Eco-evolutionary dynamics in fragmented landscapes

Peer reviewedPostprin

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. © 2021, The Author(s)

Standards of the Polish Ultrasound Society. Ultrasound examination of the portal system and hepatic vessels

Increased incidence of liver diseases, the development of liver surgery and other invasive methods for managing portal hypertension, plus an increasing number of liver transplant procedures pose more and more new challenges for ultrasonography. Ultrasonography, being an effective and clinically verified modality, has been used for several decades for diagnosing diseases of the liver, its vessels and portal hypertension. It is used for both initial and specialist diagnosis (performed in reference centers). The diagnostic value of ultrasonography largely depends on the knowledge of anatomy, physiology, pathophysiology and clinical aspects as well as on the mastering of the scanning technique. In the hands of an experienced physician, it is an accurate and highly effective diagnostic tool; it is of little use otherwise. The paper presents elements of anatomy, physiology and pathophysiology which make the portal system exceptional and the knowledge of which is crucial and indispensable for a correct examination and, above all, for the correct interpretation of results. The authors also present requirements regarding the equipment. Moreover, various technical aspects of the examination are presented and the normal morphological picture and hemodynamic parameters of healthy individuals are described. The authors discuss the most common clinical situations and rare cases during ultrasound examinations. The paper is based on the experience of the author who works in the largest center of liver diseases in Poland, and on the current literature.Wzrost zachorowań na choroby wątroby oraz rozwój chirurgii wątroby i innych inwazyjnych metod leczenia nadciśnienia wrotnego, a także zwiększająca się liczba zabiegów transplantacji wątroby wyznaczają wciąż nowe wyzwania dla ultrasonografii. Ultrasonografia, jako skuteczna i sprawdzona klinicznie metoda, stosowana jest od kilku dekad w diagnostyce chorób wątroby, jej naczyń i nadciśnienia wrotnego. Wykorzystywana jest zarówno na poziomie diagnostyki wstępnej, jak i specjalistycznej – wykonywanej w ośrodkach referencyjnych. Wartość diagnostyczna ultrasonografii w dużym stopniu zależy od znajomości anatomii, fizjologii, patofizjologii i aspektów klinicznych, a także stopnia opanowania techniki badania. W rękach doświadczonego lekarza metoda ta jest precyzyjnym i bardzo skutecznym narzędziem diagnostycznym, w przeciwnym razie jest bezużyteczna. W opracowaniu omówiono podstawowe elementy anatomii, fizjologii i patofizjologii, które stanowią o wyjątkowości układu wrotnego, a których znajomość jest kluczowa i niezbędna dla prawidłowego wykonania badania, a przede wszystkim właściwej interpretacji wyników. Przedstawiono wymagania dotyczące zaawansowania wykorzystywanej aparatury. Omówiono różne techniczne aspekty badania oraz prawidłowy obraz morfologiczny i parametry hemodynamiczne u osób zdrowych, a także najczęstsze sytuacje kliniczne i związane z nimi odchylenia od norm w wykonywanych badaniach. Prezentowana praca oparta jest na kilkunastoletnim doświadczeniu autora pracującego w największym ośrodku chirurgii wątroby w Polsce oraz na podstawie aktualnego piśmiennictwa

Standards of the Polish Ultrasound Society – update. Ultrasound examination of the visceral arteries

Ultrasound examination is a valuable method in diagnosing visceral vasoconstriction of atherosclerotic origin, as well as constriction related to the compression of the celiac trunk. Given the standard stenosis recognition criteria of >70%, the increase in peak systolic velocity (PSV) over 200 cm/s in the celiac trunk; of PSV > 275 cm/s in the superior mesenteric artery, and of PSV > 250 cm/s in the inferior mesenteric artery, the likelihood of correct diagnosis is above 90%. In the case of stenosis due to compression of the celiac trunk by median arcuate ligament of the diaphragm, a valuable addition to the regular examination procedure is to normalize the flow velocity in the vessel, i.e. the reduction in peak systolic velocity levels below 200 cm/s, and in end-diastolic velocity (EDV) levels below 55 cm/s during deep inspiration. In the case of celiac trunk stenosis exceeding 70–80%, additional information on the level of collateral circulation can be obtained by measuring the flow in the hepatic and splenic arteries – assessing the flow velocity, resistance, and pulsatility indices (which fall below 0.65 and below 1.0 in cases of stenosis of the celiac trunk with a reduced capacity of collateral circulation), as well as assessing the changes in these parameters during normal respiration and during inspiration. This paper discusses in detail the examination methods for the celiac trunk and mesenteric arteries, as well as additional procedures used to confi rm the diagnosis and pathologies affecting visceral blood flow velocity, i.e.: cirrhosis and hypersplenism. The publication is an update of the Polish Ultrasound Society guidelines published in 2011

Standards of the Polish Ultrasound Society. Ultrasound examination of the portal system and hepatic vessels

Increased incidence of liver diseases, the development of liver surgery and other invasive methods for managing portal hypertension, plus an increasing number of liver transplant procedures pose more and more new challenges for ultrasonography. Ultrasonography,being an effective and clinically verifi ed modality, has been used for several decades for diagnosing diseases of the liver, its vessels and portal hypertension. It is used for both initial and specialist diagnosis (performed in reference centers). The diagnostic value of ultrasonography largely depends on the knowledge of anatomy, physiology, pathophysiology and clinical aspects as well as on the mastering of the scanning technique. In the hands of an experienced physician, it is an accurate and highly effective diagnostic tool;it is of little use otherwise. The paper presents elements of anatomy, physiology and pathophysiology which make the portal system exceptional and the knowledge of which is crucial and indispensable for a correct examination and, above all, for the correct interpretation of results. The authors also present requirements regarding the equipment. Moreover,various technical aspects of the examination are presented and the normal morphological picture and hemodynamic parameters of healthy individuals are described. The authors discuss the most common clinical situations and rare cases during ultrasound examinations.The paper is based on the experience of the author who works in the largest center of liver diseases in Poland, and on the current literature

Does the Reaction of Inflorescences and Flowers of the Invasive <i>Prunus serotina</i> Ehrh. to Various Herbicides Give Hope for Elimination of This Species from Polish Forests?

The North American Prunus serotina Ehrh. is an invasive neophyte widespread in Polish forests. Due to the negative impact of this species on native vegetation, the most effective methods of its removal from the stands have been searched for. Our research aimed to determine whether herbicides that were applied in spring 2020 influenced morphological features of inflorescences and flowers of P. serotina in the next year of vegetation (i.e., 2021). So far, the effects of herbicides used were analysed in the same year, no later than a few weeks after their application. The experiment was carried out on the research area of 2.7 ha located in the Zielonka Forest near Poznań in Poland (N 52.5330, E 17.1015). The response of 39 P. serotina trees to six different herbicides, containing sulfonylurea derivatives, glyphosate and phenoxy herbicides was investigated. The chemicals were applied directly to the tree, to the holes made in the trunk axis. The plant material included inflorescences from 10 control trees and 29 trees treated with different herbicides. Nine morphological inflorescence and flower features and three ratios were analysed. In total 200 inflorescences and 1000 flowers were measured. Statistically significant differences between inflorescence and flower features collected from trees treated with different herbicides were demonstrated. The largest ranges of values of the studied features were found in inflorescences and flowers collected from the control trees (C-WI, C-DWH). The greatest variability of the studied features was found for C-DWH. Compared to the control trees the reduction in inflorescence size, as well as the smaller number of flowers, were recorded in the trees treated with different herbicides, irrespective of an active substance content. The use of six different herbicides—with different active substance contents to control P. serotina proves to be effective