C4:The future of solid organ transplantation from the perspective of young transplant professionals

With great interest, we read the first C4 Article titled "Current opinions in organ allocation", the result of pioneering work by the editorial board of the American Journal of Transplantation. The effort of the editorial board to realize their four C's goal, establishing a crowdsourced collaboration on current and controversial subjects, has resulted in a state-of-the-art review. Over a hundred transplant professionals contributed to this project, making it a one-of-a-kind, interdisciplinary and cross border collaboration. This article is protected by copyright. All rights reserved

Laboratory-evolved Vanillyl-alcohol Oxidase Produces Natural Vanillin

The flavoenzyme vanillyl-alcohol oxidase was subjected to random mutagenesis to generate mutants with enhanced reactivity to creosol (2-methoxy-4-methylphenol). The vanillyl-alcohol oxidase-mediated conversion of creosol proceeds via a two-step process in which the initially formed vanillyl alcohol (4-hydroxy-3-methoxybenzyl alcohol) is oxidized to the widely used flavor compound vanillin (4-hydroxy-3-methoxybenzaldehyde). The first step of this reaction is extremely slow due to the formation of a covalent FAD N-5-creosol adduct. After a single round of error-prone PCR, seven mutants were generated with increased reactivity to creosol. The single-point mutants I238T, F454Y, E502G, and T505S showed an up to 40-fold increase in catalytic efficiency (k(cat)/K-m) with creosol compared with the wild-type enzyme. This enhanced reactivity was due to a lower stability of the covalent flavin-substrate adduct, thereby promoting vanillin formation. The catalytic efficiencies of the mutants were also enhanced for other ortho-substituted 4-methylphenols, but not for p-cresol (4-methylphenol). The replaced amino acid residues are not located within a distance of direct interaction with the substrate, and the determined three-dimensional structures of the mutant enzymes are highly similar to that of the wild-type enzyme. These results clearly show the importance of remote residues, not readily predicted by rational design, for the substrate specificity of enzymes

Gender Disparities in Authorships and Citations in Transplantation Research

Background: Over the past decades, there has been a rapid change in the gender ratio of medical doctors, whereas gender differences in academia remain apparent. In transplantation research, a field already understaffed with female doctors and researchers, there is little published data on the development in proportion, citations, and funding of female researchers over the past years. Methods: To evaluate the academic impact of female doctors in transplantation research, we conducted a bibliometric analysis (01 January 1999 to 31 December 2018) of high-impact scientific publications, subsequent citations, and funding in this field. Web of Science data was used in combination with software R-Package "Gender," to predict gender by first names. Results: For this study, 15 498 (36.2% female; 63.8% male) first and 13 345 (30.2% female; 69.8% male) last author gender matches were identified. An increase in the percentage of female first and last authors is seen in the period 1999-2018, with clear differences between countries (55.1% female authors in The Netherlands versus 13.1% in Japan, for example). When stratifying publications based on the number of citations, a decline was seen in the percentage of female authors, from 34.6%-30.7% in the first group (≤10 citations) to 20.8%-23.2% in the fifth group (>200 citations), for first (P < 0.001) and last (P = 0.014) authors, respectively. From all first author name-gender matches, 6574 (41.6% female; 58.4% male, P < 0.001) publications reported external funding, with 823 (35.5% female; 64.5% male, P = 0.701) reported funding by pharmaceutical companies and 1266 (36.6% female; 63.4% male, P < 0.001) reporting funding by the National Institutes of Health. Conclusions: This is the first analysis of gender bias in scientific publications, subsequent citations, and funding in transplantation research. We show ongoing differences between male and female authors in citation rates and rewarded funding in this field. This requires an active approach to increase female representation in research reporting and funding rewarding

Centering, scaling, and transformations: improving the biological information content of metabolomics data

BACKGROUND: Extracting relevant biological information from large data sets is a major challenge in functional genomics research. Different aspects of the data hamper their biological interpretation. For instance, 5000-fold differences in concentration for different metabolites are present in a metabolomics data set, while these differences are not proportional to the biological relevance of these metabolites. However, data analysis methods are not able to make this distinction. Data pretreatment methods can correct for aspects that hinder the biological interpretation of metabolomics data sets by emphasizing the biological information in the data set and thus improving their biological interpretability. RESULTS: Different data pretreatment methods, i.e. centering, autoscaling, pareto scaling, range scaling, vast scaling, log transformation, and power transformation, were tested on a real-life metabolomics data set. They were found to greatly affect the outcome of the data analysis and thus the rank of the, from a biological point of view, most important metabolites. Furthermore, the stability of the rank, the influence of technical errors on data analysis, and the preference of data analysis methods for selecting highly abundant metabolites were affected by the data pretreatment method used prior to data analysis. CONCLUSION: Different pretreatment methods emphasize different aspects of the data and each pretreatment method has its own merits and drawbacks. The choice for a pretreatment method depends on the biological question to be answered, the properties of the data set and the data analysis method selected. For the explorative analysis of the validation data set used in this study, autoscaling and range scaling performed better than the other pretreatment methods. That is, range scaling and autoscaling were able to remove the dependence of the rank of the metabolites on the average concentration and the magnitude of the fold changes and showed biologically sensible results after PCA (principal component analysis). In conclusion, selecting a proper data pretreatment method is an essential step in the analysis of metabolomics data and greatly affects the metabolites that are identified to be the most important

Integrating functional genomics data using maximum likelihood based simultaneous component analysis

<p>Abstract</p> <p>Background</p> <p>In contemporary biology, complex biological processes are increasingly studied by collecting and analyzing measurements of the same entities that are collected with different analytical platforms. Such data comprise a number of data blocks that are coupled via a common mode. The goal of collecting this type of data is to discover biological mechanisms that underlie the behavior of the variables in the different data blocks. The simultaneous component analysis (SCA) family of data analysis methods is suited for this task. However, a SCA may be hampered by the data blocks being subjected to different amounts of measurement error, or noise. To unveil the true mechanisms underlying the data, it could be fruitful to take noise heterogeneity into consideration in the data analysis. Maximum likelihood based SCA (MxLSCA-P) was developed for this purpose. In a previous simulation study it outperformed normal SCA-P. This previous study, however, did not mimic in many respects typical functional genomics data sets, such as, data blocks coupled via the experimental mode, more variables than experimental units, and medium to high correlations between variables. Here, we present a new simulation study in which the usefulness of MxLSCA-P compared to ordinary SCA-P is evaluated within a typical functional genomics setting. Subsequently, the performance of the two methods is evaluated by analysis of a real life <it>Escherichia coli </it>metabolomics data set.</p> <p>Results</p> <p>In the simulation study, MxLSCA-P outperforms SCA-P in terms of recovery of the true underlying scores of the common mode and of the true values underlying the data entries. MxLSCA-P further performed especially better when the simulated data blocks were subject to different noise levels. In the analysis of an <it>E. coli </it>metabolomics data set, MxLSCA-P provided a slightly better and more consistent interpretation.</p> <p>Conclusion</p> <p>MxLSCA-P is a promising addition to the SCA family. The analysis of coupled functional genomics data blocks could benefit from its ability to take different noise levels per data block into consideration and improve the recovery of the true patterns underlying the data. Moreover, the maximum likelihood based approach underlying MxLSCA-P could be extended to custom-made solutions to specific problems encountered.</p

Sub-Subgiants in the Old Open Cluster M67?

We report the discovery of two spectroscopic binaries in the field of the old open cluster M67 -- S1063 and S1113 -- whose positions in the color-magnitude diagram place them approximately 1 mag below the subgiant branch. A ROSAT study of M67 independently discovered these stars to be X-ray sources. Both have proper-motion membership probabilities greater than 97%; precise center-of-mass velocities are consistent with the cluster mean radial velocity. S1063 is also projected within one core radius of the cluster center. S1063 is a single-lined binary with a period of 18.396 days and an orbital eccentricity of 0.206. S1113 is a double-lined system with a circular orbit having a period of 2.823094 days. The primary stars of both binaries are subgiants. The secondary of S1113 is likely a 0.9 Mo main-sequence star, which implies a 1.3 Mo primary star. We have been unable to explain securely the low apparent luminosities of the primary stars; neither binary contain stars presently limited in radius by their Roche lobes. We speculate that S1063 and S1113 may be the products of close stellar encounters involving binaries in the cluster environment, and may define alternative stellar evolutionary tracks associated with mass-transfer episodes, mergers, and/or dynamical stellar exchanges

Pathophysiological Changes in the Hemostatic System and Antithrombotic Management in Kidney Transplant Recipients

Nowadays, the main cause for early graft loss is renal graft thrombosis because kidney transplant outcomes have improved drastically owing to advances in immunological techniques and immunosuppression. However, data regarding the efficacy of antithrombotic therapy in the prevention of renal graft thrombosis are scarce. Adequate antithrombotic management requires a good understanding of the pathophysiological changes in the hemostatic system in patients with end-stage kidney disease (ESKD). Specifically, ESKD and dialysis disrupt the fine balance between pro- and anticoagulation in the body, and further changes in the hemostatic system occur during kidney transplantation. Consequently, kidney transplant recipients paradoxically are at risk for both thrombosis and bleeding. This overview focuses on the pathophysiological changes in hemostasis in ESKD and kidney transplantation and provides a comprehensive summary of the current evidence for antithrombotic management in (adult) kidney transplant recipients.</p

Antithrombotic Management in Adult Kidney Transplantation: A European survey study

In kidney transplantation (KTx), renal graft thrombosis (RGT) is one of the main reasons for early graft loss. Although evidence-based guidance on prevention of RGT is lacking, thromboprophylaxis is widely used. The aim of this survey was to obtain a European view of the different thromboprophylactic strategies applied in KTx. An online 22-question survey, addressed to KTx professionals, was distributed by email and via platforms of the European Society for Organ Transplantation. Seventy-five responses (21 countries, 51 centers) were received: 75% had over 10 years' clinical experience, 64% were surgeons, 29% nephrologists, and 4% urologists. A written antithrombotic management protocol was available in 75% of centers. In 8 (16%) centers, respondents contradicted each other regarding the availability of a written protocol. Thromboprophylaxis is preferred by 78% of respondents, independent of existing antithrombotic management protocols. Ninety-two percent of respondents indicated that an anticipated bleeding risk is the main reason to discontinue chronic antithrombotic therapy preoperatively. Intraoperatively, 32% of respondents administer unfractionated heparin (400-10,000 international units with a median of 5,000) in selected cases. Despite an overall preference for perioperative thromboprophylaxis in KTx, there is a high variation within Europe regarding type, timing, and dosage, most likely due to the paucity of high-quality studies. Further research is warranted in order to develop better guidelines.</p

Aggravation of fibrin deposition and microthrombus formation within the graft during kidney transplantation

In kidney transplantation, microthrombi and fibrin deposition may lead to local perfusion disorders and subsequently poor initial graft function. Microthrombi are often regarded as donor-derived. However, the incidence, time of development, and potential difference between living donor kidneys (LDK) and deceased donor kidneys(DDK), remains unclear. Two open-needle biopsies, taken at preimplantation and after reperfusion, were obtained from 17 LDK and 28 DDK transplanted between 2005 and 2008. Paraffin-embedded sections were immunohistochemically stained with anti-fibrinogen antibody. Fibrin deposition intensity in peritubular capillaries(PTC) and glomeruli was categorized as negative, weak, moderate or strong and the number of microthrombi/mm(2) was quantified. Reperfusion biopsies showed more fibrin deposition (20% to 100% moderate/strong, p < 0.001) and more microthrombi/mm(2) (0.97 ± 1.12 vs. 0.28 ± 0.53, p < 0.01) than preimplantation biopsies. In addition, more microthrombi/mm(2) (0.38 ± 0.61 vs. 0.09 ± 0.22, p = 0.02) and stronger fibrin intensity in glomeruli (28% vs. 0%, p < 0.01) and PTC (14% vs. 0%, p = 0.02) were observed in preimplantation DDK than LDK biopsies. After reperfusion, microthrombi/mm(2) were comparable (p = 0.23) for LDK (0.09 ± 0.22 to 0.76 ± 0.49, p = 0.03) and DDK (0.38 ± 0.61 to 0.90 ± 1.11, p = 0.07). Upon reperfusion, there is an aggravation of microthrombus formation and fibrin deposition within the graft. The prominent increase of microthrombi in LDK indicates that they are not merely donor-derived