Real-time processing of radar return on a parallel computer

NASA is working with the FAA to demonstrate the feasibility of pulse Doppler radar as a candidate airborne sensor to detect low altitude windshears. The need to provide the pilot with timely information about possible hazards has motivated a demand for real-time processing of a radar return. Investigated here is parallel processing as a means of accommodating the high data rates required. A PC based parallel computer, called the transputer, is used to investigate issues in real time concurrent processing of radar signals. A transputer network is made up of an array of single instruction stream processors that can be networked in a variety of ways. They are easily reconfigured and software development is largely independent of the particular network topology. The performance of the transputer is evaluated in light of the computational requirements. A number of algorithms have been implemented on the transputers in OCCAM, a language specially designed for parallel processing. These include signal processing algorithms such as the Fast Fourier Transform (FFT), pulse-pair, and autoregressive modelling, as well as routing software to support concurrency. The most computationally intensive task is estimating the spectrum. Two approaches have been taken on this problem, the first and most conventional of which is to use the FFT. By using table look-ups for the basis function and other optimizing techniques, an algorithm has been developed that is sufficient for real time. The other approach is to model the signal as an autoregressive process and estimate the spectrum based on the model coefficients. This technique is attractive because it does not suffer from the spectral leakage problem inherent in the FFT. Benchmark tests indicate that autoregressive modeling is feasible in real time

On the joint spectral density of bivariate random sequences

For univariate random sequences, the power spectral density acts like a probability density function of the frequencies present in the sequence. This dissertation extends that concept to bivariate random sequences. For this purpose, a function called the joint spectral density is defined that represents a joint probability weighing of the frequency content of pairs of random sequences. Given a pair of random sequences, the joint spectral density is not uniquely determined in the absence of any constraints. Two approaches to constraining the sequences are suggested: (1) assume the sequences are the margins of some stationary random field, (2) assume the sequences conform to a particular model that is linked to the joint spectral density. For both approaches, the properties of the resulting sequences are investigated in some detail, and simulation is used to corroborate theoretical results. It is concluded that under either of these two constraints, the joint spectral density can be computed from the non-stationary cross-correlation

Custom wheat microarray development for analysis of grain quality

BACKGROUND: Germline mutations in the SMAD4 gene lead to both juvenile polyposis syndrome and hereditary haemorrhagic telangiectasia (HHT). CASE DESCRIPTION: A 23-year-old man underwent colectomy with ileo-anal pouch anastomosis at the age of 12 due to colorectal juvenile polyposis. At follow-up, recurrent juvenile polyps in the pouch were removed. No gastric polyps were found. The family history was negative for intestinal polyposis. In addition, the patient had recurrent epistaxis. DNA testing revealed a pathogenic SMAD4 mutation: c.1558G>T; p.(Glu520*). Further examination confirmed suspected HHT. CONCLUSION: DNA testing in patients with juvenile polyposis is important for subclassification of this syndrome with implications for the management of patients and family members

Application of Brownian motion theory to the analysis of membrane channel ionic trajectories calculated by molecular dynamics

This paper shows how Brownian motion theory can be used to analyze features of individual ion trajectories in channels as calculated by molecular dynamics, and that its use permits more precise determinations of diffusion coefficients than would otherwise be possible. We also show how a consideration of trajectories of single particles can distinguish between effects due to the magnitude of the diffusion coefficient and effects due to barriers and wells in the potential profile, effects which can not be distinguished by consideration of average fluxes

A scoping review of practice recommendations for clinicians' communication of uncertainty

Background Health-care providers increasingly have to discuss uncertainty with patients. Awareness of uncertainty can affect patients variably, depending on how it is communicated. To date, no overview existed for health-care professionals on how to discuss uncertainty.Objective To generate an overview of available recommendations on how to communicate uncertainty with patients during clinical encounters.Search strategy A scoping review was conducted. Four databases were searched following the PRISMA-ScR statement. Independent screening by two researchers was performed of titles and abstracts, and subsequently full texts.Inclusion criteria Any (non-)empirical papers were included describing recommendations for any health-care provider on how to orally communicate uncertainty to patients.Data extraction Data on provided recommendations and their characteristics (eg, target group and strength of evidence base) were extracted. Recommendations were narratively synthesized into a comprehensible overview for clinical practice.Results Forty-seven publications were included. Recommendations were based on empirical findings in 23 publications. After narrative synthesis, 13 recommendations emerged pertaining to three overarching goals: (a) preparing for the discussion of uncertainty, (b) informing patients about uncertainty and (c) helping patients deal with uncertainty.Discussion and conclusions A variety of recommendations on how to orally communicate uncertainty are available, but most lack an evidence base. More substantial research is needed to assess the effects of the suggested communicative approaches. Until then, health-care providers may use our overview of communication strategies as a toolbox to optimize communication about uncertainty with patients.Patient or public contribution Results were presented to stakeholders (physicians) to check and improve their practical applicability.Analysis and support of clinical decision makin

Cellular SNF2H Chromatin-Remodeling Factor Promotes Herpes Simplex Virus 1 Immediate-Early Gene Expression and Replication

Like other DNA viruses that replicate in the nucleus, herpes simplex virus 1 (HSV-1) regulates the association of histones with its genome to promote viral replication and gene expression. We previously demonstrated that SNF2H, a member of the ISWI family of chromatin-remodeling factors, is concentrated in HSV-1 replication compartments in the nuclei of infected cells, suggesting that this cellular enzyme plays a role in viral replication. We show here that small interfering RNA (siRNA)-mediated knockdown of SNF2H in HEp-2 cells resulted in an approximately 20-fold decrease in HSV-1 replication, arguing that SNF2H promotes efficient HSV-1 replication. Decreases in HSV-1 replication were observed with multiple SNF2H-specific siRNAs, and the extent of the replication decrease correlated with the amount of SNF2H knockdown, indicating that the phenotype resulted from decreased SNF2H levels rather than off-target effects of the siRNAs. We also observed a decrease in the accumulation of immediate-early (IE) gene products in HSV-1-infected cells in which SNF2H was knocked down. Histone H3 occupancy on viral promoters was increased in HSV-1-infected cells that were transfected with SNF2H-specific siRNAs, suggesting that SNF2H promotes removal of histones from viral promoters during infection. Furthermore, chromatin immunoprecipitation (ChIP) studies showed that SNF2H associated with the HSV-1 genome during infection, which suggests that SNF2H may directly remodel viral chromatin. We hypothesize that SNF2H is recruited to viral promoters during HSV-1 infection, where it can remodel the chromatin state of the viral genome, facilitate the transcription of immediate-early genes, and enhance viral replication

Genetic counseling of patients with ovarian carcinoma:acceptance, timing, and psychological wellbeing

The new Dutch guidelines on hereditary and familial ovarian carcinoma recommend genetic testing of all patients with epithelial ovarian cancer (EOC). With this study, we aimed to obtain insight into (1) the acceptance and timing of the offer of genetic counseling in women with EOC, (2) reasons for accepting or declining genetic counseling, and (3) psychological differences between women who did and did not have genetic counseling. A multicenter questionnaire survey was performed in patients with EOC in four Dutch oncology centers. The questionnaire addressed whether, how, and when genetic counseling was offered, women's arguments to accept or decline genetic counseling, and included the Cancer Worry Scale (CWS) and the Hospital Anxiety and Depression Scale (HADS). A total of 67 women completed the questionnaire, of which 43 had genetic counseling. Despite a wide variability in the timing of the offer of genetic counseling, 89% of the women were satisfied with the timing. No significant differences were found between the CWS and HADS scores for the timing of the offer of genetic counseling and whether or not women had genetic counseling. Taking the small sample size into account, the results tentatively suggest that genetic counseling may have limited impact on the psychosocial wellbeing of women with EOC. Therefore, we assume that implementation of the new guidelines offering genetic counseling to all patients with EOC will not cause considerable additional burden to these patients

'We don't know for sure':discussion of uncertainty concerning multigene panel testing during initial cancer genetic consultations

Pre-test counseling about multigene panel testing involves many uncertainties. Ideally, counselees are informed about uncertainties in a way that enables them to make an informed decision about panel testing. It is presently unknown whether and how uncertainty is discussed during initial cancer genetic counseling. We therefore investigated whether and how counselors discuss and address uncertainty, and the extent of shared decision-making (SDM), and explored associations between counselors' communication and their characteristics in consultations on panel testing for cancer. For this purpose, consultations of counselors discussing a multigene panel with a simulated patient were videotaped. Simulated patients represented a counselee who had had multiple cancer types, according to a script. Before and afterwards, counselors completed a survey. Counselors' uncertainty expressions, initiating and the framing of expressions, and their verbal responses to scripted uncertainties of the simulated patient were coded by two researchers independently. Coding was done according to a pre-developed coding scheme using The Observer XT software for observational analysis. Additionally, the degree of SDM was assessed by two observers. Correlation and regression analyses were performed to assess associations of communicated uncertainties, responses and the extent of SDM, with counselors' background characteristics. In total, twenty-nine counselors, including clinical geneticists, genetic counselors, physician assistants-in-training, residents and interns, participated of whom working experience varied between 0 and 25 years. Counselors expressed uncertainties mainly regarding scientific topics (94%) and on their own initiative (95%). Most expressions were framed directly (77%), e.g. We don't know, and were emotionally neutral (59%; without a positive/negative value). Counselors mainly responded to uncertainties of the simulated patient by explicitly referring to the uncertainty (69%), without providing space for further disclosure (66%). More experienced counselors provided less space to further disclose uncertainty (p <0.02), and clinical geneticists scored lower on SDM compared with other types of counselors (p <0.03). Our findings that counselors mainly communicate scientific uncertainties and use space-reducing responses imply that the way counselors address counselees' personal uncertainties and concerns during initial cancer genetic counseling is suboptimal