevThe validity and usefulness of the results of SRs and meta-analyses strongly depend on their methodological rigor. Assessing bias, such as publication bias, is essential, when conducting SRs. If the publication or non-publication of research findings depends on the nature and direction of the results (definition of publication bias ) then thet al. reported that between 2005 and 2010 the proportion of meta-analyses of in vivo animal studies that assessed publication bias increased to 60% (21/35) [While principles of critically appraising SRs of clinical research are well established, their application to SRs of pre-clinical studies appears variable . Previou (21/35) . Lack ofet al. conducted their search for SRs of animal experiments in 2009/10 [et al. and Korevaar et al. and updating the evidence base for SRs of animal experiments. This SR will be part of the project, To Overcome failure to Publish nEgative fiNdings (OPEN Project), which was developed with the goal of elucidating the scope of publication bias and non-publication of studies through a series of SRs and policy evaluations (http://www.open-project.eu).Korevaar  2009/10 . It remaThe specific goals of the present SR of animal studies are: determining the number of published SRs of animal studies up to the present; investigating methodological features of SRs and meta-analyses of animal studies especially with respect to assessment of publication bias, and investigating the influence of SRs of animal studies on clinical research by examining citations of the SRs in clinical studies.et al. and Korevaar et al. [in vivo animal experiments with the purpose of reviewing animal evidence to inform human health and if they can be allocated to one of the following categories: i) investigation of the efficacy of a medical or surgical intervention; ii) investigation of the side-effects or toxicity of a medical intervention; iii) investigation of the mechanisms of action of a medical intervention; iv) investigation of risk factors ; v) investigation of effects of an exposure to a chemical substance; vi) overview of animal models for disease, and vii) investigation of diagnostic test accuracy. Articles including human studies in addition to animal studies will be considered too. As did Korevaar et al. we will exclude genome-wide association studies and animal experiments with the main purpose to learn more about fundamental biology, physical functioning or behavior and not to inform human healthcare.To allow for a valid combination of results we will use similar criteria and search strategies to Peters r et al. ,6, to idr et al. . For methttp://toxnet.nlm.nih.gov/; including Toxline, DART, and HSDB) and ScienceDirect, all from 2009 to the present (January 2013). In addition, the bibliographies of any eligible articles identified will be checked for additional references. No language restrictions will be applied. The search strategy used by Korevaar et al. has been slightly modified with the support of a librarian/information specialist. The full search strategies are displayed in Additional file We will systematically search electronic databases such as Ovid Medline, Embase, Toxnet  we will abstract the following: first author and publication year; journal ; whether the article identifies itself as an SR or meta-analysis in the title or abstract; the objective; search strategy ; whether any formal assessment of study quality was performed, and which instrument was used; number of included studies; whether any funding sources were reported for the SR and abstracted from the included studies; whether any assessment of the presence of publication bias was reported, and which method was used; any other comments on publication bias; whether any reporting guideline  for SRs was mentioned.A specifically designed data extraction form will be developed and pilot-tested. Working in teams of two, we will independently extract relevant information from each eligible article. From all eligible SRs  and a random sample of 29 SRs without meta-analysis. Limiting to articles published until 2009 allows all articles to be available in the literature for at least 3 years until our analysis. We will focus on studies likely to influence clinical decision making, such as i) randomized controlled trials; ii) matched controlled trials; iii) crossover trials; iv) uncontrolled prospective trials; v) guidelines; vi) retrospective cohort studies; vii) prospective cohort studies; viii) laboratory experiments with healthy human volunteers; ix) cross-sectional surveys, and x) case report/case series. Two reviewers will review each of the 58 studies independently and in duplicate. They will abstract the role of the citation by allocating a citation to one of the following categories: i) use of citation unrelated to animal studies in review; ii) used citation to provide at least partial justification for the study or a future study; iii) used citation to support or explain their findings; iv) used citation to discuss physiological pathways, and v) used citation to justify the measure of certain variables.Data reporting will involve a descriptive summary of meta-analyses and systematic reviews. We will report the study according to PRISMA guidelines .in vivo animal studies with special attention to the assessment of publication bias. SRs of animal studies can influence clinical care directly or indirectly through guidelines and clinical studies that are designed based on evidence from pre-clinical studies. In order to better understand the extent of that influence we plan to examine citations of identified reviews in publications of clinical studies.This SR aims to comprehensively summarize the epidemiology and methodological quality of SRs and meta-analyses of in vivo animal studies through a sensitive search strategy and inclusion of previously identified articles. We will employ two definitions of SRs: a broader one that ensures comparability with previous empirical studies and a more stringent definition that will be applied to all articles meeting the broader criteria. A limitation of our protocol is that our results might be affected by publication bias because we will not search any grey literature. We are therefore limiting the generalizability of our results about methodological quality and publication bias to the published SRs of in vivo animal studies.Our protocol has strengths and limitations. The strengths are that we will use a comprehensive approach to identify SRs and meta-analyses of This SR together with the results of other SRs in the context of the OPEN Project will raise awareness about the widespread plague of publication bias and the complexity of this issue. Moreover, these reviews will serve as a foundation for a recommendations workshop, which will enable key members of the biomedical research community  to develop future policies and guidelines to reduce the frequency of non-publication and related biases.OPEN: to Overcome Failure to Publish Negative Findings; PRISMA: Preferred Reporting Items for Systematic reviews and Meta-Analyses; SR: systematic review.We declare that all authors and contributing members have no competing interests.MB, JM, and DB conceived of the study. MB, VG and EM designed the search strategies. MB drafted the manuscript with the help of KM, JM and DB. EvE, BL, EM, VG and GS critically reviewed the manuscript for important intellectual content. All authors read and approved the final version before submission. MB, JM and DB are guarantors.Search strategy.Click here for file


It is based on the deep sequencing of ribosome protected mRNA fragments allowing the measurement of ribosome density along all RNA molecules present in the cell. At the same time, the high resolution of this technique allows detailed analysis of ribosome density on individual RNAs. Since its invention, the ribosome profiling technique has been utilized in a range of studies in both prokaryotic and eukaryotic organisms. Several studies have adapted and refined the original ribosome profiling protocol for studying specific aspects of translation. Ribosome profiling of initiating ribosomes has been used to map sites of translation initiation. These studies revealed the surprisingly complex organization of translation initiation sites in eukaryotes. Multiple initiation sites are responsible for the generation of N-terminally extended and truncated isoforms of known proteins as well as for the translation of numerous open reading frames (ORFs), upstream of protein coding ORFs. Ribosome profiling of elongating ribosomes has been used for measuring differential gene expression at the level of translation, the identification of novel protein coding genes and ribosome pausing. It has also provided data for developing quantitative models of translation. Although only a dozen or so ribosome profiling datasets have been published so far, they have already dramatically changed our understanding of translational control and have led to new hypotheses regarding the origin of protein coding genes. © 2013 John Wiley & Sons, Ltd.Ribosome profiling or ribo-seq is a new technique that provides genome-wide information on protein synthesis (GWIPS)  The race for the completion of the human genome yielded a by-product that is probably more important for modern biology than the goal of the project itself—cheap and powerful technologies for sequencing DNA. These technologies shifted the focus of researchers from studying individual molecules and pathways to studying the whole composition of molecules inside the cell. However, most of the popular high-throughput techniques provide only static information on the composition of the cell. For example, proteomics approaches such as mass-spectrometry give information on the composition of a proteome, while RNA-seq captures information on the composition of a transcriptome. An assumption is used whereby the abundance of transcripts can be interpreted as a measure of transcription levels. This assumption is problematic because of the varying stability of RNA transcripts. Because of the high variability in protein molecule half-lives, inferring gene expression levels from protein abundance is even more problematic. A high concentration of a particular protein in the cell does not necessarily mean that the corresponding gene is being highly expressed at the moment of measurement.Until recently, no simple high-throughput technique existed for measuring gene expression at the level of translation. The situation has changed with the advent of the ribosome profiling technique developed in the laboratory of Jonathan Weissman at University of California, San Francisco.The technology is the product of a propitious marriage of an existing methodology with massive parallelization offered by second-generation sequencing platforms.Because ribosome profiling reveals the exact positions of ribosomes on an mRNA transcript, two major variants of the technique have been developed: ribosome profiling of elongating ribosomes and ribosome profiling of initiating ribosomes. Elongating ribosomes can be blocked with antibiotics that inhibit either translocation  that often prevent translation of the main protein product ORF . Polysomal profiling also cannot provide information on the exact number of ribosomes on mRNAs. Because ribo-seq allows localization of the ribosomes, this information can be assessed, therefore making it a preferential approach for differential gene expression. The very first ribosome profiling study showed a 100-fold range difference in the density of ribosome footprints across different yeast transcripts expressed at a relatively high level.The ability to detect changes in the expression of genes is essential for understanding the genetic determinants of phenotypical behavior and the molecular response of the cell to changing conditions. For more than a decade, microarray techniques,Most of the published ribosome profiling studies borrowed computational approaches from RNA-seq analysis for measuring differential gene expression levels. For a number of reasons, specifically discussed at the end of this subsection and illustrated with examples throughout the entire review, treating the density of ribosome footprints on an mRNA transcript as a direct measure of its translation may generate a number of artifacts. It is likely that specialized tools for the analysis of gene expression using ribo-seq will be developed in the future. In the meantime, however, adapting RNA-seq computational approaches is sensible for obtaining approximate information. Indeed, by using such approaches, a small number of ribosome profiling studies have already provided significant insights into certain important aspects of translational control.GCN4 was found to increase sevenfold. While the translational regulation of GCN4 in response to amino acid deficiency is well established and studied,Protein synthesis is an energetically expensive anabolic process and therefore it is expected to be sensitive to the available nutrition, in particular, amino acids. To test the ability of ribo-seq to characterize changes in protein synthesis in response to starvation, Ingolia et al.Saccharomyces cerevisiae to oxidative stress. Yeast cells were treated with hydrogen peroxide and ribo-seq, and RNA-seq were carried out in parallel 5 and 30 min after the treatment. Many genes whose expression was altered at the transcriptional and translational level have been identified with this approach. The number of genes whose expression was changed greatly increased with the prolonged treatment: the transcript abundance of 116 genes was affected after 5 min and 1497 genes after 30 min with similar numbers obtained for genes whose translation was altered. Interestingly, they reported several transcribed but translationally quiescent genes whose translation is activated upon oxidative stress, for example, the Srx1 gene which encodes sulfiredoxin. The dataset of translationally regulated genes was compared with a previous study that used polysome profiling for this purpose.Geraschenko et al.While this review was in preparation, two more studies were published that explored translational response to heat shockThe discovery of RNA interference (RNAi) opened up a debate regarding the potential mechanisms of translational regulation with miRNAs see Refs –29. Whil31However, as discussed by Janas and Novina,Caenorhabditis elegans.Stadler et al. performed parallel mRNA-seq and ribo-seq to analyze the translational changes in a set of five genes  which are known targets of specific miRNAs during the different stages of larval development in While these studies did not end the debate regarding the role and the mechanisms of miRNA-mediated translational control,mTOR is a kinase that regulates global protein synthesis by phosphorylating the protein 4E-BP whose unphosphorylated form inactivates initiation factor eIF4E whose function is to bind to the mRNA 5′-cap and initiate the assembly of the initiator ribosome complex.41Two recent works employed ribo-seq to study the translational regulation mediated by mTOR. Thoreen et al.46In a recent work focused on the characterization of the RNA-binding protein LIN28A, Cho et al.47S. cerevisiae.SPS1 and SPS2 genes. The mRNA levels for both genes showed comparable changes throughout the different stages of meiosis. Yet SPS1, but not SPS2, showed a strong temporal delay in the activation of its translation.Brar et al. explored temporal changes in gene expression during meiosis in At the time of writing this review, Stern-Ginossar et al.Obviously two transcripts expressed at the same level but of different length would produce a different number of short reads aligning to them as the number of reads is proportional to the length of the transcript. Thus the absolute number of short reads derived from a particular transcript is usually normalized to the length of the transcript as well as to the total number of alignable reads, as in Cufdiff FKPM units.5′ leader seems to be an adequate substitute to avoid the oxymoron ‘translation of 5′-UTRs’. The frequent occurrence of conserved AUGs in 5′ leaders was revealed by phylogenetic analyses.The notion that only a single ORF is translated in an individual eukaryotic mRNAs and that 5′-UTR stands for ‘untranslated’ terminal region are mostly of historical interest after the discovery of functional regulatory uORFs.Another problem related to differential translation measurement lies in the method for normalizing translation efficiency over mRNA abundance. A change in mRNA abundance due to changes in transcription or mRNA stability would ultimately result in a corresponding change in the number of ribosome footprints. A simple approach to take this into account is to compare log ratios of ribosome densities over mRNA abundance. Hence, mRNA-seq data, generated in parallel with ribo-seq data, is used to correct for a possible contribution of differential cytosolic mRNA levels to the observed differential levels of actively translated mRNAs. However, Larsson et al. caution against using the commonly applied log ratio approach (ribo-seq levels divided by corresponding mRNA-seq levels) because log difference scores could correlate with cytosolic mRNA levels. The possible confounding effect of cytosolic mRNA levels may result in biological false positives and false negatives. As an alternative, Larsson et al. proposed analysis of partial variance (APV) as a more accurate correction method for cytosolic mRNA levels.53A limitation of ribosome profiling is that it allows to measure only relative changes in gene expression. Because ribo-seq does not provide information on absolute changes of translation, global suppression of translation may be misinterpreted as the activation of translation of a few unaffected genes. In RNA-seq experiments, this problem is solved with the addition of synthetic RNA molecules with a different nucleotide composition (spike-in control).Prior to ribosome profiling, measurements of translation elongation rates were carried out on individual mRNAs.59C. elegans in order to provide evidence in support of the hypothesis that translation is slowed down by wobble interactions between a codon and its anticodon.67The common interpretation of ribosome profiling data is that the density of footprints at a particular location on mRNA is proportional to the time that ribosomes spend at this location. Therefore, it is possible to calculate the average density of ribosomes on specific codons to determine their relative decoding rates. All ribosome profiling studies that addressed this issue agree that there is little relationship between codon usage frequencies and their decoding rates.Escherichia coli and Bacillus subtilis and found that the ribosome occupancy at mRNA locations correlate with purine rich Shine–Dalgarno (SD) regions upstream of the A-site codons. The SD sequence is well known for its role in translation initiation in most prokaryotessecMtnaCE. coli, at mifM in B. subtilisXbp1 mRNAThe truly unexpected observation generated by ribosome profiling was the realization that the rate of cognate tRNA selection in the A-site tRNA may not be the major factor that determines local translation elongation rates. Li et al.All studies where ribosome profiling is used for estimating local decoding rates require the detection of the A-site codon location. Ribosome profiling does not provide direct information on the locations of the A-site codons. It is inferred from the locations of ribosome footprints. At present there are two strategies. One, used in ribosome profiling in eukaryotes, sets an offset between the 5′-end of the ribosome footprint and the expected location of the A-site codon. The offset is derived from the distance between the major density peaks for the 5′-ends upstream of the starts of main coding regions (in some studies stratified according to RPF length), see Refs E. coli mRNAs. They found that in the majority of mRNAs, TF binds to the nascent peptide chain after the ribosome finishes translating about a hundred codons. TF was also found to have a strong preference for binding to ribosomes translating outer-membrane protein mRNA. To study cotranslational protein folding in mammalian cells, Han et al.Oh et al.These three studies have demonstrated the applicability of selective ribosome profiling for studying the compartmentalization of translation inside the cell as well as for elucidating the functional properties of ribosome associated factors.Ab initio annotation of genomes is particularly difficult for short ORFs because short ORFs could exist purely by chance and information on the nucleotide composition of short ORFs may not be sufficient to discriminate coding from noncoding ORFs. Ribosome profiling provides a way to find translated ORFs irrespective of their length. Most recoded genes that require nonstandard translational events, such as programmed ribosomal frameshifting, cannot be automatically identified with pure sequence analysis because of the high diversity and our poor understanding of recoding signals. Ribo-seq can be used to facilitate the discovery of novel recoded genes. It has been argued that most alternative splice isoforms may not contribute to protein synthesis.The analysis of ribosome profiling data does not necessarily depend on gene annotation and thus can be used for the verification of existing gene annotations and the identification of novel nonannotated genome features such as protein-coding genes or short translated ORFs. Protein coding genes are usually discriminated from regulatory ORFs. While it is becoming increasingly difficult to reach agreement on a formal definition of a gene,NPAS2, a gene encoding a component of the suprachiasmatic circadian clock in mammals, provides evidence for the conservation of the nORF rather than its protein sequence suggesting a role for its translation, but not for its product,The very first ribosome profiling study in yeastE. coliE. coli K12 being one of the most extensively studied organisms with an intensively annotated genome. Hence it is evident that current sequence analyses approaches do not allow the identification of all protein coding genes based on DNA sequences even in a well-studied bacterial species and that ribosome profiling is capable of improving the situation. This was further exemplified with a recent study of human cytomegalovirus (HCMV) infection where ribosome profiling of elongating and initiating ribosomes increased the number of identified translated ORFs by more than a third.14Because splicing in bacteria is uncommon, sequences of bacterial ribosome footprints can be aligned directly to genomic sequences, thus simplifying the discovery of novel protein coding genes. Strikingly the first ribosome profiling study performed in Ribosome Profiling of Initiating Ribosomes of this review) is much more appropriate for this goal.Ribosome profiling of elongating ribosomes has significant limitations for the analysis of initiation codons. When protein synthesis is initiated from multiple start codons, only the 5′-end start codon can be identified. Therefore, ribosome profiling of initiating ribosomes (described in the section cis-elements to either standard (stop codon readthrough) or to nonstandard proteinogenic amino acids (selenocysteine and pyrrolysine insertions). In addition, in the case of programmed ribosomal frameshifting, a portion of the ribosomes shift frames at specific locations in the mRNA thus terminating at a stop codon that is out-of-frame relative to the initiator codon. Michel et al.APE2, MMT2, URA8, and YLR179C). Moreover, the identified cases appear to be dependent on oxidative stress suggesting that ribosomal frameshifting plays a regulatory role in these recoded genes.23In contrast to determining the 5′ boundary of a protein coding region, ribosome profiling of initiating ribosomes provides no value for finding the 3′ boundaries of coding regions. Identifying the 3′ boundary of coding regions is problematic in the case of recoding events , the identification of translated ORFs can be made based on TIS detection. Moreover it is even simpler in comparison with ribosome footprints obtained with elongating ribosomes. Because ORFs overlap, it is very difficult to discriminate between the translation of a single frame and the translation of two overlapping ORFs occupying the same transcript location. If TISs are detected with codon precision, information regarding the framing can be determined and therefore can be used for the identification of translated ORFs.All of the studies in the previous subsection reported the existence of ORFs in different configurations relative to the main annotated ORFs with the largest proportion of them being uORFs.52In many cases translation initiates on very short ORFs, which are unlikely to produce functional peptides: among 751 translated ORFs in cytomegalovirus, 245 are shorter than 21 codons, 239 are in the range of 21–80 and only 120 are longer than 80 codons.While initiation at non-AUG codons is frequent in many bacteria, as recently as 2010, the number of non-AUG codons identified as potential translation initiation sites in humans was small. In 2011, Ivanov et al.12Ribosome Profiling of Initiating Ribosomes, initiation at alternative sites both upstream and downstream of the annotated protein coding ORFs is pervasive. Many of these events were heretofore difficult to detect and annotate. Now, advancements can be made in gene annotations by incorporating ribosome profiling data. RND3 gene which has an in-frame CUG initiating codon. CLK3 gene which Lee et al.Translation is a complex process and therefore its characterization will require the use of a combination of approaches. Ribosome profiling of elongating and initiating ribosomes was carried out in parallel in the most recent study.Translation is a process that is downstream of transcription and therefore it cannot be characterized accurately without information on the transcriptome. Therefore transcriptome sequencing and ribosomal profiling have to be carried out in parallel. Combined together, RNA-seq and different ribo-seq techniques will form a universal set of tools for characterizing the molecular state of any living cell at a very detailed level. The continual reduction in cost and time of nucleic acid sequencing will ensure the accessibility of these techniques for gene expression measurements to a very wide research community. There is little doubt that the application of this suite of techniques will grow explosively. However, the ease of the data generation will demand adequate capacity to process, interpret, store, integrate and distribute the data.85


Cerebral glucose metabolism is a reliable index of neural activity and may provide evidence for brain function in healthy adults. We studied the correlation between cerebral glucose metabolism and age under the resting-state in both sexes with position emission tomography. Statistical test of age effect on cerebral glucose metabolism was performed using the statistical parametric mapping software with a voxel-by-voxel approach ( It is now well established that normal aging is associated with a progressive decline in cognitive performance, including perception, attention, language and memory 18F] fluoro-In the resting state, the level of cerebral glucose metabolism is considered as a reliable index of neural activity However, previous reports about the relationship between the regional cerebral glucose metabolism and age are discrepant in a number of brain areas, sometimes conflicting. For example, one study indicated a decreased glucose metabolism with age in the thalamus We studied 68Ge source for attenuation correction. All subjects rested in a quiet, dark room with eyes closed and ears open for All PET investigations were performed at the Medical PET Center of Zhejiang University. PET images were acquired with Hamamatsu SHR 22000 whole-body PET scanner in two-dimensional mode. The scanner has a www.mricro.com). All PET images were spatially normalized into the Montreal Neurological Institute  standard template using SPM5. After normalization, spatial smoothing was performed by convolution, using an isotropic Gaussian kernel with The tissue concentration of FDG can be calculated from the pixel intensity values of the PET images as described by Kumar et al. The result of one-sample In the female group, regions of positive correlation between glucose metabolism and age were not found.In In the male group, significant age-related increasing in glucose metabolism was evident in the lentiform nucleus in the right sub-lobar  , Table 3Age related gyral narrowing and sulcal widening can cause artifacts in glucose metabolism. Some studies found that a decline glucose uptake with normal aging becomes insignificant after taking the partial volume effects into account In our analysis of the resting-state PET images, the glucose metabolism in the frontal lobe declines with normal aging in both the female and the male groups. It is consistent with the results of prior studies which have also used a voxel-based analysis The decline of glucose metabolism in the superior temporal gyrus with aging is significant in both sexes. Willis et al. Another observed phenomenon from this study is the asymmetry of the metabolism decline in frontal and temporal lobes, which is predominant in the male group. As described in A negative correlation between glucose metabolism and age in the caudate is observed in the male group with a less significance relatively. It has been reported by Kawachi et al. In the male group, the regions of the lentiform nucleus, thalamus, paracentral lobule, middle frontal gyrus and precuneus show the positive correlation between glucose uptake and age from our studies. The phenomenon can be explained for an increase in activity in these regions to compensate for the other regions of neuron dysfunction or loss. Scarmeas et al. Several limitations of this study should be illustrated. First, as described above, the partial volume effect ignored in this study is a confounding effect in analysis of age-related changes in the metabolism. Another issue is that estrogen use may influence cerebral glucose metabolism in adults


According to The Indonesian Medical Council, 2006, Indonesian competence-based medical curriculum should be oriented towards family medicine. We aimed to find out if the educational goal of patient-centered care within family medicine (comprehensive care and continuous care) were adequately transferred from the expected curriculum to implemented curriculum and teaching process.Discourse analysis was done by 3 general practitioners of scenarios and learning objectives of an Indonesian undergraduate medical curriculum. The coders categorized those sentences into two groups: met or unmet the educational goal of patient-centered care.Text analysis showed gaps in patient-centered care training between the scenarios and the learning objectives which were developed by both curriculum committee and the block planning groups and the way in which the material was taught. Most sentences in the scenarios were more relevant to patient-centered care while most sentences in the learning objectives were more inclined towards disease-perspectives.There is currently a discrepancy between expected patient-centered care values in the scenario and instructional materials that are being used. The "Health for All" goals as stated in the 1978 Alma Ata declaration described the need to acknowledge the patient as a person -7. CarinIn 2006, the Indonesian Medical Council, adopted a competence-based education as the basis for undergraduate medical curriculum and clearly stated the orientation of the curriculum should be towards family medicine -10. The There is often a discrepancy between "curriculum on paper" and "curriculum in action" . One stuInspired by those lessons, we have chosen to find out if the scenarios and learning objectives in an Indonesian medical school's curriculum that oriented towards family medicine practice were adequately sensitizing students to the values of patient-centered care. We used a qualitative approach by applying a discourse analysis method to explore any discrepancy between problem formulation in the scenarios (presented to the students) and its learning objectives (hidden and driven by tutors) towards a patient-centered care tutorial discussion.In most of the world, education in family practice is taken at the post graduate level . Family The current national health care and health education system in Indonesia requires six years of undergraduate medical education before becoming a physician. Planning included an additional year of internship. However, clinical education in Indonesia was department-based and there are no recognized departments of family medicine or general practice in any of the medical schools in Indonesia. It is a classic "chicken and egg dilemma": we want training programs in family medicine but there are no specialists in family medicine to teach our undergraduates and graduates. Thus, teachers for the internship program may come from general practitioners who do not possess adequate formal postgraduate education on family medicine or may come from hospital-based specialties that do not reflect the realities of health problems in the community. There are gaps in time-spent, knowledge, skillfulness and professionalism between GPs and other specialists in Indonesia.Approximately two thirds of the doctors in Indonesia are primary care doctors. Considering the essential roles of primary care doctors in this country and the lack of postgraduate clinical training, the World Health Organization (WHO) made a recommendation in 2003 that Indonesian primary care doctors should undertake additional postgraduate education as family doctors [In this study, we examined an Indonesian competence-based medical curriculum. The curriculum oriented towards family medicine practice and uses a problem based learning approach to stimulate self directed learning in which adapted from a Western medical curriculum . We chosA macro view of the curriculum shows a design around general learning objectives  for each academic year. The themes for year 1, 2 and 3 are: The Human Body System, The Life Cycle and The Multisystem or Chronic Illnesses consecutively. Each academic year theme consists of 6 blocks. Afterwards, an assessment committee guided the general guidelines of the block assessment process.At the micro level of the curriculum, the multidisciplinary block planning group designed each block, starting from re-considering the learning objectives, creating the scenarios for discussion, defining the facilitators , organizing the schedule and finally creating scenarios for the assessment as guided by the assessment committee. Each blocks containing 6 scenarios. One scenario may consist of 5-10 learning objectives known to the tutors but not to the students.We analyzed the discourse in the scenarios and the learning objectives of year 1, 2 and 3. We did not include year 4, year 5 and year 6 because they were under construction during the study period. A discourse analysis is chosen to provide rich analysis on the event and meaning beyond the analyzed-texts -21.Three coders were general practitioners from a family medicine team at an Indonesian school of medicine. The coders work in a routine primary care service and are involved in the teaching of primary care for undergraduate medical students for more than 10 years. As one of coders, the first author underwent a distance socio-cultural learning theories course  for 9 months provided by the School of Health Professional Education, Maastricht University, The Netherlands, 2010-2011. Other coders were trained in discourse-analysis methods by the first author for a total of 16 hours using international guidelines -21. We aWe used two principles representing the patient-centered care which are fundamental for primary care practices: 1. The Comprehensive Care based on the Bio-psycho-social-economic-education-environment-culture and spiritual concern towards patients and 2. The Continuous Care based on adequate understanding of five levels of prevention and the natural history of diseases -7. We deEach coder defined each sentence in each scenario and learning objectives of each block, based on the two categories. Three coders met when they finished 6 scenarios in 1 block to discuss their findings of the two categories until they reached agreement. Total coding process took 20 weeks (April-August 2010). The coding process took place in Bahasa Indonesia. The first author translated the result into English for presentation and manuscript writing purposes, after agreement of other coders.The text in scenarios and learning objectives was analyzed based on discourse analysis methods -21.Results are noted in Table Examples of sentences in the scenarios that met the educational goal of patient-centered care values:She plans to get married next month but she would not like to get pregnant until she finishes her study in the Faculty of Law." "His doctor has an appropriate recommendation for his work and family counseling after recovery". ""These sentences stimulate students to think beyond patient's health problems. The patient-centered care values were adequately expressed in the concern of comprehensive care and the continuous care towards the patient as individual, as family member and as a member of his/her society".(Agreement among three coders)Examples of sentences in the scenario that unmet the educational goal of patient-centered care values:"Please think a lot about the mechanism of the problem above". "The doctor sent her to the laboratory for a skin-scrapping and a direct skin examination test by KOH 30% stain and culture in order to find out the causative agent". "These sentences may drive students to think on the pathophysiology and procedures, in which of course fundamental for basic medical sciences; however less attention may be given to the patient as a person. The first sentence was the last sentence in the particular scenario that confronted all patient-centered messages in previous sentences. The second sentence mentioned the word 'sent' without careful acknowledgement on patient's consent". Carefully obtaining patients' consent is fundamental in comprehensive care as well as continuous care principles. Obtaining patients' consent may become one of learning objectives in this scenario, so that students may not only pay attention on the disease (diagnosis and treatment) but also paying attention on patient's concern.(Agreement among three coders)Examples of sentences in the learning objectives that met the educational goal of patient-centered care values:"Aware of the professional value as a medical doctor.""Conduct physical examination in a holistic manner according to patient's problem"."These sentences stimulate students to think beyond patient's health problems. The patient-centered care values were adequately expressed the personal care in the behavioral-socioemotional ethical concern towards patient as a person".(Agreement among three coders)Examples of sentences in the learning objectives that unmet the educational goal of patient-centered care values:"Explain etiology and classification of heart failure-New York Heart Association"."Explain the definition of diarrhea".medical knowledge' and abandon the other 6 areas of competencies of medical doctors in Indonesia that we understand from the Indonesian Medical Council, 2006"."These were common sentences we found during analyzing the learning objectives across all blocks in the year 1,2,3 undergraduate curriculum. Most of patient-centered care messages in the scenarios might be neglected when students or tutors found out these learning objectives. We understand that the basic medical sciences need these learning objectives. However, we think that most of learning objectives we analyzed were focusing only on area 2 of competency that was '(Agreement among three coders)This study found gaps in expected patient-centered care values (presented in the scenario) and mostly disease-oriented actual learning objectives (presented in tutors' book). We have assumed that patient-centered care principles must have included in the 7 general areas of competences because the curriculum was oriented towards family medicine. The spirit of patient-centered care may have been missing along the way of the development of the curriculum and educational goals in the particular medical school. However, the way block planning groups creatively translated the disease-oriented learning objectives into more patient-centered scenarios were remarkable and included the effort of hospital specialists' who were trying to be aware of the importance of patient-centered care ideals. Clinical teachers created a more patient-centered scenario in purpose to attract students' attention to learn contextual cases. Three decades experience of problem based learning approaches of the medical school reflected in this endeavor of teaching patient-centered care values.Nevertheless, there are threats to misuse the patient-centered care scenarios. First, the meaning of "contextual" clinical case. Teachers are mostly working at a teaching hospital. Lots of scenarios in later years are referring to a patient who came to the hospital. If the patient mentioned in the scenario presented in a primary health care settings, the disease description remains the same. It is not our goal to limit clinical knowledge but rather to put it into a context in which the patient is seen as more than the disease. Additionally, many presentations in primary care remain undifferentiated. It is important to teach clinical problem solving to students in order to better deal with this uncertainty . In thisSecond, "contextual" scenarios are threatened by the current learning objectives. Students did not know the learning objectives when they read a scenario during a tutorial discussion. Therefore, most of tutorial discussions may begin with curiosity on "who the patient is" and "what was going on the context of clinical cases" as expected by the block planning groups. However, the curiosity on patients' background and concern may not last long. In the end of the discussion students will likely to formulate learning goals that are leaned towards diseases than illnesses as guided by tutors who have been guided by the learning objectives. Teachers in earlier year are mostly come from pre-clinical departments and are general practitioners. However, more than half of scenarios in the first year are leaned towards basic medical sciences of anatomy, physiology and biochemistry than to understand a family as a unit of care. Therefore, in three years of basic medical education, general primary care principles are likely insufficiently covered. Our observations on several actual learning outcomes of tutorial discussion formulated by students of academic year 3 showed limited attention to patient-centered care values. Most of actual learning outcome emphasized diagnosis and treatment establishment, without touching doctor - patient and their family - interaction. However, this observation was limited in number to be included in this study.Another study in the area of effective communication showed that doctors in a teaching hospital rarely respond to patients' concern but mostly did brief diagnosis establishment and prompt treatment . FurtherWe assumed that if we included year 4 tutorial discussions that will be no significance change to our findings. This raises the concern of unmet educational goal of patient-centered care in later years of study. Moreover, year 5 and 6 are clinical rotation stages which are department based (without a family medicine department). A medical doctor trained in this context of the study may have difficulty framing the problem of one of the patient's concern rather than a simple disease to be cured. Therefore, a clear distinction between studying basic medical sciences, studying general clinical medicine, and studying hospital-based clinical sciences is needed in the context of this study ,26.One of limitations in this study is that we analyzed a curriculum of only one medical school in Indonesia. However to our knowledge, this medical school leads many medical institutions in curriculum reformation. Another limitation was that only one method of discourse analysis performed. A more multifactorial methodology may leads to improved comprehension of the curriculum and prospectus modification . The othThe current health problems in Indonesia are TB-HIV, high Maternal Mortality Rate and Infant Mortality Rate, Malaria, Dengue Fever, Malnutrition and Chronic illness such as Hypertension and Diabetes Mellitus . Basic sThe current basic medical education curriculum in Indonesia that is supposed to be oriented towards family medicine has not succeeded. We recommended appropriate patient-centered care training for medical students to be more sensitive to patients' problem. Proper undergraduate and postgraduate training on primary care practice with community based educational approaches are required.Non-financial competing interest: The authors declare an academic competing interest of teaching family medicine with patient-centered care approaches for both undergraduate and postgraduate medical education.MC designed this study and wrote the first draft of this paper. MC and ADS were two of the three coders. MAG provided advices on the content of patient-centered care in family medicine. AS contributed advices on the content of curriculum-discrepancy and guided the process of scientific writing. All four authors discussed and revised the first draft until the final version to be submitted.This study was part of an Evaluation Study of the Curriculum Development of Faculty of Medicine Gadjah Mada University under the NPT-Project, 2010. The ethical approval was obtained from the Committee Ethics UGM under the Evaluation Study of the Curriculum Development FM UGM 2010.


The mechanisms of attention control have been extensively studied with a variety of methodologies in animals and in humans. Human studies using non-invasive imaging techniques highlighted a remarkable difference between the pattern of responses in dorsal fronto-parietal regions vs. ventral fronto-parietal (vFP) regions, primarily lateralized to the right hemisphere. Initially, this distinction at the neuro-physiological level has been related to the distinction between cognitive processes associated with strategic/endogenous vs. stimulus-driven/exogenous of attention control. Nonetheless, quite soon it has become evident that, in almost any situation, attention control entails a complex combination of factors related to both the current sensory input and endogenous aspects associated with the experimental context. Here, we review several of these aspects first discussing the joint contribution of endogenous and stimulus-driven factors during spatial orienting in complex environments and, then, turning to the role of expectations and predictions in spatial re-orienting. We emphasize that strategic factors play a pivotal role for the activation of the ventral system during stimulus-driven control, and that the dorsal system makes use of stimulus-driven signals for top-down control. We conclude that both the dorsal and the vFP networks integrate endogenous and exogenous signals during spatial attention control and that future investigations should manipulate both these factors concurrently, so as to reveal to full extent of these interactions. The ability to suitably allocate processing resources is fundamental for the efficient processing of incoming sensory signals and for the generation of appropriate behavior in complex environments. The brain continuously receives a large amount of sensory signals that cannot be fully processed. Attention selection allows preferential processing of some signals and filtering out of other inputs. What are the constraints that govern this selection process, thus determining what signals should gain access to in-depth processing?Traditionally, attention research has distinguished between two types of mechanisms that contribute to the selection process. On one hand there are endogenous, top-down factors that primarily relate to the subject’s “internal” goals and intentions. On the other hand, there are exogenous, bottom-up effects that primarily relate to the characteristics “external” stimuli. Endogenous factors are associated with top-down voluntary control, while exogenous factors are associated with stimulus-driven control that is thought to take place automatically. The distinction between these two types of control can be rather intuitive: when searching for a friend in a crowd, we will voluntary shift attention from one face to another until the external input  matches our internal knowledge about the physical appearance of our friend. By contrast, in a crowd of people all dressed with dark cloths, we will quickly notice a person dressed in bright red, who will catch attention automatically. Experimentally, the impact of endogenous and exogenous factors for selection have been studied with a variety of paradigms. Somewhat related to the “real-life” examples above, visual search tasks can be used to highlight endogenous vs. exogenous factors for the allocation of spatial attention. Search tasks including a target-item “similar” to the distracters  will be slow and inefficient. The search time will depend on the number of competing distracters thus indicating that search proceeds serially with attention shifted voluntarily from one item to another item. By contrast, when the target item stands out  the search is rapid and efficient, with the red target capturing attention in an automatic manner irrespective of the number of distracters.Another way to investigate endogenous and exogenous control of spatial attention includes using variants of the Posner spatial cueing paradigm Posner, . Rather Many functional imaging and Event Related Potentials (ERPs) studies have investigated the neural basis of endogenous and exogenous visuo-spatial attention control. These highlighted the central role of the frontal and parietal lobes, with a notable distinction between the response patterns in dorsal and ventral regions. A variety of tasks requiring endogenous control of spatial attention highlighted the activation of dorsal fronto-parietal regions . These data challenge the traditional dichotomy linking the dorsal system with endogenous attention and the ventral system with exogenous attention, and indicate a novel perspective to understand the multifaceted mechanisms underlying the control of spatial attention.As noted above, a wealth of imaging evidence has associated activation of the dorsal fronto-parietal network with endogenous/voluntary attention control . In order to explicitly characterize the effect of bottom-up signals, we considered the saliency model proposed by Itti and Koch . This deIn a first study, we investigated the impact of visual salience on spatial orienting using a virtual visual environment  task, we sought to establish whether stimulus-driven attention to salient elements of a complex image has any consequence on subsequent memories of that image . The dorsal attention system is usually structurally intact in these patients: nonetheless, the activity of dorsal areas can be functionally reduced due to structural lesions of adjacent areas in the ventral attention system. Consistent with this, the study of visual ERPs suggested that in neglect patients bottom-up visual processing can be impaired at around 130 ms post-stimulus, at the level of structurally intact dorsal attention areas  may result from a common response to both valid and invalid target in the left TPJ. At the behavioral level, in the non-predictive condition the validity effect was reduced, though, not abolished. This is important because it shows that even when the general validity context of an endogenous Posner task is constant and neutral, non-predictive cuing can still bias participants’ attention. Even more importantly, the analyses of the benefits and costs, showed—quite surprisingly—that the reduction of the validity effect in the non-predictive condition was entirely explained by a drop in the costs; whereas benefits were equivalent in the predictive and non-predictive conditions . All together these findings show that: (a) the left TPJ hosts both neuronal populations coding the mismatch between cued and actual target location on invalid trials and cue-target matches on valid trials; (b) the right TPJ hosts neuronal populations coding the mismatch between cued and actual target location; (c) the validity context modulates TPJ activity during the cue period but shows no comparable influence on target-related brain response: this suggests that in fMRI studies investigating the influence of the validity effect it is suitable to disentangle cue- and target-related effects. Cue- vs. target-related effects also provides us with a possible explanation for the different findings between the study of Vossel et al. , which rIn two other studies we investigated the response pattern of the vFP system seeking to further dissociate pure stimulus-driven effects from expectation and task-relevance  and other endogenous/internal constraints. Mere bottom-up stimulus onset is insufficient to activate this network  bears some relationship with recent proposals concerning the role of “predictive coding” in visual processing  can be selectively driven by the abatement of attentional costs, whereas benefits can be maintained with both predictive and non predictive cuing . In an ensuing ERPs study . We emphasize that attention control must pick up statistical ir-/regularities of the environment and integrate these with on-line information about the current sensory input. This interaction determines the selection of the most relevant stimuli and governs the allocation of the attentional resources. At the physiological level, this is likely to require some interplay between the dorsal and the ventral attention systems. We propose that the ventral system performs moment-to-moment match/mismatch operations, comparing current expectations/predictions with the actual sensory input. The result of these operations leads to a continuous update of the expectations and predictions, which the dorsal system utilizes to control the allocation of spatial attention.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.


Despite various developments in many fields of ophthalmology, the surgical therapy of open-angle glaucoma has remained mostly unchanged over the last 30 years. Ever since the introduction of intraoperative mitomycin and postoperative subconjunctival injections of 5-fluorouracil (5-FU), trabeculectomy has not markedly been altered. These facts stand in contrast to the need for a more efficient surgical therapy for open-angle glaucoma, since one of the main disadvantages of filtering surgery is the lack of enduring success. Large-scale retrospective studies have suggested that filtering blebs become non-functional in at least 50% of patients, 5 years after surgery. This clearly demonstrates the necessity for developing techniques to reduce postoperative scarring in filtering blebs.In the current issue of Journal of Ophthalmic and Vision Research, Pakravan and colleaguesCertain questions however remain. First, interestingly, the toxicity of mitomycin applied topically on intact conjunctival epithelium is considerably less than that applied on bare sclera. Future studies may address whether this disparity is due to different durations of application (drops have relatively short period of contact with the ocular surface), variations in effective concentrations of the agent (drops may be diluted by tears), and/or due to the protective effect of an intact conjunctival epithelium. Second, it is not clear yet whether prolonged topical application of mitomycin may cause corneal stem cell insufficiency leading to problems in corneal epithelialization or dry eye due to damage to conjunctival goblet cells. Third, the risk of systemic side effects of mitomycin eye drops due to absorption through the nasolacrimal duct mucosa may additionally be addressed.In conclusion, the study by Pakravan et al may show new possibilities and open up a new avenue in the postoperative care of patients after routine trabeculectomy. Since the application of mitomycin eye drops is considerably more convenient and probably less costly, it may indeed be an alternative to postoperative subconjunctival injections of 5-FU.


The HIV epidemic in Manipur, the highest HIV prevalence state of India, is primarily driven by injecting drug use. Reliable estimate of population size of injecting drug users (IDU) is critical for aiding HIV prevention program in the state to combat drug driven HIV epidemic. The study described multiplier method, an indirect technique of estimation of IDU size in five districts of Manipur, India making use of existing records of rapid intervention and care (RIAC) programs. Number of IDUs who accessed RIAC services during the past 12 months was taken as the benchmark data for the size estimation. The benchmark data were then multiplied by the inverse of the proportion of the IDUs who reported having accessed RIAC services during the same period to derive the sizes of IDU population in each study districts. The estimated sizes of IDU population in five districts were: 7353 (95% CI: 6759-8123) in Imphal West, 5806 (95% CI: 5635-6054) in Imphal East, 3816 (95% CI: 3571-4139) in Thoubal, 2615 (95% CI: 2528-2731) in Churachandpur and 2137 (95% CI: 1979-2343) in Bishenpur district. Multiplier method seems to be a feasible indirect technique which can be applied to estimate of IDU population using existing data from intervention programs in settings like Manipur where reliable size estimation of IDU population is lacking. Injecting drug use is a global public health problem that contributes significantly to the transmission of bloodborne viral pathogens, including HIV and is responsible for an increasing proportion of new HIV infections -4. ApproHowever, despite its critical importance, reliable size estimates of drug injecting population have received little attention in this region. Societal stigma and hostility associated with illegal drug use in the region often force the IDUs to hide their identity as a drug user ,9. The hMultiplier method estimates the population size using information from two independent data sources that overlap in a known way ,11. One We carried out the study in five districts i.e. Imphal East, Imphal West, Thoubal, Bishnupur and Churachandpur. Apart from Churachandpur district that is hilly, other 4 districts are situated in plain terrain. Churachandpur is the largest and Imphal West is the most populous among the 5 districts selected for the study Table  15]. Th. Th15]. Population size estimation was done separately for each study districts. The benchmark data  used for each study districts were numbers of IDUs who received services from different RIAC centres within last 12 months and were obtained from RIAC centres through the Manipur AIDS Control Society (MACS). The benchmark figure was arrived at by combining the data of different RIAC centres. To avoid data duplication, those IDUs accessing services from outside the areas covered by a particular RIAC center were excluded from the benchmark figure. Further exclusion of IDUs receiving RIAC services from outside the study district (i.e. catchments area) were also made from the benchmark figure. Thus, a final combined revised list of those IDUs accessing services of RIAC centres in the last 12 months was prepared for each study districts in consultation with different RIAC centres.Have you accessed any services from any of the RIAC centres of the district (name of the district) at least once in the last 12 months?". Exact binomial 95% confidence interval (CI) for proportions was calculated using Epi-info 6 software .We also conducted separate anonymous interviews of IDUs to obtain information about exposures to RIAC services in the last 12 months in the month of September 2004. For obtaining IDU samples, mapping of IDU locations (hot-spots) where IDUs congregated for injecting, buying and hanging out in all the districts were carried out. Details methodology of mapping of hot-spots has been described earlier . In shorThe findings of the study are presented in Table There are several important issues that should be kept in mind for estimating population size using multiplier methods. Multiplier is a mathematically simple and straightforward method, but it requires good quality institutional record keeping (i.e. benchmark data) for accurate estimation of population size ,10,14. IAnother important issue in multiplier method is the time reference period which must be clear and same in both data sources. In our study, the time reference period taken for the benchmark data was last 12 months. But, this time reference period used in benchmark was not consistent with the definition we used to define an IDU in the survey, where only those IDUs who had injected in the last six months were interviewed. Such issues of inconsistencies in the time reference period have also been reported in other studies . But, thFor deriving an accurate multiplier, it is also essential to obtain reliable information about exposure to intervention from the respondents (IDUs) in the survey. In this study, we asked the respondents to report if they had accessed any services from RIAC centres in the last 12 months. Such longer time reference period (12 months) may however lead to recall errors of the events. Recall errors associated with longer time reference period can be minimized by shortening the time reference period. Apart from recall bias, self-reported information may also be subject to interviewer bias or socially desirable respond. To control such biases, interviewers were carefully selected and trained adequately by the investigators to build adequate skills among them to collect objective data from the respondents. In this study, 66% to 93% of IDUs reported receiving services from intervention program. These findings of this study were comparable to those found in another behavioural survey conducted among IDUs in Churachandpur and Bishenpur districts of Manipur in 2006 supporting the veracity of our results . Report Drawing a representative and random sample of IDU population is also a big challenge because of hidden nature of IDU population. However, to get representative samples of the study population and also to achieve better coverage of catchment area, we carried out an exhaustive mapping of IDU hot-spots and then respondents were selected from those hot-spots through a random selection process. Random selection of IDUs within the mapped hot-spots also helped in preventing self-selection biases or volunteerism. However, there may still be some biases in the approach adopted in this study . TherefoTo the best of our knowledge, this was the first study to estimate the size of IDU population using multiplier method in Manipur. This study revealed that estimation of population size of IDUs based purely on records of intervention programs does not represent the true size of the population as our study indicates that a sizeable proportion of IDU population remain unexposed to the intervention programs. Therefore, despite limitations, multiplier method may be used as a simple indirect tool to estimate size of IDU population utilizing the existing program data. Because of availability of IDU registries maintained by the intervention programs, the method seems to be sustainable in settings like Manipur. However, there are several key caveats which should be taken into account while using multiplier method for estimating the size of such hidden population. Understanding of some these caveats may help in the further application of this method using more recent data.The authors declare that they have no competing interests.GKM, JM and RA contributed in the conception of study design, oversaw the data acquisition, led data analysis, and drafted the manuscript. BSA contributed in data acquisition, study design, interpretation of the data and reviewing the manuscript. All the authors read the manuscript and approved the final version of the manuscript.