Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST

Given the constraints faced in the development of new drugs, the importance of drug repurposing has reached unprecedented levels. A key aspect of effective drug repurposing lies in the discovery of disease mechanisms and the identification of clusters of diseases with shared mechanistic characteristics. While various methods exist for computing candidate disease mechanisms and clusters, the absence of ground truth presents challenges in validating these predictions through in silico means. This obstacle significantly impedes the widespread adoption of in silico prediction tools, as experimentalists often hesitate to conduct wet-lab validations without clearly quantified initial plausibility. To address this issue, we introduce DIGEST (in silico validation of disease and gene sets, clusterings or subnetworks). DIGEST is a Python-based validation tool that offers multiple avenues for utilization. It is accessible as a web interface through https://digest-validation.net, as a stand-alone package, or via a REST API. DIGEST streamlines the process of in silico validation by providing fully automated pipelines. These pipelines encompass critical components such as disease and gene ID mapping, enrichment analysis, comparisons of shared genes and variants, and background distribution estimation. Additionally, DIGEST incorporates functionality to automatically update the external databases utilized by the pipelines. By employing DIGEST, users gain the ability to assess the statistical significance of candidate mechanisms in terms of functional and genetic coherence. The tool enables the computation of empirical P-values with ease, requiring only a few simple clicks. With its comprehensive and user-friendly features, DIGEST greatly facilitates the evaluation of candidate mechanisms, empowering researchers to quantify the plausibility of predicted mechanisms in a robust and efficient manner.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202

Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing

In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools have emerged to identify potential drug repurposing candidates. However, these tools often require complex installation and lack intuitive visual network mining capabilities. To tackle these challenges, we introduce Drugst.One, a platform that assists specialized computational medicine tools in becoming user-friendly, web-based utilities for drug repurposing. With just three lines of code, Drugst.One turns any systems biology software into an interactive web tool for modeling and analyzing complex protein-drug-disease networks. Demonstrating its broad adaptability, Drugst.One has been successfully integrated with 21 computational systems medicine tools. Available at https://drugst.one, Drugst.One has significant potential for streamlining the drug discovery process, allowing researchers to focus on essential aspects of pharmaceutical treatment research.Comment: 45 pages, 6 figures, 7 table

The myth of western knight : about the white fever among Japanese women

The aim of this paper is to demonstrate the specificity of male-female relationships between Japanese women and white men. The most popular approach to the problem concentrates on the perspective of white men with a yellow fever who tend to idealize Asian women perceiving them as perfect lovers or wives. However, this paper’s main intention is to analyze the problem from the side of Japanese women who are building the image of white men in contrast to Japanese men who are seen as entangled in patriarchal stereotypes and sexism. When looking for causes of the phenonenon I shall refer to Western chivalry fantasy - the term coined by Karen Ma which illustrates the fanciness of western chivalry which is built in isolation from the real facts. This feeling leads to akogare - longing for the idealized image of white man which seems to say more about women themselves and their dreams than about the objects of their adoration

The "kawaii" phenomenon as a form of aestheticization of the commonplace

The aim of the article is to broadly present the phenomenon called kawaii, which started in Japan and is now becoming popular all over the world. The term kawaii can be translated from Japanese as 'cute', 'sweet', or 'soft', but at the same time it involves other, often omitted meanings, which prevents us from the full understanding of its essence and character (the elements of kowai - 'scary' in Japanese, but also: 'grotesque', 'exaggeration', 'absurd'). The article presents not only the eaning of the term, but also the origin of the phenomenon, the different causes of its initial and spreading popularity, as well as many examples showing the level of its expansion in Japan. Kawaii will also be shown in reference to Sharon Kinsella's idea for classification. According to her, there exist four spaces on which kawaii is highly popular: food, idols, clothes, and fancy goods. The area mentioned as last refers to very characteristic kawaii goods, the essence of which is not practical use, but an aesthetical value and a metaphorical meaning which helps in creating the identity of their owners. The last part will concentrate on the effects of the kawaii phenomenon as well as the distinctive traits which - contrary to the first glance - show the 'japaneseness' of the phenomenon and classify it as a part of local culture

The spectator of the Krakow Opera and their importance for the management of the institution

Celem mojej pracy jest charakterystyka publiczności Opery Krakowskiej na tle zmian, które zachodzą obecnie w świecie opery. Z jednej więc strony, ukazuję specyfikę owych przemian; równocześnie zaś zarysowuję obraz Opery Krakowskiej – z jej misją, celami, repertuarem, zasobami oraz działaniami w sferze marketingu i public relations. Na takim tle odnoszę się do widzów Opery Krakowskiej, którzy powinni stanowić wsparcie dla zarządzania instytucją w świetle zachodzących zmian, do których opera jest zmuszona się przystosować. Stwierdzenie to, stanowiące główną tezę pracy, odnosi się zarówno do socjologicznej charakterystyki widzów, ich motywów uczestnictwa w wydarzeniach operowych, przyjmowanych sposobach odbioru, stosunku do nowoczesności, jak i do ich profilu marketingowego, co łącznie prowadzi do kompleksowego ujęcia problemu, które w swoim założeniu wpisuje się w nurt zarządzania humanistycznego. Jest to zgodne z tendencją do indywidualizacji oczekiwań odbiorców, dla których wizyta w operze stanowi sposób na poszukiwanie osobistych przeżyć; w konsekwencji zadaniem Opery staje się budowanie pogłębionych relacji z publicznością, poprzedzonych odpowiednimi badaniami, które pomogą zrozumieć ich potrzeby oraz w efekcie podjąć odpowiednie działania, mające na celu ich zaspokojenie.The aim of my thesis is to show the characteristics of the audience of the Krakow Opera against the background of the changes that are taking place in the the opera world. On the one hand, I show the specificity of these changes, when on the other I present the institution of the Krakow Opera - with its mission, objectives, repertoire, resources and activities in the field of marketing and public relations. At that background I refer to the Krakow Opera spectators who, as I argue on the basis of research, should provide support to the management of the institution in the light of the changes, which the Opera is forced to adapt. The above statement, which constitute the main thesis of my project, is proved by reference to both the sociological characteristics of the audience, their motives for participation in the events, the ways of reception, the attitude to modernity, as well as their marketing profile, what leads to the complex approach to the problem, which can be understood as the part of the humanistic management. Nowadays there is the tendency to individualize the expectations of spectators for whom a visit to the opera is the way of seeking personal experiences. Consequently, it becomes the task of the Opera to build in-depth relationships with the audience, preceded by research, which is the only way to understand the audience's needs and take action to meet them

The image of man in visual kei

Praca, zatytułowana Wizerunek mężczyzny w visual kei, stanowi próbę wskazania sposobów kreacji wizerunku artystów tej sceny, jak również różnorakich motywów, zaczerpniętych zarówno z kultury rodzimej, jak i obcych, które wpłynęły na kształtowanie fenomenu lub też stają się źródłem inspiracji do jego odnawiania i rozwoju. Visual kei nie jest gatunkiem muzycznym, lecz stylem w japońskiej muzyce, który niezwykłą wagę przykłada do wielowymiarowości przekazu jak również, do współistniejących na poziomie równoważnym z muzyką, efektów wizualnych. Opisując wizerunek artystów, którzy do niego przynależą, odnoszę się zarówno do elementów i inspiracji przejętych z Zachodu (np. glam rock, motywy gotyckie), jak i tych mających swoje korzenie w kulturze tradycyjnej. Niezwykle istotne jest również zwrócenie uwagi na elementy japońskiej popkultury, których reprezentacja wyraźnie widoczna jest w visual kei, wpisując zjawisko w ramy współczesnej kultury (np. shoujo, mangi YAOI). Dla zrozumienia wizerunku muzyków, kluczowe jest również wzięcie pod uwagę samej definicji męskości w Japonii, mocno rozwiniętej estetyki ciała oraz znaczenia cross-dressingu. W dalszej kolejności trzeba również przyjrzeć się zróżnicowanej i ambiwalentnej japońskiej estetyce, a także japońskiemu teatrowi, których znaczenie dla całego zjawiska wydaje się odgrywać niebagatelną rolę. Wielość ukazanych zagadnień umożliwia szerokie spojrzenie na scenę visual kei, której istota nie zostanie uproszczona do jednego aspektu, lecz ukazana w całej swojej barwnej różnorodności opartej na zasadzie fantazji, piękna oraz wolności.The thesis The image of man in visual kei depicts the methods of the image's creation used by the visual kei artists. However, the paper shows also different motifs taken from the native Japanese culture, and those taken from abroad, which influenced the phenomenon's origin or can be treated as the source of inspirations of visual kei revival and further development. Visual kei is not a music genre, it is a style in Japanese music, which puts a special effort on the multidimensional message and the visual effects which meaning is comparable to this of the music itself. Describing musicians' image I refer to the motifs and inspirations from the West (for example glam rock, gothic motifs), and to these which roots lie in the Japanese traditional culture. The emphasis should be put on the elements of Japanese popular culture which are so well visible in visual kei. It inscribes visual kei into the frames of contemporary Japanese culture (for example shoujo, YAOI manga). Furthermore, it is obligatory to analyze the definition of masculinity in Japan, and the meaning of body aesthetics or cross-dressing to be able to better understand visual kei. The highly diversified and ambivalent Japanese aesthetics, particularly the Japanese theater also had a strong impact on the phenomenon. The multiplicity of presented cases will lead to a wider view on the whole scene of visual kei which will not be limited to one aspect only, but rather presented in its variety based on the rule of fantasy, beauty and freedom

Potentilla chinensis aqueous extract attenuates cyclophosphamide-induced hemorrhagic cystitis in rat model

Cyclophosphamide (CYP) damages all mucosal defence lines and induces hemorrhagic cystitis (HC) leading to detrusor overactivity. Patients who undergo combined chemio-radiotherapy are at higher risk of HC. Potentilla chinensis extract (PCE) prevent oxidative stress-dependent diseases. Thus, the aim of the study was to investigate the effect of PCE on urinary bladder function in CYP-induced HC in preclinical study. 60 rats were divided into 4 groups, as follows: I—control, II—rats with CYP-induced HC, III—rats received PCE in dose of 500 mg/kg, and IV—rats with CYP-induced HC which received PCE in dose of 500 mg/kg. PCE or vehicle were administered orally for 14 days. The cystometry was performed 3 days after the last dose of the PCE. Next, urothelium thickness and oedema measurement and biochemical analyses were performed. Cyclophosphamide induced hemorrhagic cystitis. PCE had no influence on the urinary bladder function and micturition cycles in normal rats. PCE diminished the severity of CYP-induced hemorrhagic cystitis. In the urothelium the cyclophosphamide induced the elevation of CGRP, TNF-α, IL-6, IL-1β, OTC(3,) NIT, and MAL. Also, the level of T-H protein, HB-EGF, and ZO1 was decreased. Moreover, the level of ROCK1 and VAChT in detrusor muscle increased. cyclophosphamide caused an increased concentration of BDNF and NGF in the urine. In turn, PCE in cyclophosphamide-induced hemorrhagic cystitis caused a reversal of the described biochemical changes within urothelium, detrusor muscle and urine. PCE attenuates detrusor overactivity. In conclusion, our results revealed that PCE attenuates detrusor overactivity in case of cyclophosphamide-induced hemorrhagic cystitis. The potential properties of PCE appear to be important in terms of preventing of oxidative stress-dependent dysfunction of urinary bladder. PCE may become a potential supportive treatment in patient to whom cyclophosphamide-based chemotherapy is used