Correcting for heterogeneity and non-comparability bias in multicenter clinical trials with a rescaled random-effect excess hazard model.

In the presence of competing causes of event occurrence (e.g., death), the interest might not only be in the overall survival but also in the so-called net survival, that is, the hypothetical survival that would be observed if the disease under study were the only possible cause of death. Net survival estimation is commonly based on the excess hazard approach in which the hazard rate of individuals is assumed to be the sum of a disease-specific and expected hazard rate, supposed to be correctly approximated by the mortality rates obtained from general population life tables. However, this assumption might not be realistic if the study participants are not comparable with the general population. Also, the hierarchical structure of the data can induces a correlation between the outcomes of individuals coming from the same clusters (e.g., hospital, registry). We proposed an excess hazard model that corrects simultaneously for these two sources of bias, instead of dealing with them independently as before. We assessed the performance of this new model and compared it with three similar models, using extensive simulation study, as well as an application to breast cancer data from a multicenter clinical trial. The new model performed better than the others in terms of bias, root mean square error, and empirical coverage rate. The proposed approach might be useful to account simultaneously for the hierarchical structure of the data and the non-comparability bias in studies such as long-term multicenter clinical trials, when there is interest in the estimation of net survival.

Bacterial community dynamics during industrial malting, with an emphasis on lactic acid bacteria.

Characterization of the microflora during malting is an essential step towards process management and optimization. Up till now, however, microbial characterization in the malting process has mostly been done using culture-dependent methods, probably leading to biased estimates of microbial diversity. The aim of this study was to characterize the bacterial communities using two culture-independent methods, including Terminal Restriction Fragment Length Polymorphism (T-RFLP) and 454 pyrosequencing, targeting the 16S rRNA gene. Studied samples originated from two harvest years and two malting houses malting the same batch of barley. Besides targeting the entire bacterial community (T-RFLP), emphasis was put on lactic acid bacteria (LAB) (T-RFLP and 454 pyrosequencing). The overall bacterial community richness was limited, but the community structure changed during the process. Zooming in on the LAB community using 454 pyrosequencing revealed a total of 47 species-level operational taxonomic units (OTUs). LAB diversity appeared relatively limited since 88% of the sequences were covered by the same five OTUs (representing members of Weissella, Lactobacillus and Leuconostoc) present in all samples investigated. Fluctuations in the relative abundances of the dominant LAB were observed with the process conditions. In addition, both the year of harvest and malting house influenced the LAB community structure.

Collider-independent tt forward-backward asymmetries.

We introduce the forward-backward asymmetries A(u), A(d) corresponding to uu, dd → tt production, respectively, at hadron colliders. These are collider and center-of-mass independent observables, directly related to the forward-backward and charge asymmetries measured at the Tevatron and the LHC, respectively. We discuss how to extract these asymmetries from data. Because these asymmetries are collider independent, their measurement at these two colliders could elucidate the nature of the anomalous forward-backward asymmetry measured at the Tevatron. Our framework also shows in a model independent fashion that a positive Tevatron asymmetry exceeding the standard model expectation is compatible with the small asymmetry measured at the LHC.

Characterization of Tetragenococcus strains from sugar thick juice reveals a novel species, Tetragenococcus osmophilus sp. nov., and divides Tetragenococcus halophilus into two subspecies, T. halophilus subsp. halophilus subsp. nov. and T. halophilus subsp. flandriensis subsp. nov.

Most bacteria recovered so far from sugar thick juice during storage represent strains of the species Tetragenococcus halophilus. Recently, several Gram-positive, non-motile, non-spore-forming cocci with other physiological and genetic traits were isolated from sugar thick juice samples from different origins. In this study, representative isolates were investigated using a polyphasic taxonomic approach. The 16S rRNA gene sequence similarity between these isolates and their closest relative, Tetragenococcus muriaticus, was 97.4%. The level of DNA-DNA relatedness between isolate T1(T), representing the newly found Tetragenococcus isolates, and T. muriaticus was 57%. Isolate T1(T) had a DNA G+C content of 36.7 mol%. Phylogenetic data and genomic and phenotypic features demonstrated that the isolates represent a novel species, for which the name Tetragenococcus osmophilus sp. nov. is proposed with T1(T) as the type strain (=LMG 26041(T) =DSM 23765(T)). Additionally, T. halophilus isolates from high-salt and high-sugar environments showed clear differences in several physiological and genetic characteristics like RAPD fingerprints and 16S rRNA gene sequences. DNA-DNA hybridizations, however, showed 79 to 80% relatedness between osmophilic and halophilic T. halophilus isolates, demonstrating that the different strains belong to the same species. Based on the phenotypic and genotypic differences observed, as well as the different origins of the strains and the industrial relevance of thick juice degradation, two subspecies of T. halophilus are described in this manuscript: T. halophilus subsp. halophilus subsp. nov. for the strains isolated from salt media and T. halophilus subsp. flandriensis subsp. nov. for the strains isolated from sugar-rich environments, which were first isolated in Flanders, Belgium. The type strains for the subspecies are IAM 1676(T) (=LMG 11490(T) =DSM 20339(T)) and T5(T) (=LMG 26042(T) =DSM 23766(T)), respectively.

Fungal plant pathogen detection in plant and soil samples using DNA macroarrays.

PCR-based DNA array technology is one of the most suitable techniques to detect and identify multiple pathogens in a single assay. Out of the different array platforms that currently exist, membrane-based DNA macroarrays are the most convenient for plant disease diagnosis because of low costs, great sensitivity, and modest equipment requirements. Here we describe a protocol for routine detection of plant pathogens using DNA macroarrays, i.e., from sampling to analysis of hybridization results. Diagnosis can be completed within 36 h after sample collection.

Rapid detection and identification of viral and bacterial fish pathogens using a DNA array-based multiplex assay.

Fish diseases can be caused by a variety of diverse organisms, including bacteria, fungi, viruses and protozoa, and pose a universal threat to the ornamental fish industry and aquaculture. The lack of rapid, accurate and reliable means by which fish pathogens can be detected and identified has been one of the main limitations in fish pathogen diagnosis and fish disease management and has consequently stimulated the search for alternative diagnostic techniques. Here, we describe a method based on multiplex and broad-range PCR amplification combined with DNA array hybridization for the simultaneous detection and identification of all cyprinid herpesviruses (CyHV-1, CyHV-2 and CyHV-3) and some of the most important fish pathogenic Flavobacterium species, including F. branchiophilum, F. columnare and F. psychrophilum. For virus identification, the DNA polymerase and helicase genes were targeted. For bacterial identification, the ribosomal RNA gene was used. The developed methodology permitted 100% specificity for the identification of the target species. Detection sensitivity was equivalent to 10 viral genomes or less than a picogram of bacterial DNA. The utility and power of the array for sensitive pathogen detection and identification in complex samples such as infected tissue is demonstrated in this study.

Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes.

In the last two decades major changes have occurred in how microbial ecologists study microbial communities. Limitations associated with traditional culture-based methods have pushed for the development of culture-independent techniques, which are primarily based on the analysis of nucleic acids. These methods are now increasingly applied in food microbiology as well. This review presents an overview of current community profiling techniques with their (potential) applications in food and food-related ecosystems. We critically assessed both the power and limitations of these techniques and present recent advances in the field of food microbiology attained by their application. It is unlikely that a single approach will be universally applicable for analyzing microbial communities in unknown matrices. However, when screening samples for well-defined species or functions, techniques such as DNA arrays and real-time PCR have the potential to overtake current culture-based methods. Most importantly, molecular methods will allow us to surpass our current culturing limitations, thus revealing the extent and importance of the 'non-culturable' microbial flora that occurs in food matrices and production.

Protective effect of hop beta-acids on microbial degradation of thick juice during storage.

AIMS: This study assessed the value of a commercial alkaline solution of hop beta-acids (HBA) for prevention of microbial degradation of thick juice, a concentrated intermediate product in the production of beet sugar. METHODS AND RESULTS: The antimicrobial effect of different concentrations of HBA against microbial degradation of thick juice was tested in a pilot-scale storage experiment. Chemical, biochemical and microbial parameters were monitored during thick juice storage. Thick juice degradation, indicated as a decrease in pH, was generally accompanied by an increase in the count of fastidious bacteria (FB) on Columbia Agar with Sheep Blood (CAwSB), which were mainly identified as Tetragenococcus halophilus. Addition of HBA delayed juice acidification and the development of FB in a concentration-dependent manner. The susceptibility of FB to HBA was determined by plating degraded thick juice (FB > 10(5) CFU ml(-1) on CAwSB plates with different concentrations of HBA (0-160 ppm). None of the HBA concentrations tested reduced the number of FB colonies formed, but increasing HBA concentrations extended the lag time of colony formation. CONCLUSIONS: HBA produce no measurable bactericidal effect, but retard the development of FB in thick juice. Moreover, HBA do not prevent the thick juice from deteriorating, but significantly delay its degradation. SIGNIFICANCE AND IMPACT OF THE STUDY: These results indicate that adding a commercially available HBA formulation can prolong the storage life of thick juice in the sugar industry, although degradation cannot be eliminated. Future research will focus on the detailed characterization of FB consistently isolated from degraded thick juice and on determining their role in thick juice degradation.

[Evolution of epilepsy in successive pregnancies]. / Evolución de la epilepsia en gestaciones sucesivas.

INTRODUCTION: Hormonal and metabolic factors related to pregnancy itself are considered to increase the likelihood of seizure recurrence. If so, we should expect a similar evolution of epilepsy in a subsequent pregnancy. We investigated differences in evolution of non-gestational epilepsy in each pregnancy of women suffering from epilepsy. METHODS: A prospective study was conducted in order to compare seizure frequency in two successive pregnancies of more than 36 weeks duration in 12 patients. Improvement/worsening is defined as a change of +/- 50 % in the number of seizures regarding that which occurred within the previous eleven months. RESULTS: Twelve epileptic women were studied during two subsequent pregnancies. Eight of them took the same antiepileptic treatment for both pregnancies and one took no antiepileptic drug. Three worsened in the first pregnancy and two in the second. Seven patients had the same seizure frequency during both pregnancies. The total plasma antiepileptic concentrations tended to decline with the same proportion in both pregnancies if the dose remained unchanged. We observed no differences in mean hormone plasma concentrations for each quarter, within subsequent pregnancies. CONCLUSION: Except for one case with drug-resistant epilepsy, we found that the reason for the discrepancy in the frequency of the seizure between two successive pregnancies in the same patient was a sharp or rapid change in antiepileptic drug dose or non-compliance. In well controlled epileptic women a consistent evolution of epilepsy should be expected in a subsequent pregnancy, if adequate treatment is maintained.

[Neurological involvement in systemic sclerosis]. / Manifestaciones neurológicas en la esclerosis sistémica.

INTRODUCTION: Systemic sclerosis (SS) is recognized as the connective tissue disease which less frequently presents neurological complications; in recent studies it is demonstrated, however, that neurological involvement in SS is more frequent of what it had been assumed. PATIENTS AND METHODS: Clinical neurological exploration was done in 26 patients with definitive SS; an electroneurogram was carried out in 23 cases in order to determine the prevalence of central neurological pathology and of peripheral neuropathy, to define its characteristics, and to investigate possible associations with clinical parameters and with autoimmunity. RESULTS: 23 cases (88%) were females and 3 cases (12%) males; the median age was 57.5 12.0 (SD) years, while the median age to the diagnosis was 51.3 12.3 (SD) years and the median period of natural history of disease was 6.2 3.1 years. Seven patients (26.9%) showed involvement of the CNS, being the headache and the neuropsychiatric manifestations the most common conditions (11.5%). Peripheral neuropathy prevalence was 39.1% (9 cases); according to the distribution of the injury, the polyneuropathy prevailed in 30.4% of cases. With regard to the functional selectivity, the sensitive-motor forms were most frequent (55.6%); according to the most involved structure, the axonal neuropathy was most common (44.4%).Discussion. The possible pathogenic mechanisms of the neurological pathology in this disease are discussed.

[Preventive prophylactic treatment in posttraumatic epilepsy]. / Tratamiento preventivo-profiláctico de la epilepsia postraumática.

Posttraumatic epilepsy (PTE) represents about 2 3% of all the etiologies of epilepsy. The so called early seizures , which appear in the first week after the traumatic brain injury (TBI), are related to the severity of the injury; they do not have an strictly epileptic mechanism, but they become a risk factor to the development of PTE. PTE appears in 5% of all the patients suffering from all TBI, and in 15 20% of the patients suffering from a severe TBI. However, the endpoint uses to be to use antiepileptic drugs (AEDs) as prophylactic treatment in all well established PTE. The efficacy of classic antiepileptic drugs (Phenobarbital, Phenytoin, Carbamazepine, Valproate acid) to control the kindling effect has not been confirmed yet as a prophylactic treatment for PTE. Prophylactic efficacy of other drugs, like lipid peroxidation inhibitors, neuroprotectors (especially antioxidants), glutamic receptor blockers, NMDA receptor blockers, and drugs that modulate apoptosis via caspasas inhibition; however, they constitute new ways of therapeutic investigation with a strong experimental basis. Our recommended therapeutic strategy is not to administrate AEDs indiscriminately, but analyzing risk factors, designing a careful prevention for late seizures using AEDs with proven efficacy in partial seizures and with the best achievable tolerability; being also attentive to the possible use of new drugs in the future, like lipid peroxidation inhibitors, and drugs designed to inhibit other excitotoxic, ionic or oxidative processes.