bluuebunny/crossref_metadata_2025_split huggingface dataset:
How to upgrade the status of migrant languages in the European Union
Authors: Houtkamp Christopher , Marácz László 
Published: January 2022

Abstract
In this chapter, we will compare the status of traditional minority and migrant languages in the European context and its practical implications for the trade-off between mobility and inclusion. It has been observed that traditional minority languages in Central and Eastern European (CEE) states have fewer rights compared to official languages and that their status and position is best described by language hierarchies, asymmetries, subordination, and threshold restrictions. This against the background of international treaties, such as article 22 of the Charter of Fundamental Rights of the European Union (CFREU) stating that the European Union (EU) respects cultural, religious, and linguistic diversity and the charters of the Council of Europe (CoE). Although linguistic inequality is an unwanted state of affairs violating international treaties and obligations of member states, these traditional minority language cases might refer to the assignment of linguistic rights to languages of migrants. Both categories belong to the domain of the non-official, majority languages and are expected to be assigned less rights than ‘national languages’, although traditional minority languages have been assigned limited rights in terms of the personality principle next to the territoriality principle applied to the national languages. Note that the language rights of migrants in the EU are also restricted by the mobility-and-inclusion trade-off, which is detrimental to migrant languages in the national context. A solution to this inequality is provided by the fact that the personality principle is a common denominator in the assignment of linguistic rights to minority-language speakers and has already been introduced into transnational European spaces. Hence, the rights of migrant languages can be accounted for by applying the personality principle in these spaces as well. This results in a Union-wide supranational language policy for migrant languages which supports the upgrading of migrant languages in accordance with the personality principle.
Multilingualism and security
Authors: Ozoliņa Žaneta , Bambals Rihards 
Published: January 2022

Abstract
The 20th century left permanent marks on the European geographical, socio-political and linguistic maps. No EU member states other than Estonia and Latvia have five percent or more native Russian-speakers in their population, which makes the case of the Baltic States unique in the wider pan-European context. Russia, the EU’s largest neighbour, has struggled to cope with the political reality of tens of millions of Russian-speakers being left outside of its borders. The mix of ethno-linguistic borders that do not coincide with politico-geographic ones raises several security-related questions; one of them is whether language can be used as a tool of manipulation, propaganda and source of unrest in society. Russia has securitised the protection of Russian-speakers abroad as analysis of its strategic foreign, security and military policy documents proved. In countries not included in NATO and the EU, such as Georgia and Ukraine, the Russian authorities have used the protection of ethnic Russians and Russian-speakers as a legitimate reason to violate the sovereignty and indivisibility of independent nations. Any country with a substantial Russian-speaking diaspora, especially in the former Soviet territories with less power and resources than Russia, may find its national security and societal resilience put to the test. The aim of the article is to analyse potential security implications stemming from different linguistic groups from the perspective of societal security, national security, risk to state sovereignty, and security at the wider EU level, as well as to identify challenges that may arise when conflicts of international actors spill over into state domains, and cause dissent within the local population.
Eccentric exercise improves myocardial oxygen supply/demand balance with decelerating aortic diastolic pressure decay: The acute and chronic studies
Authors: Tagawa Kaname , Ra Song‐Gyu , Yoshikawa Toru , Maeda Seiji 
Published: January 2022

ABSTRACTBoth eccentric (ECC) and concentric (CON) exercises improve energy expenditure and blood lipid profile. Although ECC exercise has a more beneficial effect on these factors than CON exercise, its benefits on vital organs are still unclear. This study investigated the mode‐of‐action‐dependent effects on myocardial perfusion index. Seventeen healthy men (age: 26 ± 5 years) were randomly enrolled in CON (n = 9) and ECC (n = 8) groups. Transient exercise and regular training (three‐day a week for 4‐week) included bicep curl comprising 5‐set of 10‐repetition, each using 75% one‐repetition maximum concentric loading. The ECC group performed one‐repetition of ECC for 3‐s and CON for 1‐s, while the CON group performed one‐repetition of CON for 3‐s and ECC for 1‐s. All participants were assessed for subendocardial viability ratio (SEVR, myocardial perfusion index) and aortic diastolic pressure decay. Before study, these were found to be same for both groups. Transient (ΔSEVR: 20.3 ± 13.3%, p = 0.01; Δdecay: −0.07 ± 0.02 s−1, p < .001) and regular (ΔSEVR: 18.5 ± 12.8%, p = .001; Δdecay: −0.06 ± 0.05 s−1, p = .004) ECC (but not CON) exercises significantly increased SEVR and decelerated decay. Increased SEVR with ECC exercise was associated with decelerated decay (transient ECC: r2 = 0.56, 95% confidence interval [CI] = −0.95 to −0.10, p = .03; regular ECC: r2 = 0.53, 95% CI = −0.95 to −0.05, p = .04). These findings suggest that ECC exercise improves myocardial perfusion and diastolic pressure contour is involved in physiological mechanisms.
Hybrid‐type, multicomponent interval training upregulates musculoskeletal fitness of adults with overweight and obesity in a volume‐dependent manner: A 1‐year dose‐response randomised controlled trial
Authors: Batrakoulis Alexios , Jamurtas Athanasios Z. , Tsimeas Panagiotis , Poulios Athanasios , Perivoliotis Konstantinos , Syrou Niki , Papanikolaou Konstantinos , Draganidis Dimitrios , Deli Charikleia K. , Metsios Georgios S. , Angelopoulos Theodore J. , Feito Yuri , Fatouros Ioannis G. 
Published: January 2022

ABSTRACTThis study examined the dose‐response effects of a 1‐year hybrid‐type, multicomponent interval training programme (DoIT) on various musculoskeletal fitness parameters in inactive overweight and obese adults in a gym setting. Ninety‐seven middle‐aged (44.8 ± 5.2 years) individuals with overweight/obesity (31.2 ± 5.7 kg/m2) (66% female) were randomly assigned to the following groups: (i) no‐intervention control (CON, n = 29), (ii) DoIT performed once weekly (DoIT‐1, n = 24), (iii) DoIT performed twice weekly (DoIT‐2, n = 23) and (iv) DoIT performed thrice weekly (DoIT‐3, n = 21). DoIT was a time‐efficient, intermittent‐based, multicomponent exercise protocol using progressive loaded fundamental movement patterns with prescribed work‐to‐rest intervals (1:3–2:1) in a circuit format (2–3 rounds). Muscular strength, muscular endurance, flexibility, passive range of motion (PRoM), static balance and functional movement screen (FMS®) were assessed at baseline, 6 and 12 months following intervention. At post‐training, all exercise groups exhibited superior changes than CON in (i) muscular strength (+13%–38%, p < 0.001); (ii) muscular endurance (+42%–159%, p < 0.001); (iii) flexibility (+12%–42%, p < 0.001); (iv) PRoM (+6%–50%, p = 0.001–0.026); (v) static balance (+61%–163%, p < 0.001); and (vi) FMS (+18%–39%, p < 0.001). Although a single exercise session/week improved musculoskeletal fitness, changes demonstrated a step‐wise improvement with two and three sessions/week suggesting a dose‐dependent response. The response rate to training was 100% for all exercise groups. These findings suggest that a multicomponent exercise approach incorporating bodyweight drills and resistance‐based alternative modes performed under real‐world conditions may improve several musculoskeletal fitness indicators in a dose‐dependent manner in inactive, middle‐aged adults with overweight/obesity.Trial registration: ClinicalTrials.gov identifier: NCT03759951.
ORI-Deep: improving the accuracy for predicting origin of replication sites by using a blend of features and long short-term memory network
Authors: Shahid Mahwish , Ilyas Maham , Hussain Waqar , Khan Yaser Daanial 
Published: January 2022

AbstractReplication of DNA is an important process for the cell division cycle, gene expression regulation and other biological evolution processes. It also has a crucial role in a living organism’s physical growth and structure. Replication of DNA comprises of three stages known as initiation, elongation and termination, whereas the origin of replication sites (ORI) is the location of initiation of the DNA replication process. There exist various methodologies to identify ORIs in the genomic sequences, however, these methods have used either extensive computations for execution, or have limited optimization for the large datasets. Herein, a model called ORI-Deep is proposed to identify ORIs from the multiple cell type genomic sequence benchmark data. An efficient method is proposed using a deep neural network to identify ORIs for four different eukaryotic species. For better representation of data, a feature vector is constructed using statistical moments for the training and testing of data and is further fed to a long short-term memory (LSTM) network. To prove the effectiveness of the proposed model, we applied several validation techniques at different levels to obtain seven accuracy metrics, and the accuracy score for self-consistency, 10-fold cross-validation, jackknife and the independent set test is observed to be 0.977, 0.948, 0.976 and 0.977, respectively. Based on the results, it can be concluded that ORI-Deep can efficiently predict the sites of origin replication in DNA sequence with high accuracy. Webserver for ORI-Deep is available at (https://share.streamlit.io/waqarhusain/orideep/main/app.py), whereas source code is available at (https://github.com/WaqarHusain/OriDeep).
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs
Authors: Balabin Helena , Hoyt Charles Tapley , Birkenbihl Colin , Gyori Benjamin M , Bachman John , Kodamullil Alpha Tom , Plöger Paul G , Hofmann-Apitius Martin , Domingo-Fernández Daniel 
Published: January 2022

Abstract

Motivation
The majority of biomedical knowledge is stored in structured databases or as unstructured text in scientific publications. This vast amount of information has led to numerous machine learning-based biological applications using either text through natural language processing (NLP) or structured data through knowledge graph embedding models. However, representations based on a single modality are inherently limited.

Results
To generate better representations of biological knowledge, we propose STonKGs, a Sophisticated Transformer trained on biomedical text and Knowledge Graphs (KGs). This multimodal Transformer uses combined input sequences of structured information from KGs and unstructured text data from biomedical literature to learn joint representations in a shared embedding space. First, we pre-trained STonKGs on a knowledge base assembled by the Integrated Network and Dynamical Reasoning Assembler consisting of millions of text-triple pairs extracted from biomedical literature by multiple NLP systems. Then, we benchmarked STonKGs against three baseline models trained on either one of the modalities (i.e. text or KG) across eight different classification tasks, each corresponding to a different biological application. Our results demonstrate that STonKGs outperforms both baselines, especially on the more challenging tasks with respect to the number of classes, improving upon the F1-score of the best baseline by up to 0.084 (i.e. from 0.881 to 0.965). Finally, our pre-trained model as well as the model architecture can be adapted to various other transfer learning applications.

Availability and implementation
We make the source code and the Python package of STonKGs available at GitHub (https://github.com/stonkgs/stonkgs) and PyPI (https://pypi.org/project/stonkgs/). The pre-trained STonKGs models and the task-specific classification models are respectively available at https://huggingface.co/stonkgs/stonkgs-150k and https://zenodo.org/communities/stonkgs.

Supplementary information
Supplementary data are available at Bioinformatics online.
Preference for animate domain sounds in the fusiform gyrus of blind individuals is modulated by shape–action mapping
Authors: Bola Łukasz , Yang Huichao , Caramazza Alfonso , Bi Yanchao 
Published: January 2022

AbstractIn high-level visual areas in the human brain, preference for inanimate objects is observed regardless of stimulation modality (visual/auditory/tactile) and individual’s visual experience (sighted/blind) whereas preference for animate entities seems robust mainly in the visual modality. Here, we test a hypothesis explaining this domain difference: Object representations can be activated through nonvisual stimulation when their shapes are systematically related to action system representations, a quality typical of most inanimate objects but of only specific animate entities. We studied functional magnetic resonance imaging activations in congenitally blind and sighted individuals listening to animal, object, and human sounds. In blind individuals, the typical location of the fusiform face area preferentially responded to human facial expression sounds clearly related to specific facial actions and resulting face shapes but not to speech or animal sounds. No univariate preference for any sound category was observed in the fusiform gyrus in sighted individuals, but the expected multivoxel effects were present. We conclude that nonvisual signals can activate shape representations of those stimuli—inanimate or animate—for which shape and action computations are transparently related. However, absence of potentially competing visual inputs seems necessary for this effect to be clearly detectable in the case of animate representation.
Coronavirus Disease 2019 Messenger RNA Vaccines Associated With Delayed Onset of Breakthrough Infections and Fewer Radiographic Abnormalities
Authors: Li Xin , Chan Jacky Man Chun , Lam Bosco , Lung David Christopher , Lung Kwok Cheung , Chow Christina Kin Yi , Tam Tracey , Chiu Kelvin Hei Yeung , Hung Ling Lung , Hung Ivan Fan Ngai , Cheng Vincent Chi Chung , To Kelvin Kai Wang , Yuen Kwok Yung 
Published: January 2022

Abstract
This retrospective study of incoming travelers with coronavirus disease 2019 showed that individuals immunized by messenger RNA vaccines had significantly longer postvaccination intervals (median, 30.5 days) to breakthrough infection, lower white blood cell counts and lactate dehydrogenase levels on admission, and fewer radiographic abnormalities than those immunized by inactivated virus vaccine, who paradoxically had lower respiratory viral load.
Investigational Antifungal Agents for Invasive Mycoses: A Clinical Perspective
Authors: Lamoth Frederic , Lewis Russell E , Kontoyiannis Dimitrios P 
Published: January 2022

Abstract
Treatment of invasive fungal infections (IFIs) remains challenging, because of the limitations of the current antifungal agents (ie, mode of administration, toxicity, and drug-drug interactions) and the emergence of resistant fungal pathogens. Therefore, there is an urgent need to expand our antifungal armamentarium. Several compounds are reaching the stage of phase II or III clinical assessment. These include new drugs within the existing antifungal classes or displaying similar mechanism of activity with improved pharmacologic properties (rezafungin and ibrexafungerp) or first-in-class drugs with novel mechanisms of action (olorofim and fosmanogepix). Although critical information regarding the performance of these agents in heavily immunosuppressed patients is pending, they may provide useful additions to current therapies in some clinical scenarios, including IFIs caused by azole-resistant Aspergillus or multiresistant fungal pathogens (eg, Candida auris, Lomentospora prolificans). However, their limited activity against Mucorales and some other opportunistic molds (eg, some Fusarium spp.) persists as a major unmet need.
Early vegetation recovery of a burned Mediterranean forest in relation to post-fire management strategies
Authors: Carrari Elisa , Biagini Patrizio , Selvi Federico 
Published: January 2022

Abstract
The risk of wildfires in the Mediterranean region is expected to increase with climate change. Fire is one of the main drivers of plant diversity and composition, triggering succession processes that vary according to the fire regime and species’ regeneration traits. Human management can modulate these processes to promote the recovery of the burned soil-vegetation system, through the application of practices such as salvage logging. Effects of these managements have been studied mostly for coniferous forests, with contrasting results, while little is known about the responses of evergreen broadleaved woodlands. Here, we analysed the 34-month recovery processes of a Quercus ilex forest and an adjacent Pinus pinaster stand in central Italy with respect to their diversity, composition and plant fire-related traits, in relation to three different management strategies applied after fire. These were: (1) no intervention (NT), (2) salvage logging and mulching (SM and SMP for the pine stand), (3) salvage logging, mulching and erosion control measures (e.g. fascines for hill slope stabilization; EC). Overall, the increase of post-fire vegetation cover was negatively affected by SM and EC treatments, while their effects on ɣ- and α-diversity were positive. Species diversity was significantly lower in pine than in broadleaved plots and compositional differences associated with forest type were significant. Abundance of woody species was higher in the unsalvaged sites, except for a few species (e.g. Q. ilex), while herbaceous plants were not affected. Species composition in managed plots was different from control plots after 10 and 22 months, while differences decreased after 34 months. Effects of management strategies on the frequency of resprouters as well as on the proportion of species with persistent vs transient soil seed bank were minor; these traits were mainly driven by forest type. Our findings suggest that non-treatment is the best post-fire management strategy for a fast recovery of woody species in typical Mediterranean broadleaved forests. However, the EC strategy promoted a high diversity level, while not apparently altering species composition compared with the natural post-fire succession process.
Nordic responses to covid-19 from a health promotion perspective
Authors: Thualagant Nicole , Simonsen Nina , Sarvimäki Anneli , Stenbock-Hult Bettina , Olafsdottir Helga S , Fosse Elisabeth , Torp Steffen , Ringsberg Karin C , Forrinder Ulla , Tillgren Per 
Published: January 2022

Summary
On 30 January 2020, the disease covid-19 was declared by the World Health Organization to be an international threat to human health and on 11 March 2020, the outbreak was declared a pandemic.
The aim of this study was to analyse policy strategies developed by the five Nordic countries during the first 3 months of the pandemic from a health promotion perspective in order to identify Nordic responses to the crisis. Although the Nordic countries have a long tradition of co-operation as well as similar social welfare policies and legislation, each country developed their own strategies towards the crisis. The strategies identified were analysed from a health promotion perspective emanating from five principles: intersectorality, sustainability, equity, empowerment and a lifecourse perspective.
Denmark, Finland and Norway had lockdowns to varying degrees, whereas Sweden and Iceland had no lockdowns. Iceland implemented a test and tracking strategy from the very beginning. All countries based their recommendations and restrictions on appeals to solidarity and trust in institutions and fellow citizens. The analysis showed that the strategies in all countries could be related to health promotion principles with some differences between the countries especially regarding equity and sustainability. The Nordic governments took responsibility for protecting their citizens by developing policy strategies based on restrictions and recommendations congruent with the principles of health promotion. The findings also identified issues that will pose challenges for future pandemic strategies.
Deleterious Genetic Variation Across the NOD Signaling Pathway Is Associated With Reduced NFKB Signaling Transcription and Upregulation of Alternative Inflammatory Transcripts in Pediatric Inflammatory Bowel Disease
Authors: Ashton James J , Boukas Konstantinos , Stafford Imogen S , Cheng Guo , Haggarty Rachel , Coelho Tracy A F , Batra Akshay , Afzal Nadeem A , Williams Anthony P , Polak Marta E , Beattie R Mark , Ennis Sarah 
Published: January 2022

Abstract

Background
Inflammatory bowel disease may arise with inadequate immune response to intestinal bacteria. NOD2 is an established gene in Crohn’s disease pathogenesis, with deleterious variation associated with reduced NFKB signaling. We hypothesized that deleterious variation across the NOD2 signaling pathway impacts on transcription.

Methods
Treatment-naïve pediatric inflammatory bowel disease patients had ileal biopsies for targeted autoimmune RNA-sequencing and blood for whole exome sequencing collected at diagnostic endoscopy. Utilizing GenePy, a per-individual, per-gene score, genes within the NOD signaling pathway were assigned a quantitative score representing total variant burden. Where multiple genes formed complexes, GenePy scores were summed to create a “complex” score. Normalized transcript expression of 95 genes within this pathway was retrieved. Regression analysis was performed to determine the impact of genomic variation on gene transcription.

Results
Thirty-nine patients were included. Limited clustering of patients based on NOD signaling transcripts was related to underlying genomic variation. Patients harboring deleterious variation in NOD2 had reduced NOD2 (β = -0.702, P = 4.3 × 10-5) and increased NFKBIA (β = 0.486, P = .001), reflecting reduced NFKB signal activation. Deleterious variation in the NOD2-RIPK2 complex was associated with increased NLRP3 (β = 0.8, P = 3.1475 × 10-8) and TXN (β = -0.417, P = 8.4 × 10-5) transcription, components of the NLRP3 inflammasome. Deleterious variation in the TAK1-TAB complex resulted in reduced MAPK14 transcription (β = -0.677, P = 1.7 × 10-5), a key signal transduction protein in the NOD2 signaling cascade and increased IFNA1 (β = 0.479, P = .001), indicating reduced transcription of NFKB activators and alternative interferon transcription in these patients.

Conclusions
Data integration identified perturbation of NOD2 signaling transcription correlated with genomic variation. A hypoimmune NFKB signaling transcription response was observed. Alternative inflammatory pathways were activated and may represent therapeutic targets in specific patients.