Distributed Bayesian networks reconstruction on the whole genome scale

Background Bayesian networks are directed acyclic graphical models widely used to represent the probabilistic relationships between random variables. They have been applied in various biological contexts, including gene regulatory networks and protein–protein interactions inference. Generally, learning Bayesian networks from experimental data is NP-hard, leading to widespread use of heuristic search methods giving suboptimal results. However, in cases when the acyclicity of the graph can be externally ensured, it is possible to find the optimal network in polynomial time. While our previously developed tool BNFinder implements polynomial time algorithm, reconstructing networks with the large amount of experimental data still leads to computations on single CPU growing exceedingly. Results In the present paper we propose parallelized algorithm designed for multi-core and distributed systems and its implementation in the improved version of BNFinder—tool for learning optimal Bayesian networks. The new algorithm has been tested on different simulated and experimental datasets showing that it has much better efficiency of parallelization than the previous version. BNFinder gives comparable results in terms of accuracy with respect to current state-of-the-art inference methods, giving significant advantage in cases when external information such as regulators list or prior edge probability can be introduced, particularly for datasets with static gene expression observations. Conclusions We show that the new method can be used to reconstruct networks in the size range of thousands of genes making it practically applicable to whole genome datasets of prokaryotic systems and large components of eukaryotic genomes. Our benchmarking results on realistic datasets indicate that the tool should be useful to a wide audience of researchers interested in discovering dependencies in their large-scale transcriptomic datasets

Comparative analysis of classification techniques for topic-based biomedical literature categorisation

Introduction: Scientific articles serve as vital sources of biomedical information, but with the yearly growth in publication volume, processing such vast amounts of information has become increasingly challenging. This difficulty is particularly pronounced when it requires the expertise of highly qualified professionals. Our research focused on the domain-specific articles classification to determine whether they contain information about drug-induced liver injury (DILI). DILI is a clinically significant condition and one of the reasons for drug registration failures. The rapid and accurate identification of drugs that may cause such conditions can prevent side effects in millions of patients.Methods: Developing a text classification method can help regulators, such as the FDA, much faster at a massive scale identify facts of potential DILI of concrete drugs. In our study, we compared several text classification methodologies, including transformers, LSTMs, information theory, and statistics-based methods. We devised a simple and interpretable text classification method that is as fast as Naïve Bayes while delivering superior performance for topic-oriented text categorisation. Moreover, we revisited techniques and methodologies to handle the imbalance of the data.Results: Transformers achieve the best results in cases if the distribution of classes and semantics of test data matches the training set. But in cases of imbalanced data, simple statistical-information theory-based models can surpass complex transformers, bringing more interpretable results that are so important for the biomedical domain. As our results show, neural networks can achieve better results if they are pre-trained on domain-specific data, and the loss function was designed to reflect the class distribution.Discussion: Overall, transformers are powerful architecture, however, in certain cases, such as topic classification, its usage can be redundant and simple statistical approaches can achieve compatible results while being much faster and explainable. However, we see potential in combining results from both worlds. Development of new neural network architectures, loss functions and training procedures that bring stability to unbalanced data is a promising topic of development

The Pediatric Cell Atlas:Defining the Growth Phase of Human Development at Single-Cell Resolution

Single-cell gene expression analyses of mammalian tissues have uncovered profound stage-specific molecular regulatory phenomena that have changed the understanding of unique cell types and signaling pathways critical for lineage determination, morphogenesis, and growth. We discuss here the case for a Pediatric Cell Atlas as part of the Human Cell Atlas consortium to provide single-cell profiles and spatial characterization of gene expression across human tissues and organs. Such data will complement adult and developmentally focused HCA projects to provide a rich cytogenomic framework for understanding not only pediatric health and disease but also environmental and genetic impacts across the human lifespan

Awareness of sewing machine operators about the effect of hand massage on the sensations caused by static load

Ārstnieciskā masāžaVeselības aprūpeMedical MassageHealth CareKvalifikācijas darba tēma: „Šūšanas iekārtu operatoru informētība par rokas masāžas iedarbību uz statiskas slodzes izraisītām sajūtām”, darba autore Alina Frolova. Šūšanas iekārtu operatora darbs ir monotons, parasti ar augstu darba tempu un veselas dienas atkārtojošām elkoņa, plaukstas locītavas un pirkstu kustībām. Darbs pie kniedēšanas ierīcēm prasa neveiklu pozu un uzspiestas augšējo ekstremitāšu kustības ar augšup paceltiem pleciem, izraisot deformāciju kakla un muguras augšdaļā. Lielāko dienas daļu elkoņa un plaukstas locītavas/roku saliekšanās ar slīpu kaklu un galvu un ķermeņa augšdaļu ir radījusi augstu MSD risku (Buckle and Deveraux, 2002). Darbinieki ražošanā ir pakļautas daudziem muskuļu-sistēmas traucējumu riska faktoriem. Līdz ar to viņi ziņo par augstākiem skeleta-muskuļu veselības traucējumu rādītājiem (Schneider and Irastorzan, 2010). Pēc Darba inspekcijas rīcība esošajiem datiem 2018.gadā Latvijā 66,0% no pirmreizēji apstiprinātajiem arodslimniekiem bija sievietes (Valsts darba inspekcija, 2019). Pētījuma mērķis - Noskaidrot šūšanas iekārtu operatoru informētību par rokas masāžas iedarbību uz statiskas slodzes izraisītām sajūtām. Pētījuma jautājums - Vai šūšanas iekārtu operatori pietiekami informēti par rokas masāžas iedarbību uz statiskas slodzes izraisītām sajūtām? Literatūras apskats ietver 2 daļas: Masāžas vispārēja ietekme uz cilvēka organismu un augšējām ekstremitātēm; Statiskas slodzes ietekme uz cilvēka organismu. Pētnieciskā daļa iekļauj sevī pētījuma metodoloģiju, rezultātus un secinājumus. Pētījumā instrumenti: darba autores izstrādāta anketa. Respondenti: 100 sievietes, kas strādā tekstilizstrādājumu ražošanas nozarē. Secinājumi: šūšanas iekārtu operatori nav pietiekami informēti par rokas masāžas iedarbību uz statiskas slodzes izraisītām sajūtām. Atslēgas vārdi: masāža, ārstnieciskā masāža, augšējās ekstremitātes masāža, statiska slodze, šūšanas iekārtu operatori, informētība.Qualification thesis topic: 'Awareness of sewing machine operators on the effect of hand massage on static sensations', by Alina Frolova. The work of a sewing machine operator is monotonous, usually with a high work pace and repetitive movements of the elbow, wrist and fingers throughout the day. Working on riveting machines requires awkward postures and forced movements of the upper limbs with the shoulders up, causing deformities in the neck and upper back. Elbow and wrist/hand flexion with neck and head and upper body inclined for most of the day has resulted in a high risk of MSDs (Buckle and Deveraux, 2002). Workers in manufacturing are exposed to many risk factors for musculoskeletal disorders. Consequently, they report higher rates of musculoskeletal disorders (Schneider and Irastorzan, 2010). According to the Labour Inspectorate, in 2018, 66.0% of first-time confirmed occupational diseases cases in Latvia were women (Valsts darba inspekcija, 2019). Aim of the study - To determine the awareness of sewing machine operators on the effects of hand massage on static sensations. Research question - Are sewing machine operators sufficiently informed about the effects of hand massage on static load-induced sensations? The literature review includes 2 parts: General effects of massage on the human body and upper limbs; Effects of static loading on the human body. The research part includes the research methodology, results and conclusions. Research tools: questionnaire developed by the author. Respondents: 100 women working in the textile industry. Conclusions: sewing machine operators are not sufficiently informed about the effects of hand massage on static sensations. Keywords: massage, therapeutic massage, upper limb massage, static load, sewing machine operators, awareness

THE NATURE OF CHANGES IN THE ELDERLY’S PERSONALITY FEATURES DURING THE POSTEMPLOYMENT PERIOD

The article presents the results of the theoretical and methodological substantiation and empirical verification of the approach to investigation the changes in elderly’s personality features during postemployment period. Theoretical analysis revealed that professional activity should be considered as the significant predictor of differences in perception and adaptation of the elderly. To meet the purpose of the study the sample of research participants was split into two subgroups (employed and unemployed seniors) to reveal changes in their personality features. Results of the empirical study confirmed the significant differences in dispositional traits and other personality features among groups of employed and unemployed seniors (adaptation, self-perception, acceptation of other people, internality, dominance, time orientation, autonomy, spontaneity, self– understanding, autosympathy, sociability, flexibility in communication, self-actualization appeared to be higher among employed seniors comparing to unemployed). Employed elderlies also showed higher level on such scales as: extraversion, agreeableness, self-control, emotional stability, expressiveness in comparison to the group of unemployed ones. The group of unemployed seniors tend to experience higher level of emotional comfort, but at the same time they are characterized by high level of anxiety, frustration, loneliness, aggression and rigidity. The multiple correlation-regression analysis yielded the following hierarchy of the most informative aspects of the elderly’s adaptation. They include: spontaneity and self-realization. The findings open up new prospects for identifying the potential personality precursors of adaptation of the elderly people

Placental CX3CL1 is Deregulated by Angiotensin II and Contributes to a Pro-Inflammatory Trophoblast-Monocyte Interaction

CX3CL1, which is a chemokine involved in many aspects of human pregnancy, is a membrane-bound chemokine shed into circulation as a soluble isoform. Placental CX3CL1 is induced by inflammatory cytokines and is upregulated in severe early-onset preeclampsia. In this study, the hypothesis was addressed whether angiotensin II can deregulate placental CX3CL1 expression, and whether CX3CL1 can promote a pro-inflammatory status of monocytes. qPCR analysis of human placenta samples (n = 45) showed stable expression of CX3CL1 and the angiotensin II receptor AGTR1 throughout the first trimester, but did not show a correlation between both or any influence of maternal age, BMI, and gestational age. Angiotensin II incubation of placental explants transiently deregulated CX3CL1 expression, while the angiotensin II receptor antagonist candesartan reversed this effect. Overexpression of recombinant human CX3CL1 in SGHPL-4 trophoblasts increased adhesion of THP-1 monocytes and significantly increased IL8, CCL19, and CCL13 in co-cultures with human primary monocytes. Incubation of primary monocytes with CX3CL1 and subsequent global transcriptome analysis of CD16+ subsets revealed 81 upregulated genes, including clusterin, lipocalin-2, and the leptin receptor. Aldosterone synthase, osteopontin, and cortisone reductase were some of the 66 downregulated genes present. These data suggest that maternal angiotensin II levels influence placental CX3CL1 expression, which, in turn, can affect monocyte to trophoblast adhesion. Release of placental CX3CL1 could promote the pro-inflammatory status of the CD16+ subset of maternal monocytes

Endogenous cardiotonic steroids in chronic renal failure

Background. Previous reports demonstrated that digitalis-like cardiotonic steroids (CTS) contribute to the pathogenesis of end-stage renal disease. The goal of the present study was to define the nature of CTS in patients with chronic kidney disease (CKD) and in partially nephrectomized (PNx) rats. Methods. In patients with CKD and in healthy controls, we determined plasma levels of marinobufagenin (MBG) and endogenous ouabain (EO) and erythrocyte Na/K-ATPase activity in the absence and in the presence of 3E9 anti-MBG monoclonal antibody (mAb) and Digibind. Levels of MBG and EO were also determined in sham-operated Sprague–Dawley rats and in rats following 4 weeks of PNx. Results. In 25 patients with CKD plasma, MBG but not EO was increased (0.86 ± 0.07 versus 0.28 ± 0.02 nmol/L, P \u3c 0.01) and erythrocyte Na/K-ATPase was inhibited (1.24 ± 0.10 versus 2.80 ± 0.09 μmol Pi/mL/h, P \u3c 0.01) as compared to that in 19 healthy subjects. Ex vivo, 3E9 mAb restored Na/K-ATPase in erythrocytes from patients with CKD but did not affect Na/K-ATPase from control subjects. Following chromatographic fractionation of uremic versus normal plasma, a competitive immunoassay based on anti-MBG mAb detected a 3-fold increase in the level of endogenous material having retention time similar to that seen with MBG. A similar pattern of CTS changes was observed in uremic rats. As compared to sham-operated animals, PNx rats exhibited 3-fold elevated levels of MBG but not that of EO. Conclusions. In chronic renal failure, elevated levels of a bufadienolide CTS, MBG, contribute to Na/K-ATPase inhibition and may represent a potential target for therapy

Remote opportunities for scholars in Ukraine

Russia’s unprovoked attack on Ukraine has destroyed civilian infrastructure, including universities, research centers, and other academic infrastructure (1). Many Ukrainian scholars and researchers remain in Ukraine, and their work has suffered from major setbacks (2–4). We call on international scientists and institutions to support them