Plant MADS domain proteins are involved in a variety of developmental processes for which their ability to form various interactions is a key requisite. However, not much is known about the structure of these proteins or their complexes, whereas such knowledge would be valuable for a better understanding of their function. Here, we analyze those proteins and the complexes they form using a correlated mutation approach in combination with available structural, bioinformatics and experimental data.Correlated mutations are affected by several types of noise, which is difficult to disentangle from the real signal. In our analysis of the MADS domain proteins, we apply for the first time a correlated mutation analysis to a family of interacting proteins. This provides a unique way to investigate the amount of signal that is present in correlated mutations because it allows direct comparison of mutations in various family members and assessing their conservation. We show that correlated mutations in general are conserved within the various family members, and if not, the variability at the respective positions is less in the proteins in which the correlated mutation does not occur. Also, intermolecular correlated mutation signals for interacting pairs of proteins display clear overlap with other bioinformatics data, which is not the case for non-interacting protein pairs, an observation which validates the intermolecular correlated mutations. Having validated the correlated mutation results, we apply them to infer the structural organization of the MADS domain proteins.Our analysis enables understanding of the structural organization of the MADS domain proteins, including support for predicted helices based on correlated mutation patterns, and evidence for a specific interaction site in those proteins. New mutations continually arise and are the source of genetic diversity. They provide the material on which selection acts; in large, sexual populations, beneficial mutations will reach fixation, and most deleterious mutations will be lost. However, in the case of deleterious mutations, a compensatory mutation may occur that renders the two mutations neutral or beneficial as a pair and causes them to be preserved by selection. In protein-coding sequences, coevolution of residues can occur as compensation of changes in e.g. volume or charge, or because of the simultaneous involvement of residues in e.g. ligand binding. This implies that residues which show such correlated mutations are expected to be located close to each other in the 3 D structure of a protein. An early observation of this kind was obtained in a set of virus sequences, where the positions in the sequence that showed an identical pattern of variation were in most cases close together in the 3 D structure . SeveralA number of methods have been developed to search for correlated mutations, and their results are mostly validated by comparing with distances between residues in crystal structures. A distinction can be made between pairwise correlation methods  ,8 and inOn a higher level, similarity between phylogenetic trees is related to protein interactions in large sets of interacting families -22. HoweArabidopsis revealed the ability to form 110 different dimers [Plant MADS domain transcription factors (TFs) are involved in regulation of a variety of developmental processes such as floral transition and flower development ,28. Theyt dimers  among 27t dimers ,32.A couple of structures are available for dimers of MADS domains (followed by a domain with some homology to the I domain) -38, but Here, we present a novel approach to analyzing correlated mutations and testing their validity. We analyze correlated mutations in a family of interacting proteins. This provides a convenient way to compare correlated mutations between those proteins and assess whether correlated mutations are 'conserved' between them. Secondly, it allows comparison of correlated mutations observed between pairs of interacting proteins with those observed between pairs of non-interacting proteins, where the latter provide a unique background-model for assessment of significance of the observed intermolecular correlated mutations. Hence, our results contribute to the interpretation of correlated evolution signals.We integrate our results with available structural, bioinformatics and experimental data for the plant MADS domain proteins and in this way we obtain clues about the structural organization of these proteins and their complexes.We will first discuss sequence retrieval, followed by correlated mutation analysis and validation of the results using various types of independent data. Next, conservation of correlated mutations between homologous positions in various proteins will be analyzed, which provides a novel way to assess the amount of information correlated mutations contain. Finally, our results will be applied in prediction of protein interactions and scrutinized to obtain structural insight into the MADS proteins.The workflow followed to obtain sequences and perform further analysis is illustrated in Figure Combining the sequences with existing interaction data  allowed Correlated mutations were obtained for intra- and inter-molecular sequence alignments using CAPS (see Methods). Additional Files Residues which show correlated mutations are expected to be located close to each other in tertiary and quaternary structure. Comparison of the distribution of distances for intramolecular correlated mutation residue pairs in the crystal structure of the MADS domain shows that there is indeed a clear enrichment at low distances, compared to all residue pairs in the crystal structure Figure . The enrFor the intermolecular correlated mutation analysis, the analysis of interacting protein pairs using time correction (see Methods) shows an enrichment in residues within 15Å, compared to all residue pairs Figure . Such enThe enrichment of residues which are in contact within 15Å) across the interface is reasonably strong , but less so than what is seen for the intramolecular correlated mutation analysis. This is in line with what has been observed previously for intermolecular correlated mutation analysis (see introduction). One reason could be that the correlated mutation analysis will inherently focus on residues which are not conserved (because otherwise there will be no coevolution effect). For a large part, residues at the interface will be conserved, meaning that a lot of residue-pairs will not show up in the correlated mutation analysis. Another factor obviously is the assumption  that orthologs will have similar interaction partners, a hypothesis for which evidence exists . The cleÅ across For the intermolecular correlated mutation results, a comparison was made with motif pairs which were previously predicted to determine MADS interaction specificity ,54. The Both the previously predicted motif pairs and the correlated mutation position pairs predict connections between regions in pairs of interacting sequences. In the comparison above, this was not taken into account, but we would expect that overlap between motif pairs and correlated mutation pairs would be 'consistent' in the sense that the two motifs that constitute a motif pair each overlap with one of the two positions of a given correlated mutation pair. Analysis of the number of ortholog pairs in which a given motif pair had such consistent overlap with correlated mutation positions indicates that this is higher for the interacting pairs than for the non-interacting pairs (data not shown). There is one motif pair which overlaps consistently with a correlated mutation pair in four different interacting protein pairs, and one which overlaps consistently in three different interacting pairs. The former connects two parts of the K-domain Figure , whereasFinally, we compared the intermolecular correlated mutation positions with available Arabidopsis SNP data . For theOverall, the comparison of correlated mutation positions with structural data, interaction motifs and SNPs show the same trend: correlated mutations from interacting pairs have enrichment in signals compared to non-interacting pairs. In addition, the intramolecular correlated mutations show clear distance enrichment. Hence, all observed trends, although sometimes weak, are consistent and point towards biological significance of the observed signals.An intriguing question is whether positions with correlated mutations in various protein subfamily members are conserved for being correlated or not, because this would give further insight into the mechanism behind correlated mutations. Note that the use of the term "conservation" here is somewhat different from its most common use to describe sequence conservation, but was chosen because it best describes the phenomenon of observing a feature (correlated mutation in this case) in multiple instances of a sequence alignment . To answer this question for the MADS proteins, we investigated for all intramolecular correlated mutation pairs in a given protein whether they were detected in other MADS proteins as well, in which case they were called "conserved" in these other proteins. We first analyzed whether there is more conservation of correlated mutations for pairs of proteins with higher sequence identity, but this was not the case. Overall, 63% of the correlated mutation pairs are conserved in at least one other MADS protein, and 37% are not  of these pairs are located in each others neigbourhood in the 3 D structure , and the C-terminal domain is predicted to be unstructured.i-i+3, i-i+5 and especially i-i+4 to be connected to each other, and for residues i-i+2 to be not connected. Note that, for example, the notation i-i+3 refers to pairs of residues which are separated in the amino acid sequence by two intervening residues. This pattern is not found when instead of the predicted helices, random stretches of equal length are defined and compared with the correlated mutation positions  for the predicted helices, whereas only 10 out of 1000 randomizations (randomly selecting sequence stretches) have a similar or higher difference (p~0.01).Although structure information is only available for the MADS and I domain, it is generally assumed that the K-domain consists of coiled coils. Our correlated mutation analysis can be used to validate this assumption. We predicted coiled coils in this domain (see Methods) and compared the correlated mutation positions with these predictions. The predicted helices are listed in Additional File s Figure ; the difNext, we analyzed whether correlations were observed between helices, in order to infer their orientation with respect to each other. Because only a few intramolecular correlated mutation positions occur between predicted K-domain helices  but found no such correlation.The majority of the intramolecular correlated mutations were observed in at least two MADS proteins, i.e. they showed conservation. We found that when such conserved correlated mutations were not observed in other MADS proteins, this is mostly because these positions are more conserved and not because of uncorrelated variability in these other proteins. This analysis gives additional support to the interpretation of correlated mutations as "one mutation followed by a compensatory mutation". Such support is important because of the need to infer "coevolution" based on observed "covariation", a process in which noise can be present, as discussed in the Introduction.A possible confounding factor for intermolecular correlated mutation analysis is that we cannot be sure that the predicted orthologs in all the various species that we analyze do indeed interact. To get some further insight into this issue, we assembled a set of interacting MADS domain proteins from various species from literature ,61-67. UOur approach is unique in using a set of interacting protein pairs and a set of related non-interacting protein pairs as a reference. As the latter would be expected not to have correlations with each other, they serve as negative controls. Using these, we found i) that the overrepresentation of intermolecular residues at short distances is higher for interacting protein pairs than for non-interacting pairs; ii) that there is more consistency between results from different interacting pairs than between results from different non-interacting pairs; iii) that there is a better overlap between correlated mutation results from interacting protein pairs and our previously predicted interaction motifs than between correlated mutation results from non-interacting protein pairs and those motifs; and iv) that they have less overlap with SNPs. Although some trends are weak on their own, they are all consistent.Our results here are complementary to our previous analysis of sequence determinants of MADS protein interaction specificity . In partOur results provide understanding of structural properties of the important plant MADS proteins. In particular, our correlated mutation analysis confirms predicted helices in the K-domain, and supports a specific organization of these helices in the MADS dimers. Also, we obtain further support for an interaction region in the I domain. Hence, in addition to obtaining general insight into coevolution signals at the protein level, we also demonstrate the use of these signals to test specific hypothesis about structural properties of proteins.http://www.maizesequence.org, medicago http://www.medicago.org/genome, papaya [A set of type II MADS proteins was obtained as follows Figure . Interpr, papaya  and sorg, papaya  were sca, papaya  to obtaiNext, orthologs were assigned to the various Arabidopsis sequences. We used a "best hit" criterion, based on the value of the sequence identity  after separately aligning each of the obtained sequences with each of the Arabidopsis sequences, using Muscle . For theSubsequently, in each species separately, blastclust with sequence identity cutoff of 95% was used for each group of sequences which simultaneously were "best hits" for a given Arabidopsis sequence (the cutoff of 95% was based on the observation that this keeps the Arabidopsis MADS proteins apart). A representative for each cluster was chosen randomly, except that preference was given to Interpro-based sequences compared to blast-based sequences and sequences from the genomes were preferred over both Interpro-based sequences and blast-based sequences. In addition, at least 25% sequence identity between a sequence and the Arabidopsis sequence which was it best hit, was required.Our choice to detect orthologs using blast hits is a pragmatic one. A more elaborate and time-consuming approach would be to make use of phylogenetic trees, which however have their own degree of uncertainty. We tested how different the results would be upon application of phylogenetic relationships from previously published phylogenetic trees for the MADS domain proteins AP1 and FUL . When coTo analyze intramolecular correlated mutations, the only step to take next was to align the sequences of each Arabidopsis MADS domain protein with all its associated sequences, for which Muscle  was usedAfter alignment, the resulting sets of interaction pairs  were used as input for the correlated mutation analysis if at least 30 pairs were present. As a background model, non-interacting pairs with at least 30 associated sequence pairs were used as input.Note that the cutoff on the number of sequences (30) that we use is somewhat arbitrarily but such cutoff is clearly needed because the smaller the number of sequences, the less reliable the correlated mutation results are.CAPS  compareshttp://gobase.bcm.umontreal.ca/searches/gene.php to obtain distances between species and using Clustalw [To determine significance of these correlations, re-sampling can be performed. However, because this is computationally expensive , we chose to use a cutoff on the value of the correlation coefficient, which we set to 0.4, in agreement with previous correlated mutation analyses . This isClustalw  to buildClustalw .Although no structure for plant MADS domain proteins is available, a couple of structures of human MADS domains are available. Of these, 1tqe, 1n6j, 1egw and 3kov are crystal structures of MEF2-type MADS domains, which are most related to plant MIKC (type II) MADS domains . BecauseCorrelated mutation pairs were compared with protein structure data as follows. For all intra-and inter-molecular pairs of residues in the PDB structure 1egw, the shortest heavy-atom distance was obtained. Mapping of the Arabidopsis sequence to the structure was obtained via Muscle alignment. For this, residues 2-69 of the structure were used. For residues 2-59, which constitute the MADS domain, there is high overall sequence similarity with the plant MADS domain, and for residues 60-69 there is also reasonable sequence similarity with the first part of the plant I domain. For the various proteins, this similarity (amount of conservative substitutions) is at least 7 out of 10. However, the sequence identity with the plant I domain is lower than for the MADS domain, meaning that the results of comparison with this part of the structure could be more noisy.In addition, correlated mutation pairs were compared with previously predicted interaction motifs . Becausehttp://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_lupas.html. Default settings were used , and a window length of 14, minimum coil probability of 0.5 and minimum length of 4 residues was applied to predict coiled coil helices based on the predicted coil probabilities. Helical wheel representations were generated with http://rzlab.ucr.edu/scripts/wheel/wheel.cgiTo predict coiled coils in the K-domain, a method which compares sequences with sequences of known coiled-coil proteins  was usedi)-N(i+4) pair  and O(i)-HN(i+4) pair . The anneal.inp CNS-script was used, which applies a high-temperature torsion-angle dynamics phase followed by a torsion angle dynamics cooling phase and a second cartesian dynamics cooling phase. Ten structures were calculated, and the lowest energy structure was used. Protein structure figures were prepared using Molscript [Modelling of the structure of the MADS domain of SEP3 was performed using Modeller . Out of olscript  and Rastolscript .k is defined asFor the intramolecular correlated mutation analysis, correlated mutation positions in a given protein were compared with the homologous positions in all other proteins, and these pairs were either designated 'conserved' correlated mutation if they showed a correlated mutation as well, and 'non-conserved' correlated mutation if they did not. To compare sequence variability at 'conserved' vs 'non-conserved' sites, sequence entropy was used, which for alignment column jk is the frequency of amino acid j at position k.where PHere we describe the various random trials that were performed in order to test for statistical significance. To assess the statistical significance of the intramolecular distance enrichment, 1000 random subsets of residue pairs were generated . For these, the fraction of residues within 15Å of each other was calculated.To assess the significance of observed intermolecular short distance enrichment for correlated mutation positions, we applied a randomization procedure where the original pairs of sequences that formed an input set for CAPS were randomly shuffled. This was repeated 1000 times.To assess the significance of the observed overlap between correlated mutation residues and predicted interaction motifs, random 'correlated mutation' pairs were generated by replacing each position in an observed correlated mutation position pair with a randomly generated sequence position. In doing so, we took into account that a position could occur in several correlated mutation pairs; such position was replaced by the same random position in all its correlated mutation position pairs.Finally, to assess the statistical significance of the observed preferred sequence-distance for correlated mutation positions within helices in the K-domain, we analyzed whether similar preferred sequence-distances occurred within randomly generated stretches of the sequence. The number and length distribution of these stretches was similar to that of the predicted K-domain coils, but their position within the sequence was randomized.ADJvD and RCHJvH conceived and designed the study, and wrote the paper. ADJvD performed the experiments and analyzed the data. All authors read and approved the final manuscriptSequence identifiers for intramolecular correlated mutation analysis. This file contains the sequences identifiers of the sequences used in the intramolecular correlated mutation analysis.Click here for fileInput data for intermolecular correlated mutation analysis. This file contains the pairs of interacting proteins used for the intermolecular correlated mutation analysis.Click here for fileIntramolecular correlated mutation results. This files contains the correlated mutation pairs obtained from the intramolecular analysis.Click here for fileIntermolecular correlated mutation results. This files contains the correlated mutation pairs obtained from the intermolecular analysis.Click here for fileShort distance enrichment significance. This file contains an analysis of the statistical significance of the observed short distance enrichment for the intermolecular correlated mutations.Click here for fileCorrelated mutations that have consistent overlap with predicted interaction motifs. This file contains correlated mutations that have consistent overlap with predicted interaction motifs and are strong candidates to be important residues for protein-protein interactions of the MADS domain proteins.Click here for fileConserved correlated mutations. This file contains correlated mutations which are conserved, i.e. appearing in more than one MADS domain protein (both intramolecular and intermolecular correlated mutations).Click here for filePrediction of helices in K-domain. This file contains predicted helices in the K-domain.Click here for filePredicted intramolecular contacts between helices. This file contains contacts predicted between K-domain helices using correlated mutations.Click here for filePredicted intramolecular contacts helices - MADS/I domain. This file contains contacts predicted between K-domain helices and the MADS/I domain.Click here for fileCorrelated mutations based analysis of intermolecular MADS domain protein helix - helix interactions. This file contains an analysis of intermolecular contacts predicted between K-domain helices.Click here for file


Pediatric Rheumatology (PR) has its first impact factor. The journal has just been given an impact factor of 1.44 this June after 5 years of association with the online publisher BioMed Central. This ranks our journal 59th out of 113 pediatric journals and 22nd out of 29 rheumatology journals and we are just 5 years old  [Pediatric Rheumatology is the only journal entirely devoted to our specialty with an impact factor and as an open access journal can therefore be reached by medical students, residents, and primary care physicians and specialists, as well as non-physicians and the general public all over the world.We are pleased to announce that PR to maintain a competitive price for authors to publish who need assistance-many authors do not.We are delighted that the Pediatric Rheumatology European Society (PReS) has agreed to support this journal and align its prestigious name and reputation with us as of January 1, 2013. For the next 5 years the Society will provide financial support to Open access journals represent the future of scientific publications and many University and Research Centers in the Western world already support their researchers by covering the costs of publication in these type of journals. The American National Institutes of Health and the British Wellcome Trust require their grantees to publish open access within 12 and 6 months respectively, and as the open access movement gathers momentum , fundingPR journal will become worthy of many important pediatric rheumatology publications as the journal grows, and our impact factor increases. The link between PR and PReS does fit with one important goal of PReS and all pediatric rheumatology organizations. We wish to provide a useful, common forum for pediatric rheumatologists all over the world and stimulate the growth of pediatric rheumatology, especially in growth areas such as Africa and Asia, where our subspecialty is just beginning to mature. Our open access model should help interested physicians and other professionals learn more about our field and the diseases we care for. Ultimately, we want to do our utmost to do what we can to improve medical care for children with rheumatic and musculoskeletal diseases everywhere and help each child. Many of us in the Western World come from relatively privileged circumstances. We at PR believe it is our duty and responsibility to do what we can for every child with JIA, lupus, dermatomyositis, and other rheumatic diseases, no matter what their status and situation. We hope this effort to support PR will in turn help these children we care about. Recent educational efforts of PReS, such as our Mumbai, India symposium in November 2012, also address our need to spread the gospel of pediatric rheumatology.Meanwhile we hope that our


P < 0.001), lower donor age , shorter time on dialysis , recipient positive CMV IgG , absence of AR episodes , 0 to 1 (versus 2) HLA-B mismatch , and recipients male gender . Our results show that an early KT, younger donor age, and an optimal first year graft function are of paramount importance for long-term graft survival. Measures that address these issues  are still warranted.Kidney graft survival has been mainly evaluated using an up to 10-year threshold. Instead, in this study our aim was to evaluate predictive variables that impact long-term kidney graft survival (≥10 years). We enrolled 892 patients in our analysis: 638 patients with functioning graft at 10 years PT and 254 patients with graft failure at 10 years PT (considering patient death with a functioning graft <10 years PT as graft failure). Between groups comparisons were done using Mann-Whitney and chi-square test. To determine independent predictive variables for long-term graft survival a multivariate-adjusted logistic regression was performed. Significant predictors of long term graft survival were lower 12-month PT creatinine (OR = 0.26,  For patients with end-stage renal disease (ESRD), a successful transplant  provides significantly higher survival rates and better quality of life –3, whichWe conducted a retrospective study and analyzed data from a total of 996 kidney transplants (KT) performed between July of 1983 and June of 2000, at Hospital de Santo António, Porto, Portugal. After discharge, recipients were followed at our outpatient clinic until graft loss or death. Recipient and donor information was collected from our computed database. We included, in our analysis, all recipients with a graft survival beyond 3 months, and patients surviving beyond the first-year PT. Simultaneous multiple grafts recipients were excluded. Graft loss was defined as return to chronic dialysis, graft removal, a retransplant, or death.We enrolled 892 patients in our analysis: 638 patients with functioning graft at 10 years of followup (Group I) and 254 patients with graft failure within 10 years PT (considering patient death with a functioning graft <10 years PT as graft failure) (Group II). Delayed graft function was defined as the need for one or more dialysis treatments in the first posttransplant week. n, %) for categorical variables. P  values < 0.05 were considered statistically significant. For comparison between groups the Mann-Whitney test and chi-square test were used for continuous nonparametric variables and categorical variables, respectively. To determine independent predictive variables for long-term graft survival a multivariate-adjusted logistic regression was performed, adjusting for age and sex of the recipient, mean time on dialysis, recipient status for cytomegalovirus IgG, prior blood transfusions (<3 versus ≥3), donor's age, number of HLA-B mismatches , PRA (<30 versus ≥30%), induction with antithymoglobulin, delayed graft function, acute rejection, and serum creatinine at 12 months after KT.All statistical analysis was performed using SPSS software for Windows . Results are presented as median and interquartiles range for continuous variables and as frequency and percentages (The majority of the enrolled patients were men (59.4%), with median age 37.0 years [IQR 27.6–47.1] at the time of transplant. Median time on dialysis was 2.6 years [IQR 1.4–5.0], 96.3% were on hemodialysis. Most donors were also men (70.9%). Median posttransplant follow-up time was 176.2 months [IQR 138.2–222.4]. The median survival time of renal grafts was 149.9 months [IQR 109.6–190.8]. Enrolled population characteristics are presented in P = 0.001) and fewer pretransplant blood transfusions . As for donor characteristics both groups had similar gender distribution and serum creatinine by the time of death, but the group with longer graft function had younger donors  (The group with graft function after ten years (Group I-G I) had more frequently positive status for cytomegalovirus IgG  . P = 0.005) had less human lymphocyte antigen B (HLA-B) mismatches , lower PRA level , and lower incidence of delayed graft function , and episodes of acute rejection  were less frequent. Serum creatinine at 12 months after KT was also lower in this group .Group I being more frequently received to the induction therapy with ATG , lower donor age , shorter time on dialysis , recipient positivity for CMV IgG , absence of acute rejection episodes , 0 to 1 (versus 2) HLA-B mismatch , and recipient male gender . Recipient age at transplant, number of transfusions (<3 versus ≥3), PRA level (<30 versus ≥30%), immediate graft function and induction with ATG were not significant predictors.The multivariate analysis  showed aThis study focused only on patients with more than 10 years of followup, referring to kidney transplant performed between the year of 1983 and 2000. Major differences of this cohort of patients from kidney transplantation nowadays consist of different and less effective immunosuppression, initially based on azathioprine and prednisolone, then based on cyclosporine and evolving towards introduction of mycophenolate mofetil and tacrolimus. Infectious prophylaxis was also less effective, translating to higher incidence of CMV disease. Due to improvements related with these issues significant progress has been made in graft and patient survival rates after kidney transplant, since the 1980s , 6. The When this population was submitted to kidney transplantation expanded criteria donors were not included, and the vast majority were deceased donors (99%), but many other factors are common to most survival analyses in renal transplantation, such as donor age or gender and creatinine level at 12 months. In this study, univariate analysis and multivariate logistic model were used for analyzing factors influencing renal graft survival. Data analysis indicated that an optimal first year graft function (including absence of acute rejection episodes and creatinine level at 12 months) was of paramount importance for long-term graft survival.Several studies implicated acute rejection as a major risk factor for chronic allograft failure –12. A prThe correlation between the elevated serum creatinine levels at 12 months and graft survival has been documented in several studies , 15. In Other independent known determinants for graft survival include recipient age at transplantation, donor age, length of pretransplant dialysis, delayed graft function, and panel reactive antibody > 30% .In renal transplantation, donor age is known to have an important influence on the outcome of the graft reflecting functional renal mass . In our There is a long-standing debate about whether delayed graft function reduces the survival rate of a renal graft . SeveralTraditionally, high panel reactive antibody (PRA) has been associated with increased immunologic risk and lower kidney graft survival . In our As for HLA compatibility, it has been considered the most important independent factor for the 10-year survival rate of patients and the half-life of a patient's first renal transplant. Cecka showed 10-year survival of dead renal transplant to be of 74% when HLA was matched between the donor and recipient and stated a reduction for 58% if it was mismatched . During The impact of CMV serology in kidney transplantation showed donor CMV-seropositive kidneys to be associated with significantly reduced graft survival for CMV-seronegative recipients but not CMV-seropositive recipients . In our This study presents the limitations of any retrospective study moreover this complex cohort of patients, concerning different phases of immunosuppressive regimens and the lack of accurate information of the induction and maintenance immunosuppressive strategies used; restricts more broad inferences. Nonetheless, this is a study on a large number of patients, with a long-term followup (beyond ten years posttransplant) and we could find interesting results. In summary, modifiable risks factors as an early KT, younger donor age, number of HLA B mismatches and an optimal first-year graft function (including absence of acute rejection episodes and creatinine level at 12 months) are of paramount importance for long-term graft survival. Measures that address these issues  are still warranted.


Listeria monocytogenes as a pathogen in meningitis and bacteremia in immunosuppressed patients is high. We report a case of vascular graft infection due to Listeria monocytogenes as an example of a less well-known manifestation of listeriosis and focus on the possible treatment procedures emphasizing a management with surgical debridement but preservation of the endograft, in contrast to the gold standard treatment of vascular graft infections which consists of a removal of the graft.The awareness of  Listeria monocytogenes as a pathogen in meningitis in immunosuppressed or elderly patients is high. Also gastroenteritis, infections in pregnancy or sepsis in neonates are well-known clinical manifestations due to Listeria. However, this pathogen can cause many other types of infection. As an example, we report here the so-far 8th case of vascular graft infection due to Listeria, where in general organisms like Staphylococci, E. coli, or Streptococci are found. Our aim is to increase the awareness of Listeria as a pathogen causing other clinical syndromes in immunosuppressed patients over and above meningitis and gastroenteritis, and we focus on the treatment options in prosthetic graft infection due to Listeria reviewing the so far reported 7 cases.The awareness of Listeria monocytogenes, whereas the blood cultures remained negative. Therefore, the patient was treated with ampicillin 2 gm q4h intravenously without gentamicin because of his impaired renal function . The patient was under immunosuppression with Ciclosporine A and Mycophenolate-Mofetile after renal transplantation 2004, and he got an endovascular repair of an infrarenal aortic aneurysm with a Talent-graft in 2005. At admission, the patient's low back pain and fluctuating fever were interpreted as a sacroileitis. A MRI-scan showed no skeletal pathology but a slight enhancement of the sclerotic infrarenal aorta including an enhancement of the periaortal tissue. So, a CT guided translumbar needle aspiration of the enhancing structure was taken, and the cultures yielded growth of tion see . Under this antibiotic treatment, the CRP-level sank initially, but remained then around 120 mg/l so that gentamicin 1 mg/kg i.v. three times a day was added. At this time, the surgeon refused a surgical approach since the renal transplant was vasculated through the graft and a removal of the graft would have been a high risk for the transplanted organ. After 6 weeks of combined antibiotic therapy a new MRI showed new collections around the vascular graft down to the psoas muscle. A drainage delivered pure pus, the cultures were sterile but an in-house eubacterial PCR  was positive for Listeria. So after 2 months of conservative treatment a surgical approach was faced due to lacking improvement. Intraoperatively extensive inflammatory adhesions were found; therefore, the aneurysm with the endograft could not be removed. Only a debridement around the aneurysm and in the psoas muscle could be performed. The Mycophenolate-Mofetil dosing was reduced at that time. Two weeks thereafter and after 8 weeks of combined intravenous antibiotic therapy the patient could be discharged with an oral regimen consisting of 320 mg trimethoprim/1600 mg sulfamethoxazole twice a day. A MRI-scan 6 months later in June 2008 showed no more abscesses but a slight enhancement in the periaortic tissue as well as in the psoas muscle. In January 2009, the CRP achieved a normal level (<5 mg/l), and, in July 2009, there was no more enhancement in the MRI-scan. Nevertheless, we decided to continue the antibiotic treatment for another 2 years (until July 2011) since the patient has a stable function of his renal transplant and since a relapse of the graft infection would be disastrous for the whole situation of the patient. In March 2011, the patient is well without any symptoms.E. coli are responsible for prosthetic graft infections 10]. Althfections . Graft i010]. Altfections . In genegnancies . AccordiIn the 8 analysed cases, with one exception, the mean interval between graft implantation and onset of infection was 2 years (range 12 weeks to 10 years), indicating a hematogeneous spread of infection. Listeria occur ubiquitous are mainly ingested with contaminated food, and invasive disease evolves by hematogeneous spread from the gut . 1–5% ofThe diagnosis of graft infections can be extremely challenging. Symptoms are often nonspecific like recurrent fever and chills or back pain as it was in our case. With a sensitivity of 94% and a specificity of 85% CT-scan is considered the diagnostic test of choice [With regard to the treatment strategy, persistence or recurrence of the infection was observed in both with (case no. 2) and without (cases no. 4–8) initial removal of the prosthesis see , where a


Social psychology and related disciplines are seeing a resurgence of interest in replication, as well as actual replication efforts. But prior work suggests that even a clear demonstration that a finding is invalid often fails to shake acceptance of the finding. This threatens the full impact of these replication efforts. Here we show that the actions of two key players – journal editors and the authors of original  research findings – are critical to the broader public’s continued belief in an invalidated research conclusion. Across three experiments, we show that belief in an invalidated finding falls sharply when a critical failed replication is published in the same – versus different – journal as the original finding, and when the authors of the original finding acknowledge that the new findings invalidate their conclusions. We conclude by discussing policy implications of our key findings. Social psychologists agree that replication is essential to a healthy science, yet actual replication efforts have been extremely rare. This is largely because disciplinary incentive systems have tended to ghettoize replication efforts, relegating them to lower ranked journals or not publishing them at all But here we address a second hurdle facing replication efforts, especially those that disconfirm prior findings. Even with strong contradictory evidence in hand, original findings often continue to live on, in support of “undead theories” How can claims that do not withstand further empirical scrutiny be prevented from becoming “glorified anecdotes”  and the original authors’ reaction . Participants in these two studies were selected from a convenience sample. As evident in our earlier discussion, an attempt to replicate a prior finding using the same procedures and methods as the original study may fail to find the same effects for several different reasons. A replication attempt could “fail” because the original finding was not real or reliable. Alternatively, an attempt to replicate a real or reliable finding could fail because the replication researchers do not implement some critical part of the design, or simply due to chance. We are most interested in the role of journal editors and original authors in cases where the underlying reason for the contradictory evidence is not so ambiguous All three studies were conducted by the first author as anonymous online questionnaires with users of Amazon Mechanical Turk .www.epn.se). What research needs approval is described in Sections 3 and 4 of the Act. In brief, studies with human participants need approval only if they involve sensitive personal data  or use a method intended to physically or mentally influence a person. Our studies clearly do not involve sensitive personal data according to the definition. Further, the method of having people fill in questionnaires or make decisions do not count as intended to physically or mentally influence a person, as confirmed by a previous application by the first author to the Regional Ethical Review Board in Uppsala, Sweden.No approval was obtained. For research conducted in Sweden, need for approval is regulated by the Act concerning the Ethical Review of Research Involving Humans (2003:460), which can be accessed in official English translation at the web site of the Central Ethical Review Board , of varied educational background, completed a survey for a compensation of $0.50.Participants were asked to consider the following scenario: “Through a very credible video, widely shared on Twitter and Facebook, you learn of a remarkable finding published in a prestigious journal by a group of social scientists. The finding rings true with you, and you share it with your friends who are equally enthusiastic. When surfing the internet, you incidentally find mention of a report where some unknown researchers claim that the original finding does not hold.”the same prestigious journal as the original finding, or that it was published in a low-ranked online journal. The order of these two scenarios was counterbalanced across participants. Thereafter, participants read another two scenarios, which were identical to the previous ones up to the end, at which point the same piece of information was added to both scenarios: “The report also mentions that the researchers who reported the initial finding acknowledge that this new report indeed invalidates their original finding.” For each of the four scenarios, participants were simply asked to rate the likelihood (from 0% to 100%) that the original finding was correct or valid.In a 2-by-2 within subjects design, participants were asked to consider four different ways in which a journal editor and the authors of the original finding responded to the contradictory evidence: First, they were either told that the report was published in M = 78.9, SD = 18.9). Belief in the original finding dropped substantially if the contradictory evidence was published in the same journal , and dropped even more if it was acknowledged by the original authors . Finally, belief dropped to the lowest level  when the contradictory evidence was both published in the same journal and acknowledged by the original authors. The statistical significance of the observed pattern was confirmed in a two-way within-subjects ANOVA, which showed a main effect of journal, F = 347.37, p<.001, as well as a main effect of original authors’ reaction, F = 262.09, p<.001, and no significant interaction, F = 1.23, p = .27.While the results of Study 1 strongly support our predictions, it is possible that participants were overly influenced by the fact that the study was published in a lower status journal. For reasons outlined earlier, it is typically the case that a failure to replicate will be published in a lower status journal if it is published at all. But we wanted to rule out that the Study 1 findings were driven by the status language. Thus, we conducted a second study that closely replicated the first with a notable exception. In particular, rather than presenting participants with the relative status of the journals, we asked them to infer it.One hundred and eighty-two American users of AMT , of varied educational background, completed a survey for a compensation of $.050.Participants were told to consider the same scenario as in Study 1, with the following two changes: First, instead of “a prestigious journal”, the original finding was said to have been published in a journal called “American Journal of Behavioral Sciences.” Second, instead “unknown researchers”, the contradictory claim was now made by “other researchers.” We thus removed any indication of journal or authorial status from the scenarios.the same journal “since it is customary to publish follow-up research on a given topic in the same journal as the original finding”, or that it was published in a different journal  and the “editor of the American Journal of Behavioral Sciences rejected the paper.” The order of these two scenarios was counterbalanced across participants. Thereafter, we again presented them with the same two editorial outcome scenarios, with the addition that the original researchers acknowledged the new report invalidated their original finding. For each of the four versions of the scenario, participants estimated the validity of the original research findings, as in Study 1.Like Study 1, the second study used a 2-by-2 within subjects design to manipulate how a journal editor and the authors of the original finding responded to the contradictory evidence. First, they were told that the report was published in Finally, participants were told that “Academic journals differ in their status and prestige” and then asked which journal they would guess is the higher ranked journal: ‘American Journal of Behavioral Sciences’  or ‘The Journal of Social and Behavioral Science’ .M = 58.6, SD = 20.8). Belief in the original finding dropped substantially if the contradictory evidence was published in the same journal , and dropped even more if it was acknowledged by the original authors . Finally, belief dropped further  when the contradictory evidence was both published in the same journal and acknowledged by the original authors. A two-way within-subjects ANOVA confirmed a main effect of journal’s support, F = 108.77, p<.001, as well as a main effect of original authors’ support, F = 324.70, p<.001, and a significant interaction, F = 18.30, p<.001. This interaction may be attributable to a floor effect; 35% of participants had already reached the floor of zero in their estimations of the third scenario.p<.001, binomial test. This is important because it shows that participants inferred the relative status of ostensible journals based on what typically happens to replication studies in social psychology.Finally, among the 162 participants who indicated which journal was probably the higher ranked one, the great majority answered the journal in which the original finding was published (71%) rather than the other journal (29%), Our final study addressed three potential weaknesses of Studies 1 and 2. First, the previous studies used a within-subjects manipulation of where the replication was published and thus risked priming participants’ responses. In the third study, we instead manipulated journal using a between–subjects design. Second, Studies 1 and 2 asked respondents to make hypothetical assessments of validity without any details of the studies. We wanted to test whether the same effect of editorial decision holds when people evaluate an actual research finding. , all with at least a Master’s degree in a social science, were recruited among AMT users for a compensation of $1.Participants first read the main research findings of an original publication.A nationally representative sample of Americans first estimated the current distribution of wealth in the United States, then constructed distributions with their ideal level of inequality. Finding: Americans dramatically underestimate the current level of wealth inequality in United States. Moreover, their ideal wealth distributions are nearly egalitarian. This study, by researchers of distinction in the field, was published in one of the most prestigious journals in the field.A couple of years ago a study was conducted, which can be summarized as follows: Thereafter, participants gave subjective estimates of the likelihood that the finding is valid (we refer to this as their “first rating”). Thereafter, they were informed of the outcome of a critical failed replication study. Depending on condition, participants were either told that the replication was published in the same journal or a lower-ranked journal. More specifically, after a one sentence description  of the basic procedures and results of the failure to replicate, participants were told:The (replication) researchers argued that their measure had higher validity than the measure used in the previous study and concluded that the findings of [the original] study were invalid. The replication paper was published in [the same prestigious journal as the first paper/a relatively lower-ranked online journal ].Participants gave a new subjective estimate of the likelihood that the original finding is valid (“second rating”). Finally, participants were given a detailed summary of the specific methods and results of both the original study and the replication study (available upon request), noting that “this may of course affect your evaluation of the credibility of their findings.” After reading this information, participants made a new subjective estimate of the likelihood that the original finding is valid (“third rating”).Summing up, each respondent’s belief in the original finding was measured three times as new pieces of information were sequentially given. The differences between subsequent measures  measure the effect of each new piece of information on the respondent’s belief in the original finding.M = 73.6, SD = 21.6). We first address how simply noting the existence of a failed replication, in general terms, impacted this belief. A repeated measures ANOVA on the “first” and “second” ratings confirmed that this first piece of information led to a significant drop in belief in the original finding, F = 46.06, p<.001. As expected, this effect was moderated by condition, F = 7.82, p = .007, such that the mean drop in belief was greater when the failed replication was published in the same journal  than in a lower-rank journal . This finding is consistent with results from Studies 1 and 2.Initial belief in the original finding was high  = 15.81, p<.001. Moreover, the size of this effect did not depend on condition, F = 0.08, p = .78. That is, the mean drop in belief was similar whether the failed replication had been published in the same journal  or a lower-rank journal .We then analyzed the effect of the second piece of new information, that is, the details about the specific methods used and results obtained in the original study and the failed replication. A repeated measures ANOVA on the “second” and “third” ratings confirmed that this new information led to an additional drop in belief in the original finding, http://openscienceframework.org). Such efforts are critical to a healthy discipline. But as others have noted Owing partly to widely publicized doubts about the extent to which the discipline’s knowledge is real and replicable, calls for more replication have become increasingly prominent in social psychology. These calls have been answered by ambitious efforts to replicate a broad range of the social psychological findings  findings. The results of three studies support our claims about the roles of each of these players.First, findings from our first two studies highlight the importance of how authors of original  findings react. We found that when authors of the original findings acknowledged that new data invalidated their findings, belief in their original conclusions dropped sharply. While not a surprising finding, we think it is an important one: At an objective level, researchers are in the best position to point to any findings that invalidate their prior research conclusions. But a cursory search for how researchers typically respond to others’ failure to replicate suggests that a balanced assessment of the evidence is not the norm. Instead, our search turned up mostly combative responses, in which the original authors accused the replication researchers of not following the right procedures, or lacking the background knowledge or skillset to properly conduct a replication. Such responses are sometimes valid. But we worry that defensive postures all too often stem from a reluctance to admit we were wrong. This is unfortunate, as one journal editor noted : “Scientists should not feel attacked when other scientists report failures to replicate our work; it’s not an accusation that we did something wrong. Rather, we should see failures to replicate–and successful replications–first as compliments, because people thought our work was worth paying attention to and spending time on, and second as providing more pieces to the puzzle that is the field of psychology.” It would be naïve to think we could turn this culture of reputation guarding on its head overnight. But we hope that the resurgence of interest in replication will create better conditions for not only celebrating when we were right but also for appreciating when others have shown that we were wrong.Perhaps more important are our findings about how editorial decisions impact continued belief in discredited research findings. Across all three studies, we found that sustained belief depended heavily on whether the replication study was published in the same or different journal as the original finding. In addition, the third study demonstrated the importance of actually reading the contradictory evidence rather than just learning about its existence. It goes without saying that readers of journals in which the original paper appeared are more likely to read contradictory evidence if it is published in the same journal. These findings are particularly important when considered in light of the fact that many top journals in social psychology will not publish replications as a matter of policy Committee on Publication Ethics (see www.publicationethics.org). Most important for our current purposes is the code’s standard of “Encouraging debate,” which states that “i) Editors should encourage and be willing to consider cogent criticisms of work published in their journal.; ii) Authors of criticised material should be given the opportunity to respond; and iii) Studies reporting negative results should not be excluded.” The code of conduct suggests a best practice for editors of being open to publishing research that challenges or contradicts research previously published in the journal. A policy of not publishing failures to replicate is clearly antithetical to this code of conduct. But, from a scientific perspective, it is critical that replication efforts be given full consideration by the journal that published the original finding.One solution is for journals to subscribe to a code of conduct for journal editors like that published by the In this paper we have focused mainly on social psychology, partly due to our greater familiarity with the field. The primary reason for this focus, however, is that issues surrounding the validity of social psychological findings and the necessity of replication are the subject of intense debate within the social psychology community. However, other disciplines face many of the same problems Perhaps a more important goal for future research is to address the boundary conditions of our findings. For instance, we kept to a minimum the details of the methods and findings we presented participants in Study 3. Furthermore, it is unlikely that participants knew about the particular case on which Study 3 was based, let alone held any strongly beliefs about it. But we might expect that persistence in belief in research findings will depend on a range of factors, including the nature of those findings and the (failed) replication, how long the original finding has been accepted as true and by how many people, and so on. A better understanding of the factors that lead invalid findings to “stick” even when the evidence contradicts them could only benefit scientific progress.


The International Society for Biocuration (ISB) was created in 2009 specifically to promote biocuration, the product of multidisciplinary teams of database curators, software developers and bioinformaticians. Biocurators, whose work facilitates research and education across the life sciences, create and maintain a wide variety of online tools and databases, covering topics as diverse as biochemical structures, chromosomal features and phenotypes of mutant genes. These resources are now so essential to the biological community that databases have become integral to the daily work of most researchers. But biological databases are far from static: in addition to the need to constantly capture new knowledge , data representation must also keep pace with current research—new data types must be modeled—and improved methods of data storage, representation and analysis must be continually developed. Nevertheless, such important efforts have not always been recognized, and have often not been published in full, owing to the lack of a suitable journal.The Journal of Biological Databases and Curation, was launched in 2010 to support the growing need of the research community to discuss a range of issues related to the creation, development and maintenance of biological databases, and to strengthen communication between database developers, curators and users.DATABASE, Biocuration Virtual Issue, a special collection of articles describing work presented at the annual International Biocuration Conference.As this resonates strongly with the mission of the ISB, we are delighted to announce that DATABASE has now become the Society’s official journal. The scope of DATABASE includes many areas relevant to the endeavors of the biocuration community. Moreover, DATABASE is an open-access journal, which is critical for biocuration worldwide and one of the core values that the ISB promotes. Since its creation, DATABASE has published more than 250 articles, 50 of which have appeared in the Scholarly exchanges among scientists are invaluable for helping a discipline to realize its full potential. To this end, DATABASE and the ISB are excited to be able to work together more closely, a collaboration that we expect will enhance the visibility and impact of biocurators’ work, and hence to increase the value of the Journal to members both of the ISB and of the wider scientific community.Pascale Gaudet (Chair), Monica Munoz-Torres (Secretary), Marc Robinson-Rechavi (Treasurer), Teresa Attwood, Alex J. Michael Cherry, Renate Kania, Claire O'Donovan and Chisato Yamasaki.


Dear colleagues,Our loyal friend Dr. Kuan-Teh Jeang passed away unexpectedly on the evening of January 27, 2013. The following night and day an avalanche of emails went across the Retrovirus research community, starting in Australia, then Asia, Europe and America. Great shock and sorrow was apparent in the messages by the very many colleagues with whom Teh interacted over the years. Many of us came to know Teh  and human T-cell leukemia virus (HTLV-I), with an abundant production of more than 300 scientific publications on the molecular details of virus replication and the disease-causing mechanisms. He trained over 30 postdoctoral fellows and had been a fantastic mentor of young scientists who have since spread across the globe, from Taipei to Hong Kong, from Montpellier to Amsterdam and from Montreal to Los Angeles.Teh was a very dynamic and internationally oriented scientist and he always felt a special bond with the scientific community in Taiwan. He was born and spent his early childhood in Taiwan, and later learned to speak Mandarin fluently. He actively participated in the scientific review processes in the National Science Council and the National Health Research Institute and various universities, often travelling long distances to Taiwan to offer comments and suggestions on various aspects of science. He had deep affection towards his home land Taiwan and hence contacted the founding editor Prof. C.C. Chang and volunteered his service for the Journal of Biomedical Science (JBS) of the National Science Council of Taiwan, which was the only international journal sponsored by Taiwan government at that time. He joined the editorial board of JBS in 1994 and had been very influential since then. Teh was a stabilizing force during the formative years of JBS when the biomedical community in Taiwan was somewhat skeptical of an international journal with its Editorial Office based in Taiwan. After JBS was listed in the Journal citation Index in 1999, he was also an avid advocate for ways to improve its impact factor. It is largely due to his suggestions and sometimes unorthodox ideas that JBS jumped in the annual Impact Factor ranking. The creation of Vignettes, which was well-received by our readers, was one of those suggestions.He left our board in 2004 to free himself for an important new activity: the launch of the Retrovirology journal, where he had been editor-in-chief since then. Again his talent to kick off new initiatives paid off and Retrovirology is currently among the highest cited journals in the field of virology, all achieved in less than 10 years. Since the early years, he had been an advocate of the Open Access publishing format. He was invited for the JBS editorial board meeting last September to present his current views on this topic and gave his most insightful suggestions. Teh always kept a special interest in Taiwan and its research activities, which led to several productive collaborations. He was also a champion for advocacy of the rights of Taiwanese scientists in international scientific organizations. He was elected as Academician of the Academia Sinica in 2008.Teh was a scientist with a vision and a broad interest in all aspects of the scientific endeavors. He also was a true scientific leader, starting scientific debate, writing editorials, sitting on many committees, orchestrating new book volumes and organizing international meetings on diverse topics. For instance, he was president of the Society of Chinese Bioscientists in America (SCBA) in 2010 and voiced a strong opinion to increase the representation of Asian-American scientists in leadership positions.Teh's death is a blow to the retrovirus research community and we will sorely miss his scientific leadership. He has been central to so much of what we have done together as well as being a supportive and generous friend to many of us individually. In his spirit, several initiatives have been proposed over the last couple of days by his students and colleagues to honor his legacy. Teh was only 54 years old and the loss is devastating for the Jeang family. Our thoughts and condolences are with his wife Diane and his children David, John and Diana.Present and past members of the Editorial BoardJournal of Biomedical ScienceDr. Kuan-Teh Jeang.Click here for file


The classes for the causes of death was formalized by the International Statistical Congress that later evolved into the International Statistical Institute. International Statistical Institute later collaborated with Health Organization of the League of Nations, the precursor of the World Health Organization to incorporate the classification of morbidities, and later on the role for updating and maintenance was wholly taken over by the WHO.Hospitals are data hungry organization, and store tons of patient level data in the patient’s clinical notes. This data cannot be used in the day to day decision making because it is not standardized. That was the rationale that started the movement to standardize the clinical documentation which resulted in the development of clinical coding standards based on disease classification. Disease classification has its roots in the classes of causes of death, which started as early as mid 18th Revision) of the International Classification of Disease was carried out in 1989 and is famously known as ICD 10. ICD 10 has served its purpose very well, but with the rapid change in the technologies and way the data is managed in hospitals, it is fast becoming obsolete. Therefore WHO has decided to revise the current version of the ICD 10, and come up with ICD 11 that fulfills all the requirements a modern healthcare system. ICD 11 will be a comprehensive classification that can be used by all the different stakeholders in the healthcare environment, can be integrated into the digital hospital information system and other terminologies such as SNOMED CT. For that purpose WHO has come up with a comprehensive program to involve the different stakeholders in the development of the ICD 11 that hopefully, will be commissioned in 2015.The last revision (10


In the antisaccade task, subjects are requested to suppress a reflexive saccade towards a visual target and to perform a saccade towards the opposite side. In addition, in order to reproduce an accurate saccadic amplitude, the visual saccade vector  must be exactly inverted from one visual hemifield to the other. Results from recent studies using a correlational approach  suggest that not only the posterior parietal cortex (PPC) but also the frontal eye field (FEF) might play an important role in such a visual vector inversion process. In order to assess whether the FEF contributes to visual vector inversion, we applied an interference approach with continuous theta burst stimulation (cTBS) during a memory-guided antisaccade task. In 10 healthy subjects, one train of cTBS was applied over the right FEF prior to a memory-guided antisaccade task. In comparison to the performance without stimulation or with sham stimulation, cTBS over the right FEF induced a hypometric gain for rightward but not leftward antisaccades. These results obtained with an interference approach confirm that the FEF is also involved in the process of visual vector inversion. In the antisaccade task, subjects are requested to suppress a reflexive saccade towards a visual target and to shift their gaze towards the opposite side. In order to accurately produce antisaccades with the same amplitude, the vector leading to the presented target location must be precisely inverted by 180° into an opposite saccade vector. The posterior parietal cortex (PPC) has consistently been shown to be involved in this visual vector inversion process. In the monkey, a subset of neurons in the lateral intraparietal area (LIP) shows an early activity when the visual stimulus matches the contralateral receptive field of the cell and, later on, shows a “paradoxical” activity when the visual target is presented ipsilaterally Another oculomotor cortical area that is involved in the processing of visual information and saccade generation – and might thus be implied in visual vector inversion – is the FEF The study was approved by the Ethical Committee of the State of Bern and was carried out in accordance with the principles of the latest Declaration of Helsinki.Ten right-handed subjects volunteered for the study . Their mean age was 29 years (range 24–33 years). All participants had normal or corrected-to-normal visual acuity and gave their written informed consent prior to participation.Subjects were seated in a completely dark room, their head was stabilised by a chin rest. The chin rest minimised head movements and ensured a constant viewing distance of 120 cm. Visual stimuli were presented on a vertical panel with an embedded array of separate and equidistant light emitting diodes (LED), positioned along the horizontal meridian. Eye movements were recorded by means of an infrared corneal reflection device , with a spatial resolution of 0.1° and sampling rate of 1000 Hz. Eye movement data were stored on a computer for off-line analysis. The device was calibrated at the beginning and regularly throughout the experiment. During calibration, subjects were instructed to look at lateral targets appearing in a staircase pattern, first to the right and then to the left, with amplitudes of 8°, 10°, 12°, 14°, and 16°.At the beginning of each trial of the memory-guided antisaccade task cTBS was applied using a MagPro R30 stimulator , connected to a figure-of-eight coil . For the sham condition, a sham coil  was used. The stimulator was set to produce repetitive, biphasic pulses. Stimulation intensity was then set at 80% of the participants' individual resting motor threshold of the left small hand muscles. This stimulation intensity has been shown to be sufficient to induce behavioural effects when applied over the FEF For each condition , the subjects performed 100 trials overall, 50 towards the left  and 50 towards the right . The order of the conditions was pseudo-randomized across subjects. The experiment lasted about 20 min for each condition. The different conditions were performed during three different sessions, with an interval of at least 24 hours between sessions.In a first step, erroneous prosaccades , anticipated saccades , and trials with blinks were excluded from the main analysis. The percentage of erroneous prosaccades, anticipated saccades, and trials with blinks was computed for every subject and condition. The values were then compared between conditions by means of separate, repeated-measures analyses of variance (ANOVA) with the within-factor ‘condition’ .For each correctly executed antisaccade, gain 1 was calculated by dividing the amplitude (in degrees) of the executed antisaccade by the amplitude (in degrees) of the lateral target. Gain 2 – defined as the gain of the saccade before the mirror-positioned feedback target was presented – was calculated according to the same formula. Mean gain 1 and mean gain 2 were computed for each subject, stimulation condition, and direction. The values were then analysed by means of separate, repeated-measures ANOVA with the within-factors ‘condition’  and ‘direction’ .post-hoc tests were computed by means of Bonferroni-corrected t-tests.All 2,18 = 2.303, p = .129, Partial Eta squared (η2p) = .204). Anticipated saccades occurred in 7.377% (SEM = 2.979) of cases in the condition ‘no stimulation’, in 8.478% (SEM = 3.438) of cases in the condition ‘sham right FEF’, and in 8.938% (SEM = 3.700) of cases in the condition ‘cTBS right FEF’. There was no significant difference between conditions . Trials with blinks occurred in 4.250% of cases (SEM = 1.655) in the condition ‘no stimulation’, in 5.320% of cases (SEM = 1.656) in the condition ‘sham right FEF’, and in 4.793% (SEM = 1.147) of cases in the condition ‘cTBS right FEF’. There was no significant difference between conditions .Erroneous prosaccades occurred in 2.768% (standard error of the mean (SEM) = .930) of cases in the condition ‘no stimulation’, in 3.537% (SEM = 1.857) of cases in the condition ‘sham right FEF’, and in 5.001% (SEM = 1.817) of cases in the condition ‘cTBS right FEF’. There was no significant difference between conditions  or of the factor ‘direction’ . That is, the stimulation condition or the direction of the antisaccades per se had no significant influence on mean gain 1. However, there was a highly significant interaction between the two factors . Post-hoc testing revealed that mean gain 1 for rightward memory-guided antisaccades  was significantly lower in the condition ‘cTBS right FEF’  than in the condition ‘no stimulation’  and the condition ‘sham right FEF’ . Conversely, there was no significant difference between mean gain 1 of leftward antisaccades  in the conditions ‘no stimulation’ , ‘cTBS right FEF’ , or ‘sham right FEF’  . Moreover, there was a significant difference between mean gain 1 of leftward and rightward antisaccades in the condition ‘cTBS right FEF’ (p = .012), but not in the conditions ‘no stimulation’ or ‘sham right FEF’ (p's>.05). The results are depicted in The analysis of mean gain 1 revealed no significant main effect of the factor ‘condition’  or of the factor ‘direction’ . However, there was a significant interaction between the two factors . Post-hoc testing revealed a significant difference between mean gain 2 of leftward and rightward antisaccades in the condition ‘cTBS right FEF’ (p = .014), but not in the conditions ‘no stimulation’ or ‘sham right FEF’ (p's>.05). However, mean gain 2 for rightward memory-guided antisaccades  was not significantly different between the conditions ‘cTBS right FEF’ , ‘no stimulation’ , or ‘sham right FEF’  . There was also no significant difference in mean gain 2 of leftward antisaccades  between the conditions ‘no stimulation’ , ‘cTBS right FEF’ , or ‘sham right FEF’  .The analysis of mean gain 2 revealed similar results. There was no significant main effect of the factor ‘condition’ . For instance, in a MEG study and the FEF, it might be conceivable that visual vector inversion occurs analogously in the PPC and the FEF, i.e., very early. Future studies should shed more light on the temporal aspects of the FEF involvement in visual vector inversion, and compare them with the PPC, e.g., using a correlational approach  or a single-pulse TMS interference approach.It remains unclear whether visual vector inversion relies more prominently on the FEF or the PPC, and it is not known how the processes of visual perception and spatial working memory are exactly linked to visual vector inversion. It is well known that a subpopulation of FEF neurons encodes visual stimuli in a retinotopic coordinate system Summing up, the present study confirms that also the FEF, and not only the PPC, is an important oculomotor cortical area for visual vector inversion in humans. Since the FEF and the PPC are densely interconnected


Recent efforts in HIV-1 vaccine design have focused on immunogens that evoke potent neutralizing antibody responses to a broad spectrum of viruses circulating worldwide. However, the development of effective vaccines will depend on the identification and characterization of the neutralizing antibody epitopes. Consequently, we developed bioinformatics methods to predict epitopes using corresponding genotypes and phenotypes generated using a highly sensitive and reproducible neutralization assay.50 titers with envelope mutations, and used this information to predict antibody epitopes. Structural patches were generated as amino acid groupings based on solvent-accessibility, diameter, atomic depth, and interaction networks within 3D envelope models. These patches were then evaluated as possible antibody targets by applying a boosted algorithm comprised of machine learning and statistical models. We identified residues with statistically significant correlation with IC50 titers as sites that impact neutralization sensitivity. Residues frequently occurring within the significant patches were mapped onto envelope structures as potential antibody binding sites.Using 264 clonal envelope (gp120) sequences from a panel of multiclade HIV-1 viruses with matching neutralization titers to an array of neutralizing monoclonal antibodies , we correlated IC50 titers and patch clusters predicting neutralization response to these antibodies were located within V1/V2, and V3. The predicted response by the algorithm was highly concordant (>80%) with the neutralization sensitivity of all antibodies.Predicted epitopes were identified based on strong correlations with neutralization response to each antibody. Residues highly associated with the ICWe developed and applied computational methods to rapidly survey protein structures and identify epitope regions associated with neutralization response. This data mining algorithm can help identify immunological hotspots, and provide rapid and accurate insight into regions that are targeted by potent and broad neutralization responses. Studies are ongoing to confirm these novel epitopes.


Peer review is the mainstay of editorial decision making for medical journals. There is a dearth of evaluations of journal peer review with regard to reliability and validity, particularly in the light of the wide variety of medical journals. Studies carried out so far indicate low agreement among reviewers. We present an analysis of the peer review process at a general medical journal, Deutsches Ärzteblatt International.554 reviewer recommendations on 206 manuscripts submitted between 7/2008 and 12/2009 were analyzed: 7% recommended acceptance, 74% revision and 19% rejection. Concerning acceptance (with or without revision) versus rejection, there was a substantial agreement among reviewers (74.3% of pairs of recommendations) that was not reflected by Fleiss' or Cohen's kappa (<0.2). The agreement rate amounted to 84% for acceptance, but was only 31% for rejection. An alternative kappa-statistic, however, Gwet's kappa (AC1), indicated substantial agreement (0.63). Concordance between reviewer recommendation and editorial decision was almost perfect when reviewer recommendations were unanimous. The correlation of reviewer recommendations and citations as counted by Web of Science was low .Although our figures are similar to those reported in the literature our conclusion differs from the widely held view that reviewer agreement is low: Based on overall agreement we consider the concordance among reviewers sufficient for the purposes of editorial decision making. We believe that various measures, such as positive and negative agreement or alternative Kappa values are superior to the application of Cohen's or Fleiss' Kappa in the analysis of nominal or ordinal level data regarding reviewer agreement. Also, reviewer recommendations seem to be a poor proxy for citations because, for example, manuscripts will be changed considerably during the revision process. Introduced already in the 18Medicine is a discipline largely built on journal articles, particularly in research. Also, much of continuing medical education of doctors rests on journal articles. Those articles and the journals where they appear differ in many aspects: for example, general medical versus specialty journals, English language versus regional language journals, or research papers versus review articles. Those differences will probably be reflected in different peer review processes and results. Against this background and given how essential and ubiquitous peer review has become, it is necessary to evaluate manuscript peer review at journals. Important questions pertain to the reliability of peer review, or to its validity, operationalized, for example, as its predictive value for scientific quality .Given the sheer number of medical journals – as of July 2012, NLM's database Medline alone indexed more than 5600 periodicals Several authors concluded that peer review is an unreliable process: For example, Kappa values as a measurement of inter-rater reliability have repeatedly been reported to fall between 0 and 0.4, indicating only poor to fair agreement among reviewers To our knowledge, only one study has measured the predictive value of reviewer recommendations for scientific citations in medicine: Opthof and co-workers Accordingly, we analyzed the peer review process at our general medical journal focusing on the following questions: What is the distribution of reviewer recommendations? To what degree did the editors follow reviewer recommendations? What is the agreement among reviewers in evaluating manuscripts? Are reviewer recommendations associated with the number of future citations?www.aerzteblatt-international.de). In general, manuscripts are submitted in German and are reviewed by German speaking referees.This is a retrospective cohort study regarding reviewer assessments and citations of manuscripts submitted to Deutsches Ärzteblatt International. Deutsches Ärzteblatt International is a weekly, bilingual (German and English) general medical journal that publishes approximately 100 original and review articles per year. It is the official organ of the German Medical Association (Bundesärztekammer) and of the National Association of Statutory Health Insurance Physicians (Kassenärztliche Bundesvereinigung). As such, it is geared at the general medical public and not a specialty journal. A large share of its articles serves educational purposes. The (German) print version is distributed to all doctors in Germany, resulting in a circulation of more than 400.000 copies. In addition, all article full-texts are published (open access) in German and English via the webpage of the journal  are not included in this analysis.For all manuscripts eventually published, a citation count was carried out using the Web of Science database. All citations until December 31, 2011 were counted.Manuscript submissions, acceptance and rejection rates, numbers of reviews, and their recommendations are presented as numbers, percentages , means, and standard deviations as appropriate.For the purposes of the editorial office, reviewer recommendations 2 and 3 (accept after minor or major revision) boil down to the same suggestion: The authors should be invited to revise their manuscript. In addition, in our experience comments by reviewers that had proposed minor or major revision are not reliably different in length or specificity. Therefore, we merged recommendations 2 and 3 into a single recommendation of acceptance after revision: 1. Acceptance, 2. Acceptance after Revision, 3. Rejection. This rating was used for all further analyses including the calculation of mean recommendation scores. The reviewer recommendation score for a particular manuscript was calculated as the average of the recommendations of all referees.Several indicators of agreement are calculated to present different perspectives on the analysis of agreement measurement. A contingency table  is used to document recommendations of reviewer pairs. For those pairs, Spearman's correlation coefficient was calculated. Overall agreement of reviewer recommendations is presented as percentage and as positive and negative agreement rates for ‘accept with/without revision’ versus ‘reject’ – the latter calculated as described by Cicchetti and Feinstein Furthermore, various Kappa values are presented. Fleiss' Kappa However, Kappa values can be misleadingly low when the marginal totals are very different The association of reviewer recommendations  and number of citations was analyzed using Spearman's correlation. Citations were counted between publication (2008 to 2011) and December 31, 2011. In order to adjust for different time spans during which a paper can be cited, year of publication was added as confounding variable in a partial correlation.Between July 1, 2008 and December 31, 2009 a total of 343 original and review manuscripts were submitted to Deutsches Ärzteblatt. Of those, 137  were rejected after initial evaluation by the editors. The remaining 206  were sent out for peer review, to 3 reviewers on average . About one fourth  of the reviewed articles were rejected (n = 49), and the remaining 157  were published. Of all manuscripts submitted to Deutsches Ärzteblatt (N = 343), eventually about half were published .The total number of reviews amounted to 554. In thirty-nine reviewer statements (7.0% [5.1–9.4%]) the recommendation was acceptance without revision and in approximately one fifth of reviews the referees opted for rejection . In the vast majority acceptance after (minor of major) revision was recommended  sent out for review had a unanimous statement favoring acceptance. Almost all of those were eventually accepted . The acceptance rate was lower for manuscripts with diverging reviewer statements, that is, acceptance or acceptance after revision versus rejection: 54.2% (39 out 72 [42.6–65.4%]). When all reviewers had advised rejection (n = 7) none of the manuscript were published . When weThe probability for publication regarding a manuscript unanimously positively evaluated by the reviewers was 2.2 times higher than that of all other manuscripts, and probability for publication of manuscripts unanimously recommended for rejection was zero .For all 206 papers evaluated in 554 reviews, 529 reviewer pairs were constructed . The overall rate of concordant pairs of statements was 60.9% (n = 322); acceptance without revision: 2; acceptance after minor or major revision: 289; rejection: 31 . When thWhen the options acceptance without revision and acceptance after revision were condensed so that the 3×3 table became a 2×2 table the results differed slightly: Overall agreement was 74.3% (n = 393/529). Again, the figure was similar when only the 93 papers were analyzed that were reviewed by exactly two referees: 75.2%. The proportion of positive agreement (concerning acceptance) was 0.84 (84%) and the proportion of negative agreement (concerning rejection) was 0.31 (31%).Fleiss' kappa was 0.16, indicating poor agreement, and equal to Cohen's kappa: 0.16. The alternative kappa value (AC) by Gwet indicated substantial agreement: 0.63.The 157 articles submitted between July 1, 2008 and December 31, 2009, and eventually accepted by Deutsches Ärzteblatt International were published between 2008 and 2011. Mean reviewer rating per article was 2.12 (SD: 0.35). On average, they were cited 5.1 times (SD: 4.9) between publication and December 31, 2011 . The corThis study yielded several relevant results: Firstly, at Deutsches Ärzteblatt International referees very rarely recommended acceptance of a manuscript in unchanged fashion. A substantial share of manuscript evaluations recommended rejection of the manuscript whereas the majority recommended revision and publication. Secondly, almost all unanimous recommendations (rejection or acceptance) were followed by the editors, and when reviewer statements differed (at least one reviewer opted for rejection and at least one for acceptance) about half were finally accepted. Thirdly, and this may be the key finding of our study, reviewers agreed substantially in their recommendations to accept  but not in their recommendations to reject (agreement rate 31%). This agreement was not reflected by Fleiss' (or Cohen's) kappa (0.16) but by the alternative kappa statistic as proposed by Gwet (0.63). Fourthly, reviewer recommendations regarding an article did not predict how often it was cited.About one fifth (19.3%) of all reviewer statements at Deutsches Ärzteblatt International came with a recommendation to reject the manuscript under review. This is similar to the 17% published for the Croatian Medical Journal Various reasons may prompt reviewers to opt for turning down a manuscript, e.g., poor scientific quality, the feeling that a manuscript is better suited to another type of journal , or that the work under review is simply not good enough for a particular journal. For example, with 44% rejection was often proposed by the reviewers of The Lancet During the observation period, four out of ten submissions to Deutsches Ärzteblatt International were rejected without review, often because the editors had deemed the material inappropriate for the journal's general readership. However, it is possible that reviewers are not aware of the fact that once they are asked to evaluate a manuscript the editors have already decided that it is in principle suited for their journal.In general, the editors at Deutsches Ärzteblatt International followed reviewers' recommendations when they were unanimous for acceptance or rejection. Only in rare exceptions were papers rejected that the reviewers had unanimously considered publishable. Reasons included an evident divergence between a reviewer's recommendation and his or her specific comments or when authors did not comply with reasonable revision proposals.With regard to the recommendation to accept or revise a manuscript, agreement among reviewers was substantial. At Deutsches Ärzteblatt International one particularly important purpose of the review process is to guide the editors in their decision on whether to invite the authors to revise their manuscript or to reject. No manuscript that was eventually published was accepted without revision. Therefore, it is justified to condense all three recommendations –accept as is, revise, reject – into two: revise or reject. In three out of four pairs of manuscript evaluations this alternative was unanimous. More specifically, we found a high proportion of positive agreement (0.84) indicating that a decision to accept the manuscript  was largely unanimous. 84% of such decisions by one reviewer were in agreement with a given second reviewer. However, the low proportion of negative agreement (0.313) shows that the decision to reject was by no means unanimous, such decisions being supported by a given second reviewer in only 31% of cases.For the practical purposes of an editorial office we consider this pattern of agreement satisfactory, particularly with regard to the acceptance of manuscripts.The substantial agreement among reviewers, however, was not reflected in the conventional kappa statistics. Fleiss' and Cohen's kappa were low: 0.16 in both cases, respectively – values that are usually interpreted as poor agreement This situation, poor agreement as indicated by conventional Kappa statistics, is similar to the low kappa scores reported by Kravitz et al. However, when certain recommendation categories are selected much more frequently than others, as in the present study, it may be problematic to rely on Fleiss' or Cohen's kappa with its specific calculation of chance agreement that is compared with actual agreement. Also, it has to be borne in mind that Cohen's Kappa will depend upon the arbitrary assignment of referees as reviewer 1 or 2.Spearman's correlation coefficients for reviewer agreements were below 0.2, indicating poor agreement . This maGwet In sum, our findings challenge the view that journal peer review, in general, is unreliable.Average reviewer recommendations and citations of published manuscripts were only weakly and insignificantly correlated. When the year of publication was taken into account in order to adjust for the different duration of time periods during which a paper could be cited the association became even weaker. This result is in line with the low correlation reported by Opthof and co-authors A low predictive value of reviewer recommendations for citations may indicate poor review quality and, therefore, low validity of the reviewing process. However, in part, the result may be explained by the fact that reviewers come to their conclusions at the beginning of an often time-consuming process of revising a manuscript. Therefore, accepted versions of manuscripts differ considerably from submitted versions. In addition, depending on their idea of evaluating a manuscript for Deutsches Ärzteblatt International, experts may consider an article of educational but not necessarily of scientific merit. Also, by definition, all manuscripts that were published reached high scores. It is, therefore, possible that variance of the reviewer recommendation was low precluding high correlations. In addition, the range of citations is restricted in articles published in Deutsches Ärzteblatt International because certain often cited types of articles (such as RCTs) are rarely published in our journal. In order to obtain a representative assessment of the association of reviewer scores and citations, publications in a broad set of journals have to be analyzed. Finally, although highly valuable as a measurement of journal evaluation, citations of single articles may not be appropriate for analyzing scientific quality This study has several limitations: First of all, this is an analysis of the review process at one German general medical journal during a limited time span, and its results are certainly not representative for other journals. For example, it is conceivable that the manuscripts, the reviewers, the percentage of experts declining to review  or submitting their evaluations (3%), or other factors typical for our journal differ from other general medical journals. Still, while the concordance among reviewers measured at our journal seems to be larger than in some  other analyses, most results are similar to what has been published before.Another shortcoming is that this is a study of a convenience sample of manuscripts and no sample size calculation was carried out prior to study start: Our N (206) is below the average N of 311 that Bornmann et al. reported in their meta-analysis The citation analysis in this study is restricted to Web of Science and did not use other databases such as Scopus or Google scholar. However, while Google scholar retrieves more citations the citation accuracy is lower In an analysis of the review process at a general medical journal from Germany we found that reviewers more often recommended revision than rejection or straight acceptance. Most importantly, reviewers agreed substantially among themselves concerning acceptance but not concerning rejection; editorial decisions concurred substantially with unanimous reviewer recommendations; but recommendations and number of citations were not associated. Based on a comparison of the commonly used Cohen's (or Fleiss') Kappa statistic for measuring inter-rater reliability with an alternative Kappa statistic, we argue for a reconsideration of the widely held view that journal peer review is a process of poor reliability. Provided that our results hold up, implications of this study include the application of different agreement measurements (preferably as proposed by Cicchetti and Feinstein or by Gwet rather than applying Cohen's Kappa), and the knowledge that, in medicine, reviewer comments will not tell editors and authors much about future citations. Also, at least with regard to reviewer agreement, the peer review system seems to work well.Many of the most important questions regarding peer review, however, such as whether peer review leads to streamlining of science and whether it hampers innovation, or to what degree peer review improves manuscripts, remain open, and qualitative research will probably be needed in the search of answers