Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts

Motivation: The identity of cells and tissues is to a large degree governed by transcriptional regulation. A major part is accomplished by the combinatorial binding of transcription factors at regulatory sequences, such as enhancers. Even though binding of transcription factors is sequence-specific, estimating the sequence similarity of two functionally similar enhancers is very difficult. However, a similarity measure for regulatory sequences is crucial to detect and understand functional similarities between two enhancers and will facilitate large-scale analyses like clustering, prediction and classification of genome-wide datasets

Dutch Prospective Observational Study on Prehospital Treatment of Severe Traumatic Brain Injury: The BRAIN-PROTECT Study Protocol

Background: Severe traumatic brain injury (TBI) is associated with a high mortality rate and those that survive commonly have permanent disability. While there is a broad consensus that appropriate prehospital treatment is crucial for a favorable neurological outcome, evidence to support currently applied treatment strategies is scarce. In particular, the relationship between prehospital treatments and patient outcomes is unclear. The BRAIN-PROTECT study therefore aims to identify prehospital treatment strategies associated with beneficial or detrimental outcomes. Here, we present the study protocol. Study Protocol: BRAIN-PROTECT is the acronym for BRAin INjury: Prehospital Registry of Outcome, Treatments and Epidemiology of Cerebral Trauma. It is a prospective observational study on the prehospital treatment of patients with suspected severe TBI in the Netherlands. Prehospital epidemiology, interventions, medication strategies, and nonmedical factors that may affect outcome are studied. Multivariable regression based modeling will be used to identify confounder-adjusted relationships between these factors and patient outcomes, including mortality at 30 days (primary outcome) or mortality and functional neurological outcome at 1 year (secondary outcomes). Patients in whom severe TBI is suspected during prehospital treatment (Glasgow Coma Scale score 8 in combination with a trauma mechanism or clinical findings suggestive of head injury) are identified by all four helicopter emergency medical services (HEMS) in the Netherlands. Patients are prospectively followed up in 9 participating trauma centers for up to one year. The manuscript reports in detail the objectives, setting, study design, patient inclusion, and data collection process. Ethical and juridical aspects, statistical considerations, as well as limitations of the study design are discussed. Discussion: Current prehospital treatment of patients with suspected severe TBI is based on marginal evidence, and optimal treatment is basically unknown. The BRAINPROTECT study provides an opportunity to evaluate and compare different treatment strategies with respect to patient outcomes. To our knowledge, this study project is the first large-scale prospective prehospital registry of patients with severe TBI that also collects long-term follow-up data and ma

High yield of culture-based diagnosis in a TB-endemic setting

BACKGROUND: In most of the world, microbiologic diagnosis of tuberculosis (TB) is limited to microscopy. Recent guidelines recommend culture-based diagnosis where feasible. METHODS: In order to evaluate the relative and absolute incremental diagnostic yield of culture-based diagnosis in a high-incidence community in Cape Town, South Africa, subjects evaluated for suspected TB had their samples processed for microscopy and culture over a 21 month period. RESULTS: For 2537 suspect episodes with 2 smears and 2 cultures done, 20.0% (508) had at least one positive smear and 29.9% (760) had at least one positive culture. One culture yielded 1.8 times more cases as 1 smear (relative yield), or an increase of 12.0% (absolute yield). Based on the latter value, the number of cultures needed to diagnose (NND) one extra case of TB was 8, compared to 19 if second specimens were submitted for microscopy. CONCLUSION: In a high-burden setting, the introduction of culture can markedly increase TB diagnosis over microscopy. The concept of number needed to diagnose can help in comparing incremental yield of diagnosis methods. Although new promising diagnostic molecular methods are being implemented, TB culture is still the gold standard

Transmission of tuberculosis in a high incidence urban community in South Africa.

BACKGROUND: The objective of this study was to identify risk factors for ongoing community transmission of tuberculosis (TB) in two densely populated urban communities with a high incidence rate of TB in Cape Town, South Africa. METHODS: Between 1993 and 1998 DNA fingerprints of mycobacterial isolates from TB patients were determined by restriction fragment length polymorphism (RFLP). Cases whose isolates shared identical fingerprint patterns were considered to belong to the same cluster and to be attributable to ongoing community transmission. RESULTS: The average annual notification rate of new smear positive TB was 238/100000. In all, 1023/1526 reported patients were culture positive, and RFLP was available for 768 (75%) of the isolates from these patients. Since some patients experienced more than one infection during the study period, 797 cases were included in the analysis. Of the cases, 575/797 (72%) were clustered. Smear-positive cases and those who were retreated after default were more likely to be clustered than smear-negative and new cases, respectively. Patients from Uitsig were more often part of large clusters than were patients from Ravensmead. Age, sex, year of diagnosis, and outcome of disease were not risk factors for clustering, nor for being the first case in a cluster, although various analytical approaches were used. CONCLUSIONS: The incidence and proportion of cases that are clustered in this area are higher than reported elsewhere. An overwhelming majority of TB cases in this area is attributed to ongoing community transmission, and only very few to reactivation. This may explain the lack of demographic risk factors for clustering

On the relationship between SiF4plasma species and sample properties in ultra low-k etching processes

The temporal behavior of the molecular etching product SiF4 in fluorocarbon-based plasmas used for the dry etching of ultra low-k (ULK) materials has been brought into connection with the polymer deposition on the surface during plasma treatment within the scope of this work. For this purpose, time-resolved measurements of the density of SiF4 have been performed by quantum cascade laser absorption spectroscopy. A quantification of the non-linear time dependence was achieved by its characterization via a time constant of the decreasing SiF4 density over the process time. The time constant predicts how fast the stationary SiF4 density is reached. The higher the time constant is, the thicker the polymer film on top of the treated ultra low-k surface. A correlation between the time constant and the ULK damage was also found. ULK damage and polymer deposition were proven by Variable Angle Spectroscopic Ellipsometry and X-ray Photoelectron Spectroscopy. In summary, the observed decay of the etching product concentration over process time is caused by the suppressed desorption of the SiF4 molecules due to a more dominant adsorption of polymers. © 2020 Author(s)

The chromatin environment shapes DNA replication origin organization and defines origin classes

International audienc