We introduce and analyze a within-host dynamical model of the coevolution between rapidly mutating pathogens and the adaptive immune response. Pathogen mutation and a homeostatic constraint on lymphocytes both play a role in allowing the development of chronic infection, rather than quick pathogen clearance. The dynamics of these chronic infections display emergent structure, including branching patterns corresponding to asexual pathogen speciation, which is fundamentally driven by the coevolutionary interaction. Over time, continued branching creates an increasingly fragile immune system, and leads to the eventual catastrophic loss of immune control. The immune system is a complex adaptive system whose richness makes it an excellent model for nonlinear dynamics and biological complexity. From the basic physical and chemical interactions between foreign substances and the body's repertoire of lymphocytes, an array of complex system-wide behaviors can arise as the immune system works to recognize and eliminate harmful pathogens The adaptive immune system of vertebrates has the remarkable ability to discriminate between self and non-self agents in the body, and to remove the foreign threats when recognized. The system consists of a complex array of lymphocytes, or white blood cells, which are able to recognize foreign agents with the high binding specificity of their receptors. These receptors are assembled randomly from gene segments in the bone marrow, and those that bind to the body's own cells are negatively selected as the lymphocytes mature in the thymus. The population of mature cells in the lymph nodes then has a diverse collection of specifically shaped receptors that can bind with high affinity to complementary peptide sequences, called epitopes, on many possible types of foreign antigen During the course of an infection, mutations that alter the shape, charge, or hydrophobicity of epitopes can impair continued recognition of the infection by the initially stimulated lymphocytes shape space, in which the distance separating a pathogen and lymphocyte pair maps to a particular binding affinity . This method has been used in theoretical studies of immune system characteristics and behaviors affected by cross-reactivity, such as clonal repertoire size, self-nonself discrimination In this paper, we introduce a new model of this coevolution between the adaptive immune response and mutating pathogens. The model abstracts the chemical and molecular details of the binding interaction, while retaining important features that affect infection dynamics. We account for cross-reactivity by representing these populations on a phenotypic In a rapidly mutating infection, the interactions we model give rise to complex dynamics. We observe several qualitatively different possible outcomes of infection, including early pathogen clearance, early pathogen escape, and the development of a long-lasting chronic infection. We also show the emergence of complex structure from the dynamics of a single chronic infection, including branching patterns in the pathogen population . In thisshape space of phenotypes which determine the binding affinity To capture binding region diversity in the pathogen and T-cell populations, we describe them as densities denoted by The parameter The binding affinity mediates all interactions between pathogens and T-cells. The stimulation of T-cells by pathogens is modeled as a saturating function There can be equivalent stimulation from low-density but high-affinity, high-density but low-affinity, or a combination of such pathogen distributions. If effectivity,The killing of pathogens by T-cells is also a function of the affinity: the total killing rate of The following coupled differential equations describe pathogen and T-cell dynamics:The first term of In the absence of immune response  are shown in The mutating pathogens in The corresponding steady-state solution can be approximated from our equations in the case of non-mutating pathogens localized at a single site The terms beginning with In non-mutating systems, this approximate steady state occurs with appropriate initial conditions, such as a large initial pathogen dose  Increased homeostatic pressure thus lowers the effectiveness of the overall immune response, allowing early escape and chronic infection to occur at lower pathogen mutation rates  by the adaptive immune system. It has been suggested that chronic infections are more often controlled by innate immunity or resource constraints  or minima in the pathogen's fitness landscape. The model's assumption that all pathogens and T-cells are well-mixed means that pathogen speciation is sympatric, rather than the result of a varying spatial distribution within the population For several hundred days after the pathogen split, the joint stimulation of the two strains maintains a strong T-cell peak between them; however, eventually they separate enough for selection to favor two distinct T-cell peaks over a single central one . The immAt each branching event, both total populations increase, peaking slightly as the T-cell population splits. Click here for additional data file.


Protein complexes are key catalysts and regulators for the majority of cellular processes. Unveiling their assembly and structure is essential to understanding their function and mechanism of action. Although conventional structural techniques such as X-ray crystallography and NMR have solved the structure of important protein complexes, they cannot consistently deal with dynamic and heterogeneous assemblies, limiting their applications to small scale experiments. A novel methodological paradigm, integrative structural biology, aims at overcoming such limitations by combining complementary data sources into a comprehensive structural model. Recent applications have shown that a range of mass spectrometry (MS) techniques are able to generate interaction and spatial restraints (cross-linking MS) information on native complexes or to study the stoichiometry and connectivity of entire assemblies (native MS) rapidly, reliably, and from small amounts of substrate. Although these techniques by themselves do not solve structures, they do provide invaluable structural information and are thus ideally suited to contribute to integrative modeling efforts. The group of Brian Chait has made seminal contributions in the use of mass spectrometric techniques to study protein complexes. In this perspective, we honor the contributions of the Chait group and discuss concepts and milestones of integrative structural biology. We also review recent examples of integration of structural MS techniques with an emphasis on cross-linking MS. We then speculate on future MS applications that would unravel the dynamic nature of protein complexes upon diverse cellular states. Mass spectrometry (MS) is an analytical technique that has found wide application in biological research. The development of instrumentation and experimental workflows targeted at the identification and quantification of ever larger sets of proteins has revolutionized our understanding of the expressed proteome and how it is related to the diverse functional states of the cell . The advMass spectrometry has contributed to our understanding of protein complexes for many years. The versatility and sensitivity of mass spectrometers spurred the development of a variety of techniques. The group of Brian Chait significantly contributed to the inception of these technical developments and realized several pioneering advances. For example, limited proteolysis coupled to MS , 9 and hAmong the structural techniques employing MS, cross-linking mass spectrometry (XL-MS) has probably gained the most interest in the community of structural biologists because of its relative simplicity of implementation, reproducibility, and high information content of the obtained distance restraints. In XL-MS, the chemical linking of amino acid residues within a native protein complex are combined with the direct identification of cross-linked peptides by tandem MS. By identifying cross-links between amino acid residues that are nearby in space, XL-MS can prove the physical proximity of protein complex subunits, determine their topological arrangement, and indicate the precise location where protein domains interface. Furthermore, the length of the cross-linker defines an upper bound of the distance between the cross-linked residues that proves useful for orienting and docking known atomic structures. For a detailed account of the recent innovations in XL-MS, we refer to –19.Structural biology has been traditionally driven by high-resolution techniques such as X-ray crystallography and nuclear magnetic resonance (NMR). For many years, these techniques produced structures of isolated proteins and dimers . Once itRecently, cryo-electron microscopy (cryo-EM) emerged as an alternative method to tackle the structure of protein complexes. In most cases, cryo-EM is performed on isolated protein complexes frozen in a thin layer of amorphous ice and, therefore, does not need sample crystallization. Furthermore, cryo-EM sample preparation requires a fraction of the sample amount needed for X-ray crystallography. Recent developments in direct electron detectors and image processing software have improved the attainable resolution and extended the molecular mass range of the technique , 22. AltIn this perspective article, we describe the principles of integrative structural biology and discuss the evolving contributions of mass spectrometry to this emerging field, with a particular emphasis on XL-MS. We then discuss how innovations in structural mass spectrometry will facilitate and support the structural characterization of protein complexes in a close to native environment and the study of their dynamics in different cellular states. For many years, Brian Chait and his group have been at the forefront of such innovations and have contributed seminal work to virtually every structural technique in mass spectrometry. Here we mention some of his major discoveries in the context of this exciting and rapidly progressing field of research. We also summarize the contributions of his group along with major milestones of structural mass spectrometry in Figure Integrative structural biology is a discipline concerned with the collection of a diverse set of interaction and structural data, and their integration into an organized computational framework with the aim of proposing comprehensive structural models. By combining data from complementary techniques, it can overcome technical limitations of individual techniques and describe systems spanning wide ranges of size and complexity that may be beyond the reach of each technique. The integrative approach is particularly suitable to large, heterogeneous, and flexible complexes and has the potential to increase the throughput of structural studies , 35. IntThe typical integrative modeling workflow consists of multiple steps Figure . First, One of the earliest examples of integrative structural modeling originated from the collaborative effort of the groups of Michael Rout, Brian Chait, contributing essential mass-spectrometry data, and Andrej Sali. The work represents a milestone of modern structural biology: the molecular architecture of the yeast nuclear pore complex (NPC) , 25. TheTo integrate the heterogeneous datasets, the authors first developed an algorithm that inferred proximity and connectivity maps within each subcomplex from AP-MS data. This dataset provided the richest set of restraints for the determination of the protein configurations within the pore. Then, each protein was represented as one or more beads depending on their approximate shape and expected domain folds. A scoring function was devised integrating the positions of each protein and the distance restraints from the other experiments. The computational framework was implemented in the open source modeling suite Integrative Modeling Platform (IMP) . StartinFrom this extensive experimental and computational effort, the authors could assign a localization probability for each protein, suitable to determine their relative position within the pore. In the nuclear pore architecture, the authors could localize proteins with folds typical of coat proteins  close to the nuclear membrane confirming the evolutionary relatedness of membrane bending systems. Furthermore, the arrangement of pore spokes in vertical columns suggested that the underlying principle of assembly is driven by the hierarchical repetition of structural modules originated by gene duplication .Structural techniques in mass spectrometry cover a wide range of applications. Bottom-up workflows, where the analytes are generally peptides, can cope well with sample complexity. In the case of AP-MS, a few to hundreds of interactors can be identified in a single experiment. To date, XL-MS was successfully applied to assemblies with one to more than 80 subunits . XL-MS pIn the following, we summarize some recent developments of XL-MS and selected examples of integration of diverse MS techniques. Many of these examples build on the pioneering work achieved by the Chait group. We apologize to the many important contributions that we can unfortunately not discuss due to space limitations.One of the first reports of XL-MS in the structural field was the study of the interaction between RNA polymerase II (Pol II) and the TFIIF complex . The aut5 models was then clustered by subunit location and then assessed using the XL-MS distance restraints. The model closely matched the cryo-EM reconstruction of the proteasome regulatory particle [Manual docking of proteins can, in some cases, lead to inaccurate models. An attempt to automate protein interface docking and exhaustively sample the orientational space was applied to the interaction of the proteasomal lid with the core proteasome particle . The autparticle . This woparticle . Since tparticle –45.Although lysine residues are the most common target of cross-linking experiments, they only represent about 5% of all residues in proteins. Several groups have, therefore, developed cross-linkers that can react with other amino acids , 19. OneMany structural mass spectrometry techniques provide orthogonal information and can thus be combined to propose integrative structural models . For exaIn summary, structural techniques in mass spectrometry, when combined in an integrative framework, can elucidate the assembly and structural arrangement of macromolecular machines. Furthermore, the sensitivity of MS methods allows application to cases where only a limited amount of sample can be obtained or when the system is structurally heterogeneous. In those cases, MS approaches and integrative modeling can propose architectural and mechanistic models Figure .Figure 3Mainstream structural techniques have traditionally required large sample amounts and high sample purity. To fulfill these requirements, researchers often resorted to the expression of recombinant complex subunits of interest, first in prokaryotic and then in eukaryotic hosts , 57. WhiConversely, mass spectrometric applications have the potential to accurately and sensitively probe protein complexes at the typical sample scales of cell biology experiments. For example, a pioneering study could obtain XL-MS distance restraints from complexes expressed at endogenous levels, purified by affinity-tag from human cell lines . The croThe recent applications of XL-MS technology to natively expressed complexes both from yeast and mammalian cells opens up the possibility to study the structure of protein complexes in the context of their physiological interactors and regulators. Another emerging technique that could be applied to endogenous complexes is cryo-EM. Cryo-EM can obtain high resolution reconstructions from small sample amounts and can tolerate limited structural heterogeneity , 22. TheInsights into the function of many protein complexes would be increased if we were able to understand their changes in different cellular states . Comparing different states using XL-MS requires the ability to accurately quantify the cross-linked peptides. The group of Carol Robinson pioneered this endeavor by establishing comparative XL-MS to dissect the conformational changes of the F-ATPase upon in vitro dephosphorylation . A similWe think that quantitative cross-linking will expand the structural studies of conformational changes induced by protein binding and protein modifications and reveal the detailed mechanisms of large macromolecular complexes.E. coli anticipated the experimental feasibility [A notable limitation of the previously mentioned approaches is the requirement for sample enrichment, most commonly achieved by affinity purification of tagged proteins. Although most proteomic applications of mass spectrometry can consistently explore the complexity of the cell components, XL-MS has, until now, not achieved a similar extensive coverage. Whereas previous applications in sibility , a signisibility  a human sibility . OverallIn summary, we envisage that the combination of recent experimental developments with powerful multiplexing capability will open up the exploration of endogenous protein complexes and the study of their dynamics and interactions upon different cellular states. Such analyses are now also generally supported by the development of a software tool that accurately quantifies the cross-links generated from complexes in different states, thus identifying subtle structural and compositional differences . Further


We report on the construction of an apparatus to allow neutron scattering measurements on fluids undergoing shear. The apparatus has been used with the cold neutron small-angle-neutron-scattering (SANS) spectrometer at the NIST research reactor and will be made available to users as a permanent part of the NIST facility. It is now well established that investigations of fluids subjected to a shear are rewarding. For example, studies of the structural changes induced by shearing motions lead to a better understanding of long-range intermolecular correlations in liquids , and allThis note is to report on the construction of an apparatus which allows neutron scattering measurements to be made on fluids undergoing shear . The appThe apparatus consists of a Couette-type concentric cylinder sample cell coupled to a computer automated drive and thermal control system . NeutronThe rigid aluminum frame consists of vertical rails attached to heavy plates at bottom and top. The vertical rails are commercial structural elements of the type commonly used for optical bench construction. They have a unique cross section which allows the attachment of numerous commercially available slides, carriages, clamps, etc. allowing for easy attachment of components and accessories. A work table (WT) is attached to the rails and supports the drive motor (M). The table is drilled and tapped in a regular pattern to provide an easy method for mounting of accessories. The cell chuck (CH), mounted on the motor shaft, can accommodate cells of various sizes and has provision for precise alignment of the cell rotor (CR) axis and the motor axis. Vertical adjustment of the cell stator (CS) is accomplished with a commercial rack-and-pinion assembly (Z), which was extensively modified to improve rigidity and stability. Parallelism between the motor and stator axes is obtained by adjustment of an aligning coupling (A). Collinearity is achieved using a pair of micrometer actuated translation stages (X) and (Y). An optional torque transducer (TT) can be used to obtain rheological information about the samples.A more detailed schematic of the cell is shown in Thermostating fluid is circulated within the stator for temperature control. Temperatures are measured using a platinum resistance thermometer in contact with the thermostating fluid in the stator. The thermostating fluid is excluded from the neutron beam path by the cross-tube located inside the stator. The nominal operating temperature range for the apparatus is currently 245–373 K and is determined primarily by the range of the thermostating fluid bath controller. At elevated temperatures the motor can be cooled using an optional cooling fan.The drive motor is a state-of-the-art dc brushless servo motor. These motors have permanent magnet armatures and the fields are commutated by computer controlled switching using position feedback from a shaft resolver integral with the motor shaft. This technology allows smooth, continuous rotations under programmed conditions of acceleration, velocity, torque (velocity limited), direction, position, angle, start, stop, delay, time and any sequence thereof. These capabilities allow the precise control of all rotational parameters to an accuracy of better than 0.1% over extended periods of time.The controlling computer can be any of a number of PCs available today. Computer hardware and software are available to allow completely automatic operation of the shearing apparatus in parallel with the existing on-line data acquisition system at the NIST reactor.A velocity-torque curve for the drive system is shown in


The grades of recommendation, assessment, development and evaluation (GRADE) approach is widely implemented in systematic reviews, health technology assessment and guideline development organisations throughout the world. We have previously reported on the development of the Semi-Automated Quality Assessment Tool (SAQAT), which enables a semi-automated validity assessment based on GRADE criteria. The main advantage to our approach is the potential to improve inter-rater agreement of GRADE assessments particularly when used by less experienced researchers, because such judgements can be complex and challenging to apply without training. This is the first study examining the inter-rater agreement of the SAQAT.We conducted two studies to compare: a) the inter-rater agreement of two researchers using the SAQAT independently on 28 meta-analyses and b) the inter-rater agreement between a researcher using the SAQAT (who had no experience of using GRADE) and an experienced member of the GRADE working group conducting a standard GRADE assessment on 15 meta-analyses.There was substantial agreement between independent researchers using the Quality Assessment Tool for all domains . Comparison between the SAQAT and a standard GRADE assessment suggested that inconsistency was parameterised too conservatively by the SAQAT. Therefore the tool was amended. Following amendment we found fair-to-moderate agreement between the standard GRADE assessment and the SAQAT .Despite a need for further research, the SAQAT may aid consistent application of GRADE, particularly by less experienced researchers. The Grades of Recommendation, Assessment, Development, and Evaluation (GRADE) is the most widespread method for rating the quality of evidence and grading recommendations in healthcare . More thA key advantage of GRADE is that it can lead to transparent judgments as a clear rationale is needed for each downgrade of the quality of evidence . AnotherHowever, there are potential drawbacks to the use of GRADE. Application of GRADE can be complex, as implied by the lengthy series of guidance articles in the Journal of Clinical Epidemiology, currently standing at 15 papers , others The GRADE process may also be resource intensive. As use of GRADE is likely to increase (grading the evidence is now a recommended step within Cochrane systematic reviews ), tools To assist with GRADE assessments and address these potential issues, we have previously proposed a quality assessed tool based on a Bayesian network –6. BayesThe SAQAT provides an assessment of overall quality of evidence by formalising the structure provided by the GRADE framework in a logic model and by giving a specific weight to each of the different items considered by GRADE. This paper has two aims. First, we assess inter-rater reliability of the SAQAT. Second, we compare the SAQAT with a standard GRADE assessment empirically, exploring reasons for disagreements between the two approaches, and identifying potential areas of improvement for the semi-automated tool.SAQAT comprises two parts: a checklist and a Bayesian network. We have described the development of these in detail in other articles –6. Brief2 and Q statistics. Indirectness included items on the applicability of the population, intervention, comparator, outcome, and whether conclusions were based on a direct comparison of groups. Imprecision was based on items on the width of the confidence interval in relation to minimally important difference and sample size. Publication bias included items on the comprehensiveness of the search strategy, whether included studies had industry influence, funnel plot asymmetry and whether there was evidence of discrepancies between published and unpublished trials (see Appendix 1 for a full list of items).Risk of bias was based on items in the Cochrane risk of bias tool . InconsiWe have focused specifically on the context of randomised controlled trials (RCTs) where a meta-analysis has been conducted. Therefore we did not include factors to upgrade the evidence  as these are recommended for use only in the context of systematic reviews of non-randomised studies. Extension of the SAQAT for non-randomised studies is currently in progress.Following the development and initial piloting of the checklist we conducted a more formal evaluation of its consistency. The inter-rater agreement for each of the checklist questions is reported in another study .To evaluate the inter-rater agreement of the SAQAT, which combines the checklist with a Bayesian network, we examined a total of 29 meta-analyses from a purposive sample of systematic reviews of RCTs from the Database of Systematic Reviews of Effects (DARE). Papers were selected to ensure a diverse range of reviews from a variety of disease areas such as cardiology, diabetes, pulmonary disease, neurological conditions and oncology. Reviews on substance misuse, mental health and HIV prevention were also included. Both pharmacological and non-pharmacological interventions were considered. We also selected reviews with varying quality of reporting.http://genie.sis.pitt.edu/) was used to calculate probability distributions in the Bayesian network.The checklist was used by two authors independently for all reviews. For each review a specific population, intervention, comparison and outcome (PICO) were selected beforehand to ensure both reviewers conducted the assessment on the same PICO elements of the review. GENIE software (freely downloadable from 1- ((i-j) / (k-1)) ^2, where i = rows, j = columns, and k = number of possible ratings.We calculated weighted kappa statistics with their associated 95% confidence interval (CI) to compare agreement on ratings of quality of evidence. We interpreted the coefficients according to the following guidelines: below chance—poor; 0.01–0.20 slight agreement; 0.21–0.40 fair agreement; 0.41–0.60 moderate agreement; 0.61–0.80 substantial agreement; and 0.81–1 perfect agreement . The folWe next compared the judgements of our semi-automated tool with a standard GRADE assessment conducted by an experienced user of GRADE (CW).A purposive sample of 15 recent Cochrane reviews –25 in meQuality of evidence was assessed for each review using the standard GRADE approach and the SAQAT by two reviewers independently. Assessments were made for the five main domains , as well as overall quality of evidence. All received a rating of high, moderate, low, or very low quality.One reviewer (CW) conducted assessments for each review using standard GRADE criteria and recorded his judgements using GRADEPro software . He is aOne experienced systematic reviewer with no expert knowledge in mental health (AL) and no prior experience of conducting GRADE assessments assessed the quality of evidence using the standard list of questions from SAQAT. As in study 1, responses to the checklist questions were entered into the Bayesian network using GENIE software to calculate probability distributions for each domain and the overall quality for each review. We used these probability distributions to derive judgements in a format reflecting standard GRADE assessments.One author (NM) collated the judgements from SAQAT and the standard GRADE assessment and identified any differences in judgements. As in study 1, we calculated weighted kappas and 95% confidence intervals (CIs) between the standard GRADE and SAQAT assessments for each of the five key domains  and overall quality of evidence and used the same criteria and weights for evaluating the extent of agreement.Where the assessors always or nearly always gave the same assessment for the domain, weighted kappas could not be calculated. Therefore we also presented the rate of agreements for each domain and the overall quality of evidence assessment. In addition, we presented a table comparing ratings from GRADE and the SAQAT and summarised these discrepancies narratively. We attempted to identify which disagreements were based on differences in raters’ judgments  from those based on properties inherent to the SAQAT (e.g. how much weight is given to “unclear” risk of bias).Differences between standard GRADE and SAQAT assessments were discussed among three authors  to understand the sources of the discrepancies.Before the formal evaluation we compared our responses on one systematic review. At this initial stage we identified a different interpretation of risk of bias between the Bayesian network and the judgement of the experienced GRADE user. Our Bayesian network, consistent with the Cochrane risk of bias tool , did notOur initial analysis also suggested the ratings of inconsistency generated by the Bayesian network were considered too conservative and lacked face validity. Therefore, the weight of the probabilities associated with two elements within the inconsistency domain  and their interaction were amended. To reflect the effect of this change on the results for inconsistency and overall quality of evidence, weighted kappa scores were calculated before and after this amendment.For the overall judgement on quality of evidence there was substantial agreement between duplicate raters using the SAQAT. There was almost perfect agreement on risk of bias and imprecision factors; and substantial agreement for inconsistency, indirectness, and publication bias factors. Weighted kappa results are presented in Although there was only moderate or low agreement between raters for some checklist items  there was almost perfect agreement for the overall rating of risk of bias.There was substantial agreement for all questions assessing imprecision and this was reflected in the almost perfect agreement for rating imprecision.Agreement between raters on the applicability of populations and interventions was very low. However, there was substantial agreement on the use of surrogate outcomes and whether conclusions were based on direct comparisons. Despite the lack of agreement on questions of applicability there was almost perfect agreement on the overall ratings of indirectness. This reflects that the use of surrogate outcomes has most weight in generating the indirectness judgements.There was substantial agreement for publication bias but this was lower than for all other domains. This might partly reflect less agreement on what constitutes a sufficient grey literature search and the difficulty in identifying publication biases.Where calculable, magnitude of agreement between raters using SAQAT and standard GRADE assessment ranged from slight to moderate across domains before amending the Bayesian network within the SAQAT. After amending some parameters within the inconsistency domain of the tool and changing our assumptions about unclear reporting within the risk of bias domain, agreement across domains ranged from fair to moderate, and agreement on overall judgment increased from slight to fair .After amending the tool, agreement on the risk of bias domain increased from slight to moderate, agreement on the inconsistency domain increased from slight to fair,. Rating of other domains remained unchanged . The preA full report of all rating decisions and brief commentaries on all disagreement between GRADE and SAQAT raters before and after Bayesian network amendment is presented in Appendix 2. These disagreements are summarised below.Before amending the tool, twelve disagreements were recorded. The ratings generated by the Bayesian network were more conservative in nine of those, and in three cases, judgments differed by more than one level (moderate versus very low). After amending the inconsistency domain within the Bayesian network, the number of disagreements was reduced to seven, and one differed by more than one level. In nearly all disagreements, the overall quality of evidence ratings generated by SAQAT were more conservative than those made by the manual GRADE assessor.In several cases, differences in severity between ratings appeared to be due to an accumulation of probability for downgrading across domains within the Bayesian network. With the manual GRADE assessor, quality of evidence ratings were generally based on the sum of downgrading scores from all domains . Limitations that were considered too small to justify downgrading of a domain were less likely to be taken into account in the overall assessment. On the other hand, overall quality of evidence rating generated by the Bayesian network were affected by the accumulation of all identified limitations within each domain, however small.Disagreements on rating of risk of bias took place in nine out of 15 assessments. On three occasions, the GRADE rater downgraded the evidence due to unclear risk of bias, whereas SAQAT did not. As discussed above, this reflected a priori differences in interpretation of GRADE. The tool was amended to reflect GRADE guidance on downgrading for unclear reporting. After this, the number of disagreements was reduced to five.Other disagreements reflected differences in judgment between raters about whether risk of bias was present and/or sufficiently prevalent to justify downgrading. One of the GRADE rater’s decisions to downgrade was a context-specific judgment based on knowledge of treatment area. Where disagreements occurred, the GRADE rater’s judgments were generally more conservative than the SAQAT rater’s. All disagreements differed by one level.Before amending the tool, disagreements about inconsistency were recorded for eight assessments. SAQAT was always more conservative, and in five cases, judgments differed by three levels (i.e. no serious inconsistency to very serious inconsistency). The weight of the probabilities associated with statistical heterogeneity, overlapping confidence intervals and their interaction were amended. Following this, the number of disagreements was reduced to five, and none differed by more than one level. The most common disagreement was based on whether variability of study estimates and effect direction were clinically meaningful and therefore a sufficient reason to downgrade the quality of evidence.Only three disagreements on imprecision were recorded. In two cases, the disagreements suggested that the Bayesian network departed from the GRADE manual. The third disagreement was based on differing interpretations of what constituted a clinically meaningful effect. All disagreements differed by one level.Only one disagreement on indirectness was recorded. The disagreement was probably due to differences in knowledge of subject area between the raters (difference of one level).There was no disagreement between raters in this domain. This is likely to be due to the lack of evidence of publication bias for any of the outcomes assessed.When comparing two independent reviewers using SAQAT we found substantial agreement for overall quality and substantial to almost perfect agreement for all of the five domains of GRADE . Agreement between GRADE and SAQAT on overall quality of evidence ratings was slight, and became fair after amending assumptions about risk of bias and inconsistency within the Bayesian network. Ratings generated by the Bayesian network were sometimes more conservative than manual GRADE assessments.This is the first empirical and systematic study comparing the standard GRADE approach with a semi-automated approach incorporating the elements of GRADE into a Bayesian network. This study adds to the evidence that the SAQAT could be useful in the application of the GRADE approach.A key advantage of SAQAT is its replicability. Our study shows that SAQAT can be applied transparently and consistently by two reviewers assessing the quality of evidence from a range of systematic reviews of RCTs. Therefore, the Quality Assessment Tool may be a promising tool to improve potential replicability issues observed in previous empirical comparisons between manual GRADE assessors, where agreement between raters was sometimes more variable .Results on the comparison between SAQAT and a standard GRADE assessment are more mixed. Agreement between the two approaches varied across domains, although amendments made to assumptions within the Bayesian network improved levels of agreement. The precision of the weighted kappa estimates was low, primarily due to the relatively small sample size. Also, it is unclear how SAQAT compares to standard GRADE assessment in other health fields. Therefore further testing of the reliability of the tool using larger samples and in other areas is needed to confirm our findings.Where disagreements about overall quality of evidence occurred, ratings generated by SAQAT tended to be more conservative. This may be because, unlike manual GRADE assessment, the Bayesian network automatically takes into account the accumulation of multiple limitations in the evidence, however small. Therefore this may reflect the strength of SAQAT approach when evaluating systematic review evidence where there are multiple small probabilities of limitations in the evidence.For the analyses, only the highest probability provided by the Bayesian network was taken into account. Evidence profiles can also be presented as probability distributions representing the uncertainty underlying these judgements. These figures may be presented alongside or as an alternative to standard evidence profiles produced by GRADE Pro see .The current version of SAQAT is applicable to systematic reviews that include meta-analyses of RCTs. The GRADE approach can also be applied to meta-analyses of observational studies and narrative approaches to synthesising evidence. Further work is currently in progress to adapt and validate our approach for such reviews.Despite numerous publications about the GRADE approach and widespread use, there remain few empirical and systematic evaluations of its application. Further research on how SAQAT compares to standard GRADE assessments in other medical fields and with bigger samples is required to confirm the findings of this study.Some aspects of the GRADE framework are better supported by evidence than others. Further changes to the structure and parameterisation of SAQAT would allow qualitative and quantitative exploration of the potential weight and impact of (and interaction between) specific elements within domains, including those elements that are less certain. Methodological applications could involve mapping probabilities of bias and applying them, or formally eliciting expert opinion to generate distributions for the probabilities reflecting uncertainty appropriately.Use of SAQAT is probably most likely to benefit those with limited experience of using GRADE. However, given the complexity of GRADE, we think that experienced users of this approach may also benefit from a reminder of key criteria to help ensure consistent and repeatable quality of evidence ratings. We also think that institutions considering adopting GRADE, but concerned about the resource and training implications, may also benefit.A further benefit of using SAQAT is the potential in the future to automate the entire process of validity assessment. For example, nodes can be parameterised using text mining software or data stored by document management systems used for review production and storage (such as ARCHIE used by the Cochrane Collaboration). The benefits of automation are gaining more attention as a response to the challenges of conducting increasingly large and complex evidence syntheses in a timely manner to inform decision makers.The Semi-Automated Quality Assessment Tool (SAQAT), a checklist of questions and a Bayesian network designed to model judgements according to GRADE criteria, can produce consistent and reproducible judgements about the quality of evidence from meta-analyses of RCTs. Despite a need for further research, SAQAT may aid consistent application of GRADE, particularly by less experienced reviewers.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.


Individuals have a preferred pace at which they perform voluntary repetitive movements. Previous studies have reported that greater activation of the prefrontal cortex was observed during self-initiated movements than during externally triggered movements. The purpose of the present study is to compare the activation of the prefrontal cortex induced when the subjects performed a peg-board task at their preferred slow pace  with that induced when they performed the same task at metronome slow pace  using functional near-infrared spectroscopy. Healthy subjects performed the task while sitting in a chair. By assessing the activated channels individually, we confirmed that all of the prefrontal regions of interest were activated by both tasks. In the second-level analyses, we found that the activation detected in the frontopolar cortex  was higher during the PSP task than during the MSP task. The FPPFC is known to be at the top of prefrontal hierarchy, and specifically involved in evaluating self-generated information. In addition, the FPPFC plays a role in coordinating lateral prefrontal cortex. In the present study, the subjects evaluated and managed the internally generated PSP by coordinating the activity of other lower level prefrontal regions. Individuals are known to have a preferred pace when performing voluntary repetitive movements , and thiThe contribution of different brain areas to the internal versus external guidance of movement remains controversial. Several neuroimaging studies reported that activation of the supplementary motor area (SMA) was greater during self-initiated movements –8. HowevJahanshahi et al. compared self-initiated and externally triggered finger extensions at a mean frequency of once every 3 s using positron emission tomography (PET). The self-initiated condition involved self-generated “when to do” decisions regarding the time to initiate movements. Activation of the right dorsolateral prefrontal cortex  was greater during self-initiated than externally triggered movements . HoweverThe number of neuroimaging studies using functional near-infrared spectroscopy (fNIRS) has increased recently. The fNIRS technique was first described in 1977 . fNIRS uWe previously compared activation of the prefrontal cortex when the subjects performed a task at preferred pace and metronome pace using fNIRS. In our past and the present studies, preferred pace refers to a self-initiated condition, while metronome pace indicates the externally triggered condition defined by Jahanshahi et al. . Our subTwenty-two healthy university students  participated in the present study. All the subjects were confirmed to be right-handed by the Edinburgh Inventory . Our results showed that the activity induced by the two different tasks changed in parallel across the three time bins. Thus, even if learning and repetition had had some effect on the time course of activation in each task, it did not affect the differences in activity between the PSP and MSP tasks; therefore, any differences in activity between the two tasks were purely task dependent. This enabled us to use the oxy-Hb signals that had been averaged across the three consecutive time bins for the subsequent analyses.Before the analyses, we extracted the integral of the oxy-Hb signals for each 30 s task period separately and subjected the fNIRS data in each ROI to two-factor repeated measures analysis of variance (ANOVA), with the type of task (PSP or MSP) and three consecutive time bins as within-subject factors. No task × time-bin interactions were detected . No significant task-related differences (PSP versus MSP) were observed in other regions .In the second-level between-subject analyses, we found that the FPPFC was activated to a greater extent during the PSP task than during the MSP task [The purpose of the present study is to compare the activation of the prefrontal cortex induced when the subjects performed a pegboard task at their preferred slow pace  with that induced when they performed the same task at metronome slow pace  using fNIRS. All of the prefrontal ROIs were activated compared with the baseline (resting conditions) in both tasks. However, we detected greater FPPFC (BA 10) activation  during the PSP task than during the MSP task.By counting the numbers of activated channels (compared with the resting conditions), we confirmed that all of the prefrontal ROIs, including the DLPFC (BA 9 and 46) and VLPFC , were activated during both tasks in our study. Previous PET studies demonstrated that the DLPFC  was activated during self-initiated movements and indicated that the DLPFC holds information about preceding interresponse intervals in working memory , 10. In Comparing the activation induced by each task, we observed greater FPPFC activation during the PSP task than during the MSP task, which corresponded with the findings of previous PET studies involving similar tasks in which the FPPFC was examined , 10. DurWe consider that the main difference between the PSP and MSP tasks was whether they involved timing decisions, which are required for self-initiated movements , 10. RecThe differences between the findings of the present study and those of previous PET studies that detected activation of both the FPPFC and DLPFC during self-initiated tasks , 10 mighIn order to compare activation of the prefrontal cortex during the PSP and MSP task in the present study, we selected slow pace as the speed at which these tasks were performed. Slow pace can be easily synchronized with an external cue because it allows adequate time to prepare for the next cue. There are several reports that prefrontal cortex is independent of the frequency/speed of movement if the subjects maintain their constant pace , 42. HowOccupational therapy is a client-centered health profession that is concerned with promoting health and wellbeing through occupations. The primary goal of occupational therapy is to enable people to participate in the activities of everyday life . The larIndividuals have a preferred pace at which they perform voluntary repetitive movements. We confirmed that all of the prefrontal regions of interest were activated by both tasks. Among these prefrontal regions, we found that activation in the FPPFC (BA10) was higher during the PSP task than during the MSP task. The finding of the FPPFC involvement during the PSP task suggests that each subject evaluated and managed their internally generated PSP by coordinating the activity of other lower level prefrontal regions.


Carcinosarcomas of the ureter are rare biphasic neoplasms, composed of both malignant epithelial (carcinomatous) and malignant mesenchymal (sarcomatous) components. Carcinosarcomas of the urinary tract are exceedingly rare. We report a unique case of a carcinosarcoma of the ureter with a chondrosarcoma and small cell tumor component arising in a 68-year-old male who presented with microscopic hematuria. CT intravenous pyelogram revealed right-sided hydroureter and hydronephrosis with thickening and narrowing of the right ureter. The patient underwent robot-assisted ureterectomy with bladder cuff excision and subsequent adjuvant chemotherapy. The patient is disease-free at 32 months after treatment. We provide a brief synoptic review of carcinosarcoma of the ureter and bladder with utilization of immunohistochemical (IHC) stains and potential diagnostic pitfalls. Carcinosarcomas of the ureter are rare malignant neoplasms with only around a dozen case reports within the literature –14. TheyA 68-year-old male presented with microscopic hematuria on routine physical exam, and further work-up revealed right-sided hydronephrosis and hydroureter with a transition zone in the right ureter. The patient was referred to our institution for consideration of right-sided robot-assisted ureteral excision. Evaluation with ureteroscopy found a mass in the right mid to distal ureter that was biopsied and read as high grade urothelial carcinoma. The patient subsequently underwent robotic-assisted right distal ureterectomy with bladder cuff excision. Macroscopically, there was no distinct mass but an ulcerated and hemorrhagic mucosa in the right ureter extending 7 cm in length with concurrent stricture. Microscopic examination of this specimen revealed a biphasic neoplasm composed of both malignant epithelial and mesenchymal components . The epiImmunohistochemical studies demonstrated that the epithelial components were immunoreactive with CAM 5.2, cytokeratin 7, and focally with cytokeratin 20. The small cell carcinoma component was positive for CD56, but other neuroendocrine markers including synaptophysin and chromogranin were negative. The high grade chondrosarcoma component was not stained. The morphologic and immunoprofile was consistent with a carcinosarcoma. The tumor was muscle invasive and the pathologic stage was pT2NX, according to the AJCC 7th edition. The patient was given the option of adjuvant therapy secondary to the high grade nature of the malignacy with muscle invasion and concurrent small cell carcinoma component. He received three cycles of cisplatin and gemcitabine chemotherapy. After 32 months of follow-up, the patient is alive and disease-free with negative CT and PET scans.Carcinosarcomas are aggressive neoplasms that can occur anywhere in the body but commonly occur within the uterus in women and the bladder in men. These malignant tumors most often occur in older patients, greater than 60 years of age, and are more frequent in men than women (M : F ratio of 4 : 1) . CarcinoCarcinosarcoma of the ureter is a rare malignant tumor with poor outcomes involving frequent recurrence within months and death from disease within two years , 14. It Aggressive surgical management is the treatment of choice in management of patients with carcinosarcoma of the ureter. Literature reports suggest that nephroureterectomy is the recommended procedure for surgically treating these lesions . This poSecondary to the rarity of these lesions, low number of patients to conduct meaningful prospective studies, and lack of long term follow-up, there is no clear consensus on radiochemotherapy regimens and impact on survival. The literature suggests that the prognosis is universally poor and that neoadjuvant or adjuvant chemotherapy and radiotherapy may not improve prognosis , 14. HowGiven the concern for residual microscopic disease and final pathology in our case, the decision was made to proceed with adjuvant chemotherapy. A combination of cisplatin and gemcitabine was used. The organ of disease origin and type of epithelial component in carcinosarcomas may be important factors in deciding upon which regimen to use. In addition, some confounding variables which could account for the apparent ineffectiveness of chemotherapy regimens include improper histological classification, focality of the tumor, size and depth of invasion, distance from or involvement of the renal pelvis, and/or genetic makeup of the tumor itself (inherently aggressive and unresponsive to treatment). Our patient is currently disease-free 32 months after treatment, suggesting a role for combined surgical and oncological treatment in the management of these patients.Recognition of this rare entity is important for urologists and pathologists alike to accurately diagnose these lesions and treat them aggressively. Though overall prognosis remains poor for the majority of patients, our case suggests multimodal therapy may provide an avenue for prolonged survival in carcinosarcomas of the ureter.


Pneumatosis intestinalis, defined as gas in the bowel wall, is often first identified on abdominal radiographs or computed tomography (CT) scans. It is a radiographic finding and not a diagnosis, as the etiology varies from benign conditions to fulminant gastrointestinal disease. We report here a case of pneumatosis intestinalis associated with cetuximab therapy for squamous cell carcinoma of head and neck. The patient underwent laparotomy based on the CT scan and the result was pneumatosis intestinalis without any signs of necrotizing enterocolitis. Cetuximab is a chemotherapeutic agent that belongs to the group of chimeric monoclonal antibodies of epidermal growth factor receptor (EGFR) and has a significant role in clinical oncology regimens. Its action involves binding with high affinity to the extracellular domain of human EGFR and blocking ligand binding, resulting in the inhibition of the receptor function. Its action includes furthermore the targeting of EGFR-expressing tumor cells for cytotoxic immune cells . With reIt can be used in combination with radiation therapy for the initial treatment of locally or regionally advanced squamous cell carcinoma of head and neck or in combination with platinum-based therapy with 5-FU for the first-line treatment of patients with recurrent locoregional disease or metastatic squamous cell carcinoma of head and neck. As a single agent, is indicated for the treatment of patients with recurrent or metastatic squamous cell carcinoma of head and neck for whom prior platinum-based therapy has failed , 4.We report a case of pneumatosis cystoides intestinalis (PCI) in a patient who received first-line adjuvant chemotherapy with 5-FU and cisplatin followed by second line chemotherapy with Methotrexate after undergoing an extensive regional R1-resection of a SCC lesion on his right ear followed by parotidectomy and level II lymph node resection due to relapse of SCC to the right parotid gland. The patient during this period receives only cetuximab therapy and there are only three more cases of cetuximab-induced or cetuximab-related PCI (in combination with other chemotherapeutic agents) that have been reported in the literature, during chemotherapy for advanced colorectal cancer .An 83-year-old male underwent an extensive regional R1-resection for a SCC lesion on his right ear and reconstruction with removable skin flap in 2012, followed by parotidectomy six months later and level II lymph node resection due to relapse of the SCC to the right parotid gland. He received an adjuvant first-line chemotherapy and radiotherapy (9 cycles) with 5-FU, cisplatin and second line chemotherapy with Methotrexate 8 mg weekly, with initial good response to treatment. Unfortunately, a few months later his disease started to progress. The patient is now on chemotherapy with cetuximab (last dose 36 hours ago), without any distal metastases but with regional outspread of the disease to his right ear and mandible.The patient presented to the Emergency Department of Nicosia General Hospital with epigastric pain and vomiting during the last five days, without bloody stools. The patient was afebrile, with mild abdominal distention and without peritoneal signs. Leukocytes, amylase, and lactic acid were all within the normal ranges. Abdominal radiograph revealed free air intraperitoneally and abdominal/pelvic computed tomography revealed findings of small bowel ischemic necrosis in the presence of free intraperitoneal air and air in the intestinal wall .The clinical suspicion of bowel perforation was part of the differential diagnosis and the decision of an emergency surgical operation was made. Emergency exploratory laparotomy revealed a part of small intestine (2 m) with ischemic signs, including air bubbles and bowel edema but the bowel was considered to be viable and no resection was performed. Thorough exploration of peritoneal cavity did not reveal any other pathological signs or intestinal leak. We concluded that the findings could only be associated with the pathogenesis of pneumatosis intestinalis.Two drainage tubes were placed and the patient was sent to ICU for postsurgery follow-up and weaning. After 24 hours the patient was transferred to surgical ward for further treatment. After six days of hospitalization and complete resolution of symptoms the patient was discharged.The pathogenesis of pneumatosis intestinalis remains unclear, but the process may involve loss of mucosal integrity, increased intraluminal pressure, and finally increased intraluminal gas production as a result of bacterial overgrowth , 7. VariOur patient had no signs of peritonitis symptoms and pneumatosis intestinalis was found during CT scan. This finding suggests the need for careful clinical follow-up and a high level of suspicion of pneumatosis intestinalis for these patients and a less aggressive approach as concern of surgery. The possibility of bowel perforation and the resulting sepsis was the significant factor that worried us and led to the decision of operation. Surgery should only be performed in patients who are not responding to nonoperative treatment, especially those with signs of perforation, peritonitis, or abdominal sepsis. Some authors suggest that metabolic acidosis, elevated lactic acid, elevated amylase, and portal vein gas should be considered as indications for surgery.We experienced a rare case of pneumatosis intestinalis following chemotherapy with cetuximab agent. Although this emergency condition leads us to surgery, a more conservative approach could be the initial treatment for these patients.


We report the case of a 56-year-old woman who developed status epilepticus (SE) related to independent occipital foci as clinical manifestation of posterior reversible encephalopathy syndrome (PRES) in the background of Guillain-Barrè syndrome (GBS). SE resulted from a series of focal seizures clinically characterized by left- and rightward deviations of the head and consequent oculoclonic movements. Electroencephalography recorded independent seizure activity in both occipital regions with alternate involvement of the two cerebral hemispheres. The epileptic foci corresponded topographically to parenchymal abnormalities of PRES in the occipital lobes. The manifestation of bilateral, independent occipital seizures with alternate deviations of the head and oculoclonic movements, previously not reported in patients with PRES, highlights the acute epileptogenicity of the cerebral lesions in this syndrome. Despite the variable clinical expression of seizures due to occipital damage in PRES, the development of independent seizure activity in both occipital lobes might represent a distinctive epileptic phenomenon of this encephalopathy. Epileptic seizures are a frequent clinical manifestation of posterior reversible encephalopathy syndrome (PRES). This clinicoradiological entity, initially described by Hinchey et al. with the term reversible posterior leukoencephalopathy syndrome , may be μV), rhythmic sharp waves that frequently spread to the homolateral temporoparietal and central regions . The seizure semiology was characterized by an impairment of consciousness and lateral deviations of the head and eyes with consequent oculoclonic movements that in one case led to a secondary generalization. Particularly, the occurrence of different seizures with left- and rightward deviations of the head and eyes suggested the presence of bilateral, independent epileptic activity. Electroencephalography (EEG) recorded a series of focal epileptic discharges that alternated over the two posterior cerebral regions in close but separated periods of time Figures . The dis regions . Occipit regions  and disa regions . On the  regions . The patThe patient presented with a confusing combination of peripheral and central neurologic symptoms due to the coexistence of GBS and PRES, an unusual clinical association that remarks the potential pathogenic relationship between the two syndromes. Considering the clinical context and timing of the symptoms, it is assumable that arterial hypertension developed acutely during a phase of GBS-related autonomic dysfunction and subsequently precipitated PRES. The normalization of arterial pressure despite the absence of treatment during the follow-up period supports the assumption of an acute hypertension as the precipitating factor for PRES.Apart from the classic presentation of headache, vomiting, and visual loss, an unusual association of versive seizures characterized the clinical manifestation of PRES. Although epileptic disorders are frequently reported in this syndrome , 6, it iSE resulting from bilateral, independent occipital seizures with alternate deviations of the head and oculoclonic movements may characterize the symptomatology of PRES. Despite the variable clinical expression of seizures related to occipital damage in PRES, the development of independent seizure activity in both occipital lobes might represent a distinctive epileptic phenomenon of this syndrome.


This study was carried out for rapid and noninvasive determination of the class of sorghum species by using the manifold dimensionality reduction (MDR) method and the nonlinear regression method of least squares support vector machines (LS-SVM) combing with the mid-infrared spectroscopy (MIRS) techniques. The methods of Durbin and Run test of augmented partial residual plot (APaRP) were performed to diagnose the nonlinearity of the raw spectral data. The nonlinear MDR methods of isometric feature mapping (ISOMAP), local linear embedding, laplacian eigenmaps and local tangent space alignment, as well as the linear MDR methods of principle component analysis and metric multidimensional scaling were employed to extract the feature variables. The extracted characteristic variables were utilized as the input of LS-SVM and established the relationship between the spectra and the target attributes. The mean average precision (MAP) scores and prediction accuracy were respectively used to evaluate the performance of models. The prediction results showed that the ISOMAP-LS-SVM model obtained the best classification performance, where the MAP scores and prediction accuracy were 0.947 and 92.86%, respectively. It can be concluded that the ISOMAP-LS-SVM model combined with the MIRS technique has the potential of classifying the species of sorghum in a reasonable accuracy. Sorghum is a diverse genus consisting of both cultivated and wild species. Most of them have considerable genetic and morphological diversityThe species of S.halepense, Silk sorghum, S.sudanense and S.propinguurn are belonging to Eu-sorghum section. S.halepense and Silk sorghum are considered as the dangerous weeds which have been forbidened in China; meanwhile, Silk sorghum is also forbidened because one of its parent is S.halepense. The similarities in morphology and cytology make it difficult to classify the dangerous species, therefore the classification has to be done correctly and quickly3et al. presented the infrared spectroscopy technique as a rapid and nondestructive methodology to determine the origin of gasolineet al. discriminated the maize seed varieties based on the near infrared spectroscopyet al. monitored the viability of soybean seed by employing fourier transform near-infrared (FT-NIR) spectroscopyet al. geographically classified the Spanish and Australian Tempranillo red wines by the visible and near-infrared spectroscopyet al. classified the vinegar quality according to the total acid content through the near-infrared spectroscopy techniques and the nonlinear regression methods and obtained a satisfying resultThe method of combination of the infrared spectroscopy technique and chemometrics is considered as a promising detecting technique, which can be used to rapidly and nondestructively classify the substances. Neirivaldo The manifold learning algorithms have been used for the dimensionality reduction (DR) of the high-dimensional spectral data, and provide the important means for the feature extraction11The purpose of this study was to assess the genetic relationships among S.halepense, Silk sorghum, S.sudanense and S.propinguum on the basis of middle infrared spectroscopy (MIRS) technique and chemometrics, and provide the evidence for the classification among the four species. The paper was organized as following: Firstly, the materials and equipment for acquiring spectra were introduced. Secondly, the chemometrics methods for preprocessing and modeling were presented. Thirdly, an illustrative example of detecting the nonlinearity in the sorghum spectra was provided. Fourthly, the linear and nonlinear manifold DR methods which were used to extract the feature variables were discussed. The prediction performance using the extracted feature variables and LS-SVM regression method were compared. Finally, the conclusions were drawn.Four species of sorghum used for the experiment were collected from the regions of China, America and Argentina respectively. Their primary information were listed in −1 and the resolution was set as 4 cm−1. The samples were measured in a quartz cuvette that was a standard accessory of this spectrophotometer. The cuvette was washed with distilled water when each sample was finished. Each observation was scanned 30 times, and the 30 spectral data were taken average as the reflectance to represent each sample. The software of Spectra Manager CFR was used for spectral data acquisition and analysis. The temperature was kept at about 25 °C during the whole experiment.In this study, the Fourier Transform middle Infrared Spectrometer (Japan) of JASCO Model FT/IR-4000 was used to capture the reflectance spetrum of the samples. The range of spectra was from 7000 to 350 cmIn this section, two quantitative statistical methods including the Durbin–Watson test and the Runs test and the augmented partial residual plot (APaRP) were used to diagnose the nonlinearity of high-dimensional spectral data. Subsequently, four kinds of nonlinear DR methods of ISOMAP, LLE, LE and LTSA were presented. Finally, the nonlinear regression method of LS-SVM for modelling and forecasting was introduced.The Durbin–Watson test examines the null hypothesis that there is no correlation between the successive residuals and the alternative hypothesis that the correlation exists. To estimate the null hypothesis, statistic Two critical parameters of z) which is approximately normally distributed when the null hypothesis is true. The desired test statistic is the difference between the number of runs  represents a generalization of metric multidimensional scaling (MDS) to nonlinear manifoldsLet where Locally linear embedding (LLE) attempts to recover the global structure of nonlinear manifolds from locally linear fits, so as to preserve the local geometry of the input data in the low-dimensional space18Where Which is subjected to the constraints Laplacian eigenmaps (LE) resorts to the notion of the Laplacian of the neighborhood graph in order to compute low-dimensional projectionswhich assigns an increasing weight as the points The projections Which entails a heavy penalty for neighboring points mapped far apart.By introducing the Laplacian matrix The solution of Eq. (9) is obtained in closed form by computing the The Local Tangent Space Alignment algorithm (LTSA)LS-SVM establishes the regression model by a nonlinear mapping function The popular kernel functions include linear kernel function, polynomial kernel function, radial basis function (RBF) kernel functionIn this section, the nonlinearity of sorghum MIRS was investigated. Six illustrative examples of different DR methods were shown. The LS-SVM regression methods for modelling and forecasting were discussed. There were 180 sorghum observations used for the analysis. The samples were randomly divided into two sets including the training and the test set. The training set consisted of 140 samples, where each class consisted of 35 samples. The rest of 40 samples were used for the validation.The spectral reflectance curves of the different sorghum seeds were plotted in Spectral preprocess is a preliminary step in the chemometric analysis, which is usually performed prior to the model calibration. The goal of preprocess is to reduce the effects of length variation of light path, light scattering and to enlarge the hidden information in the original spectral dataTwo quantitative statistical methods of the Durbin–Watson test and the Run test were performed to check the nonlinearity of model. The Durbin–Watson test value In this section, six different manifold DR methods of ISOMAP, LLE, LE, LTSA, PCA and MDS were used to extract the feature spectra from the full spectral data; then, the performance of them were compared.The intrinsic dimensionality The prediction effect of ISOMAP algorithm turned out to be the best, followed by the algorithms of LTSA LLE, LE, PCA and MDS. It could be concluded that the nonlinear methods of DR obtained the superior prediction performance see .The parameters of In this section, the nonlinear model of LS-SVM was used to distinguish the sorghum samples and the performance of handling nonlinearity was discussed. The LS-SVM algorithm could be used to transform the data from the original space into the high-dimensional feature space via kernel function. The commonly used kernel functions included linear kernel, polynomial kernel and Radial basis function (RBF) kernel. The RBF kernel generally showed the optimal performance in handling the nonlinear relationship between the spectra and target attributes and could be used to reduce the complexity of computation during the training procedureThe precision-recall (PR) curves, mean average precision (MAP) scores, prediction accuracy and confusion matrices (CM) were respectively used to grade the prediction performance of models. These parameters and charts were widely used to measure the performance of learning algorithm. For the CM, each column represented the instances in a predicted class, while each row represented the instances in an actual class. As shown in The MAP score was also used to measure the overall prediction precision of model. Generally, a good model should gain a high MAP score and a large area surrounded by the PR curve. The PR curves of different LS-SVM models using different manifold methods were shown in The accuracy of prediction was shown in In this paper the manifold dimensionality reduction methods and nonlinear regression model of LS-SVM combined with MIRS techniques were presented for detecting the species of sorghum seeds. The nonlinearity of the raw spectral data was detected by the method of Durbin test, run test and APaRP. The nonlinear MDR methods of ISOMAP, LLE, LE and LTSA and linear manifold DR methods of PCA and MDS were utilized to extract characteristic variables. The extracted feature variables were used as the input of LS-SVM regression model for prediction of the class of unknown sorghum samples. The performance of prediction models were evaluated by CM, PR curves, MAP scores and prediction accuracy respectively. The ISOMAP-LS-SVM model obtained the highest MAP scores and prediction accuracy of 0.947 and 92.86% respectively. The operation of spectroscopy-based measurement is much simpler and more convenient than the traditional physical and chemical methods. Thereby, the investigation provided a superior alternative method to rapidly and accurately classify the species of sorghum seeds.How to cite this article: Chen, Y. M. et al. Combination of the Manifold Dimensionality Reduction Methods with Least Squares Support Vector Machines for Classifying the Species of Sorghum Seeds. Sci. Rep.6, 19917; doi: 10.1038/srep19917 (2016).


The time scales for cognitive information processing in the brain range, at least, from milliseconds  to many seconds , spanning several orders of magnitude. In this context the slow dynamical components can be regarded as background processes modulating adiabatically the parameters governing the fast neural activity. For the case of recurrent neural networks the slow processes then change adiabatically the attractor landscape, including the adiabatic fixed points, inducing possibly both second order bifurcations, with respect to the steady-state neural activity, and first order catastrophes.In this contribution we investigate the slow adaption of the attractor landscape of exemplary small recurrent neural networks consisting of continuous-time point neurons . The sta-5 and is characterized by a higher-order catastrophe.We rigorously examine the metadynamics of the attractor landscape for a three-neuron system, observing five different phases see Fig.  for diffWe conclude that even relatively simple recurrent networks may show highly non-trivial adapting attractor landscapes and that the study of the attractor metadynamics in the brain maybe important for a further understanding of decision processes and dynamical memory recall.


Effective communication with health care providers has been found as relevant for physical and psychological health outcomes as well as the patients' adherence. However, the validity of the findings depends on the quality of the applied measures. This study aimed to provide an overview of measures of physician-patient communication and to evaluate the methodological quality of psychometric studies and the quality of psychometric properties of the identified measures.A systematic review was performed to identify psychometrically tested instruments which measure physician-patient communication. The search strategy included three databases , reference and citation tracking and personal knowledge. Studies that report the psychometric properties of physician-patient communication measures were included. Two independent raters assessed the methodological quality of the selected studies with the COSMIN  checklist. The quality of psychometric properties was evaluated with the quality criteria of Terwee and colleagues.Data of 25 studies on 20 measures of physician-patient communication were extracted, mainly from primary care samples in Europe and the USA. Included studies reported a median of 3 out of the nine COSMIN criteria. Scores for internal consistency and content validity were mainly fair or poor. Reliability and structural validity were rated mainly of fair quality. Hypothesis testing scored mostly poor. The quality of psychometric properties of measures evaluated with Terwee et al.'s criteria was rated mainly intermediate or positive.This systematic review identified a number of measures of physician-patient communication. However, further psychometric evaluation of the measures is strongly recommended. The application of quality criteria like the COSMIN checklist could improve the methodological quality of psychometric property studies as well as the comparability of the studies' results. Over the past decades, patient-centeredness has been an internationally discussed topic in all health care associated fields Although there is no overall consensus on the operational definition of physician-patient communication Since the importance of physician-patient communication has been widely recognized, a considerable number of instruments that measure physicians' communication skills have been developed. In their review from 1995 Ong et al. The systematic review was registered in the International prospective register of systematic reviews PROSPERO (registration code: CRD42013005687).Peer-reviewed studies, published in English or German, were retrieved. We included studies, which tested psychometric properties  of instruments that measure the construct physician-patient communication. We adopted a broad definition of communication comprising verbal or non-verbal behavior, a set of communication, interaction or interpersonal skills. We included studies on communication between physicians and adult patients (≥18 years). We excluded studies that only reported communication in a subscale of a broader construct and studies that were limited to the medical education setting. Only generic instruments  were included for the reason that we found specific measures (e.g. measuring only end-of-life care) were less comparable to each other than to generic measures. The applied inclusion and exclusion criteria are displayed in www.cosmin.nl) to facilitate the selection of studies on measurement properties of measurement instruments. We also conducted a secondary search, tracking all reference lists and citations of the included full-texts for further studies of potential relevance and included articles of the authors' personal knowledge.We searched the databases PubMed, PsycINFO and EMBASE including all articles from their inception to August 15, 2013. For each data base a specific search strategy was developed based on a combination of Medical Subject Headings (MeSH) and free text terms in five domains: (i) patient (ii) physician, (iii) communication, (iv) measurement and (v) psychometrics see . FurtherFor an initial screening, all search results were imported into a reference management software (Endnote) and duplicates were removed. First, titles and abstracts were assessed to exclude clearly irrelevant records. Second, the remaining full texts were assessed for eligibility. All steps were performed independently by two team members (EC and JZ or IS or JD). The two members decided upon inclusion. Disagreements between reviewers were resolved in discussion with a third team member (JZ or IS or JD). The reviewers were not blinded to authors, date and journal of publication.Three reviewers  extracted data of the included studies on measures of physician- patient communication by using data extraction sheets. To reduce any bias that may occur with the assessment of one reviewer only, one study was independently assessed triple by EC, JZ and EM. As recommended by Mokkink et al. The following descriptive data was extracted for the measures: name of the instrument, authors, year, language, perspective (e.g. patient- or physician-reported outcome or observer rating or coding), dimensions, number of items and response scale. Furthermore, we extracted study characteristics .http://www.prisma-statement.org/). We undertook two assessments of quality, one for the methodological quality of the included studies and one that describes the psychometric quality of the included studies. For the assessment of the methodological quality of the included measures, the COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) checklist, www.cosmin.nl) the authors point out that the checklist mainly focuses on standards for studies that examine psychometric properties of Health-Related Patient-Reported Outcomes (HR-PROs). In this study, we included patient- and self-reported measures as well as observer based measures on physician-patient communication. Nevertheless, prior studies applied the COSMIN criteria to a range of measures The Center for Reviews and Dissemination and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses recommends using checklists for the appraisal of study quality the Classification System of Byrne and Long (CSBL)the Matched-pair instrument (MPI)the Generic peer feedback instrument (GPFI)In total, we included 20 measures in the review. Four measures were not clearly named by the authors; we therefore used the description from the title or abstract to abbreviate the instruments in our description, the The results of COSMIN ratings are displayed in The second COSMIN box, Reliability (Box B), could be applied to eighteen studies Measurement error (Box C) was not reported in any of the studies. The content validity box (Box D) was applied to all studies that were conducted on the initial development of the measures. Thus, eighteen studies were rated Cross-cultural validity (Box G) was only assessed in one study The evaluation of the quality of psychometric properties of the identified measures was conducted with the criteria of Terwee et al. and results are shown in This review sought to systematically examine studies on psychometric properties of measures on physician-patient communication, to investigate the methodological quality of these studies and to evaluate the quality of the psychometric properties of the identified measures. We extracted data from 25 studies examining 20 measures of physician-patient communication.Regarding the methodical quality of the studies, the results revealed a heterogeneous picture. Only two studies received an excellent or good score on internal consistency Remarkably, none of the studies on patient- or physician-reported measures received an excellent score on any psychometric property, but three of the observer ratings did. However, when ratings are examined for each study per item see , most ofQuality of psychometric properties evaluated with the Terwee et al.'s criteria In summary, the results for the methodological quality assessment show that studies reported on a median of 3 out of the nine COSMIN criteria. However, several flaws were revealed concerning the methodical quality and the quality of the psychometric properties. Content validity and hypothesis testing was of rather poor methodical quality and measurement error, criterion validity and responsiveness were almost not considered and should be addressed in future psychometric studies. The quality rating with Terwee et al.'s criteria showed that some measures received positive scores even though the methodological procedure was not always adequate. When combining the ratings of the studies on the COSMIN and Terwee et al.'s criteria, best results were received for the studies on the following measures: the SEGUE framework Our results are barely comparable to the previous reviews conducted by Ong et al. From our results, we suggest to further evaluate psychometric properties of existing measures on physician-patient communication using more rigorous methodological designs. Furthermore, there is a particular need to conduct further psychometric evaluation studies on the measures, especially to assess psychometric properties that have not been tested yet (e.g. responsiveness). However, the results from this study can be helpful for researchers to select the most appropriate measure for conducting a study on physician-patient communication. Since the included measures have different rating perspectives, the selection of a measure over another will be driven by the study aim and the feasibility in a certain study setting.A strength of this review is the detailed electronic search strategy, which was based on the COSMIN filter However, the current review has several limitations that need to be addressed. First, our review includes only generic measures for reasons of feasibility; and measures developed specifically for the medical education context or specific indications were beyond the scope of this review. Second, our search was limited to studies published in German or English. Therefore, studies published in other languages may not have been included. Third, although we believe our search strategy was very sensitive and guided by methodological recommendations for systematic reviews This systematic review provides an overview on measures on physician-patient communication and helps researchers to identify the appropriate instrument for their research purpose. Moreover, our study highlighted current gaps in the methodological quality of studies on psychometric properties and the quality of their results. We recommend that future evaluation studies on psychometric properties should apply standards like the COSMIN checklist in order to enhance quality of the studies and to increase the comparison of results.S1 FileElectronic database search strategy for EMBASE, PsycINFO Pubmed.(DOCX)Click here for additional data file.S2 FileS1 Table and S2 Table. Detailed results for the COSMIN checklist with 4-point scale rating.(DOCX)Click here for additional data file.S1 ChecklistPRISMA checklist.(DOC)Click here for additional data file.


Aneurysms in the vertebrobasilar system are rare and in the distal segment of the posterior inferior cerebellar artery they are even less frequent. Giant aneurysms are also rare in the posterior cranial fossa. Giant aneurysms of the distal posterior inferior cerebellar artery generally can have mainly compressive effects on the adjacent structures and they can be mistaken for tumors.We report the case of a 74-year-old Italian woman who presented with a complaint of dizziness. Her dizziness was found to be a result of aneurysmal dilatation arising from the distal segment of the right posterior inferior cerebellar artery. A mid-line suboccipital craniotomy was performed, and the aneurysm was clipped without post-operative deficits and with improvement in the patient’s dizziness. In our present report, we also review the literature and discuss our case with regard to the clinical and radiological features and surgical procedure performed.To the best of our knowledge, few cases of this type of aneurysm have been described in the literature. Our patient had a good outcome after surgical treatment. Aneurysms of the vertebrobasilar system account for 5% to 10% of all intracranial aneurysms, and, at the level of the distal posterior inferior cerebellar artery, they are rare, comprising less than 0.5% to 3% -6.A 74-year-old Italian woman presented to our institution with complaints of severe headache and dizziness. Her neurological examination showed nuchal rigidity  with gait ataxia. Magnetic resonance imaging (MRI) revealed a 2.8cm mass in the right cerebellar hemisphere with high signal intensity on T1-weighted images and low signal intensity on T2-weighted images, which were both associated with a peripheral signal void rim and not with peri-lesional edema. A magnetic resonance angiogram revealed aneurysmal dilatation arising from the distal segment of the right PICA and oriented medially with low signal intensity of flow only in part of the lumen and no signs of subarachnoid hemorrhage (SAH) (Figure The PICA is the greatest of the branches of the vertebral artery and is the causative vessel for aneurysms in the posterior fossa, which cause cerebral infarction and cranial nerve compression in many patients. The PICA is formed by six segments and two loops. The telovelotonsillar and cortical segments are its distal parts. The bifurcation of the basilar artery and the origin of the PICA are the most common sites from which giant aneurysms arise in the vertebrobasilar system. Other locations within the posterior cranial fossa are much less common. Computed tomography reveals giant aneurysms as oval-shaped lesions with surrounding edema and, frequently, calcification. Contrast enhancement is strictly dependent on intra-aneurysmal thrombosis, but it may not be sufficient to confirm the diagnosis of the nature of the lesion, because it cannot differentiate these lesions from tumors. MRI can demonstrate a well-defined mass, with peripheral signal void rim and no contrast-enhancing components. Angiography is the most important diagnostic modality for revealing the true nature of the lesion, especially when there are no signs or symptoms of subarachnoid bleeding -7. This Giant aneurysms of the distal PICA are very rare and often present together with posterior fossa syndrome. On the basis of reports in the literature, we conclude that, for these aneurysms, the surgical option of direct clipping should be considered the first-line treatment. This option allows definitive obliteration of the aneurysm and possible removal of space-occupying lesions, especially in cases of thrombosed aneurysms. Endovascular treatment involves significant risks of neurological deficit due to the extreme variability and tortuosity of the PICA.Written informed consent was obtained from the patient for publication of this case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.CT: Computed tomography; MRI: Magnetic resonance imaging; PICA: Posterior inferior cerebellar artery; SAH: Subarachnoid hemorrhage.The authors declare that they have no competing interests.All authors analyzed and interpreted the patient data and contributed to the writing of the manuscript. All authors read and approved the final manuscript.