KnotProt: a database of proteins with knots and slipknots.

The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints

Cancer epidemiology in Poland

W pracy przedstawiono obraz epidemiologiczny nowotworów złośliwych w Polsce, jego zmiany w czasie oraz porównanie z krajami Unii Europejskiej. Przebieg trendów czasowych umieralności w głównych lokalizacjach nowotworów złośliwych w Polsce jest podobny do obrazu nowotworowego krajów UE. Transformacja epidemiologiczna umieralności z powodu nowotworów w Polsce odbywa się w stosunku do krajów Europy Zachodniej z pewnym opóźnieniem czasowym.  Ogółem trendy epidemiologiczne wszystkich lokalizacji nowotworowych są uśrednieniem rozbieżnych trendów w zachorowaniach na poszczególne nowotwory, często zdominowanym przez zmiany trendów największych lokalizacji nowotworowych. Tak dzieje się np. u mężczyzn w Polsce w przypadku umieralności na nowotwory złośliwe płuca. W drugiej części pracy poddano analizie zjawisko zachorowalności, które także wskazuje na wyraźne zróżnicowanie trendów czasowych poszczególnych lokalizacji. Trendy częstości zachorowań mierzone bezwzględną liczbą nowo diagnozowanych chorób zależą od wielu czynników — środowiskowych czynników ryzyka (np. częstości palenia), które są modyfikowalne, ale także kluczowe znaczenie mają zmiany struktury wieku populacji. Krzywa zachorowań rośnie wykładniczo wraz ze wzrostem długości życia (czynnik niemodyfikowalny). Znaczna większość (60%) zachorowań na nowotwory złośliwe jest diagnozowana wśród osób po 65 r.ż., a w Polsce obserwuje się stały przyrost ludności w tym wieku. Trzy zjawiska są najbardziej charakterystyczne dla obrazu trendów czasowych zachorowalności z powodu nowotworów złośliwych w Polsce: 1) gwałtowny spadek zachorowań z powodu nowotworów złośliwych płuca u mężczyzn (po okresie trwającego kilka dekad wzrostu zachorowań); 2) bardzo szybki wzrost zachorowań z powodu nowotworów złośliwych prostaty, szczególnie po 1990 roku; 3) dramatyczny wzrost nowo diagnozowanych nowotworów złośliwych piersi u kobiet, który zdominował zachorowalność na nowotwory złośliwe w Polsce u kobiet (obecnie co czwarty nowo diagnozowany nowotwór u kobiet to nowotwór złośliwy piersi). Dodatkowo szczegółowej analizie epidemiologicznej poddano kilka głównych lokalizacji nowotworów złośliwych (nowotwory płuca, piersi, gruczołu krokowego, jelita grubego, szyjki macicy i żołądka) oraz przedstawiono ich po­równanie z innymi krajami.  Największy sukces w kontrolowaniu nowotworów złośliwych osiągnięto w tych schorzeniach, w których możliwa jest prewencja (przede wszystkim nowotwory złośliwe płuca u mężczyzn), ale także w tych nowotworach, gdzie możliwy jest skuteczny populacyjny skrining (nowotwory złośliwe szyjki macicy, nowotwory złośliwe piersi).This paper presents the epidemiological picture of cancer in Poland, its changes over time and a comparison with other countries of the European Union (EU). The mortality time trends for the main cancer sites in Poland are similar to those observed in other EU countries. However, the epidemiological transformation in cancer mortality in Poland is delayed with respect to countries of Western Europe. The overall epidemiological trends are an average of the individual trends for different cancers, often dominated by changes in trends for the major cancer sites. This is observed, for example, in the case of male lung cancer mortality in Poland. In the second part of the study we analysed cancer morbidity, which also demonstrated clear differences in time trends in each site. Incidence trends measured by the absolute number of newly diagnosed diseases depend on many factors. The most important factor is the modifiable environmental risk factors (e.g. smoking prevalence), as well as the changes in the age structure the population. The incidence curve grows exponentially with the increase of lifespan (a non-modifiable factor). The vast majority (60%) of cancer cases are diagnosed among people over 65 years, and in Poland a steady increase of population in this age group is observed. Three phenomena emerge as the most characteristic of the time trends of cancer morbidity in Poland. (1) A sharp decline in incidence of lung cancer in men (after a period of rising incidence that lasted for decades). (2) Rapid growth in incidence of prostate cancer, especially after 1990. (3) A dramatic increase in newly diagnosed breast cancer cases in women, which dominated the incidence of cancer in women in Poland (currently one in four of newly diagnosed cancers among women is breast cancer).In addition, a detailed epidemiological analysis was conducted for several major cancer sites (lung, breast, prostate, colorectal, cervix and stomach) and its results were compared with trends observed in other countries. The biggest success in cancer control was achieved in those cancer locations, for which prevention is possible (especially lung cancer in men), and also in those cancers, where it is possible to effectively screen a population (cervical cancer, breast cancer).

Lung cancer, the leading cause of cancer deaths among women in Europe

Wstęp. Artykuł ten ma celu przedstawienie obrazu umieralności wśród kobiet w krajach Unii Europejskiej z powodu nowotworów złośliwych płuca na tle umieralności z powodu raka piersi. Badanie ma także na celu zwrócenie uwagi na czynnik ryzyka nowotworów płuca, jakim jest palenie tytoniu — wciąż rozwijający się problem zdrowia publicznego. Materiał i metody. Materiał będący podstawą tego opracowania stanowią dane o zgonach z powodu nowotworów złośliwych płuca i piersi u kobiet w Polsce i w innych krajach Unii Europejskiej za wszystkie dostępne lata w okresie 1960–2010. Analizę trendów czasowych umieralności z powodu nowotworów złośliwych płuca i piersi przeprowadzono przy użyciu programu Joinpoint Regression Program. Analizą objęto kobiety w wieku 45–74 lat. Wyniki. Umieralność z powodu raka płuca wśród kobiet rośnie od wielu lat i w większości krajów ta przyczyna zgonów już jest lub w najbliższej dekadzie będzie najczęstszą przyczyną zgonów nowotworowych Europejek. Podsumowanie. Nowotwory złośliwe płuca stają się pierwszą przyczyną zgonów nowotworowych wśród kobiet w Europie. W większości krajów trendy czasowe umieralności wykazują tendencję wzrostową. Głównym tego powodem jest rozwój epidemii palenia tytoniu wśród kobiet. Leczenie zespołu uzależnienia od tytoniu wydaje się być najskuteczniejszym sposobem na zmianę tych niekorzystnych tendencji. Edukowanie kobiet i wskazywanie efektywnych sposobów zerwania z paleniem papierosów powinno pozostawać priorytetem w zakresie działań prewencji pierwotnej nowotworów i promocji zdrowia.Introduction. This article presents the picture of mortality from lung cancer among women in the European Union in relation to breast cancer mortality. It also draws attention to tobacco smoking as a main cause of lung cancer and still a significant public health problem. Material and methods. Data on mortality due to lung cancer and breast cancer among women in Poland and other European Union countries were derived from the WHO mortality statistics for the period 1960–2010. The analysis of time trends in mortality from lung cancer and breast cancer were performed using Joinpoint Regression Program for women aged 45–74 years. Results. Lung cancer mortality among women has been increasing for many years, and in most countries this is already or will be in the next decade, the leading cause of cancer deaths European women. Conclusions. Lung cancer is the leading cause of cancer deaths among women in Europe. In majority of countries the mortality time trends are increasing and the main reason for this is a persistent epidemic of tobacco smoking in women. Treatment of tobacco dependence seems to be the most effective way to change these negative trends. Educating women and indicating them to effective ways of smoking cessation should remain a priority of cancer primary prevention and health promotion activities

Palenie tytoniu a umieralność na choroby odtytoniowe w Europie Środkowo-Wschodniej

Tobacco smoking and smoking-attributable mortality in Central and Eastern EuropeTobacco is the major determinant of the health gap between the east (EU10) and the west part (EU15) of European Union. Over half of the excess mortality among middle-aged men in the EU10 countries might have been avoided if the tobacco consumption of these men had been the same as that of equivalent men in the EU15. The role of tobacco in shaping mortality differences between the EU10 and EU15 countries in women is less prominent than in men. Nevertheless, about one fourth of the excess mortality among middle-aged women in EU10 countries can be attributed to their higher tobacco consumption. 41% of male deaths between 35 and 64 years were attributable to tobacco smoking in the EU10 countries compared with 33% in the EU15 countries. The figures for women were 17% in the EU10 and 14% in the EU15 countries. It is worth emphasizing that, in some EU10 countries, the tobacco control policies and programmes have already produced notable results on tobacco- attributable mortality, in particular among men

Palenie tytoniu w populacji mężczyzn i kobiet w Polsce w latach 1974–2004

Tobacco smoking in male and female population, Poland 1974–2004On the basis of nation-wide randomized surveys, this paper analyzes patterns and trends of smoking prevalence in Polish adult (20+) population. In 1974, 62% of adult men and 19% of women smoked daily. In 1982, smoking rates reached the highest level ever observed in Poland (among Poles aged 20–39, 70-80% of men and  0-50% of women smoked daily). Percent of former smokers was low (15% for men, 6% for women). There was also big gender difference in prevalence of never smoking (15% in men, 70% in women). In the past two decades, substantial decline in smoking prevalence is observed. In men, decline in smoking rates (43% of daily smokers in 2000–2004), contributed to decrease in lung cancer mortality. In women, smoking rates have not changed since the mid-1980s and did not led to decrease in lung cancer mortality, however, there are three different age-specific time trends in smoking prevalence in female population

AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods

AlphaKnot is a server that measures entanglement in AlphaFold-solved protein models while considering pLDDT confidence values. AlphaKnot has two main functions: (i) providing researchers with a webserver for analyzing knotting in their own AlphaFold predictions and (ii) providing a database of knotting in AlphaFold predictions from the 21 proteomes for which models have been published prior to 2022. The knotting is defined in a probabilistic fashion. The knotting complexity of proteins is presented in the form of a matrix diagram which shows users the knot type for the entire polypeptide chain and for each of its subchains. The dominant knot types as well as the computed locations of the knot cores (i.e. minimal portions of protein backbones that form a given knot type) are shown for each protein structure. Based mainly on the pLDDT confidence values, entanglements are classified as Knots, Unsure, and Artifacts. The database portion of the server can be used, for example, to examine protein geometry and entanglement-function correlations, as a reference set for protein modeling, and for facilitating evolutional studies. The AlphaKnot server can be found at https://alphaknot.cent.uw.edu.pl/

Morbidity and mortality trends of the most common cancers in 1990–2019. Poland's position compared to other European countries

Introduction.The purpose of the study was to evaluate the trends in morbidity and mortality of the selected cancer sites in Poland against other European countries. Material and methods.Countries for analysis were selected based on geographical location. Estimates of age-adjusted incidence and mortality rates were calculated using the new European 2013 standard population. Lung, colorectal, breast, and prostate cancers were chosen. Time trends for age-standardized rates were  analyzed using Jointpoint Regression software. Results.Poland differed from other analyzed countries mainly in terms of cancer mortality. Poland is a country with one of the smallest amounts of current expenses on health care per capita, which translates into one of the highest levels of cancer mortality in both women and men. Conclusions.Compared to other countries, Poland's cancer outcomes on population level are unsatisfactory. The situation may improve with the introduction of educational and screening programs

Morbidity and mortality trends of the most common cancers in 1990–2019. Poland’s position compared to other European countries

Introduction. The purpose of the study was to evaluate the trends in morbidity and mortality of the selected cancer sites in Poland against other European countries. Material and methods. Countries for analysis were selected based on geographical location. Estimates of age-adjusted incidence and mortality rates were calculated using the new European 2013 standard population. Lung, colorectal, breast, and prostate cancers were chosen. Time trends for age-standardized rates were analyzed using Joinpoint Re­gression software. Results. Poland differed from other analyzed countries mainly in terms of cancer mortality. Poland is a country with one of the smallest amounts of current expenditures on health care per capita, which translates into one of the highest levels of cancer mortality in both women and men. Conclusions. Compared to other countries, Poland’s cancer outcomes on population level are unsatisfactory. The si­tuation may improve with the introduction of educational and screening programs