bluuebunny/crossref_metadata_2025_split huggingface dataset:
GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks
Authors: Kamal Aryan , Arnold Christian , Claringbould Annique , Moussa Rim , Servaas Nila H , Kholmatov Maksim , Daga Neha , Nogina Daria , Mueller‐Dott Sophia , Reyes‐Palomares Armando , Palla Giovanni , Sigalova Olga , Bunina Daria , Pabst Caroline , Zaugg Judith B 
Published: April 2023

AbstractEnhancers play a vital role in gene regulation and are critical in mediating the impact of noncoding genetic variants associated with complex traits. Enhancer activity is a cell‐type‐specific process regulated by transcription factors (TFs), epigenetic mechanisms and genetic variants. Despite the strong mechanistic link between TFs and enhancers, we currently lack a framework for jointly analysing them in cell‐type‐specific gene regulatory networks (GRN). Equally important, we lack an unbiased way of assessing the biological significance of inferred GRNs since no complete ground truth exists. To address these gaps, we present GRaNIE (Gene Regulatory Network Inference including Enhancers) and GRaNPA (Gene Regulatory Network Performance Analysis). GRaNIE (https://git.embl.de/grp‐zaugg/GRaNIE) builds enhancer‐mediated GRNs based on covariation of chromatin accessibility and RNA‐seq across samples (e.g. individuals), while GRaNPA (https://git.embl.de/grp‐zaugg/GRaNPA) assesses the performance of GRNs for predicting cell‐type‐specific differential expression. We demonstrate their power by investigating gene regulatory mechanisms underlying the response of macrophages to infection, cancer and common genetic traits including autoimmune diseases. Finally, our methods identify the TF PURA as a putative regulator of pro‐inflammatory macrophage polarisation.
Novel (sulfated) thyroid hormone transporters in the solute carrier 22 family
Authors: Chen Zhongli , Peeters Robin P , Flach Wesley , de Rooij Linda J , Yildiz Sena , Teumer Alexander , Nauck Matthias , Sterenborg Rosalie B T M , Rutten Joost H W , Medici Marco , Edward Visser W , Meima Marcel E 
Published: April 2023

Objective
Thyroid hormone (TH) transport represents a critical first step in governing intracellular TH regulation. It is still unknown whether the full repertoire of TH transporters has been identified. Members of the solute carrier (SLC) 22 family have substrates in common with the known TH transporters of the organic anion-transporting peptide family. Therefore, we screened the SLC22 family for TH transporters

Methods
Uptake of 1 nM of iodothyronines or sulfated iodothyronines in COS1 cells expressing SLC22 proteins was performed.

Results
We first tested 25 mouse (m) SLC22 proteins for TH uptake and found that the majority of the organic anion transporter (OAT) clade were capable of 3,3’,5-triiodothyronine and/or thyroxine (T4) transport. Based on phylogenetic tree analysis of the mouse and human (h) SLC22 family, we selected eight hSLC22s that grouped with the newly identified mouse TH transporters. Of these, four tested positive for uptake of one or more substrates, particularly hSLC22A11 showed robust (3-fold over control) uptake of T4. Uptake of sulfated iodothyronines was strongly (up to 17-fold) induced by some SLC22s, most notably SLC22A8, hSLC22A9, mSLC22A27 and mSLC22A29. Finally, the zebrafish orthologues of SLC22A6/8 drOatx and drSlc22a6l also transported almost all (sulfated) iodothyronines tested. The OAT inhibitors lesinurad and probenecid inhibited most SLC22 proteins.

Conclusions
Our results demonstrated that members of the OAT clade of the SLC22 family constitute a novel, evolutionary conserved group of transporters for (sulfated) iodothyronines. Future studies should reveal the relevance of these transporters in TH homeostasis and physiology.
Проєкт «Рік війни»: дискусійні питання медійної освіти та журналістської практики
Authors: Hudoshnyk Oksana , Bucharska Iryna , Myronenko Vladlena , Khotyun Lyudmila 
Published: April 2023

Формування професійних навичок студентів-комунікативістів під час війни ускладнене не тільки зрозумілими обмеженнями воєнного часу та 4-річним дистантом, але й унеможливленням спільнотворчості як наскрізної ідеї медійної освіти. Об’єднання студентів різних курсів факультету систем і засобів масової комунікації ДНУ в межах проєкту «Рік війни» стало мотиватором обговорення цілого комплексу дискусійних питань науково-дослідної роботи та журналістської практики як під час його створення, так і на захистах випускних робіт, на конференціях і семінарах. Одним із завдань проєкту спеціальності 061 Журналістика стало різнотематичне представлення студентства у непростих умовах воєнного повсякдення, еміграції; у пошуку відповідей на надскладні виклики трагічного року війни. Одночасно проводилася робота за декількома напрямами: соціологічне опитування (анкетування), дискурсивні практики, інтерв’ю під час війни, фоторепортаж (база даних), досвід еміграції (цикл подкастів). Закцентовано на практичних навичках студентів під час інтерв’ювання зарубіжних та українських воєнних кореспондентів, створенні довідникових архівів та напрацюванні алгоритмів їх зберігання, на медіатизації власного досвіду через творчі ініціативи та медіакритичні рефлексії. Як більшість колективних проєктів, «Рік війни» визначив ключові проблеми не тільки фахової освіти (організаційні, психологічні, фінансові чинники), але й серйозні питання методології дослідницького пошуку. Так, наприклад, у запропонованій статті у простір наукової дискусії виносяться проблеми визначення стандартів та методик усноісторичних глибинних інтерв’ю, технологій архівування свідчень, адаптації створених студентами баз даних до можливостей бібліотек та каталогів, апробації каналів поширення студентських досліджень. Пілотний факультетський проєкт відкритий до обговорення, автори і куратори – до активної співпраці.
Reflexos do isolamento social no período pandêmico para juventude
Authors: Gonçalves Severo Ricardo 
Published: April 2023

O artigo analisa os impactos da pandemia em jovens estudantes e egressos do ensino médio em escolas do Rio Grande do Sul. Com relatos de suas vivências no isolamento social, apreende-se quais questões são relevantes no referido momento. Realizaram-se 44 entrevistas online com jovens de 15 a 23 anos em três cidades: Caxias do Sul, Pelotas e Porto Alegre, entre outubro de 2020 e abril de 2021. A questão-guia da análise foi a percepção sobre o período pandêmico para suas vidas. As entrevistas tiveram focos narrativos, abordando os temas autoanálise, ensino remoto, rearranjos familiares, mudanças no trabalho e formas de interação. Percebeu-se a mudança de padrões de sociabilidade, via de regra com percepção negativa sobre o atual momento, a dificuldade na mudança das relações presenciais para virtuais, em especial, no aspecto educacional, o sentimento de isolamento e as difi culdades financeiras.
Mulheres em luta e a educação de crianças pequenas em uma ocupação urbana
Authors: Ramalho Bárbara , Diniz Carvalho Levindo , Bizzotto Luciana Maciel 
Published: April 2023

Tendo como referência os campos teóricos dos estudos anticoloniais e dos estudos da infância, o presente artigo parte da escuta de educadoras moradoras de uma ocupação urbana em Belo Horizonte e analisa as relações entre a luta por moradia e o direito à educação infantil. Para tanto, são analisados dados de uma pesquisa de doutorado que teve como espaço de investigação uma creche comunitária localizada nesse território. Os resultados do estudo apontam para: os atravessamentos da luta feminista e o papel das mulheres na reivindicação pelos direitos das crianças; a singularidade na oferta da educação infantil no contexto de uma ocupação urbana; e a pertinência da lente anticolonial para a compreensão dos processos de reivindicação de direitos de crianças e mulheres em um movimento social urbano.
Anauchen (?) kozari n. sp., a new Hypselostomatid species from Laos (Gastropoda: Stylommatophora: Pupilloidea)
Authors: Páll-Gergely Barna 
Published: April 2023

AbstractAnauchen (?) kozari n. sp. is described from Luang Prabang province, central Laos. This new species is temporarily placed in the genus Anauchen due to the similarity of its apertural barriers to those of A. messageri (Bavay & Dautzenberg, 1904). Boysidia gereti Bavay & Dautzenberg, 1904 is a junior synonym of Anauchen rochebruni (Mabille, 1887) (originally described as Hypselostoma).
Determination of morphine, codeine, thebaine, papaverine and noscapine in rat plasma by UPLC-MS/MS
Authors: Wang Ying , He Yifan , Wang Xianqin , Wen Congcong , Cao Jianbin 
Published: April 2023

AbstractIn this work, a UPLC-MS/MS assay was established for the determination of morphine, codeine, thebaine, papaverine and noscapine in rat plasma. ACQUITY UPLC BEH C18 column was employed for chromatographic separation with the mobile phase comprised acetonitrile-10 mmol L−1 ammonium acetate aqueous solution (0.05% aqueous ammonia) using gradient elution. Midazolam was used as internal standard (IS). Electrospray ionization (ESI) in positive-ion mode with reaction monitoring (MRM) was used for quantitative analysis. The calibration curves for morphine, codeine, thebaine, papaverine and noscapine demonstrated good linearity (r > 0.995) in the range of 5–500 ng mL−1 for morphine and codeine, and 1–100 ng mL−1 for thebaine, papaverine and noscapine. The intra-day and inter-day precisions of morphine, codeine, thebaine, papaverine and noscapine were within 15%, the intra-day and inter-day accuracies were 89–114%, the recovery was better than 65%, and the matrix effects were 96–112%. The developed UPLC-MS/MS assay was successfully applied in the pharmacokinetics of papaverine and noscapine.
CLL-hez társuló szteroid refrakter AIHA sikeres kezelése bruton tirozin kináz gátlóval
Authors: Balla Evelin , Jakucs János , Orosi Norbert , Hallai Henrietta 
Published: April 2023

AbsztraktA B-CLL-ben szenvedő betegeink közel 20%-a esetében a kórlefolyás során jelentkezik autoimmun betegség, melyek jelentős része jól kezelhető. Jelen esettanulmány kapcsán egy olyan betegünket mutatjuk be, aki nem ebbe a csoportba tartozik. A 2016 óta ismert, „watch and wait” stratégia mentén obszervált beteg 2018-ban gravis, DAT-pozitív haemolitikus anaemia miatt került sürgősséggel felvételre. Parenterális nagy dózisú szteroid lökésterápiát alkalmaztunk B12-és folsavpótlás mellett. Nem szűnő transzfúziós igény miatt terápiáját rituximabbal egészítettük ki. Genetikai vizsgálatok eredményére várva, az elégtelen terápiás válasz miatt R-CVP-terápiát alkalmaztunk, melyre a beteg kiválóan reagált. A várt eredmények megérkeztek: 11q- és mutálatlan IGHV-státusz igazolódott. A hatodik ciklus R-CVP után mintegy egy évvel ismételten gravis hemolízis lépett fel, ekkor – a mutálatlan IGHV-státuszra való tekintettel – ibrutinibterápia mellett döntöttünk. A beteg rapidan romló általános állapota, súlyosbodó hipoxiás tünetei, fokozódó transzfúziós igénye miatt a BTK-hatás kifejlődésére nem várhattunk: intravénás immunglobulin-terápiát alkalmaztunk, valamint a korábban elkezdett ibrutinibet folytattuk. Ezt követően a beteg állapota nagyon gyorsan javult, hemoglobinértéke rapidan emelkedett, transzfúziós igénye megszűnt. A B-CLL terápiájában egyre inkább háttérbe szorulnak a kemoterápiás rezsimek, és teret adnak az innovatív, célzott terápiáknak. Ezek a hatóanyagok a hagyományos kezelésekre nem reagáló szekunder AIHA kezelésében is igen jó eredménnyel alkalmazhatóak.
Comparative study of metaheuristics on optimal design of gravity retaining wall
Authors: Alsamia Shaymaa , Koch Edina , Hamadi Hanaa Shihab 
Published: April 2023

AbstractRetaining walls are typical geotechnical engineering applications analyzed extensively in the literature. However, the optimal design of these walls is still unsolved due to the optimization problem's complexity and the unrecognized best solver that can be used. Most similar works present a single optimizer for this problem. This work used six metaheuristics to formulate and solve the optimal gravity retaining wall problem design. The comparative study was achieved among particle swarm optimization, grey wolf optimizer, artificial bee colony, dynamic differential annealed optimization, fertilization optimization algorithm, and whale optimization algorithm. The problem and its results were discussed in detail within the respective sections.
Autophagy and LC3-associated phagocytosis: similarities and differences
Authors: Ibragimov B. R. , Skibo Yu. V. , Abramova Z. I. 
Published: April 2023

Previously, autophagy was termed as a mechanism used by the cells with a lack of essential nutrients supporting homeostasis. Over the decade of studies, autophagy proved to be a more complex, ambiguous mechanism. Its activation depends on the nature of stimulus, type of immune cells and the final result. Both canonical and non-canonical autophagy, being similar in molecular events, but showing their own distinctive features, are key processes in protecting the body from penetration of intracellular pathogens, maintaining the required level of nutrients in the cell, and removing damaged organelles and cells. Canonical autophagy probably evolved as a homeostatic response to cellular stress and nutritional deficiencies, whereas non-canonical autophagy emerged as a response to suppression of inflammation. Non-canonical autophagy, hereinafter referred to as LC3-associated phagocytosis (LAP), combines the molecular mechanism of phagocytosis with an autophagy mechanism characterized by ingestion of exogenous pathogens, formation of phagosomes (laposomes) and enhanced fusion with lysosomes, followed by degradation of their contents.Significant differences were found between the processes of LAP- and canonical autophagy, which are similar in its mechanism of action. The presence of PI3K complexes in both processes, utilization and intracellular degradation of the “cargo” which is not required for the cells and organism proceeding in the lysosomes, and involvement of almost the same proteins provide similarity of their mechanisms. However, there are differences in the initiation of the processes, e.g., different types of PI3K complexes (in autophagy, PI3K III class 1 and 2 types; in LAP PI3K III, class 3 type), usage of reactive oxygen species in LAP, different types of regulatory proteins involved (ULK1, FIP200, ATG13 , Ambra1, WIPI2, ATG14 in autophagy; and Rubicon and NOX2 in LC3-associated phagocytosis), different number of layers in the membrane structure in which lysis occurs (double-membrane autophagolysosome and single-layer membrane in laposomes) clearly depict the variety of canonical and non-canonical autophagy. The two pathways are directed for different types of biological objects, i.e., intracellular pathogens, dysfunctional proteins and organelles in autophagy, and extracellular pathogens, apoptotic bodies, bacteria, utilized in LAP, thus making these mechanisms completely different in their significance.Collectively, the new data indicate that autophagy performed via both canonical and non-canonical pathways, has evolved into a host defense mechanism capable of resisting immunological and pathogenic stress and mediating immunological tolerance to both intra- and extracellular threats. The present review discusses fundamental molecular differences between these mechanisms, as well as their role in immunity, based on the latest literature data.
Evaluation of the functional activity of CD39 ectonucleotidase in regulatory T cells in children with inflammatory bowel diseases
Authors: Radygina T. V. , Sorokina E. G. , Petrichuk S. V. , Kuptsova D. G. , Kurbatova O. V. , Potapov A. S. , Afanasyeva S. A. 
Published: April 2023

In connection with the increasing incidence and prevalence of inflammatory bowel disease (IBD), the search for prognostic markers of the effectiveness of therapy is an urgent problem. An imbalance between Th17 lymphocytes and regulatory T cells (Treg) is a major defect in the immune system leading to IBD. Extracellular ATP produced during tissue damage, rebound pro-inflammatory effects, and activates Th17 cell differentiation. Ectonucleotidase CD39 catalyzes the dephosphorylation of ATP to AMP, followed by conversion to adenosine by CD73. CD39 is expressed in various cell types, including Treg. Aim – evaluate the functional activity of CD39+ in Treg in children with IBD using the luciferin-luciferase method.68 children with IBD were examined. Of these, 28 children were in remission, 40 were in exacerbation. The number of Tregs (CD4+CD25highCD127low) expressing CD39 was estimated by flow cytometry. The ATP concentration in supernatants and cells was determined using the luciferin-luciferase test. Results are presented as median (Me) and quartiles (Q0.25-Q0.75). The significance of differences between groups was assessed using the nonparametric Mann–Whitney U test.The relative number of CD39+Treg in patients in remission of IBD was significantly higher than in patients in a state of exacerbation. A decrease in ATP concentration under the influence of CD39+Treg in patients with IBD occurred immediately upon the addition of exogenous ATP. ATP in patients in remission decreased by 44.5% (Me 54.5 (41.5-65.9)), in patients in exacerbation – by 32.5% (Me 67.5 (59.7-71.3)). At the same time, in patients in remission, the decrease in the ATP content after 5 minutes of the reaction was significantly higher than in patients in the state of exacerbation (p = 0.01), after 30 minutes of the reaction, no significant difference was found. It was shown that samples with a smaller number of cells and a lower intensity of CD39 expression in Treg had a higher activity of CD39 ectonucleotidase.For efficient ATP hydrolysis, in addition to the amount of CD39 in Treg, their functional activity is important. The assessment of the catalytic activity of CD39 in Treg in patients with IBD is most informative in the first minutes after the addition of exogenous ATP. In patients in remission, the catalytic activity of CD39 in Treg was higher than in patients in a state of exacerbation.
On the Identifiability of Cognitive Diagnostic Models: Diagnosing Students’ Translation Ability
Authors: Tabatabaee-Yazdi Mona , Samir Aynaz 
Published: April 2023

Background. In recent years Cognitive Diagnostic Models (CDMs) have attracted a great deal of attention from researchers in a variety of educational fields. However, they have not been taken into consideration in Translation Quality Assessment (TQA), in the aims of presenting fine-grained information about the strengths and weaknesses of translation students.
Purpose. The present study compares the ACDM, DINO, DINA, HO-DINA, and G-DINA models, in order to define the strengths and weaknesses of Iranian translation students and to examine whether the required translation attributes are compensatory, non-compensatory, additive, or hierarchical.
Methods. 200 BA translation students translated a two-English-text translation, which was scored by three experienced translation raters using the Translation Quality Assessment Rubric (TQAR). The professional translators, established the relationships between the TQAR items and the nine proposed target translation attributes by constructing a Q-matrix.
Results. Based on the results, HO-DINA can be considered the best-fitting model. Bibliography and technical skills, together with work methodology skills, are shown to be the most difficult attributes for translation students.
Conclusion. HO-DINA is a non-compensatory model, thus the study findings assert that for a correct response to a test item, all measurable attributes need to be mastered.
Technology-Enabled Language Leaning: Mediating Role of Collaborative Learning
Authors: Kaur Divya Jyot , Saraswat Niraja , Alvi Irum 
Published: April 2023

Background. Technology-Enabled Language learning (TELL) encourages peer communication and collaboration through its innovative instructional methods. Collaborative student activities are recognised as an important component of the instructional approach of higher education, More recently, collaborative learning in conjunction with digital teaching tools has emerged as a preferred SLA pedagogical approach. Despite growing interest in TELL, research into the effects of collaborative learning on affective factors in SLA remains unexplored.
Purpose. The aim of the proposed study is to identify factors influencing the behavioral intention of students to use WhatsApp for second language acquisition. Constructs from previous models: performance expectancy, effort expectancy, and perceived relevance (UTAUT) are tested, along with the mediating role of a new variable ‘collaborative learning’.
Methods. Using the convenience sampling technique, the sample comprises 202 undergraduates studying in Institutes in Rajasthan, India. Data collected through Google forms was analyzed through IBM SPSS ver. 26 and Smart-PLS ver. 3.2.9, using structural equation modeling.
Results. A positive and significant relationship was established between all the selected constructs. The indirect effects were positive, yet less significant than the direct effects. Moreover, the partially mediating effect of collaborating learning was affirmed. Empirical data confirms that collaborative learning acts as a mediating variable enhancing the intention to use WhatsApp for SLA.
Conclusion. The present study makes an original and innovative contribution to language studies by analysing the relationship between the predictors. Such a systematic understanding of the topic can assist instructors in designing robust future pedagogical techniques.
Is It True They Negatively Engage? Mixed Method Research of Student Engagement in EFL Online Classrooms
Authors: Alzahrani Fahad 
Published: April 2023

Background. A leading concern in teaching and learning is how to increase the degree of student engagement in learning. Within the virtual educational environment, student engagement is a real issue facing instructors and teachers. Students in online classrooms are not able to engage in the same manner as in face-to-face settings.
Purpose. This study aims to explore the impact and reception of online education on student engagement in English as a foreign language (EFL) classroom.
Method. This study adopts a mixed-method approach, in order to understand student engagement online. Longitudinal self-report surveys (SRS) filled out by 127 undergraduate students after each class session throughout a four-week period were used to assess their engagement in online language classrooms. Focus-group interview transcriptions were used to triangulate the data and provide further information about student engagement in terms of gender difference, engagement growth over time, and engagement fostering or hindrance factors in virtual learning classrooms.
Results. Analysis showed that students were generally engaged during the weeks with some variances. Cognitive-social learning engagement showed dynamics among students in virtual language classrooms. Factors such as place of engagement and students’ choice of device used to access the virtual session were found to influence student engagement in online classroom learning. Male and female students generally showed similar learning engagement in the virtual classes with disparities occurring over the study period.
Conclusion. The study results will be beneficial for researchers, instructors, and policymakers who are interested in understanding student engagement and who seek to improve the teaching experience.