bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of Nontechnical Skills During Resuscitation
Authors: Milatino Sgambati Michele A. , d'Ercole Adriana , Cascio Michela , Di Viesto Giuseppe , Visicchio Daniele , Boccardo Chiara , Pozzetti Ilaria , Milocco Mimosa , Caporale Mariagiovanna , Poggi Alessandro Delli 
Published: July 2024

Summary Statement
Nontechnical skills (hereinafter referred to as NTS), such as task management, leadership, situational awareness, communication, and decision making contribute to safe and efficient team performance. The importance during cardiopulmonary resuscitation is being increasingly emphasized. We carried out the intercultural adaptation of the TEAM score in Italian and to evaluate the reliability and validity of the resulting Italian version (i-TEAM). A forward-backward translation was made with the author called i-TEAM. Psychometric properties of the i-TEAM score were evaluated, including acceptability, construct validity, and interrater reliability. We divided the participants into 3 groups based on their experience, and we verified if there was a correlation between the final score NTS of i-TEAM and the groups. The Cronbach coefficient was 0.91 for the Total i-TEAM score. The descriptive statistics showed that there was no correlation between NTS score and experience (group). Our results show that i-TEAM has psychometric properties similar to the original score.
Variational inequality for a Timoshenko plate contacting at the boundary with an inclined obstacle
Authors: Kovtunenko Victor A. , Lazarev Nyurgun P. 
Published: July 2024

A class of variational inequalities describing the equilibrium of elastic Timoshenko plates whose boundary is in contact with the side surface of an inclined obstacle is considered. At the plate boundary, mixed conditions of Dirichlet type and a non-penetration condition of inequality type are imposed on displacements in the mid-plane. The novelty consists of modelling oblique interaction with the inclined obstacle which takes into account shear deformation and rotation of transverse cross-sections in the plate. For proposed problems of equilibrium of the plate contacting the inclined obstacle, the unique solvability of the corresponding variational inequality is proved. Under the assumption that the variational solution is smooth enough, optimality conditions are obtained in the form of equilibrium equations and relations revealing the mechanical properties of integrated stresses, moments and generalized displacements on the contact part of the boundary. Accounting for complementarity type conditions owing to the contact of the plate with the inclined obstacle, a primal-dual variational formulation of the obstacle problem is derived. A semi-smooth Newton method based on a generalized gradient is constructed and performed as a primal-dual active-set algorithm. It is advantageous for efficient numerical solution of the problem, provided by a super-linear estimate for the corresponding iterates in function spaces.
This article is part of the theme issue ‘Non-smooth variational problems with applications in mechanics’.
Exploring the performance of the topological energy method for object and damage detection from noisy and poor databases
Authors: Pena M. , Muñoz S. , Rapún M.-L. 
Published: July 2024

In this work, we study the performance of numerical methods based on the computation of topological energies to process data from synthetic and real experiments where only noisy limited-view data corresponding to a few frequencies are available. We show numerical experiments in two problems of practical interest. The first one corresponds to experimental measurements of the electromagnetic scattering produced by different objects extracted from the Fresnel database. The second one is related to synthetic experiments in a simplified model where steel welding joints are acoustically tested to identify possible flaws (air bubbles and inclusions) produced during the welding process.
This article is part of the theme issue ‘Non-smooth variational problems with applications in mechanics’.
NF-κB Epigenetic Attractor Landscape Drives Breast Cancer Heterogeneity
Authors: Lopes Francisco , Pires Bruno R. B. , Lima Alexandre A. B. , Binato Renata , Abdelhay Eliana 
Published: July 2024

ABSTRACTHeterogeneity in breast cancer (BC) subtypes within a tumor contributes to therapy resistance and cancer recurrence. Development of subtype heterogeneity results from stochastic transitions between cell types as the tumor evolves over time. Here, we sought to characterize how NF-κB contributes to the progression of the human epidermal growth factor receptor 2-positive (HER2+) breast cancer subtype. Initially, we used RNA to determine the expression levels of NF-κB, TWIST1, SIP1, and SLUG in two breast cancer (BC) cell lines, HCC-1954 and MDA-MB-231, classified as HER2+and triple-negative breast cancer (TNBC) subtypes, respectively. Then, we built and calibrated a Gene Regulatory Network (GRN) model reproducing the transcriptional regulation between these genes. For validation, we used DHMEQ-treated cells, along with published patient data and in vitro results. The model epigenetic landscape exhibits two attractor basins corresponding to both HER2+and TNBC subtypes, separated by an unstable stationary state. Stochastic fluctuations in the NF-κB levels induce spontaneous irreversible transition from HER2+to TNBC attractor basins at different times, contributing to subtype heterogeneity. The unstable state mediates this transition by providing a slow route between subtypes in the phase space that is susceptible to dynamic fluctuations. Mutations or drugs that change the availability of NF-κB alters the size of the subtype basins, changing the transition probabilities. Together, our findings enhance the established attractor landscape formulation and deepen understanding of BC heterogeneity, leading to more precise classification, prognosis, and targeted strategies for BC progression.
SAMA: a contig assembler with correctness guarantee
Authors: Salmela Leena 
Published: July 2024

AbstractIn genome assembly the task is to reconstruct a genome based on sequencing reads. Current practical methods are based on heuristics which are hard to analyse and thus such analysis is not readily available. We present a model for estimating the probability of misassembly at each position of a de Bruijn graph based assembly. Unlike previous work, our model also takes into account missing data. We apply our model to produce contigs with correctness guarantee. Our model may have further applications in downstream analysis of contigs or in any analysis working directly on the de Bruijn graph. Our experiments show that when the coverage ofk-mers is high enough, our method produces contigs with similar contiguity characteristics as state-of-the-art assemblers which are based on heuristic correction of the de Bruijn graph.
Strawberry COP9 signalosome FvCSN5A regulates plant development and fruit ripening by facilitating polyamine oxidase FvPAO5 degradation to control polyamine and H2O2homeostasis
Authors: Huang Yun , Gao Jiahui , Ji Guiming , Li Wenjing , Wang Jiaxue , Wang Qinghua , Shen Yuanyue , Guo Jiaxuan , Gao Fan 
Published: July 2024

AbstractPolyamines (PAs), mainly including putrescine, spermidine, and spermine, are essential for plant growth and development. However, the post-translational regulation of PA metabolism remains unknown. Here, we report the COP9 signalosome subunit 5A (FvCSN5A)-mediated degradation of the PA oxidase FvPAO5, which catalyzes the conversion of spermidine/spermine to produce H2O2. FvCSN5A is localized in the cytoplasm and nucleus, ubiquitously expressed in strawberry plants, and rapidly increases during fruit ripening.FvCSN5ARNA interference (RNAi) transgenic strawberries exhibit pleiotropic effects on plant development, fertility, and fruit ripening by regulating PA and H2O2homeostasis, similar toFvPAO5overexpression transgenic lines. FvCSN5A interacts with FvPAO5 in vitro and in vivo. The ubiquitination and degradation of FvPAO5 are impaired inFvCSN5ARNAi lines. Additionally, FvCSN5A interacts with cullin 1 (FvCUL1), a core component of the E3 ubiquitin-protein ligase complex. Transient genetic analysis in cultivated strawberry fruits showed that inhibitingFaPAO5expression could partially rescue the ripening phenotype ofFaCSN5ARNAi fruits. Collectively, the CSN5A-CUL1-PAO5 signaling pathway responsible for PA and H2O2homeostasis is crucial to strawberry vegetative and reproductive growth and, final to fruit ripening. Our findings may open a promising avenue for improving crop yield and quality by manipulating the CSN5-PAO5 pair.
In search for multifunctional lncRNAs
Authors: Iyengar Bharat Ravi 
Published: July 2024

AbstractLong non-coding RNAs (lncRNAs) were so named because at the time of their discovery, no corresponding protein products were known. Despite the lack of evidence for translation, many lncRNAs perform essential cellular functions such as regulation of gene expression. Recent studies show that many lncRNAs, including those with known regulatory functions, bind to ribosomes and are translated, suggesting that RNAs can perform two different kinds of functions (a phenomenon known in proteins, called moonlighting). Using a formal mathematical model, I show that execution of one function limits that of the other. However, an RNA can transition from one function to the other, simply by a spatiotemporal regulation of its interacting partners. I further studied the properties of proteins encoded in functional human lncRNAs and found that many of them have complex sequences, and some of them can even adopt stable 3D structures. These findings may encourage further exploration of moonlighting lncRNAs, their regulation, and their role in the evolution of new protein coding genes.
Radiobiological meta-analysis of the response of prostate cancer to high dose rate brachytherapy
Authors: Kölmel Eva G , Pombar Miguel , Pardo-Montero Juan 
Published: July 2024

AbstractBackground and purposeClinical studies have shown a marked reduction in tumor control in prostate cancer treated with radically hypofractionated high-dose-rate brachytherapy (HDR-BT). The purpose of this study was to analyze the dose-response of prostate cancer treated with HDR-BT, specifically aiming at investigating the potential failure of the linear-quadratic (LQ) model to describe the response at large dosesper-fraction.Materials and methodsWe collated a dataset of dose-response to HDR-BT (3258 patients). The analysis was conducted separately for low and intermediate risk, resulting in 21 schedules (1643 patients) and 22 schedules (1615 patients), respectively. Data were fitted to tumor control probability models based on the LQ model, the linear-quadratic-linear (LQL), and a modification of the LQ model to include the effect of reoxygenation during treatment.ResultsThe LQ cannot fit the data unless the α/β is allowed to be very high (∼[20-100] Gy, 95% confidence interval). If the α/β is constrained to be low (< 8 Gy) the LQ model cannot reproduce the clinical results, and the LQL model, which includes a moderation of radiation damage with increasing dose, significantly improves the fitting. On the other hand, the reoxygenation model does not match the results obtained with the LQL.ConclusionThe clinically observed reduction in tumor control in prostate cancer treated with radical HDR-BT is better described by the LQL model. Using the best-fitting parameters, the BED for a 20 Gy × 1 treatment (95 Gy) is far less than that of a conventional 2 Gy × 37 fractionation (184 Gy). These results may assist in the design of radical HDR-BT treatment.
Unremodeled plasma membrane GPI-anchored proteins trigger aberrant clathrin-mediated endocytosis
Authors: Chen Li , Banfield David K. 
Published: July 2024

AbstractThe plasma membrane has a complex organization that includes the polarized distribution of membrane proteins as well as lipids. Glycosylphosphatidylinositol-anchored proteins (GPI-AP) are ubiquitously expressed in eukaryotes and represent a functionally diverse group of proteins some of which are critical for the organization and function of the plasma membrane. Here we investigated how the plasma membrane of yeast cells responded to the accumulation of GPI-APs in which phosphoethanolamine (EtNP) had not been removed from mannose 2 (Man2) of the GPI moiety. The persistence of EtNP on Man2 prevented cleavage of a subset of GPI-APs, but the proteins were not endocytosed. Man2 unremodeled GPI-APs increased lipid disorder and generated a stress response whereby abnormal ubiquitin- and clathrin-dependent endocytosis was triggered. The resulting stress-induced endocytosis disrupted the trafficking repertoire of a subset of plasma membrane proteins. These proteins were redirected, via the multivesicular body, to numerous small vacuoles for degradation. Our findings highlight the critical importance GPI-AP Man2 remodeling for maintaining the integrity and homeostasis of the plasma membrane.
Investigating the structure of Schizotypy through the “Multidimensional Schizotypy Scale” and “Oxford-Liverpool Inventory”: an Exploratory network analysis approach in the healthy population
Authors: Sarti Pierfrancesco , Surbeck Werner , Cecere Giacomo , Dannecker Noemi , Horisberger Rahel , Kallen Nils , Omlor Wolfgang , Steiner Anna , Palpella Dario , Langer Nicolas , Blom Johanna M.C. , Homan Philipp 
Published: July 2024

AbstractBackgroundSchizophrenia spectrum disorders and schizotypy share traits across positive, negative, and disorganized domains. Instruments like MSS and O-LIFE provide insights into these dimensions. Despite challenges posed by cultural variations and measurement methodologies, these instruments offer nuanced perspectives on the spectrum of schizotypy, spanning from its expression as a personality trait to its potential implications in clinical settings.MethodsThrough an Exploratory Graph Analysis (EGA) applied to a sample of 1059 healthy subjects, we compare the resulting networks with the original factorial structure of the two questionnaires and explore how each one conceptualizes schizotypy. Comparing both models quantitatively and qualitatively these models, we seek to elucidate the unique insights provided by each instrument regarding the spectrum of schizotypy as a personality trait.ResultsEGA analyses unveiled a three-dimensional structure plus an additional one consisting of items related to the concept of “Disconnection”. Confirmatory factor analysis showed this four-dimensional model outperformed others. High reliability and strong factor saturation were observed for all four factors.O-LIFE’s EGA revealed a complex structure, refined to four factors removing items with low fitting indices from the scale. Confirmatory analysis validated a final model with robust reliability and well-defined factor structures across the new “Cognitive and Behavioural Disorganization”, “Introversion”, “Unusual Experiences”, and “Environmental Pressure” factors.ConclusionsThis study improves the understanding of schizotypy by proposing new MSS and O-LIFE factor structures via EGA. Both scales uniquely contribute to schizotypy assessment in healthy populations, warranting further research to validate and refine these new domains across diverse populations.
Detecting HRD in whole-genome and whole-exome sequenced breast and ovarian cancers
Authors: Abbasi Ammal , Steele Christopher D. , Bergstrom Erik N. , Khandekar Azhar , Farswan Akanksha , Mckay Rana R. , Pillay Nischalan , Alexandrov Ludmil B. 
Published: July 2024

ABSTRACTBreast and ovarian cancers harboring homologous recombination deficiency (HRD) are sensitive to PARP inhibitors and platinum chemotherapy. Conventionally, detecting HRD involves screening for defects inBRCA1,BRCA2, and other relevant genes. Recent analyses have shown that HRD cancers exhibit characteristic mutational patterns due to the activities of HRD-associated mutational signatures. At least three machine learning tools exist for detecting HRD based on mutational patterns. Here, using sequencing data from 1,043 breast and 182 ovarian cancers, we trained Homologous Recombination Proficiency Profiler (HRProfiler), a machine learning method for detecting HRD using six mutational features. HRProfiler’s performance is assessed against prior approaches using additional independent datasets of 417 breast and 115 ovarian cancers, including retrospective data from a clinical trial involving patients treated with PARP inhibitors. Our results demonstrate that HRProfiler is the only tool that robustly and consistently predicts clinical response from whole-exome sequenced breast and ovarian cancers.SIGNIFICANCEHRProfiler is a novel machine learning approach that harnesses only six mutational features to detect clinically useful HRD from both whole-genome and whole-exome sequenced breast and ovarian cancers. Our results provide a practical way for detecting HRD and caution against using individual HRD-associated mutational signatures as clinical biomarkers.
Social Determinants of Health and Healthcare Utilization Disparities among Older Adults with and Without Cognitive Impairment
Authors: Rahemi Zahra , Shalhout Sophia Z. , Bacsu Juanita-Dawne R. , Petrovsky Darina V. , Zanwar Preeti Pushpalata , Adams Swann Arp 
Published: July 2024

AbstractThe purpose of this study was to determine the healthcare utilization patterns in a national sample of older adults across several social determinants of health factors (ethnicity, gender, race, education) with normal and dementia/impaired cognition. We used datasets from the Health and Retirement Study (HRS, 2018) to evaluate healthcare utilization, including metrics such as hospital and nursing home stays, hospice care, and number of visits to the doctor. Logistic models were used to predict healthcare utilization separately in those with normal cognition and dementia. Our final sample comprised 15,607 adults (mean age: 65.2 normal cognition, mean age 71.5 dementia). Hispanics with normal cognition were less likely to stay in a hospital than non-Hispanic respondents (OR: 0.52-0.71, p<0.01). Being female was associated with a higher risk for shorter nursing home days (OR: 1.41, p<0.01) and doctor visits (OR: 1.63-2, p<0.01) in cognitively normal older adults. Being female was associated with a lower risk for hospital stay in those with dementia (OR: 0.50-0.78, p<0.01). Respondents identifying as Black or other races with dementia were less likely to experience nursing home days (OR: 0.42, p<0.04). Black respondents with normal cognition were less likely to experience doctor visits (OR: 0.32-0.37, p<0.01). Those with more than a high school education in both groups were more likely to experience doctors’ visits. The study points to the continued disparities in healthcare utilization linked to participants’ social determinants of health factors and cognition.
VIRAL METAGENOMIC SURVEY OF CASPIAN SEALS
Authors: Karamendin K , Goodman SJ , Kasymbekov Y , Kumar M , Nuralibekov  , Kydyrmanov A 
Published: July 2024

AbstractViral diseases of pinnipeds cause substantial mortality and morbidity and can influence population demography. Viral metagenomic studies can therefore play an important role in pinniped health assessments and disease surveillance relevant to both individual species and in a ‘One Health’ context. This study used a metagenomic approach with high throughput sequencing to make the first assessment of viral diversity in Caspian seals (Pusa caspica), the only marine mammal species endemic to the Caspian Sea. Sequencing libraries from 35 seals sampled 2009-2020 were analysed, finding sequences from the viral familiesPicornaviridae, Adenoviridae, Circoviridae, Herpesviridae, Papillomaviridae, Caliciviridae, Orthomyxoviridae, Anelloviridae, Smacoviridae, CruciviridaeandParvoviridae. The similarity of viral contigs from Caspian seal to sequences to those recovered from other pinnipeds ranged from 63.74% (San Miguel sea lion calicivirus) to 78.79% (Seal anellovirus 4). Some may represent novel viral species, but overall, the viral repertoire of Caspian seals is similar to available viromes from other pinnipeds. Among the sequences recovered were partial contigs for influenza B, representing only the second such molecular identification in marine mammals. This work provides a foundation for further studies of viral communities in Caspian seals, the diversity of viromes in pinnipeds more generally, and contributes data relevant for disease risk assessments in marine mammals.
A new pathway in central metabolism mediates nutrient control of development and antibiotic production byStreptomyces
Authors: Li Chao , Urem Mia , Kotsogianni Ioli , Lau Josephine , Elsayed Somayah S. , Martin Nathaniel I. , McNae Iain W. , Voskamp Patrick , Mayer Christoph , Rigali Sébastien , Pannu Navraj , Abrahams Jan Pieter , Schada von Borzyskowski Lennart , van Wezel Gilles P. 
Published: July 2024

ABSTRACTThe amino sugarN-acetylglucosamine (GlcNAc) plays a central role in primary metabolism and is a key signaling molecule for the onset of morphological and chemical differentiation ofStreptomyces. The global nutrient-sensory regulator DasR acts as the gatekeeper of development in streptomycetes, and its activity is modulated by aminosugar phosphates. Here, we report the discovery of a novel pathway in aminosugar metabolism that governs GlcNAc sensing. GlcNAc-6P is converted into a toxic metabolite via two new enzyme functions, namely dehydration ofN-acetylglucosamine-6-phosphate by NagS to form 6P-Chromogen I, a reaction that has not yet been described in the textbooks, and its subsequent deacetylation by NagA producing a cytotoxic structural analogue of ribose. The latter reveals an unexpected promiscuous activity for GlcNAc-6P deacetylase NagA. The crystal structures of NagS apoenzyme and NagS in complex with its substrate GlcNAc-6P or its inhibitor 6-phosphogluconate were resolved at 2.3 Å, 2.6 Å, and 1.7 Å resolution, respectively. Detailedin vivoandin vitrostudies resolved the key residues of the NagS catalytic site. Thus, we have uncovered a novel pathway in aminosugar metabolism that sheds new light on nutrient-mediated control of development and antibiotic production inStreptomyces.
Generation of 1.6 GeV single-particle proton beams
Authors: Zhou Kai , Han Yanliang , Li Zhiping , Jing Hantao , Yu Yongji 
Published: July 2024

We present a scattering slow extraction method employing a rotating foil in the Rapid Cycling Synchrotron (RCS) to produce a stable 1.6 GeV single-particle proton beam at CSNS. The foil scatters particles on the beam’s edge over multiple turns, with those at large scattering angles being separated and extracted through a Lambertson magnet. By adjusting the scatter foil’s rotational speed and position, we can precisely control the intensity and repetition rate of the extracted beam. This approach enables the efficient extraction of extremely low-intensity proton beams from CSNS-II/RCS. By setting single-particle collimators in the downstream beamline, a single-particle proton beam is achieved. Using 4y, we simulated the scattering slow extraction process in detail, confirming that a stable 1.6 GeV single-particle proton beam can be extracted, the beam energy can be adjusted from 0.8 to 1.6 GeV using the degrader, the time interval between adjacent single protons can be adjusted from hundreds of nanoseconds to tens of microseconds, to meet the needs of different experiments. Both the beam loss and the residual radiation doses are kept at low levels.

Published by the American Physical Society
2024