Miracle-dz/UniFAR-FTUs huggingface dataset:
X‐ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double‐strand break repair impacting cell and cancer biology

Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIVBRCT–Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.
PEDOT/WO3 Hybrid Nanofiber Architectures for High Performance Electrochromic Devices

This study focuses on the electrochromic device (ECD) applications of poly(3,4-ethylenedioxythiophene)/tungsten oxide (PEDOT/WO3) hybrid nanofibers prepared via electrospinning method. Nanoporous WO3 films were initially electrosynthesized on Pt sheet. The PEDOT layer was electropolymerized onto the entire surface of the WO3 nanoporous host framework in the presence of different ionic liquids: 1-butyl-3-methylimidazolium tetrafluoroborate (BMIMBF4), 1-butyl-3-methylimidazolium hexafluorophosphate (BMIMPF6), 1-butyl- 3-methylimidazolium bis(trifluoromethylsulfonyl) imide (BMIMTFSI), and 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl) imide (BMPTFSI). The morphological features and elemental surface characterization of hybride nanofibers were monitored by scanning electron microscopy and energy dispersive X-ray spectroscopy. ECDs changed color reversibly from transparent to light brown by switching from +3 V to −3 V. It was found that the highest optical modulation of 47.89 % and maximum coloration efficiency of 363.72 cm2/C is achieved for PEDOT/WO3/BMIMPF6 based electrochromic device. Hybrid nanofibers exhibited excellent long term stability even after 1000 chronoamperometric cycles. This work could not only push forward the facile preparation of PEDOT/WO3 nanofibers but also represent, for the first time, the possibility that the hybrid nanofibers could be a promising material for the highly efficient ECDs.
A General Kinetic-Optical Model for Solid-State Reactions Involving the Nano Kirkendall Effect. The Case of Copper Nanoparticle Oxidation

Oxidation of copper nanoparticles (NPs) and other solid-state reactions have been shown recently to involve the nanoscale Kirkendall effect (NKE). The process, resulting in the formation of internal voids, has been rarely considered in most of the simple reaction kinetic models currently available. Here we present a general solid-state reaction kinetic model based on the assumption of steady-state diffusion profiles for rationalizing the evolution of the optical behavior observed in plasmonic Cu NPs undergoing solid-state oxidation to Cu2O. While the model is applied here to an oxidation process, it is applicable in principle to any system showing Kirkendall voiding. An analytical expression of the rate law for spherical NPs is derived, and implications of the model are discussed. By combining the general kinetic model with Mie scattering solutions under the quasi-static approximation, the extinction cross section of Cu NPs as a function of the Cu-to-Cu2O conversion fraction is modeled, for NPs of differe.
Psychometric properties of the Mindsets of Depression, Anxiety, and Stress Scale (MDASS) in Chinese young adults and adolescents

Mindset has been found to be closely related to mental health symptoms. Yet no scale for the Mindsets of Depression, Anxiety, and Stress (MDASS) has been validated. This study developed a 12‐item MDASS with four items in each domain and examined its psychometric properties among young adults and adolescents.
Improving Patient Activation among Older Veterans: Results from a Social Worker-Led Care Transitions Intervention

ABSTRACT Older veterans enrolled in the Veterans Health Administration (VHA) often use both VHA and non-VHA providers for their care. This dual use, especially around an inpatient visit, can lead to fragmented care during the time of transition post-discharge. Interventions that target patient activation may be valuable ways to help veterans manage complex medication regimens and care plans from multiple providers. The Care Transitions Intervention (CTI) is an evidence-based model that helps older adults gain confidence and skills to achieve their health goals post-discharge. Our study examined the impact of CTI upon patient activation for veterans discharged from non-VHA hospitals. In total, 158 interventions were conducted for 87 veterans. From baseline to follow-up there was a significant 1.7-point increase in patient activation scores, from 5.4 to 7.1. This association was only found among those who completed the intervention. The most common barriers to completion were difficulty reaching the veteran by phone, patient declining the intervention, and rehospitalization during the 30 days post-discharge. Care transitions guided by social workers may be a promising way to improve patient activation. However, future research and practice should address barriers to completion and examine the impact of increased patient activation on health outcomes.
Unsulfated biotechnological chondroitin by itself as well as in combination with high molecular weight hyaluronan improves the inflammation profile in osteoarthritis in vitro model

Several studies suggest that inflammation has a pivotal role during the progression of osteoarthritis (OA) and cytokines have been identified as the main process mediators. This study aimed to explore the ability to modulate the main OA pro‐inflammatory biomarkers of novel gels (H‐HA/BC) based on high molecular weight hyaluronan (H‐HA) and unsulfated biotechnological chondroitin (BC). For the first time, BC was tested also in combination with H‐HA on human primary cells isolated from pathological knee joints. Specifically, the experiments were performed using an OA in vitro model based on human chondrocytes and synoviocytes. To evaluate the anti‐inflammatory effects of H‐HA/BC in comparison with H‐HA and BC single gels, NF‐kB, COMP‐2, MyD88, MMP‐13 and a wide range of cytokines, known to be specific biomarkers in OA (e.g., IL‐6, IL‐8, and TNF‐α), were evaluated. In addition, cell morphology and proliferation occurring in the presence of either H‐HA/BC or single components were assessed using time‐lapse video microscopy. It was shown that synovial fluids and cells isolated from OA suffering patients, presented a cytokine pattern respondent to an ongoing inflammation status. H‐HA and BC significantly reduced the levels of 23 biomarkers associated with cartilage damage. However, H‐HA/BC decreased significantly 24 biological mediators and downregulated 19 of them more efficiently than the single components. In synoviocytes cultures, cytokine analyses proved that H‐HA/BC gels re‐established an extracellular environment more similar to a healthy condition reducing considerably the concentration of 11 analytes. Instead, H‐HA and BC significantly modulated 7 (5 only with a longer treatment) and 8 biological cytokines, respectively. Our results suggest that H‐HA/BC beyond the viscosupplementation effect typical for HA‐based gels, can improve the inflammation status in joints and thus could be introduced as a valid protective and anti‐inflammatory intraarticular device in the field of Class III medical devices for OA treatments.
Mechanistic aspects of carotenoid health benefits – where are we now?

Abstract Dietary intake and tissue levels of carotenoids have been associated with a reduced risk of several chronic diseases, including cardiovascular diseases, type 2 diabetes, obesity, brain-related diseases and some types of cancer. However, intervention trials with isolated carotenoid supplements have mostly failed to confirm the postulated health benefits. It has thereby been speculated that dosing, matrix and synergistic effects, as well as underlying health and the individual nutritional status plus genetic background do play a role. It appears that our knowledge on carotenoid-mediated health benefits may still be incomplete, as the underlying mechanisms of action are poorly understood in relation to human relevance. Antioxidant mechanisms – direct or via transcription factors such as NRF2 and NF-κB – and activation of nuclear hormone receptor pathways such as of RAR, RXR or also PPARs, via carotenoid metabolites, are the basic principles which we try to connect with carotenoid-transmitted health benefits as exemplified with described common diseases including obesity/diabetes and cancer. Depending on the targeted diseases, single or multiple mechanisms of actions may play a role. In this review and position paper, we try to highlight our present knowledge on carotenoid metabolism and mechanisms translatable into health benefits related to several chronic diseases.
Effect of Moderately but Persistently Elevated Lipid Levels on Risks of Stroke and Myocardial Infarction in Young Korean Adults

Background Identifying predictive markers for future atherosclerotic cardiovascular diseases may be helpful to motivate young adults to promote healthy lifestyle. We sought to determine the association between persistently elevated low‐density lipoprotein‐cholesterol (LDL‐C) and/or triglyceride levels and the atherosclerotic cardiovascular diseases risks in young adults. Methods and Results We conducted a nationwide population‐based cohort study of 1 887 853 statin‐naive adults aged 20 to 39 years, with LDL‐C <190 mg/dL, using the Korean National Health Insurance Service database. Persistently elevated LDL‐C and triglyceride levels were defined by ≥3 measurements of ≥160 and ≥175 mg/dL, respectively. The primary outcome was a composite of stroke and myocardial infarction. Among the study population, 11 121 (0.59%) and 167 373 (8.87%) had persistently elevated LDL‐C and triglycerides, respectively. During a median follow‐up of 5.2 years, 2170 and 1537 incidences of stroke (0.16%) and myocardial infarction (0.23%) occurred. Persistently elevated LDL‐C levels were significantly associated with increased risks of the primary outcome, with an adjusted hazard ratio (HR) of 1.396 (95% CI, 1.005–1.940). This association was independent of high‐density lipoprotein cholesterol. Persistently elevated triglycerides were significantly associated with increased risks of the primary outcome (HR, 1.120; 95% CI, 1.015–1.236), but attenuated after adjustment for high‐density lipoprotein cholesterol. Conclusions Persistently elevated LDL‐C and triglyceride levels were associated with atherosclerotic cardiovascular diseases risk in young Korean adults without severe hypercholesterolemia. These lipid abnormalities should be considered risk factors in young adults since their effects on lifetime atherosclerotic cardiovascular diseases risk may become more pronounced over the life course.
b2bTools: online predictions for protein biophysical features and their conservation

Abstract We provide integrated protein sequence-based predictions via https://bio2byte.be/b2btools/. The aim of our predictions is to identify the biophysical behaviour or features of proteins that are not readily captured by structural biology and/or molecular dynamics approaches. Upload of a FASTA file or text input of a sequence provides integrated predictions from DynaMine backbone and side-chain dynamics, conformational propensities, and derived EFoldMine early folding, DisoMine disorder, and Agmata β-sheet aggregation. These predictions, several of which were previously not available online, capture ‘emergent’ properties of proteins, i.e. the inherent biophysical propensities encoded in their sequence, rather than context-dependent behaviour (e.g. final folded state). In addition, upload of a multiple sequence alignment (MSA) in a variety of formats enables exploration of the biophysical variation observed in homologous proteins. The associated plots indicate the biophysical limits of functionally relevant protein behaviour, with unusual residues flagged by a Gaussian mixture model analysis. The prediction results are available as JSON or CSV files and directly accessible via an API. Online visualisation is available as interactive plots, with brief explanations and tutorial pages included. The server and API employ an email-free token-based system that can be used to anonymously access previously generated results.
Synonym Replacement based on a Study of Basic-level Nouns in Swedish Texts of Different Complexity

Basic-level terms have been described as the most important to human categorisation. They are the earliest emerging words in children’s language acquisition, and seem to be more frequently occurring in language in general. In this article, we explored the use of basic-level nouns in texts of different complexity, and hypothesise that hypernyms with characteristics of basic-level words could be useful for the task of lexical simplification. We conducted two corpus studies using four different corpora, two corpora of standard Swedish and two corpora of simple Swedish, and explored whether corpora of simple texts contain a higher proportion of basic-level nouns than corpora of standard Swedish. Based on insights from the corpus studies, we developed a novel algorithm for choosing the best synonym by rewarding high relative frequencies and monolexemity, and restricting the climb in the word hierarchy not to suggest synonyms of a too high level of inclusiveness.
A Baseline Document Planning Method for Automated Journalism

In this work, we present a method for content selection and document planning for automated news and report generation from structured statistical data such as that offered by the European Union’s statistical agency, EuroStat. The method is driven by the data and is highly topic-independent within the statistical dataset domain. As our approach is not based on machine learning, it is suitable for introducing news automation to the wide variety of domains where no training data is available. As such, it is suitable as a low-cost (in terms of implementation effort) baseline for document structuring prior to introduction of domain-specific knowledge.
Word Alignment Dissimilarity Indicator: Alignment Links as Conceptualizations of a Focused Bilingual Lexicon

Starting from the assumption that different word alignments of translations represent differing conceptualizations of cross-lingual equivalence, we assess the variation of six different alignment methods for English-to-Spanish translated and post-edited texts. We develop a word alignment dissimilarity indicator (WADI) and compare it to traditional segment-based alignment error rate (AER). We average the WADI scores over the possible 15 different pairings of the six alignment meth-ods for each source token and correlate the averaged WADI scores with translation process and product measures, including production duration, number of insertions, and word translation entropy. Re-sults reveal modest correlations between WADI and production duration and insertions, as well as a moderate correlation be-tween WADI and word translation entropy. This shows that differences in alignment decisions reﬂect on variation in translation decisions and demonstrates that aggregate WADI score could be used as a word-level feature to estimate post-editing difﬁculty.
Exploring the Importance of Source Text in Automatic Post-Editing for Context-Aware Machine Translation

Accurate translation requires document-level information, which is ignored by sentence-level machine translation. Recent work has demonstrated that document-level consistency can be improved with automatic post-editing (APE) using only target-language (TL) information. We study an extended APE model that additionally integrates source context. A human evaluation of fluency and adequacy in English–Russian translation reveals that the model with access to source context significantly outperforms monolingual APE in terms of adequacy, an effect largely ignored by automatic evaluation metrics. Our results show that TL-only modelling increases fluency without improving adequacy, demonstrating the need for conditioning on source text for automatic post-editing. They also highlight blind spots in automatic methods for targeted evaluation and demonstrate the need for human assessment to evaluate document-level translation quality reliably.
CoDeRooMor: A new dataset for non-inflectional morphology studies of Swedish

The paper introduces a new resource, CoDeRooMor, for studying the morphology of modern Swedish word formation. The approximately 16.000 lexical items in the resource have been manually segmented into word-formation morphemes, and labeled for their categories, such as prefixes, suffixes, roots, etc. Word-formation mechanisms, such as derivation and compounding have been associated with each item on the list. The article describes the selection of items for manual annotation and the principles of annotation, reports on the reliability of the manual annotation, and presents tools, resources and some first statistics. Given the”gold” nature of the resource, it is possible to use it for empirical studies as well as to develop linguistically-aware algorithms for morpheme segmentation and labeling (cf statistical subword approach). The resource will be made freely available.
Knowledge Distillation for Swedish NER models: A Search for Performance and Efficiency

The current recipe for better model performance within NLP is to increase model size and training data. While it gives us models with increasingly impressive results, it also makes it more difficult to train and deploy state-of-the-art models for NLP due to increasing computational costs. Model compression is a field of research that aims to alleviate this problem. The field encompasses different methods that aim to preserve the performance of a model while decreasing the size of it. One such method is knowledge distillation. In this article, we investigate the effect of knowledge distillation for named entity recognition models in Swedish. We show that while some sequence tagging models benefit from knowledge distillation, not all models do. This prompts us to ask questions about in which situations and for which models knowledge distillation is beneficial. We also reason about the effect of knowledge distillation on computational costs.
Fine-grained Named Entity Annotation for Finnish

We introduce a corpus with fine-grained named entity annotation for Finnish, following the OntoNotes guidelines to create a resource that is cross-lingually compatible with existing annotations for other languages. We combine and extend two NER corpora recently introduced for Finnish and revise their custom annotation scheme through a combination of automatic and manual processing steps. The resulting corpus consists of nearly 500,000 tokens annotated for over 50,000 mentions categorized into the 18 OntoNotes name and numeric entity types. We evaluate this resource and demonstrate its compatibility with the English OntoNotes annotations by training state-of-the-art mono-, bi- and multilingual deep learning models, finding both that the corpus allows highly accurate recognition of OntoNotes types at 93% F-score and that a comparable level of tagging accuracy can be achieved by a bilingual Finnish-English NER model.
Sound source and pseudo-sound in the near field of a circular cylinder in subsonic conditions

Abstract It is well known that the pressure fluctuations on both sides of a cylinder and those in its oscillating near-wake region are both sound sources at low Reynolds and Mach numbers. However, assessment of the propagating capacity and quantification of the radiating versus non-radiating components of these two sound sources are not currently available for this important benchmark aeroacoustic problem. Here, we isolate the radiating acoustic sound sources from the non-radiating hydrodynamic pseudo-sounds by applying the wavelet decomposition technique of Mancinelli et al. (J. Fluid Mech., vol. 813, 2017), previously used in subsonic jet-noise experiments, to decompose the cylinder near-field pressure fluctuations obtained from our direct numerical simulations. Rigorous independence and convergence analyses of the wavelet decomposition procedure are performed. It is found that the radiating acoustic component strongly dominates over the non-radiating hydrodynamic component at near-field locations above and upstream of the cylinder. In the oscillating near-wake region, the hydrodynamic component dominates over the acoustic component at most frequencies, except at the vortex shedding frequency where they exhibit comparable strengths. Furthermore, within the oscillating near-wake region, the overall sound pressure level associated with the hydrodynamic pressure fluctuations exceeds that associated with the acoustic pressure fluctuations. Away from the oscillating near-wake region, the hydrodynamic pressure fluctuations decrease dramatically while the acoustic counterparts decay slowly, demonstrating that the hydrodynamic pressure fluctuation does not propagate, and that the acoustic pressure fluctuation is the only component to propagate to the far field.
Self-similarity of turbulent jet flows with internal and external intermittency

Abstract The combined effect of internal and external intermittency on the statistical properties of small-scale turbulence is investigated in temporally evolving, planar turbulent jet flows at different Reynolds numbers using highly resolved direct numerical simulations. In turbulent jet flows, the phenomenon of external intermittency originates from a sharp layer, known as the turbulent/non-turbulent interface, that separates the turbulent core from the surrounding irrotational fluid. First, it is shown that low-order and higher-order structure functions in both the core and the shear layer of the jet satisfy complete self-preservation, which means that structure functions are invariant with time and collapse over the entire range of scales, regardless of the set of length and velocity scales used for normalization. Next, the impact of external intermittency on small-scale turbulence is studied along the cross-wise direction by the self-similarity of structure functions. It is shown that structure functions exhibit from the centre toward the edge of the flow a growing departure from self-similarity and the prediction of classical scaling theories. By analysing statistics conditioned on the turbulent portion of the jet, it is demonstrated that this departure is primarily due to external intermittency and the associated similarity-breaking effect.