Isolation and Genetic Characterization of a Novel Adenovirus Associated with Mass Mortality in Great Cormorants (Phalacrocorax carbo).

High mortality in great cormorants (Phalacrocorax carbo) was registered on the Alakol Lake in eastern Kazakhstan in 2021 when about 20% of juveniles died. High-throughput sequencing revealed the presence of a putative novel cormorant adenovirus significantly divergent from known aviadenoviruses. We suggest that this cormorant adenovirus can be considered an emerging threat to the health and conservation of this species.

Aislamiento y caracterización genética de un nuevo adenovirus asociado con la mortalidad masiva en cormoranes grandes (Phalacrocorax carbo). En 2021 se registró una alta mortalidad de cormoranes grandes (Phalacrocorax carbo) en el lago Alakol, en el este de Kazajstán, cuando murieron alrededor del 20% de las aves jóvenes. La secuenciación de alto rendimiento reveló la presencia de un supuesto nuevo adenovirus de cormorán significativamente divergente de los aviadenovirus conocidos. Sugerimos que este adenovirus de cormorán puede considerarse una amenaza emergente para la salud y conservación de esta especie.

Inter-Rater Reliability of Collateral Status Assessment Based on CT Angiography: A Retrospective Study of Middle Cerebral Artery Ischaemic Stroke.

The importance of assessing the collateral status (CS) in patients with ischaemic stroke (IS) has repeatedly been emphasised in clinical guidelines. Various publications offer qualitative or semiquantitative scales with gradations corresponding to the different extents of the collaterals, visualised mostly on the basis of CTA images. However, information on their inter-rater reliability is limited. Therefore, the aim of this study is to investigate the inter-rater reliability of the scales for collateral assessment. CTA images of 158 patients in the acute period of IS were used in the study. The assessment of CS was performed by two experts using three methodologies: the modified Tan scale, the Miteff scale, and the Rosenthal scale. Cohen's kappa, weighted kappa and Krippendorff's alpha were used as reliability measures. For the modified Tan scale and the Miteff and Rosenthal scales, the weighted kappa values were 0.72, 0.49 and 0.59, respectively. Although the best measure of consistency was found for the modified Tan scale, no statistically significant differences were revealed among the scales. The impact of the CS on the degree of neurological deficit at discharge was shown for the modified Tan and Rosenthal scales. In conclusion, the analysis showed a moderate inter-rater reliability of the three scales, but was not able to distinguish the best one among them.

Prevalence and genetic diversity of coronaviruses, astroviruses and paramyxoviruses in wild birds in southeastern Kazakhstan.

Wild birds are natural reservoirs of many emerging viruses, including some zoonoses. Considering that the territory of Kazakhstan is crossed by several bird migration routes, it is important to know pathogenic viruses circulating in migratory birds in this region. Therefore, the aim of this study was to identify the host range, diversity and spatial distribution of avian paramyxoviruses, coronaviruses, and astroviruses in free-ranging wild birds in the southeastern region of Kazakhstan. For this purpose, we collected tracheal and cloacal swabs from 242 wild birds belonging to 51 species and screened them using conventional PCR assays. Overall, 4.1% (10/242) and 2.9% (7/242) of all examined birds tested positive for coronaviruses and astroviruses, respectively. Coronaviruses were found in the orders Pelecaniformes (30%; 3/10), Charadriiformes (30%; 3/10), Columbiformes (20%; 2/10), Anseriformes (10%; 1/10), and Passeriformes (10%; 1/10). All detected strains belonged to the genus Gammacoronavirus. Astroviruses were detected in birds representing the orders Passeriformes (57%; 4/7), Coraciiformes (14%; 1/7), Charadriiformes (14%; 1/7), and Columbiformes (14%; 1/7). Paramyxoviruses were observed in only two birds (0.8%; 2/242). Both strains were closely related to the species APMV-22, which had not been previously detected in Kazakhstan. Phylogenetic analysis of the partial RdRp gene sequences of the virus strains revealed three different clades of astroviruses, two clades of coronaviruses, and one clade of paramyxoviruses. The results of this study provide valuable information on the diversity and spatial distribution of paramyxoviruses, coronaviruses, and astroviruses in wild birds in southeastern Kazakhstan and highlight the importance of further thorough monitoring of wild birds in this region.

Application of Radiomics in Vesselness Analysis of CT Angiography Images of Stroke Patients.

Development of vascular collaterals in a lesion area is one of the key factors that determine not only the choice of treatment for ischemic stroke (IS) patients, but also outcome and therapy effectiveness. The main method for examining the vessels' ramification is CT angiography (CTA). CTA analysis may be improved by incorporating filters designed to extract more features about vessels and quantify their level of development. This work suggests the usage of radiomics methods in the analysis of vesselness measure calculated from CTA images. Vesselness measurement is based on the analysis of the Hessian matrix with a few modifications dictated by practical aspects of this issue. The developed algorithm was implemented as a filter that generates a new 3D image, every voxel of which has the probability of belonging to a vessel-like structure. Further analysis of the distribution of vesselness in the lesion area and in the intact contralateral area was conducted with the methods from the open library PyRadiomics. A set of radiomics features was calculated. Preliminary analysis on a sample of 30 IS patients showed the presence of significant differences between afflicted and intact hemispheres.

Cormorants as Potential Victims and Reservoirs of Velogenic Newcastle Disease Virus (Orthoavulavirus-1) in Central Asia.

Virulent strains of avian orthoavulavirus 1, historically known as Newcastle disease virus (NDV), are widespread and cause high levels of mortality in poultry worldwide. Wild birds may play an important role in the maintenance of Avian orthoavulavirus 1 in nature. Prior to 2014, most of the lentogenic NDV strains isolated from Central Asia were obtained from the avian order Anseriformes (ducks and geese). Wild birds were monitored from 2014-2016 to detect the circulation of NDV. A total of 1522 samples belonging to 73 avian species were examined, and 26 positive samples were identified. The isolates of Avian orthoavulavirus 1 belonged to three genotypes: viruses from doves (Columbiformes) and cormorants (Suliformes) were attributed to the velogenic genotypes VI and XIII, respectively, while the isolate from poultry belonged to lentogenic genotype I. The isolation of Avian orthoavulavirus 1 from doves may confirm their role as a reservoir of pigeon paramyxoviruses (antigenic variant of the genotype VI NDV) in nature and indicates the potential threat of introduction of velogenic strains into the poultry population. Our study describes an epizootic scenario in Kazakhstan among cormorants with mortality among juveniles of up to 3 wk of age and isolation of the NDV from apparently healthy birds. These observations may support the idea that cormorants are one of the potential reservoirs and victims of velogenic Avian orthoavulavirus 1 in Central Asia. The seasonal migrations of cormorants may partially contribute to viral dissemination throughout the continent; however, this hypothesis needs more evidence.

Cormoranes como posibles víctimas y reservorios del virus velogénicos de la enfermedad de Newcastle (Orthoavulavirus-1) en Asia Central. Las cepas virulentas del Orthoavulavirus aviar 1, históricamente conocido como virus de la enfermedad de Newcastle (NDV), están muy extendidas y causan altos niveles de mortalidad en avicultura en todo el mundo. Las aves silvestres pueden desempeñar un papel importante en el mantenimiento del Orthoavulavirus aviar 1 en la naturaleza. Antes del año 2014, la mayoría de las cepas de Newcastle lentogénicas aisladas de Asia Central se obtenían del orden aviar Anseriformes (patos y gansos). Las aves silvestres fueron monitoreadas entre los años 2014 y 2016 para detectar la circulación de virus de Newcastle. Se examinaron un total de 1522 muestras pertenecientes a 73 especies de aves, y se identificaron 26 muestras positivas. Los aislamientos de Orthoavulavirus aviar 1pertenecían a tres genotipos: los virus de palomas (Columbiformes) y de cormoranes (Suliformes) se atribuyeron a los genotipos velogénicos VI y XIII, respectivamente, mientras que los aislamientos de aves comerciales pertenecieron al genotipo lentogénico I. El aislamiento del Orthoavulavirus aviar 1 lentogénico de las palomas puede confirmar su papel como reservorio de los paramixovirus de paloma (variantes antigénicas del genotipo VI del virus de Newcastle) en la naturaleza e indica la amenaza potencial de la introducción de cepas velogénicas en la población avícola. Este estudio describe un escenario epizoótico en Kazajstán entre cormoranes con mortalidad de aves jóvenes de hasta tres semanas de edad y aislamiento del virus de Newcastle de aves aparentemente sanas. Estas observaciones pueden apoyar la idea de que los cormoranes son uno de los reservorios potenciales y también víctimas del Orthoavulavirus aviar 1 velogénico en Asia Central. Las migraciones estacionales de cormoranes pueden contribuir parcialmente a la diseminación viral en todo el continente; Sin embargo, esta hipótesis requiere de más evidencia.

Virtual Planning of Extra-Intracranial Bypass with Numerical Investigation of Hemodynamics.

Planning of bypass surgery for patients with complex cerebral aneurysms is a very complicated task. It is important to take into consideration personal anatomy and hemodynamics and make additional investigations, but unfortunately, they don't give a guarantee of good postoperative results. Recent medical imaging and computational fluid dynamics (CFD) can be helpful for the prediction of effectiveness of selected surgical technique. In the current research with the use of CT and PC-MRI data we applied computational modeling in order to make quantitative assessment of potential changes of blood flow distribution after the surgery. Virtual version of bypass surgery showed preservation of sufficient blood flow, what was confirmed with modeling results after operation. Moreover, successful verification with PC-MRI data in control sections was made. The research has shown that virtual planning with the estimation of blood flow changes can be introduced into clinical practice for simplifying and increasing efficiency of planning process.

A Platform for Collection and Analysis of Image Data on Stroke.

Identifying imaging biomarkers (IBs) of stroke remains a priority in neurodiagnostics. There is a number of different methods for image analysis and learning rules applicable in this field, but all of them require large arrays of DICOM images and clinical data. In order to amass such dataset,we havedesigneda platform for systematic collection of clinical data and medical images in different modalities. The platform provides easy-to-use tools to create formalized radiology reports, contour and tag the regions of interest (ROIs) on the DICOM images, and extract radiomics data. Subsequent analysis of the obtained data will allow identifying the most relevant IBs that predict clinical outcome and possible complications. The results of the analysis will be used to develop predictive algorithms for stroke diagnostics.

Bayesian Data Analysis for Revealing Causes of the Middle Pleistocene Transition.

Currently, causes of the middle Pleistocene transition (MPT) - the onset of large-amplitude glacial variability with 100 kyr time scale instead of regular 41 kyr cycles before - are a challenging puzzle in Paleoclimatology. Here we show how a Bayesian data analysis based on machine learning approaches can help to reveal the main mechanisms underlying the Pleistocene variability, which most likely explain proxy records and can be used for testing existing theories. We construct a Bayesian data-driven model from benthic δ18O records (LR04 stack) accounting for the main factors which may potentially impact climate of the Pleistocene: internal climate dynamics, gradual trends, variations of insolation, and millennial variability. In contrast to some theories, we uncover that under long-term trends in climate, the strong glacial cycles have appeared due to internal nonlinear oscillations induced by millennial noise. We find that while the orbital Milankovitch forcing does not matter for the MPT onset, the obliquity oscillation phase-locks the climate cycles through the meridional gradient of insolation.

Bayesian framework for simulation of dynamical systems from multidimensional data using recurrent neural network.

We suggest a new method for building data-driven dynamical models from observed multidimensional time series. The method is based on a recurrent neural network with specific structure, which allows for the joint reconstruction of both a low-dimensional embedding for dynamical components in the data and an evolution operator. The key link of the method is a Bayesian optimization of both model structure and the hypothesis about the data generating law, which is needed for constructing the cost function for model learning. First, the performance of the method is successfully tested in the situation when a signal from a low-dimensional dynamical system is hidden in noisy multidimensional observations. Second, the method is used for building the data-driven model of the low frequency variability (LFV) in the quasigeostrophic model of the Earth's midlatitude atmosphere-a high-dimensional chaotic system. It is demonstrated that the key regimes of the atmospheric LFV are reproduced correctly in data simulations by means of the obtained model.

Signatures of human-commensalism in the house sparrow genome.

House sparrows (Passer domesticus) are a hugely successful anthrodependent species; occurring on nearly every continent. Yet, despite their ubiquity and familiarity to humans, surprisingly little is known about their origins. We sought to investigate the evolutionary history of the house sparrow and identify the processes involved in its transition to a human-commensal niche. We used a whole genome resequencing dataset of 120 individuals from three Eurasian species, including three populations of Bactrianus sparrows, a non-commensal, divergent house sparrow lineage occurring in the Near East. Coalescent modelling supports a split between house and Bactrianus sparrow 11 Kya and an expansion in the house sparrow at 6 Kya, consistent with the spread of agriculture following the Neolithic revolution. Commensal house sparrows therefore likely moved into Europe with the spread of agriculture following this period. Using the Bactrianus sparrow as a proxy for a pre-commensal, ancestral house population, we performed a comparative genome scan to identify genes potentially involved with adaptation to an anthropogenic niche. We identified potential signatures of recent, positive selection in the genome of the commensal house sparrow that are absent in Bactrianus populations. The strongest selected region encompasses two major candidate genes; COL11A-which regulates craniofacial and skull development and AMY2A, part of the amylase gene family which has previously been linked to adaptation to high-starch diets in humans and dogs. Our work examines human-commensalism in an evolutionary framework, identifies genomic regions likely involved in rapid adaptation to this new niche and ties the evolution of this species to the development of modern human civilization.

CFD Modelling of Local Hemodynamics in Intracranial Aneurysms Harboring Arterial Branches.

The main cause of non-traumatic subarachnoid haemorrhage is an intracranial aneurysm's rupture. The choice of treatment approach is exceptionally difficult in cases of aneurysms with additional branches on the aneurysm's dome or neck. The impact of the arterial branches on local hemodynamics is still unclear and controversial question. At the same time, up-to-date methods of image processing and mathematical modeling provide a way to investigate the hemodynamic environment of aneurysms. The paper discusses hemodynamic aspects of aneurysms harboring arterial branch through the use of patient-specific 3D models and computational fluid dynamics (CFD) methods. The analysis showed that the presence of the arterial branches has a great influence on flow streamlines and wall shear stress, particularly for side wall aneurysm.

Method for reconstructing nonlinear modes with adaptive structure from multidimensional data.

We present a detailed description of a new approach for the extraction of principal nonlinear dynamical modes (NDMs) from high-dimensional data. The method of NDMs allows the joint reconstruction of hidden scalar time series underlying the observational variability together with a transformation mapping these time series to the physical space. Special Bayesian prior restrictions on the solution properties provide an efficient recognition of spatial patterns evolving in time and characterized by clearly separated time scales. In particular, we focus on adaptive properties of the NDMs and demonstrate for model examples of different complexities that, depending on the data properties, the obtained NDMs may have either substantially nonlinear or linear structures. It is shown that even linear NDMs give us more information about the internal system dynamics than the traditional empirical orthogonal function decomposition. The performance of the method is demonstrated on two examples. First, this approach is successfully tested on a low-dimensional problem to decode a chaotic signal from nonlinearly entangled time series with noise. Then, it is applied to the analysis of 250-year preindustrial control run of the INMCM4.0 global climate model. There, a set of principal modes of different nonlinearities is found capturing the internal model variability on the time scales from annual to multidecadal.

Principal nonlinear dynamical modes of climate variability.

We suggest a new nonlinear expansion of space-distributed observational time series. The expansion allows constructing principal nonlinear manifolds holding essential part of observed variability. It yields low-dimensional hidden time series interpreted as internal modes driving observed multivariate dynamics as well as their mapping to a geographic grid. Bayesian optimality is used for selecting relevant structure of nonlinear transformation, including both the number of principal modes and degree of nonlinearity. Furthermore, the optimal characteristic time scale of the reconstructed modes is also found. The technique is applied to monthly sea surface temperature (SST) time series having a duration of 33 years and covering the globe. Three dominant nonlinear modes were extracted from the time series: the first efficiently separates the annual cycle, the second is responsible for ENSO variability, and combinations of the second and the third modes explain substantial parts of Pacific and Atlantic dynamics. A relation of the obtained modes to decadal natural climate variability including current hiatus in global warming is exhibited and discussed.

Navigated transcranial magnetic stimulation in amyotrophic lateral sclerosis.

INTRODUCTION: Amyotrophic lateral sclerosis (ALS) is a set of disorders associated with preferential degeneration of both upper and lower motor neurons. Navigated transcranial magnetic stimulation (nTMS) is a tool used to perform noninvasive functional brain mapping. We aimed to assess function of upper motor neurons in ALS. METHODS: nTMS was performed on 30 patients with ALS (mean age 54.4 ± 12.1 years) and 24 healthy volunteers (mean age 32.7 ± 13.3 years). RESULTS: The resting motor threshold (MT) was significantly higher in ALS patients compared with controls (P < 0.001). The mean map areas were smaller in patients with ALS than in healthy individuals, although some patients with short disease duration had extended maps. CONCLUSIONS: Motor area maps serve as markers of upper motor neuron damage in ALS. Further research may elucidate the pathogenic mechanisms of the neurodegenerative process and aid in development of diagnostic and prognostic markers.