Dynamics of the human gut phageome during the antibiotics therapy

Antibiotics are widely used in all sorts of the medical procedures. Without them, modern medical practice is not possible. As much as they are inevitable, they have severe adverse effects in promoting the antibiotic resistance. Each antibiotic therapy has a profound impact on the human gut. Firstly antibiotics select resistant bacteria what results in rapid changes of the taxonomical composition of the human gut. Secondly, the antibiotic pressure prompts the horizontal gene transfer including transduction that is intermediated by the phages, what advances spread of the resistance. Although the taxonomical composition restores after a month from the therapy, the bacteria get enriched with the genes conferring resistance to antibiotics. We have analyzed changes in the microbiome and phageome of the two people throughout the antibiotic therapy and subsequent recovery time. Analysis of the phage genomes is bioinformatically tricky as phages have complex genomic structures and there are no reliable reference databases. Therefore, we developed a novel comprehensive pipeline for the time-series analysis of the metagenomic datasets focusing on the function and changes in the phage sequences. We observed the phages respond to the antibiotic therapy, and are enriched with antibiotic-resistant genes

Dokàd zmierzasz, Ukraino? What Future for Ukraine? Point of View No. 11, June 2005

No abstract

Bioinformatics approaches to study antibiotics resistance emergence across levels of biological organization.

The Review on Antimicrobial Resistance predicts that in thirty years infections with antibiotic-resistant microorganisms will become one of the leading causes of death. The discovery of new antibiotics has so far been too slow to ensure continuous use of antibiotics in the face of growing resistance. Therefore, efforts to curb resistance emergence gain in importance. These efforts comprise two complementary strategies. The first focuses on the mechanisms of resistance emergence, in the hope that it would enable development of pharmacological agents constraining resistance emergence. The second aims at improving antibiotic use practices, based on studies of the impact of antibiotics on resistance emergence within patient populations. Antibiotic resistance emerges in bacterial cells, negatively influences the human gut microbiome, and transfers between people. Hence, antibiotic resistance has impacts across several levels of biological organization. This thesis describes four projects, which concerned various aspects of antibiotics resistance. The first two projects deal with basic resistance emergence mechanisms, on the level of bacterial strains and bacterial consortia, whereas the other two deal with finding better practices for antibiotic use on a population level. During the first project, I analyzed changes in genomes of MRSA strains isolated from several patients throughout antibiotic therapies and developing MRSA infections. I observed changes in number and types of virulence factors responsible for interacting with the human body, which are attributed to mobile genetic elements. In the second project, I showed that, prompted by antibiotic therapy, within the human gut microbiome resistance transfers from bacterial genomes onto plasmids, prophages, and free phages. Hence, resistance emergence depends not only on the antibiotic therapy but also on the state of the gut microbiome, which again results from the patients’ overall health and previous antibiotic therapies. The third project, SATURN, employed machine learning methods for a large set of data regarding patients’ demographics, comorbidities, antibiotic therapies, surgeries, and colonization with multi-drug resistant bacteria. The final classifiers were made available on the AskSaturn website where the doctors can compare antibiotic therapies based on the probability of colonization with multi-drug resistant bacteria. The fourth project, Tübiom, focused on the antibiotic-influenced gut microbiomes of the healthy population. The first two projects rely on genome and metagenome sequencing data. For them, I designed specialized bioinformatics analysis pipelines. The latter two projects use mixed data, which were analyzed with machine learning algorithms. These projects also involved web development and data visualization. Although each of the projects requires different data and methods, each of them provides a crucial part in a pipeline aiming at utilizing gut microbiome information in medical practice to constrain resistance emergence

The "other" in court : Islam and Muslims in Polish judicial opinions published online

Muslims are a marginal minority in Poland, but research shows that they are often subject to negative perceptions and hostility from the majority. Orientalist stereotypes about Islam and the people associated with it are widespread and often reproduced in the media. Research from North America and the European Court of Human Rights suggests that such prejudices can affect the adjudication of cases involving Muslims. It may be presumed that Poland is no exception to that, and this assumption was the starting point for our empirical study. To date, there have been no studies on the perception of Muslims and Islam in the Polish legal system. This article presents the results of a qualitative thematic analysis of 57 judicial opinions issued by the common courts in Poland and published online, in which Islam or being Muslim was mentioned. The cases were categorised and texts of the judicial opinions closely analysed (with computer-assisted qualitative data analysis software) to identify recurring themes. The findings of this first exploratory study show that stereotypical representations and the “‘Othering” of Muslims do indeed occur in Polish courts, with some judges repeating Orientalist tropes that have become normalised in Polish society

Wpływ pandemii COVID-19 na ubóstwo energetyczne w UE

The last two years of the pandemic contributed to the increase in energy poverty in the European Union. Energy poverty is becoming more and more common, for many reasons, such as rising fuel prices, hard coal, CO2 emission fees. Energy poverty is understood as a situation where heating costs exceed 10% of income. Energy poverty is defined by the EPEE as “the lack of resources to keep heating at an adequate level at a fair price”. The article will present statistical data on energy poverty based on various indicators in 2018-2020 in EU countries. In addition, the current climate and energy policy in the EU and its assumptions as well as its impact on energy poverty are described. In addition, programs in EU countries that have significantly contributed to improving the situation of energy poverty will be indicated.Ostatnie dwa lata pandemii przyczyniły się do zwiększenia się ubóstwa energetycznego w państwach Unii Europejskiej. Ubóstwo energetyczne jest coraz powszechniejsze, z wielu powodów, takich jak rosnące ceny paliw, węgla kamiennego, opłat emisji CO2. Ubóstwo energetyczne rozumiane jest jako sytuacja, w której koszty ogrzewania przekraczają 10% dochodów. Ubóstwo energetyczne zostało zdefiniowane przez EPEE1 jako „brak środków na utrzymanie ogrzewania na odpowiednim poziomie za uczciwą cenę”. W artykule zostaną przedstawione dane statystyczne dotyczące ubóstwa energetycznego na podstawie różnych wskaźników w latach 2018–2020 w państwach UE. Ponadto opisano aktualną politykę klimatyczno-energetyczną w UE i jej założenia oraz jej wpływ na ubóstwo energetyczne. Dodatkowo wskazane zostaną programy w państwach UE, które istotnie wpłynęły na poprawę sytuacji ubóstwa energetycznego

Statistical Analysis of Soft Commodities Returns in the Period 2007-2016

Soft commodities, often referred to as tropics, constitute a significant element of international trade and are also important to the Polish economy. Moreover, Polish investors may invest in foreign markets of soft commodities through commodity-linked ETFs, offered by some brokerage houses. Obviously, each investment decision should be preceded by an analysis of asset performance. This paper provides results of statistical analysis of soft commodities returns over the period January 2007 to December 2016. They reveal the existence of weak positive correlation between the returns, non-normal distributions, negative trends, and serial autocorrelation

Hydrogels as effective wound dressings in support of wounds treatment

In recent years, the topic of effective wound treatment has become growing in importance due to the increasing rate for their diagnosis, but also because of the raising awareness of wound healing issues. One of the essential parts of the treatment is the use of appropriate wound dressings that actively support the natural healing process. This draws attention to the potential of hydrogel wound dressings, which, as non-adhesive, soft and flexible polymeric products with a high water content, can act as a safe contact layer, reduce pain levels, maintain an appropriate level of moisture and promote autolytic debridement. Hydrogel wound dressings are available in two physical forms, i.e. semi-solid (amorphous hydrogel) and solid (hydrogel sheet). A review of scientific literature shows that they are materials with many benefits in the treatment of dry or weakly exuding and necrotic wounds. However, their use in the management of infected and high exudate wounds is limited. There is therefore a need for their further development to help improve chemical, physical and biological properties, thereby expanding their functionality. Current studies focused on two main strategies, i.e. 1) enhancing therapeutic efficacy by incorporating into the system an active substance with anti-inflammatory and antibacterial activity, or 2) implementing various sensors, that detect, or respond to, environmental stimuli. In order to obtain a product of adequate quality and durability of use, an important part of the research is a detailed evaluation of the properties of the designed materials. Adequate elasticity, mechanical strength, swelling and absorption capacity, as well as internal structure are all factors that need to be examined to assess the functionality of the designed materials as wound dressings. The present review is aimed at systematizing the knowledge of hydrogel wound dressings and identifying future research directions. The work includes a description of their properties, available forms, composition and testing methods

Turystyka, eksport towarowy, pomoc rozwojowa i przekazy jako narzędzia przełamania stagnacji społeczno-gospodarczej w państwach Globalnego Południa o niekorzystnym położeniu geograficznym oraz najsłab

Przedmiotem artykułu jest identyfikacja i ocena zależności pomiędzy wpływami z turystyki, eksportu towarowego, pomocy rozwojowej i przekazów w 83 państwach Globalnego Południa. Państwa te zostały pogrupowane ze względu na cechy geograficzne, które w znacznym stopniu hamują rozwój społeczno-gospodarczy na: małe rozwijające się państwa wyspiarskie, państwa bez dostępu do morza (śródlądowe). Państwa te określono na potrzeby artykułu państwami o niekorzystnym położeniu geograficznym. Dodatkowo wyróżniono grupę państw najsłabiej rozwiniętych. Zależność pomiędzy czterema zmiennymi stanowiła punkt wyjścia do zbadania i oceny związku pomiędzy nimi a obecnym poziomem rozwoju społeczno-gospodarczego w analizowanych państwach Południa. W badaniu zastosowano charakterystyki dla czterech zmiennych w poszczególnych grupach państw, takie jak: średnia, mediana, odchylenie standardowe, współczynnik zmienności, skośność, minimum oraz maksimum. Do identyfikacji zależności pomiędzy zmiennymi wykorzystany został współczynnik korelacji r−Spearmana. Badanie wskazało, że we wszystkich analizowanych państwach, na podstawie uzyskanych wyników, można było zauważyć silny dodatni związek pomiędzy turystyką a eksportem towarowym. W tych państwach, które szczególnie intensywnie rozwijały specjalizację turystyczną (eksport produktu turystycznego) przekładało się to na przełamanie stagnacji gospodarczej i przyspieszenie procesów rozwojowych

Assessment of Efficiency of Investment in Companies Belonging to the Rare Earth Metals Sector

Purpose – This paper aimed at assessing the efficiency of investment in companies belonging to the rare earth elements sector and examining the stability of the results. Research method – The following performance measures were used in the study: modified Sharpe and Omega, Sortino, Calmar, Sterling and Burke ratios. The investigation is based on daily quotations of selected companies whose business activities were related to extraction, processing and recycling of rare earth metals in the period: from July 2018 to June 2023 and MVIS® Global Rare Earth/Strategic Metals Index representing the global market. Results – The analysis for the entire period revealed a worse performance of investments in rare earth stocks than investment in risk-free assets. Only AREC outperformed other securities offering the best results for 3 of 6 ratios. To examine the stability of the results, the total investigation period was divided into 5 subperiods and all performance ratios were determined for each of them. A strong variation of results did not allow to recognise stable patterns. When the results for the entire investigation period were used as a benchmark, only MVREMX offered stable and attractive results of modified Sharpe ratio outperforming the five-year value in 4 out of 5 subperiods. Originality / value / implications / recommendations – This study provides a new insight into the rare earths sector regarding its growing international importance and the efficiency of investments into listed rare earth firms. The examination uses two-dimensional measures offering the advantage of simultaneously combining return and risk into a single performance number. 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