bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanisms of APOBEC3 mutagenesis in human cancer cells
Authors: Petljak Mia , Dananberg Alexandra , Chu Kevan , Bergstrom Erik N. , Striepen Josefine , von Morgen Patrick , Chen Yanyang , Shah Hina , Sale Julian E. , Alexandrov Ludmil B. , Stratton Michael R. , Maciejowski John 
Published: July 2022

AbstractThe APOBEC3 family of cytosine deaminases has been implicated in some of the most prevalent mutational signatures in cancer1–3. However, a causal link between endogenous APOBEC3 enzymes and mutational signatures in human cancer genomes has not been established, leaving the mechanisms of APOBEC3 mutagenesis poorly understood. Here, to investigate the mechanisms of APOBEC3 mutagenesis, we deleted implicated genes from human cancer cell lines that naturally generate APOBEC3-associated mutational signatures over time4. Analysis of non-clustered and clustered signatures across whole-genome sequences from 251 breast, bladder and lymphoma cancer cell line clones revealed that APOBEC3A deletion diminished APOBEC3-associated mutational signatures. Deletion of both APOBEC3A and APOBEC3B further decreased APOBEC3 mutation burdens, without eliminating them. Deletion of APOBEC3B increased APOBEC3A protein levels, activity and APOBEC3A-mediated mutagenesis in some cell lines. The uracil glycosylase UNG was required for APOBEC3-mediated transversions, whereas the loss of the translesion polymerase REV1 decreased overall mutation burdens. Together, these data represent direct evidence that endogenous APOBEC3 deaminases generate prevalent mutational signatures in human cancer cells. Our results identify APOBEC3A as the main driver of these mutations, indicate that APOBEC3B can restrain APOBEC3A-dependent mutagenesis while contributing its own smaller mutation burdens and dissect mechanisms that translate APOBEC3 activities into distinct mutational signatures.
Hijacking of transcriptional condensates by endogenous retroviruses
Authors: Asimi Vahid , Sampath Kumar Abhishek , Niskanen Henri , Riemenschneider Christina , Hetzel Sara , Naderi Julian , Fasching Nina , Popitsch Niko , Du Manyu , Kretzmer Helene , Smith Zachary D. , Weigert Raha , Walther Maria , Mamde Sainath , Meierhofer David , Wittler Lars , Buschow René , Timmermann Bernd , Cisse Ibrahim I. , Ameres Stefan L. , Meissner Alexander , Hnisz Denes 
Published: July 2022

AbstractMost endogenous retroviruses (ERVs) in mammals are incapable of retrotransposition; therefore, why ERV derepression is associated with lethality during early development has been a mystery. Here, we report that rapid and selective degradation of the heterochromatin adapter protein TRIM28 triggers dissociation of transcriptional condensates from loci encoding super-enhancer (SE)-driven pluripotency genes and their association with transcribed ERV loci in murine embryonic stem cells. Knockdown of ERV RNAs or forced expression of SE-enriched transcription factors rescued condensate localization at SEs in TRIM28-degraded cells. In a biochemical reconstitution system, ERV RNA facilitated partitioning of RNA polymerase II and the Mediator coactivator into phase-separated droplets. In TRIM28 knockout mouse embryos, single-cell RNA-seq analysis revealed specific depletion of pluripotent lineages. We propose that coding and noncoding nascent RNAs, including those produced by retrotransposons, may facilitate ‘hijacking’ of transcriptional condensates in various developmental and disease contexts.
Kinetics of anti-nucleocapsid IgG response in COVID-19 immunocompetent convalescent patients
Authors: Movsisyan Mariam , Chopikyan Armine , Kasparova Irina , Hakobjanyan Gohar , Carrat Fabrice , Sukiasyan Meline , Rushanyan Marieta , Chalabyan Mariam , Shariff Sanobar , Kantawala Burhan , Keshishyan Anna , Hovhannisyan Alvard , Hakobyan Armine , Petrosyan Gayane , Minasyan Armen , Muradyan Armen , Mekinian Arsene , Yenkoyan Konstantin 
Published: July 2022

AbstractThe comprehension of a long-term humoral immune response against SARS-CoV-2 can shed light on the treatment and vaccination strategies of COVID-19 disease, improving the knowledge about this virus infection and/or re-infection. We assessed the IgG antibodies against SARS-CoV-2 nucleocapsid (N) protein (anti-SARS-CoV-2 (N) IgG) in 1441 COVID-19 convalescent patients within 15 months longitudinal study from middle-developed country. The main inclusion criteria was positive RT– PCR result on nasopharyngeal swab samples at least one month before antibody testing and absence of any induced or inherited immunodeficiency. 92.7% of convalescent patients’ serum contained anti-SARS-CoV-2 (N) IgG and only 1.3% of patients had a delayed antibody response. In the majority of convalescent patients’ the durability of antibodies lasted more than one year. The kinetics of anti-SARS-CoV-2 (N) IgG took a bell-shaped character—increased first 25–30 weeks, then started to decrease, but were still detectable for more than 15 months. We found that on the one hand anti-SARS-CoV-2 humoral response level correlates with disease severity, on the other, in particular, the level of peak antibodies correlates with age—older patients develop more robust humoral response regardless of sex, disease severity and BMI.
A retrospective analysis of peri-operative medication errors from a low-middle income country
Authors: Abbasi Shemila , Rashid Saima , Khan Fauzia Anis 
Published: July 2022

AbstractIdentifying medication errors is one method of improving patient safety. Peri operative anesthetic management of patient includes polypharmacy and the steps followed prior to drug administration. Our objective was to identify, extract and analyze the medication errors (MEs) reported in our critical incident reporting system (CIRS) database over the last 15 years (2004–2018) and to review measures taken for improvement based on the reported errors. CIRS reported from 2004 to 2018 were identified, extracted, and analyzed using descriptive statistics and presented as frequencies and percentages. MEs were identified and entered on a data extraction form which included reporting year, patients age, surgical specialty, American Society of Anesthesiologist (ASA) status, time of incident, phase and type of anesthesia and drug handling, type of error, class of medicine, level of harm, severity of adverse drug event (ADE) and steps taken for improvement. Total MEs reported were 311, medication errors were reported, 163 (52%) errors occurred in ASA II and 90 (29%) ASA III patient, and 133 (43%) during induction. During administration phase 60% MEs occurred and 65% were due to human error. ADEs were found in 86 (28%) reports, 58 of which were significant, 23 serious and five life-threatening errors. The majority of errors involved neuromuscular blockers (32%) and opioids (13%). Sharing of CI and a lesson to be learnt e-mail, colour coded labels, change in medication trolley lay out, decrease in floor stock and high alert labels were the low-cost steps taken to reduce incidents. Medication errors were more frequent during administration. ADEs were occurred in 28% MEs.
High-accuracy virtual testing of air conditioner’s digital twin focusing on key material’s deformation and fracture behavior prediction
Authors: Fu Shaohua , Wan Zhenping , Lu Weifeng , Liu Huaican , Zhang Peng’e , Yu Bo , Tan Jianming , Pan Feng , Liu Zhigang 
Published: July 2022

AbstractThe concept of digital twin has been introduced for some time, yet one fundamental element of digital twin, digital material, has not been thoroughly studied. To interact with the physical product, the digital twin should always truthfully reflect the responses under various stimuli. In this paper, the deformation and fracture behavior of high impact polystyrene (HIPS) under the influencing factors of strain rate and stress triaxiality are studied to construct the material’s digital model. A digital twin of air conditioner product is further built and tested under virtual drop test. Comparing to experimental results, the acceleration curve, crazing induced whitening and the fracture events can all be captured by the digital twin. Our work demonstrates the importance of material characterization as an essential step to construct an accurate digital twin and shows a promising future of digital twin in virtual testing to replace traditional “trial and error” experiments.
Mutational induction in SARS-CoV-2 major lineages by experimental exposure to neutralising sera
Authors: Brandolini Martina , Dirani Giorgio , Taddei Francesca , Zannoli Silvia , Denicolò Agnese , Arfilli Valentina , Battisti Arianna , Manera Martina , Mancini Andrea , Grumiro Laura , Marino Maria Michela , Gatti Giulia , Fantini Michela , Semprini Simona , Sambri Vittorio 
Published: July 2022

AbstractThe ongoing evolution of SARS-CoV-2 and the emergence of new viral variants bearing specific escape mutations responsible for immune evasion from antibody neutralisation has required a more accurate characterisation of the immune response as one of the evolutive forces behind viral adaptation to a largely immunised human population. In this work, culturing in the presence of neutralising sera vigorously promoted mutagenesis leading to the acquisition of known escape mutations on the spike as well as new presumptive escape mutations on structural proteins whose role as target of the neutralizing antibody response might have been thus far widely neglected. From this perspective, this study, in addition to tracing the past evolution of the species back to interactions with neutralising antibody immune response, also offers a glimpse into future evolutive scenarios.
Grape seed proanthocyanidin extract inhibits DNA and protein damage and labile iron, enzyme, and cancer cell activities
Authors: Habib Hosam M. , El-Fakharany Esmail M. , Kheadr E. , Ibrahim Wissam H. 
Published: July 2022

AbstractGrape seed extract from (Vitis vinifera) (VGSE) is an excellent source of various polyphenols that exhibit highly potent antioxidant and disease prevention properties. Although numerous biological activities, with potential for improving human health, have been reported for VGSE, there is a lack of data relating to the health benefits of VGSE on DNA damage, protein damage, labile iron activity, and enzyme inhibitory effects. This investigation demonstrated, for the first time, that VGSE inhibits DNA and BSA damage and labile iron activity in-vitro. Moreover, VGSE also inhibited in-vitro activities of AChE, tyrosinase, and α-amylase. VGSE treatment significantly reduced viability of MCF-7, Hep-G2, Caco-2, and Huh-7 cells after 48-h treatments. The results obtained provide additional support for the purported health benefits of VGSE and reinforce its potential in disease prevention and therapy, especially in relation to cancer.
On the mixed Kibria–Lukman estimator for the linear regression model
Authors: Chen Hongmei , Wu Jibo 
Published: July 2022

AbstractThis paper considers a linear regression model with stochastic restrictions,we propose a new mixed Kibria–Lukman estimator by combining the mixed estimator and the Kibria–Lukman estimator.This new estimator is a general estimation, including OLS estimator, mixed estimator and Kibria–Lukman estimator as special cases. In addition, we discuss the advantages of the new estimator based on MSEM criterion, and illustrate the theoretical results through examples and simulation analysis.
Relationship between cognition and treatment adherence to disease-modifying therapy in multiple sclerosis: a prospective, cross-sectional study
Authors: Giedraitiene N. , Taluntiene V. , Kaubrys G. 
Published: July 2022

AbstractLess than half of patients with chronic diseases, including multiple sclerosis (MS), adhere to their prescribed medications. Treatment selection is essential for patient adherence. The aim of this study was to explore the potential factors influencing nonadherence to disease-modifying therapies (DMTs) in MS. This prospective, cross-sectional study was performed at the Multiple Sclerosis Center between 2018 and 2021. In total, 85 patients were eligible for final analysis. Forty-one patient (48.2%) with MS were non-adherent to DMT. Male sex, oral administration of drugs, and longer treatment duration were associated with nonadherence. The mean Expanded Disability Status Scale score did not differ between the adherent and non-adherent patients (p > 0.05). Patients with a higher score on the Symbol Digit Modalities Test, who were receiving self-injection therapy, had shorter treatment duration, and higher disability, were more likely to be adherent to DMT than those without. To minimize nonadherence in patients with MS, the patient’s information processing speed should be considered before DMT initiation, and appropriate treatment options should be discussed.
Single-cell transcriptome of the mouse retinal pigment epithelium in response to a low-dose of doxorubicin
Authors: Lee Hyungwoo , Lee Ho-Yeon , Chae Jae-Byoung , Park Chul-Woo , Kim Chaekyu , Ryu Ja-Hyoung , Jang Jiwon , Kim Namshin , Chung Hyewon 
Published: July 2022

AbstractCellular senescence of the retinal pigment epithelium (RPE) is thought to play an important role in vision-threatening retinal degenerative diseases, such as age-related macular degeneration (AMD). However, the single-cell RNA profiles of control RPE tissue and RPE tissue exhibiting cellular senescence are not well known. We have analyzed the single-cell transcriptomes of control mice and mice with low-dose doxorubicin (Dox)-induced RPE senescence (Dox-RPE). Our results have identified 4 main subpopulations in the control RPE that exhibit heterogeneous biological activities and play roles in ATP synthesis, cell mobility/differentiation, mRNA processing, and catalytic activity. In Dox-RPE mice, cellular senescence mainly occurs in the specific cluster, which has been characterized by catalytic activity in the control RPE. Furthermore, in the Dox-RPE mice, 6 genes that have not previously been associated with senescence also show altered expression in 4 clusters. Our results might serve as a useful reference for the study of control and senescent RPE.
Stellar limb darkening
Authors: Kostogryz N. M. , Witzke V. , Shapiro A. I. , Solanki S. K. , Maxted P. F. L. , Kurucz R. L. , Gizon L. 
Published: July 2022

Context. The detection of the first exoplanet paved the way for the era of transit-photometry space missions with revolutionary photometric precision, whose aim is to discover new exoplanetary systems around different types of stars. With this high precision, it is possible to derive the radii of exoplanets very accurately, which is crucial for constraining their type and composition. However, it requires an accurate description of their host stars, especially their center-to-limb variation of intensities (so-called limb darkening) as it affects the planet-to-star radius ratio determination.
Aims. We aim to improve the accuracy of limb-darkening calculations for stars with a wide range of fundamental parameters.
Methods. We used the recently developed 1D Merged Parallelized Simplified ATLAS code to compute model atmosphere structures and to synthesize stellar limb darkening on a very fine grid of stellar parameters. For the computations, we utilized the most accurate information on chemical element abundances and mixing-length parameters, including convective overshoot. The stellar limb darkening was fitted using the two most accurate limb darkening laws: the power-2 and 4-parameter nonlinear laws.
Results. We present a new extensive library of stellar model atmospheric structures, the synthesized stellar limb darkening curves, and the coefficients of parameterized limb-darkening laws on a very fine grid of stellar parameters in the Kepler, TESS, CHEOPS, and PLATO passbands. The fine grid allows the sizable errors, introduced by the need to interpolate, to be overcome. Our computations of solar limb darkening are in a good agreement with available solar measurements at different view angles and wavelengths. Our computations of stellar limb darkening agree well with available measurements of Kepler stars. A new grid of stellar model structures, limb darkening, and their fitted coefficients in different broad passbands are provided in online tables available at the CDS.
Using the polarization properties of double radio relics to probe the turbulent compression scenario
Authors: Stuardi C. , Bonafede A. , Rajpurohit K. , Brüggen M. , de Gasperin F. , Hoang D. , van Weeren R. J. , Vazza F. 
Published: July 2022

Context.Radio relics are megaparsec-sized synchrotron sources located in the outskirts of some merging galaxy clusters. Binary-merging systems with a favorable orientation may host two almost symmetric relics, named double radio relics.Aims.Double radio relics are seen preferentially edge-on and, thus, constitute a privileged sample for statistical studies. Their polarization and Faraday rotation properties give direct access to the relics’ origin and magnetic fields.Methods.In this paper, we present a polarization and rotation measure (RM) synthesis study of four clusters hosting double radio relics, namely 8C 0212+703, Abell 3365, and PLCK G287.0+32.9; previously missing polarization studies; and ZwCl 2341+0000, for which conflicting results have been reported. We used 1–2 GHz Karl G. Jansky Very Large Array observations. We also provide an updated compilation of known double radio relics with important observed quantities. We studied their polarization and Faraday rotation properties at 1.4 GHz and we searched for correlations between fractional polarization and physical resolution, the distance from the cluster center, and the shock Mach number.Results.The weak correlations found between these quantities are well reproduced by state-of-the-art magneto-hydrodynamical simulations of radio relics, confirming that merger shock waves propagate in a turbulent medium with tangled magnetic fields. Both external and internal Faraday depolarization should play a fundamental role in determining the polarization properties of radio relics at 1.4 GHz. Although the number of double radio relics with RM information is still low, their Faraday rotation properties (i.e., rest-frame RM and RM dispersion below 40 rad m−2and non-Gaussian RM distribution) can be explained in the scenario in which shock waves with Mach numbers larger than 2.5 propagate along the plane of the sky and compress the turbulent intra-cluster medium.
À propos du document de l’Agence nationale de la recherche
Les apports de la génomique à l’agroécologie
Authors: Hainzelin Étienne 
Published: July 2022

Comment les outils de la génomique peuvent-ils concrètement contribuer à la transition agroécologique de la production agricole ? Cette question est traitée au travers de l’analyse d’un corpus des 1 200 projets de recherche dans les différents domaines de la génomique, financés par l’Agence nationale de la recherche (ANR) entre 2005 et 2019. L’analyse débouche sur une proposition de quatre pistes prioritaires pour les recherches futures en génomique pour l’agroécologie.
Isolated toughness for path factors in networks
Authors: Wang Sufang , Zhang Wei 
Published: July 2022

Let ℋ be a set of connected graphs. Then an ℋ-factor is a spanning subgraph ofG, whose every connected component is isomorphic to a member of the set ℋ. An ℋ-factor is called a path factor if every member of the set ℋ is a path. Letk ≥ 2 be an integer. By aP≥k-factor we mean a path factor in which each component path admits at leastkvertices. A graphGis called a (P≥k, n)-factor-critical covered graph if for anyW ⊆ V(G) with |W| = nand anye ∈ E(G − W),G− Whas aP≥k-factor coveringe. In this article, we verify that (1) an (n + λ + 2)-connected graphGis a (P≥2, n)-factor-critical covered graph if its isolated toughnessI(G) >n+λ+2/2λ+3, wherenandλare two nonnegative integers; (2) an (n+ λ + 2)-connected graphGis a (P≥3, n)-factor-critical covered graph if its isolated toughnessI(G) >n+3λ+5/2λ+3, wherenandλbe two nonnegative integers.
Eine theoriegeleitete Implementierung von Messinstrumenten in der physiotherapeutischen Versorgung einer Stroke Unit
Authors: Paus Annalena , Grafe Marion , Stenzel Romina , Heitmann Steffen , Brümmer Werner 
Published: July 2022

Zusammenfassung
Hintergrund Der Einsatz von Messinstrumenten objektiviert und unterstützt die klinische Entscheidungsfindung von Physiotherapierenden bei Planung, Durchführung und Evaluation einer Therapie. Die dadurch erhaltenen Informationen ermöglichen eine patientenzentrierte Versorgung und haben das Potential, die interprofessionelle Kommunikation zu verbessern. Trotz der genannten Vorteile findet die Nutzung von Messinstrumenten im klinischen Alltag bislang keine ausreichende Anwendung.
Ziel Systematische Implementierung von Messinstrumenten in die physiotherapeutische Versorgung der Stroke Unit des Universitätsklinikums Münster mithilfe des „Implementation of Change Model“. Zudem wird evaluiert, ob durch eine Anwendung des Modells eine gesteigerte Nutzung der Messinstrumente festgestellt werden kann.
Methode Zur Implementierung von Messinstrumenten wurde das Implementation of Change Model schrittweise mit diversen Methoden umgesetzt. Zur Ergebnisevaluation wurden quantitative (Fragebogenerhebung) und qualitative Forschungsmethoden (Fokusgruppendiskussion) angewandt.
Ergebnisse Nach Abschluss der Erprobungsphase, Auswertung der Dokumentation, der Befragungen sowie einer Diskussion zeigte sich, dass durch Anwendung des Implementation of Change Models die Nutzung von Messinstrumenten bei Patient*innen mit Schlaganfall gesteigert werden konnte. Aus Sicht der Befragten nahm die Überzeugung über den klinischen Nutzen von Messinstrumenten zu. Es konnte auch eine subjektive Verbesserung der Qualität der Behandlung festgestellt werden.
Schlussfolgerung Das Implementation of Change Model eignet sich zur systematischen Anwendung durch eine Gruppe von Physiotherapierenden in der Akutversorgung, wodurch sich die Nutzung von Messinstrumenten bei Patient*innen mit Schlaganfall steigerte. Es wird empfohlen, weitere Erkenntnisse mit einer größeren Gruppe von Therapierenden und in anderen Versorgungsbereichen durchzuführen.