Mycobacterium leprae that predominantly attacks the skin and peripheral nerves, leading to progressive impairment of motor, sensory and autonomic function. Little is known about how this peripheral neuropathy affects corticospinal excitability of handgrip muscles. Our purpose was to explore the motor cortex organization after progressive peripheral nerve injury and upper-limb dysfunction induced by leprosy using noninvasive transcranial magnetic stimulation (TMS).Leprosy is an endemic infectious disease caused by In a cross-sectional study design, we mapped bilaterally in the primary motor cortex (M1) the representations of the hand flexor digitorum superficialis (FDS), as well as of the intrinsic hand muscles abductor pollicis brevis (APB), first dorsal interosseous (FDI) and abductor digiti minimi (ADM). All participants underwent clinical assessment, handgrip dynamometry and motor and sensory nerve conduction exams 30 days before mapping. Wilcoxon signed rank and Mann-Whitney tests were performed with an alpha-value of p<0.05.Dynamometry performance of the patients’ most affected hand (MAH), was worse than that of the less affected hand (LAH) and of healthy controls participants (p = 0.031), confirming handgrip impairment. Motor threshold (MT) of the FDS muscle was higher in both hemispheres in patients as compared to controls, and lower in the hemisphere contralateral to the MAH when compared to that of the LAH. Moreover, motor evoked potential (MEP) amplitudes collected in the FDS of the MAH were higher in comparison to those of controls. Strikingly, MEPs in the intrinsic hand muscle FDI had lower amplitudes in the hemisphere contralateral to MAH as compared to those of the LAH and the control group. Taken together, these results are suggestive of a more robust representation of an extrinsic hand flexor and impaired intrinsic hand muscle function in the hemisphere contralateral to the MAH due to leprosy.Decreased sensory-motor function induced by leprosy affects handgrip muscle representation in M1. Mycobacterium leprae that predominantly attacks both skin and peripheral nerves, resulting in persistent distal hand atrophy and the loss of sensory and autonomic functions. In this study, we employ a noninvasive tool named transcranial magnetic stimulation (TMS) to map the handgrip muscle representation in the primary motor cortex of patients affected by leprosy. The findings of this study support that the decrease or loss of sensory afferent neurons and/or impairment in the strength of peripheral muscles in the ulnar/median territory verified in leprosy patients alters the handgrip function leading to cortical motor reorganization in the corresponding affected hand muscles.Leprosy is an endemic disease caused by  Mycobacterium leprae [Leprosy, also known as Hansen's disease, is a chronic human granulomatous bacilliferous infection caused by the obligate intracellular organism m leprae . Leprosym leprae ,3. The bm leprae .Nerve damage may happen before, during or after treatment with the multidrug therapy (MDT) recommended by World Health Organization. In other words, even after bacteriological cure, leprosy can cause permanent physical disabilities and deformities. The installation of those deformities contributes to social exclusion, psychological disorders, and self-stigma, as has been recorded in studies about social participation and quality of life. Since 1985, 14 million individuals have received MDT [A considerable amount of literature has been published on leprosy. Several studies have focused on understanding the basic aspects of leprosy, such as genetics , 7, physThe adult brain is capable of profound plasticity after peripheral lesions ,22,23,24Motor cortex plasticity has also been demonstrated after peripheral lesions caused by amputation and/or phantom pain ,28,29,30It remains unknown if and how the human motor cortex reorganizes after the typical gradual peripheral nerve damage provoked by leprosy. In the present study, we used single-pulse TMS mapping to evaluate motor organization in M1 after MDT in adult chronic leprosy patients with persistent hand disabilities. We hypothesized that patients with chronic damage in upper limb peripheral nerve caused by leprosy could present changes in corticospinal excitability as well as in hand grip muscle representation organization in M1.This study employed a cross-section design where a transcranial magnetic stimulation (TMS) mapping protocol was used to evaluate the cortical representation of selected hand muscles in M1 contralateral and ipsilateral to the most affected hand in chronic leprosy patients and healthy subjects in Hospital Federal Clementino Fraga Filho, RJ, Brazil, over the period of 2009 to 2013.All participants provided written, informed consent, consistent with the Declaration of Helsinki. The Human Research Ethics Committee  approved this study.Six right-handed adult patients with chronic leprosy, grade 2 disability  with the shoulder and wrist at a neutral position with the forearm supported and the elbow positioned at 90 degrees ,42,43. TLeprosy neuropathy, despite being primarily demyelinating, frequently leads to axonal loss. Nerve conduction studies are considered the most objective method of assessing nerve function  to confiPatients in this study were examined in a nerve conduction study approximately 30 days before the TMS mapping. The ENMG protocol for the study of motor conduction of median and ulnar nerves was performed. The amplitude of the compound muscle action potentials (CMAP) as well as the latencies and motor conduction velocity (MCV) were measured. For the sensory conduction study in the same nerves, the compound sensory action potential amplitude (CSAP), distal latency and velocity of sensory conduction velocity (SCV) were measured. The skin temperature was measured and maintained above 32 degrees Celsius.Prior to the TMS session, an image of the head of every subject was obtained using magnetic resonance imaging (MRI) using a neuronavigation system (3space Fastrack–Polhemus Isotrack II) to ensure the accurate positioning of the TMS coil. At the beginning of the experiment, the 3D location of 200 points on the scalp was measured using an electromagnetic position sensor to co-register the MRI with the actual position of the subject’s head . A plastDuring the experiment, subjects remained awake, seated in a plastic comfortable chair with pillows placed under the forearms/hands, and his/her jewelry, glasses, watches and other potentially conducting or magnetic objects worn on the head or arms were removed to prevent interactions with the magnetic field, consistent with a TMS guide . The skiSurface EMG recordings were obtained using surface 8 mm, Ag/AgCl electrodes (Medtronic Adhesive Disposable Surface Electrodes) placed on the skin over the muscle bellies, and the centers of the electrodes were placed approximately 1.5 cm apart. A ground electrode was placed ipsilaterally above the epicondylus, laterally at the elbow joint. Surface EMG signals were amplified and band pass filtered . The signal was subsequently digitized at a sampling rate of 15.000 Hz  and stored on a desktop computer for offline analysis. Custom-made MATLAB software  was used to measure the latency and peak-to-peak MEP amplitudes. The MEPs mean amplitudes recorded at each stimulated point was subsequently calculated and projected onto the brain to create a cortical muscle representation map. We visually inspected the EMG profiles to ensure that all muscles were electrically silent for each TMS pulse. When it was not the case, the trial was rejected and stimulation at that point was repeated.TMS mapping of four hand target muscles was performed using a MagVenture-MagPro R30  connected to a figure-of-eight cooled coil . The elicited electric field was directed in the lateral to medial direction with the coil held in a tangential position with the handle perpendicular to the midsagittal line.Before mapping, the FDS hot spot  was located. Subsequently the resting motor threshold, which corresponds to the minimal intensity of stimulation at the hotspot eliciting MEPs larger than 50 μV in at least 50% of 10 trials, was determined according to the threshold-hunting paradigm . Once thx,y) coordinate was calculated as:ai represents the mean amplitude, and xi and yi represents the stimulated coordinate position.After data collection, the average latency and amplitude of the MEPs for each site was calculated. The mean amplitude obtained per coordinate was then normalized per participant by dividing the mean amplitudes by the maximum mean amplitudes collected in the hotspots. The center of gravity (COG), map area (number of active sites) and muscle overlaps were measured from MEP normalized values. The COG was defined as the map location representing the amplitude-weighted center of the area of excitability . The COGThe Euclidean equation was applied to determine the distance between COG locations in the same hemisphere, whereas the map area was defined as sum of active sites with >50 μV/MEP. The muscle overlap parameter was defined as the TMS stimulation points that generated simultaneous MEPs in all four-target muscles ,50.Descriptive and nonparametric analyses were performed using STATISTICA 7.0  and GraphPad Prism 6 . To study the handgrip (dynamometry), TMS map area and COG we used a Wilcoxon matched-pairs signed rank test. The Mann-Whitney test was chosen to analyze the TMS motor threshold and MEP amplitudes. For all statistical tests, the alpha level was set to p<0.05.M.leprae courses with a distal to proximal pattern, with an initial ulnar nerve sensory impairment followed by injury in motor fibers as well, described in the literature as impairment of conduction of nerve impulse [The ENMG exam was used to assess the bilateral ulnar/median nerve conduction in leprosy patients.  impulse  and decr impulse . If not Firstly, we compared grip force in both upper-limbs of control subjects and found no significant difference . The average of the grip strength in both upper limbs of the control group  was then compared with that of patients. Lower grip strength was found for the MAH as compared to the control group (p = 0.031). Lower grip strength was also found in the MAH (p = 0.031) as compared with the less affected hand (LAH) in the patient’s group. These results are shown in The percentage of TMS machine output (motor threshold), and the distance in time observed between the TMS stimulation artifact and the MEP onset (latency) were measured at the FDS muscle hotspot. Moreover, MEP average peak-to-peak (amplitude) was measured from the FDS, APB, FDI and ADM muscle hotspots. We found a significant difference in motor threshold (MT) for the FDS muscle between the MAH and the control group (p = 0.041) as well as between the LAH and the control group , as well as for FDI amplitudes between the hemisphere contralateral to the MAH and those of the LAH (p = 0.031) as well as between those of the hemisphere contralateral to the MAH and the control group , diagnosed with serious right upper limb nerve damage, no MEP response could be elicited in the tested intrinsic muscles , even with 99% of the TMS machine output. Great variability in map area was observed for all other patients and control subjects.A Wilcoxon test was applied to compare the FDS, APB, FDI and ADM map areas between hemispheres in leprosy patients  of each muscle was compared within and between hemispheres. Differences in the absolute COGs between the hemispheres indicate whether these areas are equidistant from the midline, or whether any asymmetry exists. Moreover, the position of the COGs of each muscle in the same hemisphere might indicate either an overlap or a reorganization of the motor maps. The Wilcoxon test showed no significant differences between hemispheres neither in patients nor in paired controls. Likewise, no significant differences in distance between COGs were observed between the patients and control subjects for all pairs of muscles.The present study was the first to use transcranial magnetic stimulation (TMS) to examine the organization of the primary motor cortex (M1) of patients diagnosed with leprosy and portraying claw-hand deformity. Results show motor cortical changes in leprosy patients after the so-called "cure" of the Hansen's bacillus infection using multidrug therapy.The main findings of this study can be summarized as follows. First, grip force assessment showed lower grip strength in the patients’ most affected hand (MAH) compared to the less affected hand (LAH) as well as to the control group. This result is indicative of functional impairment of the patients’ MAH. Moreover, patients had lower resting motor threshold (MT) for the FDS muscle in the hemisphere contralateral to the MAH as compared to the hemisphere contralateral to the LAH. Notwithstanding, higher motor thresholds in both hemispheres were found for this muscle in patients as compared to matched control participants. Finally, motor evoked potential (MEP) amplitudes of the intrinsic hand muscle FDI were lower in the hemisphere contralateral to the MAH as compared to those of the LAH and to the control group. Although the representational motor maps in patients and controls showed great variability, the FDI and ADM muscles in patients tended to have smaller areas in the hemisphere contralateral to the MAH than those obtained in that of the LAH or in matched control subjects. No difference within or between subjects was found for COG and distance between COGs. These results are discussed below.Measurement of handgrip strength has gained attention as a simple, non-invasive marker of muscle strength of upper extremities, suitable for clinical use. This assessment reflects the maximum strength derived from combined contraction of extrinsic and intrinsic hand muscles, leading to the flexion of hand joints . DigitalPatients with chronic ulnar/median nerve impairment were herein shown to exhibit a significant decrease in grip strength in the MAH when compared to the LAH as well as to control participants. Accordingly, Rajkumar, Premkumar and Richard  observedTarget muscles  were mapped employing the motor threshold of the FDS muscle at rest (MT). This choice was based on the fact that the median nerve (which supplies the FDS muscle) exhibited control-like ENMG parameters in our cohort  for the FDS muscle in the hemisphere contralateral to MAH as compared to the hemisphere contralateral to the LAH. Accordingly, previous studies in humans suffering traumatic amputation of the upper limb showed that the MT of the amputated limb is lower (average 10–17%) in the hemisphere contralateral to the lost limb than that of the ipsilateral hemisphere ,74,75,76MEP values collected in FDS hotspot in the hemisphere contralateral to the MAH were also higher than those of control subjects, consistent with the observations of Zanette et al, . Higher Smaller MEP amplitudes were found for the FDI muscle of the MAH as compared to the LAH and the control group. Although the map area of the tested intrinsic hand muscles was highly variable both within patients and in control subjects, smaller map areas were also found for the FDI and ADM muscles in the motor cortex contralateral to the MAH as compared to the LAH. These results are in line with those found herein for ENMG and grip strength, and furthers results obtained in hand allograft suggesting that the extent of intrinsic hand muscle representation in M1 associate with hand function .During whole handgrip, the extrinsic muscles provide the major gripping force . The FDSLeprosy patients usually exhibit a mixed variety of peripheral nerve injuries with sensorimotor impairment, thereby increasing the cortical plasticity challenge and the variability of results . IndiviS1 Table## not found; FDS: Flexor Digitorum Superficialis; APB: Abductor Pollicis Brevis; FDI: First Dorsal Interosseous; ADM: Abductor Digiti Minimi; RH: right hemisphere; LH: left hemisphere. In all leprosy patients the left hand was the most affected. The active sites were considered when the motor evoked potential (MEP) value was at least 50μV. Grey color represents subjects enrolled in the statistical analysis.Legend: ** not tested; (DOCX)Click here for additional data file.S2 Table## not found; "Sites" correspond to the number of overlapping points with simultaneous responses on the four target muscles within each hemisphere. %/Percentage of active sites considering all stimulated points. Grey color represents subjects enrolled in the statistical analysis Click here for additional data file.


The tractable, layered architecture of the olfactory bulb (OB), and its function as a relay between odor input and higher cortical processing, makes it an attractive model to study how sensory information is processed at a synaptic and circuit level. The OB is also the recipient of strong neuromodulatory inputs, chief among them being the central cholinergic system. Cholinergic axons from the basal forebrain modulate the activity of various cells and synapses within the OB, particularly the numerous dendrodendritic synapses, resulting in highly variable responses of OB neurons to odor input that is dependent upon the behavioral state of the animal. Behavioral, electrophysiological, anatomical, and computational studies examining the function of muscarinic and nicotinic cholinergic receptors expressed in the OB have provided valuable insights into the role of acetylcholine (ACh) in regulating its function. We here review various studies examining the modulation of OB function by cholinergic fibers and their target receptors, and provide putative models describing the role that cholinergic receptor activation might play in the encoding of odor information. The network of cholinergic fibers acts as a major neuromodulatory system in the brain. It is not only implicated in the pathophysiology of neurodegenerative disorders like Alzheimer’s disease, but it also plays a central role in the functioning of the healthy brain. The release of ACh by these fibers is involved in the enhancement of sensory perception during wakefulness, particularly during periods of sustained attention . StudyinFigure 1). Projections from ORNs that recognize the same odor epitope converge onto about two (of about two thousand) glomeruli in the ipsilateral bulb . Other interneuron types and subtypes have been described  into defined structures called glomeruli  and sparser projections to other OB layers  with some atypical glomeruli showing much denser innervation . When unilateral naris occlusion was performed on postnatal day 2, the pattern and intensity remained unchanged up to postnatal day 12. However, significant reductions in intensities were observed in the ipsilateral bulb of the adult . In addition, the patterning was lost during this period. These results suggest that odor-induced activity is required for the maintenance and patterning of the cholinergic innervation.Occluding sensory input to the bulb from one naris revealed that cholinergic input is modulated by olfactory activity . A possible mechanism for this inhibition is the shunting of ORN inputs due to the increase in the membrane conductance of MCs upon the opening of a large number of channels, particularly the nAChRs and GABA receptors. Thus, the receptors act as high pass filters that attenuate weak signals while allowing stronger ones to pass, thus setting odor detection thresholds.A major site for nAChR regulation is the glomerulus of the OB. Consistent with autoradiographic studies  functionPotentially important players in the increased GABA release within the glomerulus upon nAChR activation are the ET cells , a populFigure 5A) within the EPL. Activation of M1-mAChRs, via mobilization of endoplasmic reticulum store calcium, release GABA onto the MCs at the dendrodendritic synapses between GCs and MCs  cells, while also inhibiting the basal firing of the GABAergic granule and PG cells . This ob animals . Further animals . This ob animals .Activation of basal forebrain cholinergic neurons also results in the sharpening of M/T cell responses so that when these inputs are activated, M/T cell responses to the optimal odorant  are enhanced, while responses to non-optimal odorants are suppressed . It shouOur knowledge of cholinergic modulation of the OB output is far from complete as we are still discovering the extent of receptor distribution and cell types that they can act upon. The functional role that the α7 receptor plays in modulating OB function is still unresolved. Anatomical studies have revealed that α7 nAChRs are highly expressed in the glomerulus , while bSimilarly, we have no information on the role M2-mAChRs play in the cholinergic modulation of the bulbar output. Anatomical evidence suggests that these receptors are localized on GC synapses in the EPL, on second-order GABAergic neurons in the infra-mitral cell layer, and on some juxtaglomerular GABAergic interneurons, suggesting complex inhibition/disinhibition roles for these receptors on MC output .Our knowledge of the function and regulation of various juxtaglomerular interneurons is incomplete as well. For example, the short axon cells, a type of juxtaglomerular cells that mediates interglomerular inhibition , have beThe vast repertoire of cholinergic receptor subtypes expressed throughout the brain exhibit a variety of physiological properties. These include the sensitivity of these receptors to ACh, as well as their desensitization rates. A major puzzle in the field of cholinergic function is to understand the roles played by these different receptor subtypes. Cholinergic transmission in the brain can be broadly classified as occurring via two modes, synaptic, and diffusion-based, resulting in the release of ACh with concentrations that vary over orders of magnitude. Varying concentrations of ACh acting on receptor subtypes exhibiting a myriad of sensitivity and desensitizing properties indicate a dynamic control of sensory processing over multiple timescales that is dependent on the behavioral state of the animal.in vivo work have shown that during light sleep or awake immobility, a low, tonic level of ACh primarily activate mAChRs expressed on GCs . This model, therefore, predicts a role for both tonic and phasic modulation for cholinergic inputs  where early loss of olfactory discrimination and anosmia has been reported . ChangesThe cholinergic hypothesis for diseases like AD has had dominance for many decades  and has Figure 3). Unilateral naris occlusion results in a loss of pruning of incoming cholinergic fibers in the adult and results in diffuse innervation of the OB similar to that seen in young (day 12) animals . The key process in cholinergic modulation of OB functions, appears to be GABAergic signaling. Activation of nAChRs drives glomerular inhibition via the indirect excitation of PG cells. This allows for normalization of glomerular excitation, setting thresholds for transfer of information. The excitation of MCs and ET cells by nAChRs also increase baseline firing, potentially providing a template for net negative readouts in firing frequencies, as well .A simple model, based on current state of our knowledge, would postulate that nAChR activity dominates at the glomerular microcircuit, while mAChRs control the GC-driven modulation of MC firing . Ongoing efforts at further localizing the relevant receptors and at manipulating cholinergic inputs in awake animals performing olfactory tasks will shed more light on this important modulation of a sensory modality by cholinergic processes.At the same time mAChR-driven excitation of GCs and their modulation of GABAergic signaling at the GC-MC dendrodendritic synapses allows for lateral inhibition. Recovery from inhibition across MCs aids in synchronizing firing which is thought to facilitate the integration of incoming information at a population level (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.


RNA-binding proteins (RBPs) are pivotal in orchestrating several steps in the metabolism of RNA in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Here, we employed CLIP (cross-linking immunoprecipitation)-seq datasets for 60 human RBPs and RIP-ChIP (RNP immunoprecipitation-microarray) data for 69 yeast RBPs to construct a network of genome-wide RBP- target RNA interactions for each RBP. We show in humans that majority (~78%) of the RBPs are strongly associated with their target transcripts at transcript level while ~95% of the studied RBPs were also found to be strongly associated with expression levels of target transcripts when protein expression levels of RBPs were employed. At transcript level, RBP - RNA interaction data for the yeast genome, exhibited a strong association for 63% of the RBPs, confirming the association to be conserved across large phylogenetic distances. Analysis to uncover the features contributing to these associations revealed the number of target transcripts and length of the selected protein-coding transcript of an RBP at the transcript level while intensity of the CLIP signal, number of RNA-Binding domains, location of the binding site on the transcript, to be significant at the protein level. Our analysis will contribute to improved modelling and prediction of post-transcriptional networks. Progress in proteomics together with other omics technologies have now convincingly shown the existence of an additional and perhaps more important gene regulatory layer in cellular networks, which acts in concert with other layers of regulation to control gene expression and translation in a highly coordinated complex system defined as post-transcriptional regulatory network. For instance, in one of the large-scale omics studies comparing transcriptome and proteome levels it was shown that ~30% of the variance in protein abundance in yeast cannot be explained by mRNA expression levels4458in-vivo binding sites of RBPs at the single nucleotide level29303133348363725In prokaryotes, functionally related genes are often organized into operons to facilitate co-expression and to reduce expression fluctuation among the resulting protein products1112131516914462021222425In this study, we map the CLIP binding sites of 60 RBPs on to the human genome to construct a RBP – RNA network. Further, we examined the correlation of each RBP’s expression at both transcript and protein levels with the target RNAs to see how these correlation patterns change. We then analyzed different factors impacting the change in expression patterns through a comprehensive two level analysis using different modelling techniques namely multivariate regression modelling, stepwise linear regression and Elastic net. We observed a higher level of association between the protein expressions of RBPs with their target transcripts compared to transcript level expression. Our results indicate that RBPs at both proteomic and transcriptomic levels play an important role in coordinating expression changes of the target RNAs and this can be explained by various factors governing the functions of these RBPs.As shown in versus control associations; 1) Significantly Congruent (SC) : RBPs would belong to this class if the distribution of RBP – target correlation coefficients have their median correlation coefficient significantly higher than that seen in the control set of transcripts  2) Significantly incongruent (SIC) : RBPs would belong to this class if the distribution of RBP – target correlation coefficients have their median correlation coefficient significantly lower than that seen in the control set of transcripts  3) No Significant change (NSC) : If no significant change in the median correlation coefficient is observed between the targets and the control sets, those RBPs would belong to this class. RBPs grouped into these three classes are supported by robust set of p–values as illustrated in 38versus control transcripts for all the 60 RBPs organized into SC (36 RBPs), SIC (11 RBPs) and NSC (13 RBPs) classes. Overall, we found that 78.33% of the RBPs comprised of SC and SIC classes, exhibited significant association with their targets at the transcript level, at a p-value threshold of 0.05.To understand how RBPs are associated with their targets, we correlated the expression of one of the protein coding transcripts  of each RBP with the expression of the target transcripts across 16 human tissues and compared it with control set of transcripts . To address the issue of the size of the control set, we also randomly sampled the control set of transcripts by sampling 100 times to extract each time the same number of randomly selected transcripts as the number of target transcripts, which is referred to as the control-matched set. As a result of computing the spearman correlations between a RBP transcript and its target as well as non-target (control) transcripts, RBPs were divided into three classes based on comparing the distribution of correlation coefficients for targets To understand, whether our observation of finding RBP – target expression correlations to be significantly non-random, is generic and conserved across organisms, we analyzed the RBP – RNA network of the yeast genome using the same workflow . Since humans and yeast are evolutionary distant, we hypothesized that the yeast genome would be an ideal model to show the generality of our observations across different species. The network used in this study45While we found that RBPs show good degree of associations with their targets in both the human and yeast genomes when the transcript levels of RBPs are employed, protein expression levels of RBPs in matched tissues or experimental conditions is rather limited. However, recent genome-wide protein levels for multiple human tissues resulting from the Human Proteome Map facilitate addressing this question, albeit using limited number of samples . After identifying and mapping equivalent RNA-seq and proteomic samples, we correlated the protein expression data across nine tissues for each RBP with the corresponding target as well as control transcripts’ expression levels from the RNA-seq dataset and organized the RBPs in to three classes – SC, SIC and NSC. To further understand and dissect our findings on RBP – target associations, we performed a comparative analysis of the outcomes for various human RBPs to see how these correlation patterns change within the transcript or protein levels and from the transcript to the protein levels of RBPs. Further, we observed that 12 RBPs exhibited similar trends at both the transcript and protein levels with six of them belonging to SC category and six belonging to the SIC category. To further understand the behavior of these 12 RBPs (sync RBPs) and how they are different compared to others (non-sync RBPs), we analyzed different network centrality measures using igraphAs listed in As listed in In summary, we find that RBPs exhibit significant co-expression patterns with their target RNAs although the extent and direction of co-expression can vary between RBPs and among members of the same RBP family. They show strong association with their targets at both protein and transcript levels, however a higher level of association was observed at the protein level. Most of the RBPs show different level of association at the protein and transcript level with only 20% of them showing similar trends at both the levels. Intensity of the clip signal, number of RNA binding domains and location of the binding site on the transcript prove to be important features which can explain the association observed at the protein level while number of target transcripts, number of protein coding transcripts for the selected RBP and length of selected protein coding transcript explain the associations seen at the transcript level. On further dissecting the analysis, at the transcript centric level, we observe that the type of target transcript and the distance of the binding site from the 5′ or 3′ end of the transcript are the important factors. We also found contrasting trends i. e, same RBP can be an SC at the transcript level while being classified as an SIC RBP at the protein level - classified based on the expression associations of the RBPs with their target transcripts at the transcript and protein levels. It is interesting to note that different features were found to be significant at these two levels possibly suggesting the rational for the observed differences in directionality of the associations.In this study, we present genome-scale evidence that majority of the RBPs are correlated in expression levels with their post-transcriptionally controlled target transcripts in both the human and yeast genomes. To our knowledge this is the first study to report such an association in post-transcriptional regulatory networks and strengthens our understanding of the relationship between RBPs and their cognate targets. Our observations suggest that in disease conditions, expression associations between RBPs and target transcripts are likely altered. Hence, prognostic RBPs can be identified by comparing the extent and number of associations in healthy versus disease expression cohorts, enabling a means of rapidly profiling for RBP biomarkers in developmental diseases, cancer and other complex disorders45http://www.ebi.ac.uk/arrayexpress) under the accession number E-MTAB-513. To study the correlation of protein expression levels of RBPs with RNA levels of RBP target transcripts, we downloaded mass spectrometry based proteomic data for over 17,000 human proteins across 30 tissues/cell lines  from Human Proteome Atlas (HPA)To obtain a comprehensive understanding of the RBP-RNA interaction networks on a genome- wide scale and to study the characteristics of binding sites of RBPs on their target RNAs, we downloaded Crosslinking Immunoprecipitation followed by high-throughput sequencing (CLIP-Seq) data from CLIPdb database505253Several studies have shown that RBPs bind 200–300 nucleotides around the observed splice sites, which generally possess the identifiable sequence features56Transcript level expression was quantified for the downloaded RNA-seq data using Sailfish v0.6.3To identify a representative protein coding transcript encoding for an RBP among all the annotated transcripts in the RNA-seq data, a protein coding transcript with the highest mean expression level across all the 16 tissues was chosen. Spearman correlation was calculated between the transcript level expression of each RBP and every target as well as non-target transcript’s expression levels across the 16 tissues to generate correlation coefficients for the three different categories of transcripts namely RBP target transcripts, RBP control matched and RBP control all, defined above. Similarly, for the protein expression data upon mapping the tissues from this dataset with the tissues available in the RNA-seq dataset, we found 9 common tissues and hence spearman correlations were computed between the protein expression level of each RBP and its target as well as non-target transcript’s expression level from RNA-seq data which resulted in three categories of correlation coefficients for each RBP see . BoxplotTo understand what factors and the extent to which they might be contributing to the observed correlation patterns at the transcript and protein levels of RBPs, we employed multivariate modelling at two different levels, referred to as the RBP centric level and the transcript centric level in this study. We employed three different feature selection/reduction methods to identify the robust set of contributing features, namely – the lm function, the step LR function and the ElasticNetAt the RBP centric level, our goal was to understand and identify the general features which can likely explain the observed association between RBPs and their targets. These included nine features namely number of target transcripts controlled by an RBP, median CLIP signal of a RBP, number of RNA-binding domains in a RBP, number of documented protein interactions of a RBP, number of protein coding transcripts encoded by a RBP, total number of annotated transcripts by the gene encoding for RBP, length of the selected protein coding transcript, median of all the distances between the binding site of RBP and to the closest end of the transcript and correlation between mRNA-protein levels of an RBP, which could play a role in influencing the median correlation coefficient of all the target transcripts for each RBP. At the transcript centric level, our goal was to uncover the contribution of the transcript specific features such as CLIP signal on the target transcript, distance of binding site with respect to the 5′ or 3′ end of the transcript, length as well as type of the transcript on the correlation coefficient of each target transcript for each RBP. A detailed description of each of these features is listed in http://downloads.yeastgenome.org/published_datasets/Waern_2013_PMID_23390610/ for S. cerevisiae strain S288C reference genome sequence version R64-1-1We hypothesized that the observed correlation patterns of RBPs with their target transcripts is conserved across species. To test this hypothesis, we used the post-transcriptional regulatory network of 69 RBPs and 24,932 RBP-RNA interactions in the yeast genomeHow to cite this article: Nishtala, S. et al. Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks. Sci. Rep.6, 25711; doi: 10.1038/srep25711 (2016).


The developmental pathophysiology of autism spectrum disorders (ASD) is currently not fully understood. However, multiple lines of evidence suggest that the behavioral phenotype may result from dysfunctional inhibitory control over excitatory synaptic plasticity. Consistent with this claim, previous studies indicate that adults with Asperger’s Syndrome show an abnormally extended modulation of corticospinal excitability following a train of repetitive transcranial magnetic stimulation (rTMS). As ASD is a developmental disorder, the current study aimed to explore the effect of development on the duration of modulation of corticospinal excitability in children and adolescents with ASD. Additionally, as the application of rTMS to the understanding and treatment of pediatric neurological and psychiatric disorders is an emerging field, this study further sought to provide evidence for the safety and tolerability of rTMS in children and adolescents with ASD. Corticospinal excitability was measured by applying single pulses of TMS to the primary motor cortex both before and following a 40 s train of continuous theta burst stimulation. 19 high-functioning males ages 9–18 with ASD participated in this study. Results from this study reveal a positive linear relationship between age and duration of modulation of rTMS after-effects. Specifically we found that the older participants had a longer lasting response. Furthermore, though the specific protocol employed typically suppresses corticospinal excitability in adults, more than one third of our sample had a paradoxical facilitatory response to the stimulation. Results support the safety and tolerability of rTMS in pediatric clinical populations. Data also support published theories implicating aberrant plasticity and GABAergic dysfunction in this population. Autism spectrum disorder (ASD) is diagnosed clinically, based on the key symptoms including qualitative impairments in social communication and the presence of restricted and repetitive behaviors . HoweverSeveral lines of evidence suggest that an impairment of GABAergic transmission may be critical in the pathophysiology of ASD see . While iEmpirical support for the role of aberrant GABA signaling in the pathophysiology of ASD comes from both human and animal model research. A recent study conducted by glutamic acid decarboxylase (GAD) 65 and 67; p = 0.054) positive correlation between the GABA signal and age. Among the many roles of GABAergic circuits during development, one is lateral inhibition across neighboring minicolumns in the cortex. Consistent with an impairment in GABAergic transmission, postmortem studies have found a reduction in the horizontal spacing between minicolumns  paradigms  to explore the effect of development on the response to the cTBS paradigm. As the application of rTMS to the understanding and treatment of pediatric neurological and psychiatric disorders is an emerging field , this stTable 1 for demographic characteristics of the sample). All participants gave informed consent or assent, which was also obtained from a parent or guardian to participate in the study. The study was reviewed and approved by the institutional review board at Boston Children’s Hospital. Participants were recruited through local community advertisement. All participants had IQ > 80 based on the Weschler Abbreviated Scale of Intelligence (WASI). All met DSM-IV-TR criteria for Autism, Asperger’s Syndrome or PDD-NOS, and met criteria for ASD on the Autism Diagnostic Observation Schedule, Module 4 (ADOS). Some participants also had comorbid symptoms including inattention, anxiety, irritability, and obsessive-compulsive behaviors (See Table 1). All participants were given a comprehensive neurological exam by a board-certified pediatric neurologist (Alexander Rotenberg) to confirm normal gross motor and fine motor function. Lastly, all participants were screened following published recommendations  and specifically GABAergic inhibition, cTBS was applied to the primary motor cortex. The cTBS paradigm used in the current study was identical to that described by To measure TMS induced MEPs, EMG surface electrodes were placed in a belly tendon montage over the FDI muscle of participants’ right hands. Raw signals were amplified and bandpass-filtered between 20 and 2000 Hz. EMG signals were sampled at a rate of 5000 Hz. All stimulation (single-pulse TMS and TBS) was delivered using a hand-held 70 mm figure-of-eight coil attached to a Magstim Super Rapid stimulator . The coil was placed tangentially to the scalp with the handle pointing posteriorly. All stimulation was applied over the hand area of the left motor cortex and individually localized for each participant based on the optimal position for eliciting MEPs in the right FDI. The stimulation intensity for baseline and post-TBS single pulses was set at 120% of each individual’s resting motor threshold (RMT) while the TBS itself was delivered at 80% of AMT. RMT and AMT were defined following recommendation from the International Federation of Clinical Neurophysiology. RMT was defined as the minimum single-pulse TMS intensity required to induce an MEP in the contralateral FDI of >50 μV peak-to-peak amplitude on more than five out of ten consecutive trials while the target muscle was at rest. AMT was defined as the minimum single-pulse TMS intensity required to induce an MEP in the contralateral FDI of >200 μV peak-to-peak amplitude on more than five out of ten consecutive trials while the target muscle was held at approximately 20% of the maximal contraction. To precisely target the stimulation site (primary motor cortex) and keep the brain target constant throughout the stimulation session, we used a frameless stereotactic neuronavigation system .Data were analyzed using MatLab version 8.1 and SPSS version 22. Data analysis followed the methods described and applied in previous studies in our laboratory , 2012. ACubic spline interpolation was used to create smooth curves through the data points. Spline interpolation is a piecewise continuous function defined by third-degree polynomials in the intervals of a limited range of known data points . The use of spline interpolation on TMS data has been validated  and usedA natural log transformation was applied to the data prior to analysis as tests of normality indicated that the data was significantly different than normal. A Pearson product-moment correlation coefficient was calculated to assess the degree of relationship between age and duration of response to cTBS.Immediately following the TMS session a side effects questionnaire was completed by the experimenter. Participants were asked to report whether they experienced any of the following side effects: headache, neck pain, scalp pain or irritation, difficulty hearing, thinking or concentrating, change in mood, or any other change or side effect they experienced. The experimenter also noted whether the participant experienced a syncopal event or seizure. The participant also received a call the day after the TMS session and was once again asked to report whether they experienced any of the above side effects or to report any other side effect they experienced after they left the hospital. If the participant reported any side effect either immediately following the stimulation or the following day, its severity and duration were documented.All participants tolerated TBS and single-pulse stimulation without serious adverse event. One participant had a mild headache after stimulation that was alleviated with a single acetaminophen dose. Two participants had mild fatigue after the session that resolved the following day. No other adverse events were reported.M = 46.3 min, SD = 29.3 min). The results of the analysis indicated that there was a significant positive linear relationship between age and duration of response .A Pearson product-moment correlation coefficient was calculated to test the hypothesis that a linear relationship existed between age and duration of response to cTBS. As described above, response to the cTBS protocol was defined as duration of effect as defined by the number of minutes following cTBS before the participant returned to baseline excitability levels . Additional analyses were conducted excluding the seven participants who facilitated and the significant positive correlation between age and duration of response remained  with a Mean duration of 49.2 min (SD = 33.8 min). The subgroup of participants who displayed the paradoxical facilitation response was not predicted by comorbid symptoms or medication .In addition to the planned analyses, it was noted that unlike our previous study that included only adult participants, a third of the participants  had a paradoxical facilitation in response to the cTBS protocol  concentrations in individuals with ASD. This is further supported by a study reporting paradoxical increases in hyperactivity in six out of seven and aggression in seven out of seven children with ASD who were treated with diazepam  have not yet been well validated for this application. We chose the left hemisphere as it is typically the dominant hemisphere for both right- and left-handed individuals. Second, although motor abnormalities are not considered core symptoms of ASD, many studies have reported motor deficits in individuals with ASD, including alterations in motor milestone development , clumsinOur results support the safety and tolerability of TBS in the pediatric ASD populations. As we continue to enhance our understanding of the relationship between the response to cTBS with GABAergic inhibition and GABAergic dysfunction with ASD pathophysiology we suggest that cTBS may be a practical biomarker of GABAergic dysfunction in this population.Lindsay M. Oberman designed the study, collected the data, analyzed the data, and wrote the manuscript. Alvaro Pascual-Leone contributed to the study design, interpretation of the data, and the writing of the manuscript, Alexander Rotenberg contributed to the study design, interpretation of the data, supervised and contributed to data collection, and contributed to writing of the manuscript.Alvaro Pascual-Leone serves on the scientific advisory boards for Nexstim, Neuronix, Starlab Neuroscience, Neuroelectrics, and Neosync; and is listed as an inventor on several issued and pending patents on the real-time integration of transcranial magnetic stimulation (TMS) with electroencephalography (EEG) and magnetic resonance imaging (MRI). Alexander Rotenberg is listed as an inventor on a patent for apparatus and method of use of TMS in epilepsy. He is a co-founder of Neuromotion Inc.


Klein and Sorra's theory of innovation implementation suggests that the effectiveness of implementing an innovation results from both a climate that supports, rewards, and expects implementation as well as from the fit between the innovation and the intended users' values. Although the authors propose that innovation-values fit moderates the effect of implementation climate on implementation effectiveness, this relationship has never been tested. In addition, most of the evidence supporting the use of Klein and Sorra's theory in health services research is from qualitative studies, while most of the quantitative use of the theory occurs in information systems implementation research. Therefore, the goal of this study is to quantitatively test in a health services context the proposed relationship in which innovation-values fit moderates the effect of implementation climate on implementation.We tested the theory of innovation implementation using structural equation modeling (SEM) among 481 physician participants in the National Cancer Institute's Community Clinical Oncology Program (CCOP).Overall the hypothesized SEM model fit well. Our results indicated that both implementation climate and innovation-values fit were significantly associated with implementation effectiveness among CCOP physicians (p <0.05). In addition, including innovation-values fit as a moderator improved the overall fit of our SEM. The moderator explained 2.6% of the variation in implementation effectiveness and approached statistical significance (p = 0.06).Our study advances innovation implementation theory and field of dissemination and implementation research. The results of this study extend the scientific literature by not only empirically examining the theory of innovation implementation in a health services setting, but also by testing whether innovation-values fit moderates the effect of implementation climate on implementation effectiveness. These results can help guide further research regarding implementation climate, implementation effectiveness, and innovation-values fit, all key constructs in implementation research.This work was supported by the National Cancer Institute (R25CA116339 and R01CA124402) at the National Institutes of Health.


The brain integrates multiple sensory inputs, including somatosensory and visual inputs, to produce a representation of the body. Spinal cord injury (SCI) interrupts the communication between brain and body and the effects of this deafferentation on body representation are poorly understood. We investigated whether the relative weight of somatosensory and visual frames of reference for body representation is altered in individuals with incomplete or complete SCI (affecting lower limbs’ somatosensation), with respect to controls. To study the influence of afferent somatosensory information on body representation, participants verbally judged the laterality of rotated images of feet, hands, and whole-bodies  in two different postures (participants’ body parts were hidden from view). We found that (i) complete SCI disrupts the influence of postural changes on the representation of the deafferented body parts  and (ii) regardless of posture, whole-body representation progressively deteriorates proportionally to SCI completeness. These results demonstrate that the cortical representation of the body is dynamic, responsive, and adaptable to contingent conditions, in that the role of somatosensation is altered and partially compensated with a change in the relative weight of somatosensory versus visual bodily representations. Most of us can effortlessly coordinate movements and somatosensations371718Prior to the experiment, 16 controls, 11 individuals with incomplete SCI, and 11 individuals with complete SCI  completeThe VMIQ showed that all individuals with SCI and controls were equally able to perform mental imagery both in first- and third-person perspective . No significant differences between the three groups in terms of general imagery abilities were found . Similarly, the handedness inventory showed that the three groups were homogeneous in terms of hand dominance, with a strong preference for the right with respect to the left hand  and not differing between them in terms of right hand preference  and left hand preference .Posture-related effects hinted to a differential weight of somatosensation in the representation of deafferented body parts (feet). The analysis of RTs showed the significant main effect of posture , accounted for by the overall slower responses in the crossed postural condition (1325 ms) with respect to the straight postural condition . The significant interaction between posture and group , indicated that only controls and the incomplete SCI group were slower in mentally rotating feet while their own feet were crossed . Conversely, in the complete SCI group the difference in mental rotation task performed in the crossed (1257ms) and straight condition (1272ms) was not significant. In other words, only the complete SCI group failed to show the posture-dependent change in mental rotation of foot images . InteresPosture-related effects showed preserved representation of unaffected body parts (hands). RT analysis showed the significant main effect of posture , accounted for by the slower responses in the crossed (1296ms) with respect to the straight condition . This pattern was significant in each group when tested separately  . The posThe properties of mental rotation of body images hinted to lesion-dependent adjustments of whole-body representation. Importantly, statistical significance was not reached by the interaction between group and posture either for RTs [F = 0.38] or accuracy [F = 0.21] . HoweverSCI dramatically impairs or even definitively prevents the exchange of afferent and efferent input between the brain and the body27schema refers to the online representation of the somatosensory information about one’s own bodyimage refers to the pictorial component of the body representation373839The absence of posture-dependent modulation of RTs in the mental rotation of foot images after complete SCI can be interpreted as a sign of a changed relative weight of different frames of reference to represent the body. Thus the weight of somatosensory representations was diminished while the weight of visual representations was augmented. In contrast to a winner-take-all perspective, this interpretation is in line with the idea that we are able to integrate and assign different weights to different sources of sensory information as a function of their reliabilityIt might be argued that the heterogeneity of lesion levels in the incomplete SCI group could have affected the correlation between RTs and lesion completeness. However, despite this structural heterogeneity, functionally the large majority of the incomplete SCI group  showed homogeneous and only mild somatosensory symptoms at the lower limbs  somatosensory information (as in paraplegia following SCI) on mental processing of the representation of the disconnected body parts. This influence becomes progressively weaker as a function of  loss of afferent somatosensation. Existing models of sensory-motor integration support the existence of prediction mechanisms able to anticipate the motoret al.et al.et al.et al.et al.et al.Body representation after SCI has been considered both as disturbed39How can the present results be transferred to rehabilitation ? With the main aim of promoting beneficial neural plasticity and restoring brain activitySCI interrupts the brain-body interactions but its consequences on body representation are mostly unknown. Here we investigated the influence of SCI on the interplay between somatosensory and visual reference frames in the context of body representation. Our results hint at possible changes in the relative weighting of different source(s) of sensory information on which body representation is grounded. The main outcomes of the present study can be summarized in three main points. First, using the mental rotation task, we provided a quantifiable measure (RTs) of the effects of SCI on body representation. Second, we contrasted local  and global (full-body) representations of the body, specifying the selective effects of SCI on affected versus preserved representations. Third, we directly compared the effects of total and partial somatosensory loss on body representations. On this basis, we further proposed that the present data can be clinically applied, in that mental rotation of bodily images is a direct, non-strenuous, and controlled approach to investigate body representations that could be implemented in standard assessment and rehabilitation protocols.The experimental procedure was approved by the local Ethics Committee of the Canton of Zurich (EK-04/2006) and the study was carried out in accordance with the Declaration of Helsinki. All participants were informed of the study procedures and signed a written informed consent. Prior to the experiment, all the 38 participants . In particular, for the VMIQ first we compared the ability to perform mental imagery in first- and third-person perspective within each group, and then we analyzed the general imagery abilities across groups by averaging the values of the two imagery perspectives within each group and comparing the results between groups. In the same vein, for the handedness inventory we first compared the right- and left-lateralized preferences within each group and then we tested whether the distribution of preferences for one hand was different across groups.VMIQ and Handedness scores were analyzed using the two-tailed t-test approach  has an advantage (shorter latencies) with respect to mental rotation away from the midsagittal plane RT was defined as the time between the stimulus onset and the onset of the participant’s verbal response. Accuracy was defined as the percentage of correct responses in relation to the total number of trials. Trials with incorrect responses (accuracy) or with RTs falling out of the range between 500ms and 3500ms were excluded from the analysesHow to cite this article: Ionta, S. et al. Spinal cord injury affects the interplay between visual and sensorimotor representations of the body. Sci. Rep.6, 20144; doi: 10.1038/srep20144 (2016).


With the advent of high-throughput sequencing technologies large-scale identification of microsatellites became affordable and was especially directed to non-model species. By contrast, few efforts have been published toward the automatic identification of polymorphic microsatellites by exploiting sequence redundancy. Few tools for genotyping microsatellite repeats have been implemented so far that are able to manage huge amount of sequence data and handle the SAM/BAM file format. Most of them have been developed for and tested on human or model organisms with high quality reference genomes.polymorphic SSR retrieval (PSR), a read counter and simple sequence repeat (SSR) length polymorphism detection tool. It is written in Perl and was developed to identify length polymorphisms in perfect microsatellites exploiting next generation sequencing (NGS) data. PSR has been developed bearing in mind plant non-model species for which de novo transcriptome assembly is generally the first sequence resource available to be used for SSR-mining. PSR is divided into two modules: the read-counting module  identifies all the reads that cover the full-length of perfect microsatellites; the comparative module (PSR_poly_finder) detects both heterozygous and homozygous alleles at each microsatellite locus across all genotypes under investigation. Two threshold values to call a length polymorphism and reduce the number of false positives can be defined by the user: the minimum number of reads overlapping the repetitive stretch and the minimum read depth. The first parameter determines if the microsatellite-containing sequence must be processed or not, while the second one is decisive for the identification of minor alleles. PSR was tested on two different case studies. The first study aims at the identification of polymorphic SSRs in a set of de novo assembled transcripts defined by RNA-sequencing of two different plant genotypes. The second research activity aims to investigate sequence variations within a collection of newly sequenced chloroplast genomes. In both the cases PSR results are in agreement with those obtained by capillary gel separation.In this note we describe PSR has been specifically developed from the need to automate the gene-based and genome-wide identification of polymorphic microsatellites from NGS data. It overcomes the limits related to the existing and time-consuming efforts based on tools developed in the pre-NGS era. The development of EST-SSR markers was historically based on collection of sequence data of complementary DNAs (cDNAs) generated using the Sanger sequencing technology. Some useful tools have been made available for the detection and localization of both perfect and imperfect microsatellites along genome and mRNA sequences [http://www.bioinformatics.org/ftp/pub/msatfinder/; http://pgrc.ipk-gatersleben.de/misa/).Simple sequence repeat (SSR), also known as short tandem repeats (STRs), variable number tandem repeats (VNTRs) or microsatellite markers, are repetitive stretches of 1–6 nucleotide units randomly spread in eukaryotic genomes. Microsatellites typically vary in length between 5 and 40 repeat units and can be classified as perfect or imperfect: in the first case, the repeat unit is arranged in head to tail manner without any interruption; in the second case the repeat unit includes insertions, deletions or substitutions of bases. In addition, SSRs can be of two types: simple or compound (i.e. two adjacent distinct SSRs are separated by a certain number of nucleotides). A further categorization allows SSRs to be recognized as genomic SSRs (gSSRs) and expressed sequence tag (EST)-SSRs; the latter result from transcribed regions of a genome, are associated with functionally annotated genes and are supposed to be more conserved among related species/genera. SSRs are very polymorphic due to the high mutation rate affecting the number of repeat units and have several advantages over other molecular markers: they allow the identification of multiple alleles at single locus [locus bearing in mind the short size of NGS reads and the difficulties this type of sequence data arises in the correct identification of polymorphic SSRs. An additional effort has been freshly published [loci. In this paper, we present polymorphic SSR retrieval (PSR) a Perl package developed to identify polymorphic SSRs from NGS data and provide quantitative information to each call. Unlike the aforementioned tools, PSR has been developed in a context where de novo transcriptome assembly is generally the first sequence resource for non-model plant species to be used for SSR-mining and downstream investigations.Generally, these tools are equipped with additional programs able to design primers for microsatellite flanking regions. One of the most common approaches to the detection of length polymorphisms relies on the random selection of SSRs and on the analysis of PCR products on high-resolution gels . Since tlocus , 15, 16.locus  to analylocus , RepeatSlocus  and the locus  are the PSR is a Perl package, conceived as a modular and flexible tool, developed to identify polymorphic SSRs from NGS data. The PSR package and the user manual are available at the following URL: http://sourceforge.net/projects/polyssr/.PSR workflow is shown in Fig. Psr_read_retrieval aims at the identification of all the reads that align to the reference sequences covering the full-length of perfect microsatellites. We decided to focus on perfect microsatellite only, because the total length of the reads obtained by the Illumina sequencing instruments rarely exceeds the 100 high quality nucleotides. These constraints appear to limit polymorphism discovery only to short polymorphic SSRs, but as it is evident from data in Table locus. Indeed, in case SSRs are located at the ends of the read, the microsatellite-containing sequences are discarded since they can strongly affect the call of polymorphic sites  that includes the type and the size of identified microsatellites and their localization within the reference sequences. The second input file stores read alignments against reference sequences for each genotype under investigation. The latter can be genome sequences or de novo assembled transcripts depending on the type of microsatellites under study.Based on our experience and on results by Highnam et al. , we suggPsr_read_retrieval should be run as many times as the number of genotypes under investigation  and the minimum read depth (−p), for length polymorphism to be called. By default the values of these parameters are fixed to 10 and 30, respectively.Then, all the table-wise text files are fed into the locus.To give a clear example, a microsatellite is analysed in case at least ten reads overlap the repetitive stretch and it is called as heterozygous if 30 % or more of the reads supports the identification of the minor allele. In case of polyploid genotypes, the user can fine-tune the value of the “p” parameter in order to support the detection of all the putative alleles at each Filtering by a minimum number of reads supports variant calls and by minimum read depth within the microsatellite interval helps to reduce false positive calls.Psr_poly_finder produces as final output a table-wise text file where the first two columns report the identifiers of microsatellite-containing sequences and the type of the identified microsatellite; the remaining columns include one or more (in case of heterozygosity) SSR allele sizes per genotype.PSR reliability and effectiveness, the package has been tested in the identification of polymorphic SSRs in (1) a collection of de novo assembled transcripts defined by RNA-sequencing of two different plant genotypes; (2) a set of newly sequenced chloroplast genomes.In order to evaluate PSR, were assessed by capillary electrophoresis and eight of them showed the expected length polymorphism  only in five cases.In the first case, ten randomly selected polymorphic microsatellites, as they were identified by sm Table . Only onPSR combined with capillary gel separation was used to assess whether in silico identified length polymorphisms represented sequencing/assembling errors or, alternatively, real genotype-specific sequence variations. In seven cases out of eight, the size of the microsatellite supported by the highest number of reads was confirmed by capillary electrophoresis  that do not completely span the microsatellite. Furthermore, in case of EST-SSRs, the quality of the reference transcriptome may negatively affect read alignment as a first step and, subsequently, read count. Finally, differences can be the result of PCR slippage products of repetitive stretches or can be ascribed to errors generated by PCR-based NGS technologies, especially in case of monomeric microsatellites [It is very likely that differences from in silico and wet-lab experiments depend on the amount of reads tellites .PSR, a Perl Package developed for the detection of length polymorphisms and for the automatic comparative analysis at microsatellite loci. Indeed, the availability of polymorphic SSR markers is an essential requirement for plant community since it serve as basic resources for QTL mapping, molecular breeding, genetic diversity analysis and SSR fingerprinting for food traceability. All these and further applications, motivated us to develop and distribute PSR within plant community.The ability of next generation sequencing technologies to produce large amounts of sequence data accelerated microsatellite identification and facilitated the discovery of polymorphic SSRs. In addition, NGS resulted in the development of new specialised tools and file formats that support the management of huge amount of sequence data. However, as far as we know, few automatic and efficient systems have been developed so far for detecting both gene-based and genome-wide polymorphic microsatellites from NGS data. In this note we proposed Project name: PSR—polymorphic SSR retrievalhttp://sourceforge.net/projects/polyssr/Project home page: Operating system(s): tested on Linux and Mac OS XProgramming language: PerlOther requirements: BioPerl, MySQLLicense: GNU GPL 3Restrictions to use by non-academics: None.


Though the hunger-reduction phenomenon reported during ketogenic diets is well-known, the underlying molecular and cellular mechanisms remain uncertain. Ketosis has been demonstrated to exert an anorexigenic effect via cholecystokinin (CCK) release while reducing orexigenic signals e.g., via ghrelin. However, ketone bodies (KB) seem to be able to increase food intake through AMP-activated protein kinase (AMPK) phosphorylation, gamma-aminobutyric acid (GABA) and the release and production of adiponectin. The aim of this review is to provide a summary of our current knowledge of the effects of ketogenic diet (KD) on food control in an effort to unify the apparently contradictory data into a coherent picture. Hunger and satiety are two important mechanisms involved in body weight regulation. Even though humans can regulate food intake by will, there are systems within the central nervous system (CNS) that regulate food intake and energy expenditure. This complex network, whose control center is spread over different brain areas, receives information from adipose tissue, the gastrointestinal tract (GIT), and from blood and peripheral sensory receptors. The actions of the brain's hunger/satiety centers are influenced by nutrients, hormones and other signaling molecules. Ketone bodies are the major source of energy in the periods of fasting and/or carbohydrate shortage and might play a role in food intake control.The hypothalamus is the brain's main center responsible for hunger/satiety (H/S) control. In the theory that Mayer proposed more than 60 years ago, he assigned a central role to glucose levels in the H/S control: the so-called “glucostatic theory” Mayer, . Mayer sIn 1953, Kennedy proposed the lipostatic hypothesis suggesting that lipid metabolites could also be involved in food regulation Kennedy, .Glucose-sensitive neurons have been identified in a number of CNS regions including the metabolic control centers of the hypothalamus. Medeiros et. al. have used patch-clamp electrophysiology to examine whether neurons in a specific specialized region known as the subfornical organ (SFO), an area where the blood-brain barrier is not present, are also glucose sensitive or not. These experiments demonstrated that SFO neurons are glucose-responsive and that SFO is an important sensor and integrative center of circulating signals of energy status  and other key proteins that transduce glucose signals are expressed at low levels. Glucose also exerts a hormonal-like action on neurons; electrophysiological recordings demonstrated, for example, that hypoglycemia activates growth hormone-releasing hormone (GHRH) neurons, suggesting a mechanistic link between low blood glucose levels and growth hormone release  concentrations are present at many sites throughout the brain and may play a key role in the neural control of energy and glucose homoeostasis. Central administration of oleate, for example, inhibits food intake and glucose production in rats. This suggests that daily variations in plasma FA concentrations could be detected by the CNS as a signal that contributes to the regulation of energy balance /CD36. Translocase is a FA transporter/receptor that activates downstream signaling even in the absence of intracellular metabolism , the periventricular nucleus (PVN) and the dorsomedial hypothalamic nucleus (DMH)  the short-term  occurring at the beginning and end of a single meal; it also includes the length between meals and b) the long-term regulation  that is influenced by such factors as body fat deposition.The SS providing information to the brain mainly send information to the nucleus of the solitary tract (NTS). These signals are generated in the GIT and abdominal viscera, as well as in the oral cavity and provide information about mechanical and chemical properties of food. The information is transmitted via vagal and spinal nerve to the NTS. The ASs arrive to the median eminence through ARC or through the blood-brain barrier (BBB). All these afferents are integrated in a complex and not fully understood network.Hormones like leptin and insulin, both secreted into the blood, reflect the stored body fat. These hormones can pass the BBB and stimulate specific receptors. Hypothalamic areas are richly supplied by axons from ARC, which has greater concentrations of leptin and insulin receptors than any other hypothalamic site . The neurophysiological pathways suggest that feeding is regulated by a feedback loop, where the hypothalamus provides the long-term regulatory input to the NTS, which acts as a setpoint  plays a central role in the control of energy balance. Many molecules produced by the GIT exert hunger or satiety effects on the brain. Ghrelin is a peptide produced mainly by the stomach's oxyntic cells that stimulates ghrelin secretion in the hypophysis and has some neuroendocrine activities. However, its orexigenic properties are the most relevant to us and ghrelin is the only known peripheral orexigenic hormone Date, . CholecyThe gut-brain link is important not only for the hormones produced by the gut, but also for the long-term body weight regulation. Studies in mice indicate that the gut microbiome influences both sides of the energy balance by contributing to nutrient absorption and regulating host genes that affect adiposity [however there are conflicting reports C-AcAc for PET use. They found in rats that after 10 days of KD (11)C-AcAc brain uptake increased up to 8-fold, an increase comparable to those measured after 48 h of fasting . The potential ability of PUFA to block seizure activity in the brain is speculated to be associated with KD. Some mechanisms are thought to be a direct inhibition of voltage-gated sodium and calcium channels, modulation of a lipid-sensitive potassium channel, the activity of the sodium pump to limit neuronal excitability, or the induction of expression and activity of proteins in the mitochondria, thereby inducing a neuroprotective effect by partially inhibiting the production of reactive oxygen species (ROS)  and glutamate regulation. Wu et al. demonstrated that GABAergic signaling from the NPY/AgRP neurons to the parabrachial nucleus  is involved in many regulatory sensory stimuli including taste and gastric distension, regulate feeding behavior. GABA signaling seems to prevent animals from anorexia when AgRP neurons were destroyed  hypothesis works against the hunger-suppressive role of KD: it has been demonstrated that the hypothalamic ROS increase through NADPH oxidase is required for the eating-inhibitory effect of insulin (Jaillard et al., Although the hunger-reducing effect of KD is well-documented, its main mechanisms of action are still elusive. The global picture is complicated by the contradictory role of ketosis on anorexigenic and orexigenic signals (summarized in Figure 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.


Identification of causes and immediate adjustment to treatment of acute thrombocytopenia occurring in patients in the intensive care unit is required to avoid imminent complications. Hence it is important to train awareness and clinical decision making of students in the medical curriculum. Therefore, real-life cases were transferred into an interactive eLearning platform comprising the steps of patient assessment and therapeutic decisions.Heparin-induced platelet count decrease is an immune-mediated prothrombotic disorder, resulting from an adverse drug reaction  of the General Hospital of Vienna on extracorporeal life support (ECMO). The man underwent bypass surgery six days ago in a peripheral hospital and is concomitantly suffering from an active infection. On the fourth day at ICU a platelet count decrease has been noticed.Students are now challenged to identify possible differential diagnoses and further to apply the 4Ts-scoring system. The 4Ts comprise the components Thrombocytopenia, Timing, Thrombosis, and other causes of thrombocyte decrease  as screening for patients scored below four points and ELISA assays are performed.Patients suspected of heparin-induced thrombocytopenia need continuous monitoring with regard to platelet count and new thrombosis  are shown to students with interactive evaluation possibility. For training purposes, the case includes a patient suffering from instantly occurring HIT-complications, i.e., intracerebral thromboembolism, where students are confronted with the symptoms and possible diagnostic methods.Clinical reasoning is considered to consist of intuitive and analytical components (Croskerry, Implementation of the interactive case-based teaching method into the Medical Curriculum in Vienna was initiated in 2014. For teaching purposes, real-life clinical patient cases are transferred from the general hospital information management into an online platform provided by the Medical University of Vienna. Data anonymisation is performed automatically through the transmission system. Teachers and students provide knowledge to add background information, program relevant questions as well as a feedback system to give direction to the reasoning process.Results associated with the evaluation of these newly adjusted and improving curriculum-elements (Turk et al., To summarize, students should practice everyday patient evaluation and learn the value of interdisciplinary team communication as well as the application of the 4Ts score and crucial disease pathophysiology.In the future, the concept of interactive case-based learning methods should be developed further and established as a training program for residents. Case-based question-driven learning provides a solid basis for associative and procedural learning that is necessary in clinical reasoning processes. In order to provide a diversity of case-based learning materials several other domains establish their learning cases in eLearning/blended learning scenarios. The basic didactic principle and the institutional framework were installed project-related (Turk et al., The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Literature has revealed the importance of quantifying resting scapular posture in overhead athletes as well as quantifying scapular kinematics during dynamic movement. Prior to this project much of the attention in throwing research had been focused on the position of the humerus without description of the positioning of the scapula. Therefore, it was the purpose of this study to present scapular kinematics during pitching in youth baseball players. Twenty-five youth baseball players , with no history of injury, participated in the study. Scapular kinematics at the events of maximum humeral external rotation (MER) and maximum humeral internal rotation (MIR) during the pitching motion were assessed three-dimensionally while pitching fastballs for strikes. Results revealed that at the event of MER, the scapula was in a position of retraction, upward rotation and a posterior tilt. While at the event of MIR, the scapula was protracted, upward rotated and tilted anteriorly. The scapula plays a pivotal role in normal upper extremity movement. In addition, it is the major link in the proximal (lower extremity) to distal (upper extremity) transfer of velocity, energy and forces . Any typScapular dyskinesis has been defined as any observable alteration in scapular position or motion . These tDuring throwing, the scapula must be able to fully retract to allow for the proper cocking position, and then fully protract throughout the acceleration phase . In addiAlterations in scapular positioning have been implicated in shoulder injury . In addiTwenty-five youth baseball players  participated in the study. The selection criteria included coach recommendation, years of pitching experience (at least two years), and no injury within the past six months. Coach recommendation was sought to ensure that the participants were experienced pitching competitively for at least two years. Moreover, none of the participants reported that they had ever suffered an injury to their throwing arm. Nor did any participants suffer from any pain or stiffness in their upper or lower extremity following extensive throwing sessions. The Auburn University’s Institutional Review Board approved all testing protocols. Prior to data collection all testing procedures were explained to each participant and their parent(s)/legal guardian(s) and informed consent and participant assent were obtained. All participants were tested during their fall throwing season and had not thrown prior to their arrival for testing.The MotionMonitor™  synchronized with an electromagnetic tracking system  was used to collect data. The electromagnetic tracking system had been validated for tracking humeral movements, producing trial-by trial interclass correlation coefficients for axial humerus rotation in both loaded and non-loaded conditions in excess of 0.96 . With elth order Butterworth filter with a cutoff frequency of 13.4 Hz  to ensure the sensors remained secure throughout testing. Sensors were attached to the following locations: (1) the posterior/medial aspect of the torso at C7, (2) posterior/medial aspect of the pelvis at S1, (3–4) bilateral distal/posterior aspect of the upper arm, (5) the flat, broad portion of the acromion of the scapula, (6–7) bilateral distal/posterior aspect of the forearm, (8–9) bilateral distal/posterior aspect of the lower leg, and (10–11) bilateral distal/posterior aspect of the upper leg . A twelf 13.4 Hz . Reliabi 13.4 Hz .Euler angle decompositions were used to determine scapular  and humeral  orientation with respect to the thorax. The first scapular rotation was defined around the y-axis /external rotation (−)). Rotation about the y-axis is also referred to as scapular protraction  and retraction . The second scapular rotation was about the x-axis (upward (+)/downward rotation (−)), and the third scapular rotation was defined as rotation about the z-axis (anterior (−)/posterior tilting (+)). Anterior tilting was defined when the inferior angle of the scapula moved away from the thorax. Humeral angles were also defined relative to the thorax. Humeral orientation was determined as rotation about the y-axis of the humerus (plane of elevation), rotation about the z-axis (elevation), and rotation about the y-axis  . Plane oOnce the sensors were attached, the participant was given an unlimited time to perform their own specified pre-competition warm-up routine. Average warm-up time was 10 min. Once the participants deemed themselves warm, they were instructed on the protocol. They were required to throw maximal effort four-seam fastballs for strikes over a regulation distance  to a catcher. A JUGS radar gun  positioned in the direction of the throw determined ball speed. The fastest of the four-seam fastballs for strikes was selected for analysis .The scapular position and orientation were analyzed at the events of MER and MIR of the pitching motion. Data were analyzed for descriptive statistics of means and standard error of the mean using IBM SPSS Statistics 20 . The dependent variables measured were scapular kinematics  at the pitching events of MER and MIR.Scapular kinematic data (means and standard error of the mean) are presented for positions of rest, MER and MIR in The purpose of this study was to present the first documentation of scapular kinematics during pitching in youth baseball players; particularly, scapular kinematics at the events of MER and MIR during the pitching motion. The results indicate that at the event of MER, the scapula was in a position of retraction, upward rotation and a posterior tilt. While at the event of MIR, the scapula was protracted, upward rotated and tilted anteriorly. The results of the current study are similar to previously published literature of the scapular position at 90º of humeral elevation  Table 4Table 4.A major role of the scapula is retraction, to allow for the shoulder to be in a position of approximately 90º of abduction and maximum external rotation in the cocking phase of the baseball pitch  as in ouIn addition to scapular retraction at MER, the scapula also was in a position of upward rotation and a posterior tilt. A decrease in upward rotation is thought to result in a decrease in subacromial space as the humerus is abducted . DecreasEfficient acceleration of the shoulder into internal rotation requires scapular protraction . As the The current study presents the position of the scapula at two events of MER and MIR during pitching in youth. The current data are in agreement with previous studies examining scapular kinematics at the position of humeral elevation at 90º. Though only few have examined baseball pitchers (Myers et al., 2007; The authors of this study recognize a couple of methodological limitations that must be addressed. First, motion analysis using sensors attached to the skin are susceptible to skin artifact. To account for this we only examined positions below 120º of arm elevation, as kinematic data of the scapula are reliable in humeral elevation angles below 120º . AdditioUnderstanding the position of the scapula during overhead throwing can assist coaches, strength and conditioning specialists and sports medicine personnel in appropriate pre-throwing exercises to target the musculature about the scapula. With repetitive throwing, scapular kinematics may become susceptible to injury, thus focusing on scapular stability as a precursor to throwing could possibly assist in maintaining scapular kinematics during throwing.