Showing papers by "Jagiellonian University published in 2021"

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Structure-based protein function prediction using graph convolutional networks.

Abstract: The rapid increase in the number of proteins in sequence databases and the diversity of their functions challenge computational approaches for automated function prediction. Here, we introduce DeepFRI, a Graph Convolutional Network for predicting protein functions by leveraging sequence features extracted from a protein language model and protein structures. It outperforms current leading methods and sequence-based Convolutional Neural Networks and scales to the size of current sequence repositories. Augmenting the training set of experimental structures with homology models allows us to significantly expand the number of predictable functions. DeepFRI has significant de-noising capability, with only a minor drop in performance when experimental structures are replaced by protein models. Class activation mapping allows function predictions at an unprecedented resolution, allowing site-specific annotations at the residue-level in an automated manner. We show the utility and high performance of our method by annotating structures from the PDB and SWISS-MODEL, making several new confident function predictions. DeepFRI is available as a webserver at https://beta.deepfri.flatironinstitute.org/ .

White Analytical Chemistry: An approach to reconcile the principles of Green Analytical Chemistry and functionality

Abstract: The concept of White Analytical Chemistry (WAC) is presented as an extension of Green Analytical Chemistry (GAC). We propose the 12 WAC principles as an alternative to the known 12 GAC principles. In addition to green aspects, WAC takes into account other key criteria affecting the quality of the method, analytical (red) and practical (blue). In reference to the RGB color model, according to which mixing of red, green and blue light beams gives the impression of whiteness, a white analytical method shows the coherence and synergy of the analytical, ecological and practical attributes. Whiteness can also be quantified, based on the assessment of individual principles, as a convenient parameter useful in comparisons and selecting optimal method. WAC is closer to the idea of sustainable development due to a more holistic view, as it strives for a compromise that avoids an unconditional increase in greenness at the expense of functionality.

Patients with COVID-19: in the dark-NETs of neutrophils.

Abstract: SARS-CoV-2 infection poses a major threat to the lungs and multiple other organs, occasionally causing death. Until effective vaccines are developed to curb the pandemic, it is paramount to define the mechanisms and develop protective therapies to prevent organ dysfunction in patients with COVID-19. Individuals that develop severe manifestations have signs of dysregulated innate and adaptive immune responses. Emerging evidence implicates neutrophils and the disbalance between neutrophil extracellular trap (NET) formation and degradation plays a central role in the pathophysiology of inflammation, coagulopathy, organ damage, and immunothrombosis that characterize severe cases of COVID-19. Here, we discuss the evidence supporting a role for NETs in COVID-19 manifestations and present putative mechanisms, by which NETs promote tissue injury and immunothrombosis. We present therapeutic strategies, which have been successful in the treatment of immunο-inflammatory disorders and which target dysregulated NET formation or degradation, as potential approaches that may benefit patients with severe COVID-19.

Jet energy scale and resolution measured in proton-proton collisions at s =13 TeV with the ATLAS detector

Abstract: Jet energy scale and resolution measurements with their associated uncertainties are reported for jets using 36-81 fb$^{-1}$ of proton-proton collision data with a centre-of-mass energy of $\sqrt{s}=13$ TeV collected by the ATLAS detector at the LHC. Jets are reconstructed using two different input types: topo-clusters formed from energy deposits in calorimeter cells, as well as an algorithmic combination of charged-particle tracks with those topo-clusters, referred to as the ATLAS particle-flow reconstruction method. The anti-$k_t$ jet algorithm with radius parameter $R=0.4$ is the primary jet definition used for both jet types. Jets are initially calibrated using a sequence of simulation-based corrections. Next, several $\textit{in situ}$ techniques are employed to correct for differences between data and simulation and to measure the resolution of jets. The systematic uncertainties in the jet energy scale for central jets ($|\eta| 2.5$ TeV). The relative jet energy resolution is measured and ranges from ($24 \pm 1.5$)% at 20 GeV to ($6 \pm 0.5$)% at 300 GeV.

Endothelial function in cardiovascular medicine: a consensus paper of the European Society of Cardiology Working Groups on Atherosclerosis and Vascular Biology, Aorta and Peripheral Vascular Diseases, Coronary Pathophysiology and Microcirculation, and Thrombosis.

Abstract: Endothelial cells (ECs) are sentinels of cardiovascular health. Their function is reduced by the presence of cardiovascular risk factors, and is regained once pathological stimuli are removed. In this European Society for Cardiology Position Paper, we describe endothelial dysfunction as a spectrum of phenotypic states and advocate further studies to determine the role of EC subtypes in cardiovascular disease. We conclude that there is no single ideal method for measurement of endothelial function. Techniques to measure coronary epicardial and micro-vascular function are well established but they are invasive, time-consuming, and expensive. Flow-mediated dilatation (FMD) of the brachial arteries provides a non-invasive alternative but is technically challenging and requires extensive training and standardization. We, therefore, propose that a consensus methodology for FMD is universally adopted to minimize technical variation between studies, and that reference FMD values are established for different populations of healthy individuals and patient groups. Newer techniques to measure endothelial function that are relatively easy to perform, such as finger plethysmography and the retinal flicker test, have the potential for increased clinical use provided a consensus is achieved on the measurement protocol used. We recommend further clinical studies to establish reference values for these techniques and to assess their ability to improve cardiovascular risk stratification. We advocate future studies to determine whether integration of endothelial function measurements with patient-specific epigenetic data and other biomarkers can enhance the stratification of patients for differential diagnosis, disease progression, and responses to therapy.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): a Systemic Infection.

Abstract: To date, seven identified coronaviruses (CoVs) have been found to infect humans; of these, three highly pathogenic variants have emerged in the 21st century. The newest member of this group, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected at the end of 2019 in Hubei province, China. Since then, this novel coronavirus has spread worldwide, causing a pandemic; the respiratory disease caused by the virus is called coronavirus disease 2019 (COVID-19). The clinical presentation ranges from asymptomatic to mild respiratory tract infections and influenza-like illness to severe disease with accompanying lung injury, multiorgan failure, and death. Although the lungs are believed to be the site at which SARS-CoV-2 replicates, infected patients often report other symptoms, suggesting the involvement of the gastrointestinal tract, heart, cardiovascular system, kidneys, and other organs; therefore, the following question arises: is COVID-19 a respiratory or systemic disease? This review aims to summarize existing data on the replication of SARS-CoV-2 in different tissues in both patients and ex vivo models.

The LOFAR Two-meter Sky Survey: Deep Fields Data Release 1. I. Direction-dependent calibration and imaging

Abstract: The Low Frequency Array (LOFAR) is an ideal instrument to conduct deep extragalactic surveys. It has a large field of view and is sensitive to large-scale and compact emission. It is, however, very challenging to synthesize thermal noise limited maps at full resolution, mainly because of the complexity of the low-frequency sky and the direction dependent effects (phased array beams and ionosphere). In this first paper of a series, we present a new calibration and imaging pipeline that aims at producing high fidelity, high dynamic range images with LOFAR High Band Antenna data, while being computationally efficient and robust against the absorption of unmodeled radio emission. We apply this calibration and imaging strategy to synthesize deep images of the Bootes and Lockman Hole fields at ~150 MHz, totaling ~80 and ~100 h of integration, respectively, and reaching unprecedented noise levels at these low frequencies of ≲30 and ≲23 μ Jy beam−1 in the inner ~3 deg2 . This approach is also being used to reduce the LOTSS-wide data for the second data release.

European Green Deal – legal and financial challenges of the climate change

Abstract: The European Green Deal announced by the European Commission in December 2019 is a roadmap meant to foster the transition of the European Union towards the climate-neutral economy by reducing carbon emissions towards 55% by 2030 and achieving carbon neutrality by 2050. By putting the EGD in a boarder perspective of evolving, constitutional rationale of environmental protection in the EU legal order, this contribution examines horizontal, legal dimension and financial implications of the green transition. The challenge ahead of the Union is now how to transform the ambitious climate agenda into efficient legal and economic instruments ‘in a fair way, leaving no one behind’. This paper argues that EGD is a great opportunity, but in order to turn it into a success, it must be strongly anchored in the concepts pertaining to the constitutional framework of the EU legal order, in particular, the concepts of solidarity, sustainable development and high level of environmental protection.

Associations between green/blue spaces and mental health across 18 countries

Abstract: Living near, recreating in, and feeling psychologically connected to, the natural world are all associated with better mental health, but many exposure-related questions remain. Using data from an 18-country survey (n = 16,307) we explored associations between multiple measures of mental health (positive well-being, mental distress, depression/anxiety medication use) and: (a) exposures (residential/recreational visits) to different natural settings (green/inland-blue/coastal-blue spaces); and (b) nature connectedness, across season and country. People who lived in greener/coastal neighbourhoods reported higher positive well-being, but this association largely disappeared when recreational visits were controlled for. Frequency of recreational visits to green, inland-blue, and coastal-blue spaces in the last 4 weeks were all positively associated with positive well-being and negatively associated with mental distress. Associations with green space visits were relatively consistent across seasons and countries but associations with blue space visits showed greater heterogeneity. Nature connectedness was also positively associated with positive well-being and negatively associated with mental distress and was, along with green space visits, associated with a lower likelihood of using medication for depression. By contrast inland-blue space visits were associated with a greater likelihood of using anxiety medication. Results highlight the benefits of multi-exposure, multi-response, multi-country studies in exploring complexity in nature-health associations.

Chitosan nanoparticles as a promising tool in nanomedicine with particular emphasis on oncological treatment.

Abstract: The study describes the current state of knowledge on nanotechnology and its utilization in medicine. The focus in this manuscript was on the properties, usage safety, and potentially valuable applications of chitosan-based nanomaterials. Chitosan nanoparticles have high importance in nanomedicine, biomedical engineering, discovery and development of new drugs. The manuscript reviewed the new studies regarding the use of chitosan-based nanoparticles for creating new release systems with improved bioavailability, increased specificity and sensitivity, and reduced pharmacological toxicity of drugs. Nowadays, effective cancer treatment is a global problem, and recent advances in nanomedicine are of great importance. Special attention was put on the application of chitosan nanoparticles in developing new system for anticancer drug delivery. Pre-clinical and clinical studies support the use of chitosan-based nanoparticles in nanomedicine. This manuscript overviews the last progresses regarding the utilization, stability, and bioavailability of drug nanoencapsulation with chitosan and their safety.

Towards a rigorous understanding of societal responses to climate change

Abstract: A large scholarship currently holds that before the onset of anthropogenic global warming, natural climatic changes long provoked subsistence crises and, occasionally, civilizational collapses among human societies. This scholarship, which we term the 'history of climate and society' (HCS), is pursued by researchers from a wide range of disciplines, including archaeologists, economists, geneticists, geographers, historians, linguists and palaeoclimatologists. We argue that, despite the wide interest in HCS, the field suffers from numerous biases, and often does not account for the local effects and spatiotemporal heterogeneity of past climate changes or the challenges of interpreting historical sources. Here we propose an interdisciplinary framework for uncovering climate-society interactions that emphasizes the mechanics by which climate change has influenced human history, and the uncertainties inherent in discerning that influence across different spatiotemporal scales. Although we acknowledge that climate change has sometimes had destructive effects on past societies, the application of our framework to numerous case studies uncovers five pathways by which populations survived-and often thrived-in the face of climatic pressures.

Muon reconstruction and identification efficiency in ATLAS using the full Run 2 pp collision data set at √ s = 13 TeV

Abstract: This article documents the muon reconstruction and identification efficiency obtained by the ATLAS experiment for 139 $$\hbox {fb}^{-1}$$ fb - 1 of pp collision data at $$\sqrt{s}=13$$ s = 13 TeV collected between 2015 and 2018 during Run 2 of the LHC. The increased instantaneous luminosity delivered by the LHC over this period required a reoptimisation of the criteria for the identification of prompt muons. Improved and newly developed algorithms were deployed to preserve high muon identification efficiency with a low misidentification rate and good momentum resolution. The availability of large samples of $$Z\rightarrow \mu \mu $$ Z → μ μ and $$J/\psi \rightarrow \mu \mu $$ J / ψ → μ μ decays, and the minimisation of systematic uncertainties, allows the efficiencies of criteria for muon identification, primary vertex association, and isolation to be measured with an accuracy at the per-mille level in the bulk of the phase space, and up to the percent level in complex kinematic configurations. Excellent performance is achieved over a range of transverse momenta from 3 GeV to several hundred GeV, and across the full muon detector acceptance of $$|\eta |<2.7$$ | η | < 2.7 .

The origins and spread of domestic horses from the Western Eurasian steppes.

Abstract: Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture11,12. Analysis of 273 ancient horse genomes reveals that modern domestic horses originated in the Western Eurasian steppes, especially the lower Volga-Don region.

The orchard plot: Cultivating a forest plot for use in ecology, evolution, and beyond.

Abstract: "Classic" forest plots show the effect sizes from individual studies and the aggregate effect from a meta-analysis. However, in ecology and evolution, meta-analyses routinely contain over 100 effect sizes, making the classic forest plot of limited use. We surveyed 102 meta-analyses in ecology and evolution, finding that only 11% use the classic forest plot. Instead, most used a "forest-like plot," showing point estimates (with 95% confidence intervals [CIs]) from a series of subgroups or categories in a meta-regression. We propose a modification of the forest-like plot, which we name the "orchard plot." Orchard plots, in addition to showing overall mean effects and CIs from meta-analyses/regressions, also include 95% prediction intervals (PIs), and the individual effect sizes scaled by their precision. The PI allows the user and reader to see the range in which an effect size from a future study may be expected to fall. The PI, therefore, provides an intuitive interpretation of any heterogeneity in the data. Supplementing the PI, the inclusion of underlying effect sizes also allows the user to see any influential or outlying effect sizes. We showcase the orchard plot with example datasets from ecology and evolution, using the R package, orchard, including several functions for visualizing meta-analytic data using forest-plot derivatives. We consider the orchard plot as a variant on the classic forest plot, cultivated to the needs of meta-analysts in ecology and evolution. Hopefully, the orchard plot will prove fruitful for visualizing large collections of heterogeneous effect sizes regardless of the field of study.

Going Full-TILT Boogie on Document Understanding with Text-Image-Layout Transformer

Abstract: We address the challenging problem of Natural Language Comprehension beyond plain-text documents by introducing the TILT neural network architecture which simultaneously learns layout information, visual features, and textual semantics. Contrary to previous approaches, we rely on a decoder capable of unifying a variety of problems involving natural language. The layout is represented as an attention bias and complemented with contextualized visual information, while the core of our model is a pretrained encoder-decoder Transformer. Our novel approach achieves state-of-the-art results in extracting information from documents and answering questions which demand layout understanding (DocVQA, CORD, SROIE). At the same time, we simplify the process by employing an end-to-end model.

Modeling the Depositional Environment of the Sandstone Reservoir in the Middle Miocene Sidri Member, Badri Field, Gulf of Suez Basin, Egypt: Integration of Gamma-Ray Log Patterns and Petrographic Characteristics of Lithology

Abstract: Understanding the depositional setting of siliciclastics reservoir is fundamental process to exploration and development of hydrocarbon reservoirs and to the multi-phase cycle of the oil and gas industry. Typically, core samples from existing or potential reservoirs can be used for interpretation of depositional environment. However, the lack of core samples in certain reservoirs represents a challenge for reservoir development plans and further exploration. To overcome the absence of core samples in the middle Miocene Sidri Member in the Badri field, Gulf of Suez, this study aimed to reconstruct its depositional settings by coupling well logging patterns and petrographic characterization of ditch cuttings. Consequently, 30 thin section samples representing the reservoir section of four wells were described in detail and standard petrographic characteristics were determined. Then, gamma-ray (GR) log patterns of the studied reservoir wells were used for interpretation of depositional environment. Petrographic analysis indicates that the sandstone reservoir is fine- to medium-grained arkose with dominant siliceous cement and composed mainly of quartz, feldspars, and lithic fragments. Pores reflecting primary and secondary porosity as well as inter-granular pores are dominant. The facies analysis indicates that the studied member has a heterogeneous nature and rapid facies change; its main lithofacies are blocky sandstones, intercalated sandstones and shales, and shales. Three electrofacies were interpreted in the studied section: (1) electrofacies-A (blocky sandstones), which is characterized by a cylindrical-shaped (right boxcar) GR trend; (2) electrofacies-B (intercalated sandstones and shales), which is characterized by an irregular log trend with serrated shape; and (3) electrofacies-C (shales), which is characterized by irregular GR trend and has no character. The interpreted results indicate a tidal channel depositional setting for electrofacies-A, mixed tidal flat depositional setting for electrofacies-B, and low relief offshore mudstone depositional setting for electrofacies-C. Finally, the results illustrate how the coupling of GR patterns with the analysis of petrographic characteristics can be used to understand the depositional setting of a hydrocarbon reservoir that lacks core samples. This work could be useful for assessment of reservoir distribution and quality, for reduction of uncertainty during field development, as well as for providing useful insight to similar hydrocarbon reservoirs elsewhere.

To which world regions does the valence–dominance model of social perception apply?

Abstract: Over the past 10 years, Oosterhof and Todorov’s valence–dominance model has emerged as the most prominent account of how people evaluate faces on social dimensions. In this model, two dimensions (valence and dominance) underpin social judgements of faces. Because this model has primarily been developed and tested in Western regions, it is unclear whether these findings apply to other regions. We addressed this question by replicating Oosterhof and Todorov’s methodology across 11 world regions, 41 countries and 11,570 participants. When we used Oosterhof and Todorov’s original analysis strategy, the valence–dominance model generalized across regions. When we used an alternative methodology to allow for correlated dimensions, we observed much less generalization. Collectively, these results suggest that, while the valence–dominance model generalizes very well across regions when dimensions are forced to be orthogonal, regional differences are revealed when we use different extraction methods and correlate and rotate the dimension reduction solution.

Stress Path Analysis for Characterization of In Situ Stress State and Effect of Reservoir Depletion on Present-Day Stress Magnitudes: Reservoir Geomechanical Modeling in the Gulf of Suez Rift Basin, Egypt

Abstract: A reservoir geomechanical modeling has been attempted in the hydrocarbon-bearing Miocene formations in the offshore Badri field, Gulf of Suez, Egypt. Pore pressure established from the direct downhole measurements indicated sub-hydrostatic condition in the depleted mid-Miocene Hammam Faraun and Kareem reservoirs. Vertical stress (Sv) estimated using bulk density data yielded an average of 0.98 PSI/feet (22.17 MPa/km) gradient. Magnitudes of minimum (Shmin) and maximum (Shmax) horizontal stresses were deduced from the poro-elastic model. Relative stress magnitudes (Sv ≥ Shmax > Shmin) reflect a normal faulting tectonic stress in the Badri field. Pore pressure and stress perturbations (ΔPP and ΔSh) in the depleted reservoirs investigated from actual measurements recognized ‘stress path’ values of 0.54 and 0.59 against the Hammam Faraun and Kareem Formations, respectively. These stress path values are far away from the normal faulting limit (0.68), indicating induced normal faulting or fault reactivation to be unlikely at the present depletion rate.

Sensitivity of the Cherenkov Telescope Array to a dark matter signal from the Galactic centre

Abstract: We provide an updated assessment of the power of the Cherenkov Telescope Array (CTA) to search for thermally produced dark matter at the TeV scale, via the associated gamma-ray signal from pair-annihilating dark matter particles in the region around the Galactic centre. We find that CTA will open a new window of discovery potential, significantly extending the range of robustly testable models given a standard cuspy profile of the dark matter density distribution. Importantly, even for a cored profile, the projected sensitivity of CTA will be sufficient to probe various well-motivated models of thermally produced dark matter at the TeV scale. This is due to CTA's unprecedented sensitivity, angular and energy resolutions, and the planned observational strategy. The survey of the inner Galaxy will cover a much larger region than corresponding previous observational campaigns with imaging atmospheric Cherenkov telescopes. CTA will map with unprecedented precision the large-scale diffuse emission in high-energy gamma rays, constituting a background for dark matter searches for which we adopt state-of-the-art models based on current data. Throughout our analysis, we use up-to-date event reconstruction Monte Carlo tools developed by the CTA consortium, and pay special attention to quantifying the level of instrumental systematic uncertainties, as well as background template systematic errors, required to probe thermally produced dark matter at these energies.

Tapping into non-English-language science for the conservation of global biodiversity.

Abstract: The widely held assumption that any important scientific information would be available in English underlies the underuse of non-English-language science across disciplines. However, non-English-language science is expected to bring unique and valuable scientific information, especially in disciplines where the evidence is patchy, and for emergent issues where synthesising available evidence is an urgent challenge. Yet such contribution of non-English-language science to scientific communities and the application of science is rarely quantified. Here, we show that non-English-language studies provide crucial evidence for informing global biodiversity conservation. By screening 419,679 peer-reviewed papers in 16 languages, we identified 1,234 non-English-language studies providing evidence on the effectiveness of biodiversity conservation interventions, compared to 4,412 English-language studies identified with the same criteria. Relevant non-English-language studies are being published at an increasing rate in 6 out of the 12 languages where there were a sufficient number of relevant studies. Incorporating non-English-language studies can expand the geographical coverage (i.e., the number of 2° × 2° grid cells with relevant studies) of English-language evidence by 12% to 25%, especially in biodiverse regions, and taxonomic coverage (i.e., the number of species covered by the relevant studies) by 5% to 32%, although they do tend to be based on less robust study designs. Our results show that synthesising non-English-language studies is key to overcoming the widespread lack of local, context-dependent evidence and facilitating evidence-based conservation globally. We urge wider disciplines to rigorously reassess the untapped potential of non-English-language science in informing decisions to address other global challenges. Please see the Supporting information files for Alternative Language Abstracts.