InVADo: Interactive Visual Analysis of Molecular Docking Data.

Molecular docking is a key technique in various fields like structural biology, medicinal chemistry, and biotechnology. It is widely used for virtual screening during drug discovery, computer-assisted drug design, and protein engineering. A general molecular docking process consists of the target and ligand selection, their preparation, and the docking process itself, followed by the evaluation of the results. However, the most commonly used docking software provides no or very basic evaluation possibilities. Scripting and external molecular viewers are often used, which are not designed for an efficient analysis of docking results. Therefore, we developed InVADo, a comprehensive interactive visual analysis tool for large docking data. It consists of multiple linked 2D and 3D views. It filters and spatially clusters the data, and enriches it with post-docking analysis results of protein-ligand interactions and functional groups, to enable well-founded decision-making. In an exemplary case study, domain experts confirmed that InVADo facilitates and accelerates the analysis workflow. They rated it as a convenient, comprehensive, and feature-rich tool, especially useful for virtual screening.

Haplotype sequence collection of ABO blood group alleles by long-read sequencing reveals putative A1-diagnostic variants.

In the era of blood group genomics, reference collections of complete and fully resolved blood group gene alleles have gained high importance. For most blood groups, however, such collections are currently lacking, as resolving full-length gene sequences as haplotypes (ie, separated maternal/paternal origin) remains exceedingly difficult with both Sanger and short-read next-generation sequencing. Using the latest third-generation long-read sequencing, we generated a collection of fully resolved sequences for all 6 main ABO allele groups: ABO∗A1/A2/B/O.01.01/O.01.02/O.02. We selected 77 samples from an ABO genotype data set (n = 25 200) of serologically typed Swiss blood donors. The entire ABO gene was amplified in 2 overlapping long-range polymerase chain reactions (covering ∼23.6 kb) and sequenced by long-read Oxford Nanopore sequencing. For quality validation, 2 samples per ABO group were resequenced using Illumina and Pacific Biosciences technology. All 154 full-length ABO sequences were resolved as haplotypes. We observed novel, distinct sequence patterns for each ABO group. Most genetic diversity was found between, not within, ABO groups. Phylogenetic tree and haplotype network analyses highlighted distinct clades of each ABO group. Strikingly, our data uncovered 4 genetic variants putatively specific for ABO∗A1, for which direct diagnostic targets are currently lacking. We validated A1-diagnostic potential using whole-genome data (n = 4872) of a multiethnic cohort. Overall, our sequencing strategy proved powerful for producing high-quality ABO haplotypes and holds promise for generating similar collections for other blood groups. The publicly available collection of 154 haplotypes will serve as a valuable resource for molecular analyses of ABO, as well as studies about the function and evolutionary history of ABO.

HLA-DRB1*15:01 is a co-receptor for Epstein-Barr virus, linking genetic and environmental risk factors for multiple sclerosis.

The strongest genetic and environmental risk factors for MS, an inflammatory CNS disease, are HLA-DRB1*15:01 and EBV. This work shows that HLA-DRB1*15:01 acts as a co-receptor for EBV infection of a B cell line, suggesting a mechanistic link between both risk factors for MS.

Donor-specific alloreactive T cells can be quantified from whole blood, and may predict cellular rejection after renal transplantation.

Preformed cellular alloreactivity can exist prior to transplantation and may contribute to rejection. Here, we used a rapid flow-cytometric whole-blood assay to characterize the extent of alloreactive T cells among 1491 stimulatory reactions from 61 renal transplant candidates and 75 controls. The role of preformed donor-specific alloreactive T cells in cellular rejection was prospectively analyzed in 21 renal transplant recipients. Alloreactive CD8+ T cells were more frequent than respective CD4+ T cells, and these levels were stable over time. CD8+ T cells were effector-memory T cells largely negative for expression of CD27, CD62L, and CCR7, and were susceptible to steroid and calcineurin inhibitor inhibition. Alloreactivity was more frequent in samples with higher number of HLA mismatches. Moreover, the percentage of individuals with alloreactive T cells was higher in transplant candidates than in controls. Among transplant candidates, 5/61 exhibited alloreactive CD8+ T cells against most stimulators, 23/61 toward a limited number of stimulators, and 33/61 did not show any alloreactivity. Among 21 renal transplant recipients followed prospectively, one had donor-specific preformed T-cell alloreactivity. She was the only patient who developed cellular rejection posttransplantation. In conclusion, donor-specific alloreactive T cells may be rapidly quantified from whole blood, and may predict cellular rejection after transplantation.

Slovenia: health system review

The Health Systems in Transition (HiT) profiles are country-based reports that provide a detailed description of a health system and of policyinitiatives in progress or under development. HiTs examine different approaches to the organization, financing and delivery of health services and therole of the main actors in health systems; describe the institutional framework, process, content and implementation of health and health care policies; and highlight challenges and areas that require more in-depth analysis. Life expectancy in Slovenia has improved since 1993, reaching 78.5 years in 2007. This value is comparable to those of other European Union (EU) Member States (those belonging to the EU prior to 2004, plus those joining the EU on 1 May 2004 (EU25)), but slightly below the average of the EU MemberStates before the enlargement of May 2004 (EU15) and significantly above the respective average value of the countries that joined the EU in May 2004 and January 2007 (EU12). Health care services in Slovenia are financed mainly bycontributions to compulsory health insurance, premiums for voluntary health insurance (VHI) and through taxes. Although entitlement to health care services is universal in Slovenia, access to some health care services is limited due to lack of providers (for example, dental care) or long waiting times (for example, for certain operations). Health care services at the primary level are provided mainly by state-owned primary health care institutions as well as by independent general practitioners (GPs). Providers of primary health care act as gatekeepers for specialist services. Slovenia’s health care system has undergone major changes since the countryachieved independence in 1991. This momentum of constant change was retained during the period from 2002 to 2007 and was based on a white paper published by the Ministry of Health and on the World Bank project “A Management Model or Health Care”. Reform policy during this period included, inter alia, reform of health care financing (for example, payment for hospital services is now based on diagnosis-related groups (DRGs)); introduction of clinical guidelines by the Ministry of Health to increase quality of health care; cancellation of compulsory insurance (Health Insurance Institute of Slovenia (HIIS)) debts; and subsequent introduction of a convergence programme to limit HIIS expenditure. Furthermore, a risk-equalization scheme for VHI was introduced in 2005, which aims to reduce cream-skimming between voluntary health insurers and to equalize the variations in risk structure between private health insurance companies.

Latvia: health system review

The Health Systems in Transition (HiT) profiles are country-based reports that provide a detailed description of a health system and of policyinitiatives in progress or under development. HiTs examine different approaches to the organization, financing and delivery of health services and therole of the main actors in health systems; describe the institutional framework, process, content and implementation of health and health care policies; and highlight challenges and areas that require more in-depth analysis. The life expectancy in Latvia has improved over the last two decades and was 71.1 years in 2005. This value is comparable to those in other eastern Europeanand former Soviet Union countries but is the lowest among the Baltic and Nordic countries. Health care services in Latvia are financed mainly by taxation through the state budget as well as by out-of-pocket (OOP) payments, voluntary healthinsurance (VHI) and other direct payments. Although entitlement to health care services is universal in Latvia, equity in access to services is compromised due to high levels of OOP payments by consumers. Health care services at the primary level are provided mainly by general practitioners (GP) who work independently and act as gatekeeper for specialized services. Latvia’s health care system has undergone major changes since the country achieved independence in 1991. Reform policy since then has included amongst others: adoption of a Public Health Strategy in 2001 (which aims at developingan integrated approach of prevention and treatment at all levels of the health care system), reform of health care financing (e.g. payment for hospital services, introduction of a primary health care payment system based on capitation and fund holding, pooling and channelling of almost all funds for health care through the centralized State Compulsory Health Insurance Agency (SCHIA)), regulations of the pricing system for pharmaceuticals and introduction of a centralized health management information system. However, patients and health care consumers are concerned with regard to quality of the health careservices, long waiting lists and access to specialized care.

Evaluation of use of Epstein-Barr viral load in patients after allogeneic stem cell transplantation to diagnose and monitor posttransplant lymphoproliferative disease.

Epstein-Barr virus (EBV)-induced posttransplant lymphoproliferative disease (PTLD) continues to be a serious complication following transplantation. The aim of the present study was to evaluate the EBV load as a parameter for the prediction and monitoring of PTLD. The EBV load was analyzed by a quantitative competitive PCR with 417 whole-blood samples of 59 patients after allogeneic stem cell transplantation (SCT). The EBV load was positive for all 9 patients with PTLD and for 17 patients without PTLD. The viral loads of patients with manifest PTLD differed from the loads of those without PTLD (median loads, 1.4 x 10(6) versus 4 x 10(4) copies/microg of DNA; P < 0.0001). A threshold value of 10(5) copies/microg of DNA showed the best diagnostic efficacy (sensitivity, 87%; specificity, 91%). However, in patients with less than three major risk factors for PTLD, the positive predictive value of this threshold was rather low. One week prior to the manifestation of PTLD, the EBV load was as low in patients who developed PTLD as in patients without disease (median, 2.2 x 10(4) copies/microg of DNA; P was not significant). EBV DNA tested positive first at 20 to 71 days prior to the clinical manifestation of PTLD and occurred with the same delay after transplantation regardless of disease (median delay, 52 versus 63 days; P was not significant). EBV DNA was detected earlier in patients with primary infections than in those with reactivations (33 versus 79 days; P = 0.01), but the peak levels were similar in the two groups. EBV primary infection or EBV reactivation is frequent in patients after allogeneic SCT but results in PTLD only in a subgroup of patients. Although evaluation of the EBV load has limitations, the EBV load represents a valuable parameter to guide therapy.