A Reconstruction Algorithm for Photoacoustic Imaging based on the Nonuniform FFT

Fourier reconstruction algorithms significantly outperform conventional back-projection algorithms in terms of computation time. In photoacoustic imaging, these methods require interpolation in the Fourier space domain, which creates artifacts in reconstructed images. We propose a novel reconstruction algorithm that applies the one-dimensional nonuniform fast Fourier transform to photoacoustic imaging. It is shown theoretically and numerically that our algorithm avoids artifacts while preserving the computational effectiveness of Fourier reconstruction.Comment: 22 pages, 8 figure

On regularization methods of EM-Kaczmarz type

We consider regularization methods of Kaczmarz type in connection with the expectation-maximization (EM) algorithm for solving ill-posed equations. For noisy data, our methods are stabilized extensions of the well established ordered-subsets expectation-maximization iteration (OS-EM). We show monotonicity properties of the methods and present a numerical experiment which indicates that the extended OS-EM methods we propose are much faster than the standard EM algorithm.Comment: 18 pages, 6 figures; On regularization methods of EM-Kaczmarz typ

Predictors for surgical site infection in patients undergoing therapeutic or prophylactic intra-abdominal onlay mesh (IPOM) implantation in clean and contaminated surgical fields.

BACKGROUND Prophylactic intra-abdominal onlay mesh (IPOM) implantation has been shown to reduce the rate of fascial dehiscence and incisional hernia. However, surgical site infection (SSI) in presence of an IPOM remains a concern. The aim of this study was to assess predictors for SSI following IPOM placement in hernia and non-hernia abdominal surgery in clean and contaminated surgical fields. METHODS Observational study including patients undergoing IPOM placement at a Swiss tertiary care hospital 2007-2016. IPOM implantation was performed in hernia and non-hernia elective and emergency abdominal surgery, including contaminated and infected surgical fields. The incidence of SSI was prospectively assessed by Swissnoso according to CDC criteria. The effect of disease- and procedure-related factors on SSI was assessed in multivariable regression analysis, adjusting for patient-related factors. RESULTS A total of 1072 IPOM implantations were performed. Laparoscopy was performed in 415 patients (38.7%), laparotomy in 657 patients (61.3%). SSI occurred in 172 patients (16.0%). Superficial, deep, and organ space SSI were found in 77 (7.2%), 26 (2.4%), and 69 (6.4%) patients, respectively. Multivariable analysis revealed emergency hospitalization (OR 1.787, p = 0.006), previous laparotomy (1.745, p = 0.029), duration of operation (OR 1.193, p < 0.001), laparotomy (OR 6.167, p < 0.001), bariatric (OR 4.641, p < 0.001), colorectal (OR 1.941, p = 0.001), and emergency (OR 2.510, p < 0.001) surgery, wound class ≥ 3 (OR 3.878, p < 0.001), and non-polypropylene mesh (OR 1.818, p = 0.003) as independent predictors for SSI. Hernia surgery was independently associated with a lower risk for SSI (OR 0.165, p < 0.001). CONCLUSION This study revealed emergency hospitalization, previous laparotomy, duration of operation, laparotomy, as well as bariatric, colorectal, and emergency surgery, abdominal contamination or infection, and usage of non-polypropylene mesh as independent predictors for SSI. In contrast, hernia surgery was associated with a lower risk for SSI. The knowledge of these predictors will help to balance benefits of IPOM implantation against the risk for SSI

Sparse Regularization with lql^q Penalty Term

We consider the stable approximation of sparse solutions to non-linear operator equations by means of Tikhonov regularization with a subquadratic penalty term. Imposing certain assumptions, which for a linear operator are equivalent to the standard range condition, we derive the usual convergence rate $O(\sqrt{\delta})$ of the regularized solutions in dependence of the noise level $\delta$. Particular emphasis lies on the case, where the true solution is known to have a sparse representation in a given basis. In this case, if the differential of the operator satisfies a certain injectivity condition, we can show that the actual convergence rate improves up to $O(\delta)$.Comment: 15 page

Murine Gammaretrovirus Group G3 Was Not Found in Swedish Patients with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Fibromyalgia

BACKGROUND: The recent report of gammaretroviruses of probable murine origin in humans, called xenotropic murine retrovirus related virus (XMRV) and human murine leukemia virus related virus (HMRV), necessitated a bioinformatic search for this virus in genomes of the mouse and other vertebrates, and by PCR in humans. RESULTS: Three major groups of murine endogenous gammaretroviruses were identified. The third group encompassed both exogenous and endogenous Murine Leukemia Viruses (MLVs), and most XMRV/HMRV sequences reported from patients suffering from myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Two sensitive real-time PCRs for this group were developed. The predicted and observed amplification range for these and three published XMRV/HMRV PCRs demonstrated conspicuous differences between some of them, partly explainable by a recombinatorial origin of XMRV. Three reverse transcription real-time PCRs (RTQPCRs), directed against conserved and not overlapping stretches of env, gag and integrase (INT) sequences of XMRV/HMRV were used on human samples. White blood cells from 78 patients suffering from ME/CFS, of which 30 patients also fulfilled the diagnostic criteria for fibromyalgia (ME/CFS/FM) and in 7 patients with fibromyalgia (FM) only, all from the Gothenburg area of Sweden. As controls we analyzed 168 sera from Uppsala blood donors. We controlled for presence and amplifiability of nucleic acid and for mouse DNA contamination. To score as positive, a sample had to react with several of the XMRV/HMRV PCRs. None of the samples gave PCR reactions which fulfilled the positivity criteria. CONCLUSIONS: XMRV/HMRV like proviruses occur in the third murine gammaretrovirus group, characterized here. PCRs developed by us, and others, approximately cover this group, except for the INT RTQPCR, which is rather strictly XMRV specific. Using such PCRs, XMRV/HMRV could not be detected in PBMC and plasma samples from Swedish patients suffering from ME/CFS/FM, and in sera from Swedish blood donors

Molecular Insights into Reprogramming-Initiation Events Mediated by the OSKM Gene Regulatory Network

Somatic cells can be reprogrammed to induced pluripotent stem cells by over-expression of OCT4, SOX2, KLF4 and c-MYC (OSKM). With the aim of unveiling the early mechanisms underlying the induction of pluripotency, we have analyzed transcriptional profiles at 24, 48 and 72 hours post-transduction of OSKM into human foreskin fibroblasts. Experiments confirmed that upon viral transduction, the immediate response is innate immunity, which induces free radical generation, oxidative DNA damage, p53 activation, senescence, and apoptosis, ultimately leading to a reduction in the reprogramming efficiency. Conversely, nucleofection of OSKM plasmids does not elicit the same cellular stress, suggesting viral response as an early reprogramming roadblock. Additional initiation events include the activation of surface markers associated with pluripotency and the suppression of epithelial-to-mesenchymal transition. Furthermore, reconstruction of an OSKM interaction network highlights intermediate path nodes as candidates for improvement intervention. Overall, the results suggest three strategies to improve reprogramming efficiency employing: 1) anti-inflammatory modulation of innate immune response, 2) pre-selection of cells expressing pluripotency-associated surface antigens, 3) activation of specific interaction paths that amplify the pluripotency signal