ForMAX - a beamline for multiscale and multimodal structural characterization of hierarchical materials.

The ForMAX beamline at the MAX IV Laboratory provides multiscale and multimodal structural characterization of hierarchical materials in the nanometre to millimetre range by combining small- and wide-angle X-ray scattering with full-field microtomography. The modular design of the beamline is optimized for easy switching between different experimental modalities. The beamline has a special focus on the development of novel fibrous materials from forest resources, but it is also well suited for studies within, for example, food science and biomedical research.

What is the ecotoxicity of a given chemical for a given aquatic species? Predicting interactions between species and chemicals using recommender system techniques.

Ecotoxicological safety assessment of chemicals requires toxicity data on multiple species, despite the general desire of minimizing animal testing. Predictive models, specifically machine learning (ML) methods, are one of the tools capable of solving this apparent contradiction as they allow to generalize toxicity patterns across chemicals and species. However, despite the availability of large public toxicity datasets, the data is highly sparse, complicating model development. The aim of this study is to provide insights into how ML can predict toxicity using a large but sparse dataset. We developed models to predict LC50-values, based on experimental LC50-data covering 2431 organic chemicals and 1506 aquatic species from the ECOTOX-database. Several well-known ML techniques were evaluated and a new ML model was developed, inspired by recommender systems. This new model involves a simple linear model that learns low-rank interactions between species and chemicals using factorization machines. We evaluated the predictive performances of the developed models based on two validation settings: 1) predicting unseen chemical-species pairs, and 2) predicting unseen chemicals. The results of this study show that ML models can accurately predict LC50-values in both validation settings. Moreover, we show that the novel factorization machine approach can match well-tuned, complex, ML approaches.

Specific antibody deficiency in children with recurrent respiratory infections: a controlled study with follow-up.

Specific antibody deficiency (SAD) to unconjugated pneumococcal vaccine (PPV) is an established primary B cell immunodeficiency. The occurrence and natural history of SAD in children is unclear. We conducted an observational study to identify SAD in children with recurrent respiratory infections. Ninety-nine children, mean age 5·9 (range 2-16) years, with recurrent or severe infections were vaccinated with PPV; serum antibody concentrations for serotypes 4, 6B, 9V, 14, 18C, 19F and 23F were measured before and 2 weeks after vaccination with enzyme immunoassay. The retrospective control group consisted of 89 healthy children matched for age and gender. No children had received previous conjugated pneumococcal vaccine (PCV) or PPV. The structured history of infectious diseases of all participants was collected. Ten of 91 (11%) children (eight excluded due to immunoglobulin G subclass deficiency) with recurrent respiratory infections had SAD. In the control group, three children (3%) responded inadequately to PPV (P = 0·05). Most children with SAD also had many other minor immune defects. After 0·5-5 years (medium 3·8), eight children with SAD were revaccinated with PPV; five responded adequately and three inadequately. Two SAD children were revaccinated with PCV, one developed an adequate and one an inadequate response. Two children with SAD received treatment with intravenous immunoglobulin; the remaining eight children recovered without replacement therapy during the follow-up. SAD is common in young children with recurrent respiratory infections, but it is often transient and resolves itself within a few years without specific treatment.

Epidemiological aspects of viral haemorrhagic septicaemia virus genotype II isolated from Baltic herring, Clupea harengus membras L.

This study was carried out to clarify the role of wild fish, especially Baltic herring, Clupea harengus membras L., in the epidemiology of viral haemorrhagic septicaemia virus (VHSV) in brackish water in Finland. Baltic herring with no visible signs of disease were collected from the Archipelago Sea, the Gulf of Bothnia and the eastern Gulf of Finland. In total, 7580 herring were examined by virus isolation as 758 pooled samples and 3029 wild salmonid broodfish as pooled samples during 2004-2006. VHSV was isolated from 51 pooled herring samples in bluegill fibroblast-2 cells, but not in epithelioma papulosum cyprini cells. The majority of isolations were from the coastal archipelago and from fish caught during the spawning season. Based on glycoprotein (G) gene sequences, the virus was classified as a member of genotype II of VHSV. Pairwise comparisons of the G gene regions of herring isolates revealed that all the isolates were closely related, with 98.8-100% nucleotide homology. Phylogenetic analyses revealed that they were closely related to the strains isolated previously from herring and sprat, Sprattus sprattus (L.), in Gotland and to the VHSV isolates from European river lamprey, Lampetra fluviatilis (L.), in the rivers that flow into the Bothnian Bay. The infection in Baltic herring is likely to be independent of the VHSV Id epidemic in farmed rainbow trout, Oncorhynchus mykiss (Walbaum).

Extremely high prevalence of multidrug resistant tuberculosis in Murmansk, Russia: a population-based study.

Drug resistance and molecular epidemiology of tuberculosis (TB) in the Murmansk region was investigated in a 2-year, population-based surveillance of the civilian population. During 2003 and 2004, isolates from all culture-positive cases were collected (n = 1,226). Prevalence of multi-drug resistance (MDR) was extremely high, as 114 out of 439 new cases (26.0%), and 574 out of 787 previously treated cases (72.9%) were resistant to at least isoniazid (INH) and rifampin (RIF). Spoligotyping of the primary MDR-TB isolates revealed that most isolates grouped to the Beijing SIT1 genotype (n = 91, 79.8%). Isolates of this genotype were further analyzed by IS6110 RFLP. Sequencing of gene targets associated with INH and RIF resistance further showed that the MDR-TB strains are highly homogeneous as 78% of the MDR, SIT1 strains had the same resistance-conferring mutations. The genetic homogeneity of the MDR-TB strains indicates that they are actively transmitted in Murmansk.

First encounter of European bat lyssavirus type 2 (EBLV-2) in a bat in Finland.

In Finland, rabies in bats was suspected for the first time in 1985 when a bat researcher, who had multiple bat bites, died in Helsinki. The virus isolated from the researcher proved to be antigenically related to rabies viruses previously detected in German bats. Later, the virus was typed as EBLV-2b. Despite an epidemiological study in bats 1986 and subsequent rabies surveillance, rabies in bats was not detected in Finland until the first case in a Daubenton's bat (Myotis daubentonii) was confirmed in August 2009. The bat was paralysed, occasionally crying, and biting when approached; it subsequently tested positive for rabies. The virus was genetically typed as EBLV-2. This is the northernmost case of bat rabies ever detected in Europe. Phylogenetic analyses showed that the EBLV-2b isolate from the human case in 1985 and the isolate from the bat in 2009 were genetically closely related, demonstrating that EBLV-2 may have been circulating in Finland for many years.

Rabies control in Finland: a 12-year experience of human and veterinary surveillance.

Little is known about the public health burden of rabies in rabies-free countries. In these countries, the surveillance of suspected and treated cases serves as a substitute for estimating the risk and burden of human rabies because deaths due to rabies are extremely rare. Suspected rabies exposures among Finnish inhabitants were characterized using data from the National Infectious Disease Registry as well as animal surveillance data from the Finnish Food Safety Authority Evira, 1995-2006. In total, 195 suspected rabies exposures were reported (incidence 3/million inhabitants/year). Exposures were equally common among both genders and the median age was 35 years. Exposures were more common among 20- to 49-year olds than among other age groups. Less than one-third of the exposures occurred in Finland (incidence of indigenous exposures 0.9/million inhabitants/year). Indigenous rabies exposures were most frequently reported in southeastern Finland, with cats and dogs as the main sources. The high prevalence in the Baltic countries and Russia poses a risk for rabies reintroduction. The present control of wildlife rabies appears successful and important. The import of animals from endemic areas, however, remains a risk, which can be reduced by increasing public awareness of the disease, vaccination of imported animals and better rabies control in endemic countries.

Borreliosis: recent research, diagnosis, and management.

Lyme borreliosis (LB) is a tick-borne infection caused by the spirochete Borrelia burgdorferi sensu lato. The disease covers a wide spectrum of clinical manifestations affecting the skin, nervous and musculoskeletal systems, the heart, and the eyes. The diagnosis must be based on clinical suspicion and on symptoms and signs observed during a thorough interview and examination of the patient. Laboratory results either support or oppose the conclusions that are drawn from history and clinical examination. Antibiotic therapy is curative in most patients with LB. Unfortunately, some patients develop chronic symptoms, such as arthritis, that do not respond to antibiotics. In these patients, treatment with non-steroidal anti-inflammatory drugs or corticosteroids is recommended, while the role of immunomodulatory drugs, such as tumour necrosis factor (TNF)-alpha inhibitors, remains open. In this review we focus, after presenting the history and basics of LB, on the pathogenesis, diagnosis, and treatment of LB, as well as on recent advances in selected aspects of the field.

Duration of antibiotic treatment in disseminated Lyme borreliosis: a double-blind, randomized, placebo-controlled, multicenter clinical study.

Despite rather strict recommendations for antibiotic treatment of disseminated Lyme borreliosis (LB), evidence-based studies on the duration of antibiotic treatment are scarce. The aim of this multicenter study was to determine whether initial treatment with intravenous ceftriaxone (CRO) for 3 weeks should be extended with a period of adjunct oral antibiotic therapy. A total of 152 consecutive patients with LB were randomized in a double-blind fashion to receive either amoxicillin (AMOX) 1 g or placebo (PBO) twice daily for 100 days. Both groups received an initial treatment of intravenous CRO 2 g daily for 3 weeks, followed by the randomized drug or PBO. The outcome was evaluated using the visual analogue scale at the follow-up visits. The final analysis included 145 patients, of whom 73 received AMOX and 72 PBO. Diagnoses of LB were categorized as either definite or possible, on the basis of symptoms, signs, and laboratory results. The diagnosis was definite in 52 of the 73 (71.2%) AMOX-treated patients and in 54 of the 72 (75%) PBO patients. Of the patients with definite diagnoses, 62 had neuroborreliosis, 45 arthritis or other musculoskeletal manifestations, and 4 other manifestations of LB. As judged by the visual analogue scale and patient records, the outcome after a 1-year follow-up period was excellent or good in 114 (78.6%) patients, controversial in 14 (9.7%) patients, and poor in 17 (11.7%) patients. In patients with definite LB, the outcome was excellent or good in 49 (92.5%) AMOX-treated patients and 47 (87.0%) PBO patients and poor in 3 (5.7%) AMOX-treated patients and 6 (11.1%) PBO patients (difference nonsignificant, p = 0.49). Twelve months after the end of intravenous antibiotic therapy, the levels of antibodies against Borrelia burgdorferi were markedly decreased in 50% of the patients with definite LB in both groups. The results indicate that oral adjunct antibiotics are not justified in the treatment of patients with disseminated LB who initially receive intravenous CRO for 3 weeks. The clinical outcome cannot be evaluated at the completion of intravenous antibiotic treatment but rather 6-12 months afterwards. In patients with chronic post-treatment symptoms, persistent positive levels of antibodies do not seem to provide any useful information for further care of the patient.

25-Hydroxyvitamin D levels in serum at the onset of multiple sclerosis.

Past sun exposure and vitamin D supplementation have been associated with a reduction in the risk of MS. We measured the serum concentration of 25-hydroxyvitamin D (25[OH]D) at the time of MS diagnosis in 40 MS patients and 40 controls. We found no difference in the serum levels of 25(OH)D between MS patients and controls when all samples or samples obtained during winter months were compared, but MS patients had significantly lower serum 25(OH)D concentrations in June to September than the controls. The vitamin D stores were adequate for bone metabolism (> 37 nmol/L) in 70% of MS patients throughout the year and within the hypovitaminosis level (< 37 nmol/L) in 30% of MS patients at some time of the year. During MS-relapses, 25(OH)D levels were lower than in remission, but mostly within the reference range observed in relation with normal bone metabolism. We conclude that the vitamin D stores in most MS patients are adequate for their normal bone metabolism. However, lower vitamin D levels during MS relapses than in remission suggest that vitamin D could be involved in the regulation of the clinical disease activity of MS. The optimal serum levels of vitamin D for the regulation of immune responses remain to be determined.

Probiotics in the treatment of atopic eczema/dermatitis syndrome in infants: a double-blind placebo-controlled trial.

BACKGROUND: Probiotic bacteria are suggested to reduce symptoms of the atopic eczema/dermatitis syndrome (AEDS) in food-allergic infants. We aimed to investigate whether probiotic bacteria have any beneficial effect on AEDS. METHODS: Follow-up of severity of AEDS by the Severity Scoring of Atopic Dermatitis (SCORAD) index in 230 infants with suspected cow's milk allergy (CMA) receiving, in a randomized double-blinded manner, concomitant with elimination diet and skin treatment, Lactobacillus GG (LGG), a mixture of four probiotic strains, or placebo for 4 weeks. Four weeks after the treatment, CMA was diagnosed with a double-blind placebo-controlled (DBPC) milk challenge in 120 infants. RESULTS: In the whole group, mean SCORAD (at baseline 32.5) decreased by 65%, but with no differences between treatment groups immediately or 4 weeks after the treatment. No treatment differences were observed in infants with CMA either. In IgE-sensitized infants, however, the LGG group showed a greater reduction in SCORAD than did the placebo group, -26.1 vs-19.8 (P=0.036), from baseline to 4 weeks after the treatment. Exclusion of infants who had received antibiotics during the study reinforced the findings in the IgE-sensitized subgroup. CONCLUSION: Treatment with LGG may alleviate AEDS symptoms in IgE-sensitized infants but not in non-IgE-sensitized infants.

Prospective evaluation of the GenoType assay for routine identification of mycobacteria.

In order to evaluate the proficiency of the GenoType Mycobacteria strip hybridization assay (Hain Lifescience, Nehren, Germany) for the routine identification of mycobacteria, the assay was used to identify 178 clinical isolates during a 6-month prospective study. The GenoType results were compared to the identification results obtained with AccuProbe (GenProbe, San Diego, CA, USA) or 16S rDNA sequencing, and an overall agreement of 89.3% between GenoType and the two reference methods was reached. The GenoType assay is, thus, a rapid and reliable method for the identification of clinically important mycobacteria, and it is well suited for use in a routine laboratory.

Application of Bacillus anthracis PCR to simulated clinical samples.

We evaluated PCR for the detection of Bacillus anthracis DNA from simulated clinical specimens relevant for the microbiological diagnosis of anthrax or exposure to B. anthracis spores. In simulated blood specimens, the lowest limit of detection was 400 CFU per mL of blood, which may be sufficient for samples from patients with septic anthrax. Screening nasal swabs by PCR may not be sensitive enough to rule out dangerous exposure to anthrax spores, as a minimum of 2000 spores per sample was required for detectable amplification. As spores survived some standard DNA purification methods, special attention should be paid to laboratory safety when preparing samples possibly containing live spores.

Performance of BACTEC 960 Mycobacteria growth indicator tube in the susceptibility testing of genetically characterized Mycobacterium tuberculosis isolates.

In this study, the 7H10 agar proportion method was compared with the BACTEC TB-460 and BACTEC MGIT 960 systems (BD Biosciences, USA) for the susceptibility testing of 22 genetically characterized Mycobacterium tuberculosis isolates for isoniazid, rifampin, streptomycin, and ethambutol. The 7H10 agar proportion method agreed with the resistant genotype in 87.3%, BACTEC TB-460 in 92.7%, and the MGIT in 96.4% of the cases, showing the high sensitivity of MGIT in the detection of resistant isolates.

Interaction between Borrelia burgdorferi and immature human dendritic cells.

Antigen uptake and the following maturation of dendritic cells (DCs) are pivotal to the initiation of specific antimicrobial immune responses. DCs also play an important role in the recruitment and activation of the cells of the innate immune system. We have examined the interactions of DCs with Borrelia burgdorferi to find explanations for the difficulties the human immune system has in dealing with the bacterium. Phagocytosis of B. burgdorferi by immature DCs and the effect of the bacterium on the maturation and interleukin-8 (IL-8) secretion of DCs were studied. Borreliae were phagocytized and processed into fragments by DCs; narrow tube-like pseudopods and broad pseudopods were used for the engulfment. The immature DC population gained a heterogeneous appearance within 2 h of incubation with the borreliae. A 24 h coculture with borreliae induced maturation and IL-8 secretion in the DCs in a manner comparable with the effect of lipopolysaccharides. All strains studied, including a mutant strain lacking outer surface proteins A and B, were capable of inducing these responses. Thus, our results did not show any clear inadequacy concerning the way DCs are dealing with B. burgdorferi. However, further studies on the subject are required.

Sublethal concentrations of complement can effectively opsonize Borrelia burgdorferi.

The fate of borreliae invading a human may depend on the early innate response they induce. The interactions of human complement system and neutrophils with two strains of the Lyme borreliosis spirochete Borrelia burgdorferi were studied. Borrelia burgdorferi sensu stricto B31 (resistant to a 28% concentration of normal human serum (NHS)) and Borrelia garinii Bg A218/98 (sensitive to 7% NHS) were examined. Both strains induced neutrophil oxidative burst in a complement-dependent manner. B31 required the presence of 7% NHS, but Bg A218/98 required the presence of only 0.7% NHS for optimal induction of the burst. At all concentrations of NHS, the proportion of the spirochetes with C3bi on their surfaces and the relative amount of C3bi bound per spirochete were larger with Bg A218/98 than with B31. Bg A218/98 was able to induce an oxidative burst, when provided with serum with blocked classical pathway of complement, whereas B31 required the presence of the classical pathway. We suggest a role for the opsonizing effect of complement in controlling borreliae that are either resistant to direct killing by complement or located in the compartments of the human body at sublethal concentrations of the same.

Rapid identification of Bordetella pertussis pertactin gene variants using LightCycler real-time polymerase chain reaction combined with melting curve analysis and gel electrophoresis.

Recently, eight allelic variants of the pertactin gene (prn1-8) have been characterized in Bordetella pertussis strains isolated in Europe and the United States. It has been suggested that the divergence of the pertactin types of clinical isolates from those of the B. pertussis vaccine strains is a result of vaccine-driven evolution. Sequencing of the prn, which is relatively time-consuming, has so far been the only method for the differentiation of prn types. We have developed a rapid real-time polymerase chain reaction assay suitable for large-scale screening of the prn type of the circulating strains. This method correctly identified the prn type of all tested 41 clinical isolates and two Finnish vaccine strains. The method is simple and reliable and provides an alternative for sequencing in pertussis research.

Characterization of the adhesin of Escherichia coli F18 fimbriae.

Previous research has suggested that the adhesin encoded by the F18 fimbrial operon in Escherichia coli is either the FedE or FedF protein. In this work, we show that anti-FedF antibodies, unlike anti-FedE serum, were able to inhibit E. coli adhesion to porcine enterocytes. Moreover, specific adhesion to enterocytes was shown with purified FedF-maltose binding protein.

Complement evasion by Borrelia burgdorferi: serum-resistant strains promote C3b inactivation.

The most characteristic features of the Lyme disease pathogens, the Borrelia burgdorferi sensu lato (s.l.) group, are their ability to invade tissues and to circumvent the immune defenses of the host for extended periods of time, despite elevated levels of borrelia-specific antibodies in serum and other body fluids. Our aim in the present study was to determine whether B. burgdorferi is able to interfere with complement (C) at the level of C3 by accelerating C3b inactivation and thus to inhibit the amplification of the C cascade. Strains belonging to different genospecies (Borrelia garinii, B. burgdorferi sensu stricto, and Borrelia afzelii) were compared for their sensitivities to normal human serum and abilities to promote factor I-mediated C3b degradation. B. burgdorferi sensu stricto and B. afzelii strains were found to be serum resistant. When the spirochetes were incubated with radiolabeled C3b, factor I-mediated degradation of C3b was observed in the presence of C-resistant B. afzelii (n = 3) and B. burgdorferi sensu stricto (n = 1) strains but not in the presence of C-sensitive B. garinii (n = 7) strains or control bacteria (Escherichia coli, Staphylococcus aureus, and Enterococcus faecalis). Immunoblotting and radioligand binding analyses showed that the C-resistant strains had the capacity to acquire the C inhibitors factor H and factor H-like protein 1 (FHL-1) from growth medium and human serum. A novel surface protein with an apparent molecular mass of 35 kDa was found to preferentially bind to the N terminus region of factor H. Thus, the serum-resistant B. burgdorferi s.l. strains can circumvent C attack by binding the C inhibitors factor H and FHL-1 to their surfaces and promoting factor I-mediated C3b degradation.

LCx Mycobacterium tuberculosis assay is valuable with respiratory specimens, but provides little help in the diagnosis of extrapulmonary tuberculosis.

BACKGROUND: Commercial nucleic acid amplification tests, designed for the detection of Mycobacterium tuberculosis DNA/RNA in respiratory samples, are often applied also in nonrespiratory specimens in order to verify the diagnosis of extrapulmonary tuberculosis. AIM. To evaluate the value of the Abbott LCx Mycobacterium tuberculosis assay for the diagnosis of pulmonary and extrapulmonary tuberculosis based on routine clinical laboratory results. METHODS: The assay was used to analyse 350 respiratory and 826 nonrespiratory specimens from 961 patients, of whom 3.6% had culture-proven tuberculosis. The results obtained by the LCx assay were compared with the records on mycobacterial isolates of the national reference laboratory and, in the case of positive findings, with clinical data. RESULTS: In comparison with culture, the sensitivity, specificity and positive/negative predictive value of the assay on respiratory specimens were 87.5%, 99.7%, 93.3% and 99.4%, respectively. With nonrespiratory specimens, the overall sensitivity, specificity and positive/negative predictive value of the LCx assay were 73.3%, 98.0%, 40.7% and 99.5%, respectively. When clinical and histological data were also included, the positive predictive value of LCx with nonrespiratory specimens was 45.8%. CONCLUSION: Critical interpretation of the nucleic acid amplification results obtained from nonrespiratory specimens is necessary in both laboratory and clinical settings.