A Universal Antigen-Ranking Method to Design Personalized Vaccines Targeting Neoantigens against Melanoma

Background: The main purpose of this article is to introduce a universal mathematics-aided vaccine design method against malignant melanoma based on neoantigens. The universal method can be adapted to the mutanome of each patient so that a specific candidate vaccine can be tailored for the corresponding patient. Methods: We extracted the 1134 most frequent mutations in melanoma, and we associated each of them to a vector with 10 components estimated with different bioinformatics tools, for which we found an aggregated value according to a set of weights, and then we ordered them in decreasing order of the scores. Results: We prepared a universal table of the most frequent mutations in melanoma ordered in decreasing order of viability to be used as candidate vaccines, so that the selection of a set of appropriate peptides for each particular patient can be easily and quickly implemented according to their specific mutanome and transcription profile. Conclusions: We have shown that the techniques that are commonly used for the design of personalized anti-tumor vaccines against malignant melanoma can be adapted for the design of universal rankings of neoantigens that originate personalized vaccines when the mutanome and transcription profile of specific patients is considered, with the consequent savings in time and money, shortening the design and production time.

Diagnostics in assisted human reproduction

The World Health Organization (WHO) estimates that 50-80 x 10(6) couples in the world are infertile, i.e. 7-15% of all couples of reproductive age (15-45 years old). The term infertility refers to couples who have been unable to conceive children for at least 1 year of regular unprotected intercourse. Although the frequency and origin of infertility varies, approximately 40-60% of the aetiology of infertility in the population studied is due to female causes. The introduction of assisted reproduction techniques, which offer couples the best opportunities for pregnancy, has opened a vast field of knowledge in reproductive biology. The medical history must be taken meticulously, with enough time to obtain the largest possible amount of relevant information. It is recommended that both partners be included in the initial work-up. In recent decades, technological progress has been favoured with the development of a great variety of diagnostic tests. Moreover, a very valuable tool helping to solve this problem has gained strength and is available to everybody - so-called 'evidence-based medicine'. There are three categories in infertility diagnostic tests. The first category includes tests showing a well-established correlation with pregnancy, e.g. semen analysis, tubal patency with hysterosalpingography or laparoscopy, and ovulation detection. The second category includes patients whose results are not consistently related to pregnancy. Here, these tests include sperm penetration assay in the zona-free hamster oocyte, post-coital tests, sperm penetration into cervical mucus, and tests to detect anti-sperm antibodies. The third group includes patients whose tests are not correlated with pregnancy. The relevant tests include endometrial biopsy, the presence of varicocele, and Chlamydia detection tests. Tests for infertility are often expensive. Since these patients are usually anxious and eager and will do almost anything to have a child, care must be taken to avoid exploitation of their hopes with unnecessary procedures. This text now reviews and updates the procedures used to investigate infertility.

Complexity and fragility in ecological networks

A detailed analysis of three species-rich ecosystem food webs has shown that they display skewed distributions of connections. Such graphs of interaction are, in fact, shared by a number of biological and technological networks, which have been shown to display a very high homeostasis against random removals of nodes. Here, we analyse the responses of these ecological graphs to both random and selective perturbations (directed against the most-connected species). Our results suggest that ecological networks are very robust against random removals but can be extremely fragile when selective attacks are used. These observations have important consequences for biodiversity dynamics and conservation issues, current estimations of extinction rates and the relevance and definition of keystone species.

High levels of cytokine-producing cells in the lung tissues of patients with fatal hantavirus pulmonary syndrome

Hantavirus pulmonary syndrome (HPS) is characterized by the rapid onset of pulmonary edema and a high case-fatality rate. Hantavirus antigens have been demonstrated in pulmonary capillary endothelial cells, but the mechanisms causing capillary leakage remain unclear. Immunohistochemical staining was used to enumerate cytokine-producing cells (monokines: interleukin [IL]-1alpha, IL-1beta, IL-6, and tumor necrosis factor [TNF]-alpha; lymphokines: interferon-gamma, IL-2, IL-4, and TNF-beta) in tissues obtained at autopsy from subjects with HPS. High numbers of cytokine-producing cells were seen in the lung and spleen tissues of HPS patients, but only low numbers in the livers and kidneys. A modest increase in the numbers of cytokine-producing cells was detected in the lungs of patients who died with non-HPS acute respiratory distress syndrome (ARDS), and very few (or no) cytokine-producing cells were detected in the lungs of patients who died of causes other than ARDS. These results suggest that local cytokine production may play an important role in the pathogenesis of HPS.