Lumpy Skin Disease Virus Genome Sequence Analysis: Putative Spatio-Temporal Epidemiology, Single Gene versus Whole Genome Phylogeny and Genomic Evolution

Lumpy Skin Disease virus is a poxvirus from the genus Capripox that mainly affects bovines and it causes severe economic losses to livestock holders. The Lumpy Skin Disease virus is currently dispersing in Asia, but little is known about detailed phylogenetic relations between the strains and genome evolution. We reconstructed a whole-genome-sequence (WGS)-based phylogeny and compared it with single-gene-based phylogenies. To study population and spatiotemporal patterns in greater detail, we reconstructed networks. We determined that there are strains from multiple clades within the previously defined cluster 1.2 that correspond with recorded outbreaks across Eurasia and South Asia (Indian subcontinent), while strains from cluster 2.5 spread in Southeast Asia. We concluded that using only a single gene (cheap, fast and easy to routinely use) for sequencing lacks phylogenetic and spatiotemporal resolution and we recommend to create at least one WGS whenever possible. We also found that there are three gene regions, highly variable, across the genome of LSDV. These gene regions are located in the 5' and 3' flanking regions of the LSDV genome and they encode genes that are involved in immune evasion strategies of the virus. These may provide a starting point to further investigate the evolution of the virus.

Evidence of Lumpy Skin Disease Virus Transmission from Subclinically Infected Cattle by Stomoxys calcitrans

Lumpy skin disease virus (LSDV) is a vector-transmitted capripox virus that causes disease in cattle. Stomoxys calcitrans flies are considered to be important vectors as they are able to transmit viruses from cattle with the typical LSDV skin nodules to naive cattle. No conclusive data are, however, available concerning the role of subclinically or preclinically infected cattle in virus transmission. Therefore, an in vivo transmission study with 13 donors, experimentally inoculated with LSDV, and 13 naïve acceptor bulls was performed whereby S. calcitrans flies were fed on either subclinical- or preclinical-infected donor animals. Transmission of LSDV from subclinical donors showing proof of productive virus replication but without formation of skin nodules was demonstrated in two out of five acceptor animals, while no transmission was seen from preclinical donors that developed nodules after Stomoxys calcitrans flies had fed. Interestingly, one of the acceptor animals which became infected developed a subclinical form of the disease. Our results show that subclinical animals can contribute to virus transmission. Therefore, stamping out only clinically diseased LSDV-infected cattle could be insufficient to completely halt the spread and control of the disease.

Development and Validation of a New DIVA Real-Time PCR Allowing to Differentiate Wild-Type Lumpy Skin Disease Virus Strains, Including the Asian Recombinant Strains, from Neethling-Based Vaccine Strains

The current epidemic in Asia, driven by LSDV recombinants, poses difficulties to existing DIVA PCR tests, as these do not differentiate between homologous vaccine strains and the recombinant strains. We, therefore, developed and validated a new duplex real-time PCR capable of differentiating Neethling-based vaccine strains from classical and recombinant wild-type strains that are currently circulating in Asia. The DIVA potential of this new assay, seen in the in silico evaluation, was confirmed on samples from LSDV infected and vaccinated animals and on isolates of LSDV recombinants (n = 12), vaccine (n = 5), and classic wild-type strains (n = 6). No cross-reactivity or a-specificity with other capripox viruses was observed under field conditions in non-capripox viral stocks and negative animals. The high analytical sensitivity is translated into a high diagnostic specificity as more than 70 samples were all correctly detected with Ct values very similar to those of a published first-line pan capripox real-time PCR. Finally, the low inter- and intra-run variability observed shows that the new DIVA PCR is very robust which facilitates its implementation in the lab. All validation parameters that are mentioned above indicate the potential of the newly developed test as a promising diagnostic tool which could help to control the current LSDV epidemic in Asia.

Recombinant LSDV Strains in Asia: Vaccine Spillover or Natural Emergence?

From 2017 to 2019, several vaccine-like recombinant strains of lumpy skin disease virus (LSDV) were discovered in Kazakhstan and neighbouring regions of Russia and China. Shortly before their emergence, the authorities in Kazakhstan launched a mass vaccination campaign with the Neethling-based Lumpivax vaccine. Since none of the other countries in the affected region had used a homologous LSDV vaccine, it was soon suspected that the Lumpivax vaccine was the cause of these unusual LSDV strains. In this study, we performed a genome-wide molecular analysis to investigate the composition of two Lumpivax vaccine batches and to establish a possible link between the vaccine and the recent outbreaks. Although labelled as a pure Neethling-based LSDV vaccine, the Lumpivax vaccine appears to be a complex mixture of multiple CaPVs. Using an iterative enrichment/assembly strategy, we obtained the complete genomes of a Neethling-like LSDV vaccine strain, a KSGP-like LSDV vaccine strain and a Sudan-like GTPV strain. The same analysis also revealed the presence of several recombinant LSDV strains that were (almost) identical to the recently described vaccine-like LSDV strains. Based on their InDel/SNP signatures, the vaccine-like recombinant strains can be divided into four groups. Each group has a distinct breakpoint pattern resulting from multiple recombination events, with the number of genetic exchanges ranging from 126 to 146. The enormous divergence of the recombinant strains suggests that they arose during seed production. The recent emergence of vaccine-like LSDV strains in large parts of Asia is, therefore, most likely the result of a spillover from animals vaccinated with the Lumpivax vaccine.

An overview of state-of-the-art image restoration in electron microscopy

In Life Science research, electron microscopy (EM) is an essential tool for morphological analysis at the subcellular level as it allows for visualization at nanometer resolution. However, electron micrographs contain image degradations such as noise and blur caused by electromagnetic interference, electron counting errors, magnetic lens imperfections, electron diffraction, etc. These imperfections in raw image quality are inevitable and hamper subsequent image analysis and visualization. In an effort to mitigate these artefacts, many electron microscopy image restoration algorithms have been proposed in the last years. Most of these methods rely on generic assumptions on the image or degradations and are therefore outperformed by advanced methods that are based on more accurate models. Ideally, a method will accurately model the specific degradations that fit the physical acquisition settings. In this overview paper, we discuss different electron microscopy image degradation solutions and demonstrate that dedicated artefact regularisation results in higher quality restoration and is applicable through recently developed probabilistic methods.

Simultaneous degradation estimation and restoration of confocal images and performance evaluation by colocalization analysis

A novel method for joint restoration and estimation of the degradation of confocal microscope images is presented. The observed images are degraded due to two sources: blurring due to the band-limited nature of the optical system [modelled by the point spread function (PSF)], and Poisson noise contaminates the observations due to the discrete nature of the photon detection process. The proposed method iterates noise reduction, blur estimation and deblurring, and applies these steps in two phases, i.e. a training phase and a restoration phase. In the first phase, these three steps are iterated until the blur estimation converges. Noise reduction and blur estimation are performed using steerable pyramids, and the deblurring is performed by the Richardson-Lucy algorithm. The second phase is the actual restoration. From then on, the blur estimation is used as a criterion to measure the image quality. The iterations are stopped when this measure converges, a result that is guaranteed. The integrated method is completely automatic, and no prior information on the image is required. The method has been given the name SPERRIL (Steerable Pyramid-based Estimation and Regularized Richardson-Lucy restoration). Compared with existing techniques by both objective measures and visual observation, in the SPERRIL-restored images noise is better suppressed.

A case of childhood sarcoidosis

Cutaneous sarcoidosis is rare in children. We report a case of a 5-year-old Bangladeshi girl who presented with fever, a papular eruption on the lower limbs and trunk, malaise, anorexia and weight loss. There was multisystem involvement with marked hepatosplenomegaly, generalized lymphadenopathy, parotid fullness and chronic uveitis. Pulmonary infiltrates were seen on the chest X-ray. Histology of a skin biopsy showed naked noncaseating granulomata and PCR for Mycobacterium tuberculosis was negative. A clinical diagnosis of sarcoidosis was made. The patient was treated with oral prednisolone (2 mg/kg per day). An excellent clinical response with resolution of the rash and improvement of extracutaneous signs was noted within 3 months and she remains well on low-dose prednisolone on alternate days. We discuss the presentation and management of sarcoidosis in children, and highlight the potential difficulty in differentiating this from disseminated tuberculosis.

State-of-the-art techniques for lossless compression of 3D medical image sets

This paper explains the basic principles of lossless two-dimensional (2D) and three-dimensional (3D) image coding at a high level of abstraction. It discusses also a new inter-frame technique for lossless video coding based on intra-frame prediction and inter-frame context modelling. The performance of this technique is compared to that of state-of-the-art 2D coders on CT and MRI data sets from the Visual Human Project. The results show that the inter-frame technique outperforms state-of-the-art intra-frame coders, i.e. Calic and JPEG-LS. The improvement in compression ratio is significant in the case of CT data but is rather small in the case of MRI data.

An imaging system with calibrated color image acquisition for use in dermatology

We propose a novel imaging system useful in dermatology, more precisely, for the follow-up of patients with an increased risk of skin cancer. The system consists of a Pentium PC equipped with an RGB frame grabber, a three-chip charge coupled devices (CCD) camera controlled by the serial port and equipped with a zoom lens and a halogen annular light source. Calibration of the imaging system provides a way to transform the acquired images, which are defined in an unknown color space, to a standard, well-defined color space called sRGB. sRGB has a known relation to the CIE1 XYZ and CIE L*a*b* colorimetric spaces. These CIE color spaces are based on the human vision, and they allow the computation of a color difference metric called CIE deltaE*ab, which is proportional to the color difference, as seen by a human observer. Several types of polynomial RGB to sRGB transforms will be tried, including some optimized in perceptually uniform color spaces. The use of a standard and well-defined color space also allows meaningful exchange of images, e.g., in teledermatology. The calibration procedure is based on 24 patches with known color properties, and it takes about 5 minutes to perform. It results in a number of settings called a profile that remains valid for tens of hours of operation. Such a profile is checked before acquiring images using just one color patch, and is adjusted on the fly to compensate for short-term drift in the response of the imaging system. Precision or reproducibility of subsequent color measurements is very good with (deltaE*ab) = 0.3 and deltaE*ab < 1.2. Accuracy compared with spectrophotometric measurements is fair with (deltaE*ab) = 6.2 and deltaE*ab < 13.3.

Quantitative analysis of the neonatal brain by ultrasound

Clinical research has shown a clear correlation between white matter disorders of the neonatal brain and neuromotoric handicap at a later age. Ultrasound imaging is a proven method to detect the white matter damage at an early stage. However, since subjective visual examination of the images by neonatologists not always leads to an unambiguous diagnosis, a need for quantitative characterization is felt. Reproducibility is the first requirement in order to be able to perform objective quantitative analysis. This paper proposes a software-based method to compensate for variable acquisition factors that negatively affect the reproducibility of the measurements. The results of some basic experiments will illustrate the usefulness of the developed compensation algorithm.

Lossless quantization of Hadamard transform coefficients

This paper shows that an n x 1 integer vector can be exactly recovered from its Hadamard transform coefficients, even when 0.5 n log(2)(n) of the (less significant) bits of these coefficients are removed. The paper introduces a fast "lossless" dequantization algorithm for this purpose. To investigate the usefulness of the procedure in data compression, the paper investigates an embedded block image coding technique called the "LHAD" based on the algorithm. The results show that lossless compression ratios close to the state of the art can be achieved, but that techniques such as CALIC and S+P still perform better.

Corrections to "JPEG dequantization array for regularized decompression"

An error in the theoretical derivations leading up to the main equation of the above correspondence by Prost et al. is pointed out, and corrections are presented. Due to the error, the experimentally obtained "optimal" parameters are really only suboptimal.

Adaptive noise removal from biomedical signals using warped polynomials

This paper presents the time-warped polynomial filter (TWPF), a new interval-adaptive filter for removing stationary noise from nonstationary biomedical signals. The filter fits warped polynomials to large segments of such signals. This can be interpreted as low-pass filtering with a time-varying cut-off frequency. In optimal operation, the filter's cut-off frequency equals the local signal bandwidth. However, the paper also presents an iterative filter adaptation algorithm, which does not rely on the (complicated) computation of the local bandwidth. The TWPF has some important advantages over existing adaptive noise removal techniques: it reacts immediately to changes in the signal's properties, independently of the desired noise reduction; it does not require a reference signal and can be applied to nonperiodical signals. In case of quasiperiodical signals, applying the TWPF to the individual signal periods leads to an optimal noise reduction. However, the TWPF can also be applied to intervals of fixed size, at the expense of a slightly lower noise reduction. This is the way nonquasiperiodical signals are filtered. The paper presents experimental results which demonstrate the usefulness of the interval-adaptive filter in several biomedical applications: noise removal from ECG, respiratory and blood pressure signals, and base line restoration of electro-encephalograms (EEG's).

ECG data compression with time-warped polynomials

This paper presents a new adaptive compression method for ECG's. The method represents each R-R interval by an optimally time-warped polynomial. It achieves a high-quality approximation at less than 250 bits/s. The article shows that the corresponding rates for other transform based schemes (the DCT and the DLT) are always higher. Also, the new method is less sensitive to errors in QRS detection and it removes more (white) noise from the signal. The reconstruction errors are distributed more uniformly in the new scheme and the peak error is usually lower. The reconstruction method is also useful for adaptive filtering of noisy ECG signals.

Data compression of ECG's by high-degree polynomial approximation

A method for the compression of ECG data is presented. The method is based on high-degree polynomial expansions. Data rates of about 350 bits per second are achievable at an acceptable signal quality. The high compression is obtained by a carefully selected subdivision of the ECG signal into intervals that make optimal use of the special properties of the polynomial base functions. Each interval corresponds to one ECG period. The method is compared to the discrete cosine transform and is found to yield a significantly higher data compression for a given signal quality (quantified by mean squared error and peak error).

Intermittent positive pressure ventilation and high frequency ventilation in dogs with experimental bronchopleural fistulae

This study evaluated respiratory and cardiovascular responses of canines in whom bilateral bronchopleural fistulae were created surgically, and in whom ventilation was varied between intermittent positive pressure ventilation (IPPV) and high frequency ventilation (HFV). An Emerson prototype ventilator was used for HFV at rates of 300-1400/min at driving pressures of 2.5, 5.0, and 10 psi. Gas exchange was judged by arterial and mixed venous blood gases. Cardiac performance was measured by cardiac index, heart rate, stroke index, stroke work index, systemic and pulmonary vascular pressures and resistances. Ventilation during IPPV with the fistula open resulted in a statistically significant increase in PaCO2 and a decrease in PaO2 when compared to both HFV modes. Variations in cardiac function in these open-chested animals were insignificant for all variables tested except pulmonary artery pressures which rose significantly in the IPPV group.