bluuebunny/crossref_metadata_2025_split huggingface dataset:
A tradeoff between enterovirus A71 particle stability and cell entry
Authors: Catching Adam , Te Yeh Ming , Bianco Simone , Capponi Sara , Andino Raul 
Published: November 2023

AbstractA central role of viral capsids is to protect the viral genome from the harsh extracellular environment while facilitating initiation of infection when the virus encounters a target cell. Viruses are thought to have evolved an optimal equilibrium between particle stability and efficiency of cell entry. In this study, we genetically perturb this equilibrium in a non-enveloped virus, enterovirus A71 to determine its structural basis. We isolate a single-point mutation variant with increased particle thermotolerance and decreased efficiency of cell entry. Using cryo-electron microscopy and molecular dynamics simulations, we determine that the thermostable native particles have acquired an expanded conformation that results in a significant increase in protein dynamics. Examining the intermediate states of the thermostable variant reveals a potential pathway for uncoating. We propose a sequential release of the lipid pocket factor, followed by internal VP4 and ultimately the viral RNA.
Economic valuation of temperature-related mortality attributed to urban heat islands in European cities
Authors: Huang Wan Ting Katty , Masselot Pierre , Bou-Zeid Elie , Fatichi Simone , Paschalis Athanasios , Sun Ting , Gasparrini Antonio , Manoli Gabriele 
Published: November 2023

AbstractAs the climate warms, increasing heat-related health risks are expected, and can be exacerbated by the urban heat island (UHI) effect. UHIs can also offer protection against cold weather, but a clear quantification of their impacts on human health across diverse cities and seasons is still being explored. Here we provide a 500 m resolution assessment of mortality risks associated with UHIs for 85 European cities in 2015-2017. Acute impacts are found during heat extremes, with a 45% median increase in mortality risk associated with UHI, compared to a 7% decrease during cold extremes. However, protracted cold seasons result in greater integrated protective effects. On average, UHI-induced heat-/cold-related mortality is associated with economic impacts of €192/€ − 314 per adult urban inhabitant per year in Europe, comparable to air pollution and transit costs. These findings urge strategies aimed at designing healthier cities to consider the seasonality of UHI impacts, and to account for social costs, their controlling factors, and intra-urban variability.
Multi-omics for studying and understanding polar life
Authors: Clark M. S. , Hoffman J. I. , Peck L. S. , Bargelloni L. , Gande D. , Havermans C. , Meyer B. , Patarnello T. , Phillips T. , Stoof-Leichsenring K. R. , Vendrami D. L. J. , Beck A. , Collins G. , Friedrich M. W. , Halanych K. M. , Masello J. F. , Nagel R. , Norén K. , Printzen C. , Ruiz M. B. , Wohlrab S. , Becker B. , Dumack K. , Ghaderiardakani F. , Glaser K. , Heesch S. , Held C. , John U. , Karsten U. , Kempf S. , Lucassen M. , Paijmans A. , Schimani K. , Wallberg A. , Wunder L. C. , Mock T. 
Published: November 2023

AbstractPolar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss ‘omics’ approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.
The transcriptional and phenotypic characteristics that define alveolar macrophage subsets in acute hypoxemic respiratory failure
Authors: Morrell Eric D. , Holton Sarah E. , Lawrance Matthew , Orlov Marika , Franklin Zoie , Mitchem Mallorie A. , DeBerg Hannah , Gersuk Vivian H. , Garay Ashley , Barnes Elizabeth , Liu Ted , Peltan Ithan D. , Rogers Angela , Ziegler Steven , Wurfel Mark M. , Mikacenic Carmen 
Published: November 2023

AbstractThe transcriptional and phenotypic characteristics that define alveolar monocyte and macrophage subsets in acute hypoxemic respiratory failure (AHRF) are poorly understood. Here, we apply CITE-seq (single-cell RNA-sequencing and cell-surface protein quantification) to bronchoalveolar lavage and blood specimens longitudinally collected from participants with AHRF to identify alveolar myeloid subsets, and then validate their identity in an external cohort using flow cytometry. We identify alveolar myeloid subsets with transcriptional profiles that differ from other lung diseases as well as several subsets with similar transcriptional profiles as reported in healthy participants (Metallothionein) or patients with COVID-19 (CD163/LGMN). We use information from CITE-seq to determine cell-surface proteins that distinguish transcriptional subsets (CD14, CD163, CD123, CD71, CD48, CD86 and CD44). In the external cohort, we find a higher proportion of CD163/LGMN alveolar macrophages are associated with mortality in AHRF. We report a parsimonious set of cell-surface proteins that distinguish alveolar myeloid subsets using scalable approaches that can be applied to clinical cohorts.
The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli
Authors: Rashid Fatema-Zahra M. , Crémazy Frédéric G. E. , Hofmann Andreas , Forrest David , Grainger David C. , Heermann Dieter W. , Dame Remus T. 
Published: November 2023

AbstractNucleoid associated proteins (NAPs) maintain the architecture of bacterial chromosomes and regulate gene expression. Thus, their role as transcription factors may involve three-dimensional chromosome re-organisation. While this model is supported by in vitro studies, direct in vivo evidence is lacking. Here, we use RT-qPCR and 3C-qPCR to study the transcriptional and architectural profiles of the H-NS (histone-like nucleoid structuring protein)-regulated, osmoresponsive proVWX operon of Escherichia coli at different osmolarities and provide in vivo evidence for transcription regulation by NAP-mediated chromosome re-modelling in bacteria. By consolidating our in vivo investigations with earlier in vitro and in silico studies that provide mechanistic details of how H-NS re-models DNA in response to osmolarity, we report that activation of proVWX in response to a hyperosmotic shock involves the destabilization of H-NS-mediated bridges anchored between the proVWX downstream and upstream regulatory elements (DRE and URE), and between the DRE and ygaY that lies immediately downstream of proVWX. The re-establishment of these bridges upon adaptation to hyperosmolarity represses the operon. Our results also reveal additional structural features associated with changes in proVWX transcript levels such as the decompaction of local chromatin upstream of the operon, highlighting that further complexity underlies the regulation of this model operon. H-NS and H-NS-like proteins are wide-spread amongst bacteria, suggesting that chromosome re-modelling may be a typical feature of transcriptional control in bacteria.
Atomic-scale probing of short-range order and its impact on electrochemical properties in cation-disordered oxide cathodes
Authors: Li Linze , Ouyang Bin , Lun Zhengyan , Huo Haoyan , Chen Dongchang , Yue Yuan , Ophus Colin , Tong Wei , Chen Guoying , Ceder Gerbrand , Wang Chongmin 
Published: November 2023

AbstractChemical short-range-order has been widely noticed to dictate the electrochemical properties of Li-excess cation-disordered rocksalt oxides, a class of cathode based on earth abundant elements for next-generation high-energy-density batteries. Existence of short-range-order is normally evidenced by a diffused intensity pattern in reciprocal space, however, derivation of local atomic arrangements of short-range-order in real space is hardly possible. Here, by a combination of aberration-corrected scanning transmission electron microscopy, electron diffraction, and cluster-expansion Monte Carlo simulations, we reveal the short-range-order is a convolution of three basic types: tetrahedron, octahedron, and cube. We discover that short-range-order directly correlates with Li percolation channels, which correspondingly affects Li transport behavior. We further demonstrate that short-range-order can be effectively manipulated by anion doping or post-synthesis thermal treatment, creating new avenues for tailoring the electrochemical properties. Our results provide fundamental insights for decoding the complex relationship between local chemical ordering and properties of crystalline compounds.
Construction of ultrasonically treated collagen/silk fibroin composite scaffolds to induce cartilage regeneration
Authors: Yu Shunan , Shu Xiong , Chen Lei , Wang Chao , Wang Xinyu , Jing Jinzhu , Yan Guoqiang , Zhang Yanzhuo , Wu Chengai 
Published: November 2023

AbstractA novel tissue-specific functional tissue engineering scaffold for cartilage repair should have a three-dimensional structure, good biosafety and biological activity, and should be able to promote cartilage tissue regeneration. This study aimed to determine the effect of ultrasound-treated collagen/silk fibroin (Col/SF) composite scaffolds with good mechanical properties and high biological activity on cartilage repair. The characteristics of the scaffolds with different Col/SF ratios (7:3, 8:2, and 9:1) were determined by scanning electron microscopy, Fourier-transform infrared spectroscopy, and porosity, water absorption, and compression tests. In vitro evaluations revealed the biocompatibility of the Col/SF scaffolds. Results suggested that the optimal ratio of Col/SF composite scaffolds was 7:3. The Col/SF scaffolds induced adipose-derived stem cells to undergo chondrogenic differentiation under chondrogenic culture conditions. The efficiency of Col/SF scaffolds for cartilage regeneration applications was further evaluated using an in vivo model of full-thickness articular cartilage defects in New Zealand rabbits. The Col/SF scaffolds effectively promoted osteochondral regeneration as evidenced by macroscopic, histological, and immunohistochemical evaluation. The study demonstrates that ultrasound-treated Col/SF scaffolds show great potential for repairing cartilage defects.
The assessment of atlantoaxial joint involvement in patients with rheumatoid arthritis, results from an observational “real-life” study
Authors: Di Muzio Claudia , Conforti Alessandro , Bruno Federico , Currado Damiano , Berardicurti Onorina , Navarini Luca , Pavlych Viktoriya , Di Cola Ilenia , Biaggi Alice , Di Donato Stefano , Marino Annalisa , Lorusso Sebastiano , Ursini Francesco , Barile Antonio , Masciocchi Carlo , Cipriani Paola , Giacomelli Roberto , Ruscitti Piero 
Published: November 2023

AbstractAtlantoaxial joint is a possible affected site during rheumatoid arthritis (RA) and, in this work, we evaluated its occurrence and associated characteristics in a “real-life” cohort. By a medical records review study of RA patients longitudinally followed-up, the occurrence of severe atlantoaxial joint involvement was estimated (incidence proportion and incidence rate per 1000 person-years at risk). Regression analyses were also exploited to evaluate possible associated factors. Based on these findings, a prospective recruitment was performed to build a descriptive cross-sectional study in evaluating a subclinical atlantoaxial joint involvement in patients with the same clinical characteristics. Retrospectively, 717 patients (female 56.6%, age 64.7 ± 12.3 years) were studied. The incidence proportion of severe atlantoaxial joint involvement was 2.1% [1.5–2.5], occurring in 15 out of 717 patients, and identified by both MRI and CT scan. Considering over 3091 person-years, an incidence rate of 5.2 × 1000 [2.9–8.3] person-years was estimated. Regression analyses suggested that male gender, a longer disease duration, ACPA positivity and extra-articular manifestations resulted to be significantly associated with a severe atlantoaxial joint involvement. Given these findings, 30 asymptomatic patients were selected according to these clinical characteristics and underwent MRI of cervical spine. To date, almost 50% of these asymptomatic patients showed a subclinical atlantoaxial joint involvement. The occurrence of the severe atlantoaxial joint involvement in RA patients was estimated in a “real-life” setting. Male gender, ACPA positivity, long disease duration, and extra-articular manifestations could be associated with the severe atlantoaxial joint involvement in RA. MRI could provide a useful clinical tool to early evaluate the atlantoaxial joint involvement in RA, also in asymptomatic patients.
Volatile aroma and physicochemical characteristics of freeze-dried coconut water using different encapsulating agents
Authors: Tanongkankit Yardfon , Eadmusik Sunee , Detchewa Pakkawat , Budsabun Tanakwan , Panphut Wattana , Jakkranuhwat Nattakan , Rittisak Sriwiang , Nonthanum Panadda , Phungamngoen Chanthima 
Published: November 2023

AbstractThis research studied how different types and concentrations of encapsulating agents impacted freeze-dried coconut water products. Volatile aroma and physicochemical product characteristics were evaluated. The encapsulating agents were maltodextrin 4–8% (w/v), polydextrose 4–8% (w/v) and xanthan gum 0.1–0.3% (w/v). A plate freezer and an air blast freezer were used to pre-freeze the coconut water before drying. Freezing time had no impact on moisture content and water activity. The flavor compounds of coconut water is composed of alkanes, aldehyde, ketones, organic acids and some other flavor substances. Encapsulating agents are the main factors affecting the flavor of coconut water. Optimal conditions for producing dried coconut water were adding polydextrose at a concentration of 8%. Volatile compounds were assessed under different conditions of SPME- GC-TOFMS. The composition of flavor compounds in coconut water is complex and mainly includes esters, aldehydes, and phenols. Results showed that encapsulating agents improved the volatile aroma of dried coconut water products.
Probabilistic analysis of agent-based opinion formation models
Authors: Devia Carlos Andres , Giordano Giulia 
Published: November 2023

AbstractWhen agent-based models are developed to capture opinion formation in large-scale populations, the opinion update equations often need to embed several complex psychological traits. The resulting models are more realistic, but also challenging to assess analytically, and hence numerical analysis techniques have an increasing importance in their study. Here, we propose the Qualitative Outcome Likelihood (QOL) analysis, a novel probabilistic analysis technique aimed to unravel behavioural patterns and properties of agent-based opinion formation models, and to characterise possible outcomes when only limited information is available. The QOL analysis reveals which qualitative categories of opinion distributions a model can produce, brings to light their relation to model features such as initial conditions, agent parameters and underlying digraph, and allows us to compare the behaviour of different opinion formation models. We exemplify the proposed technique by applying it to four opinion formation models: the classical Friedkin-Johnsen model and Bounded Confidence model, as well as the recently proposed Backfire Effect and Biased Assimilation model and Classification-based model.
Higher HDL cholesterol levels are associated with increased markers of interstitial myocardial fibrosis in the MultiEthnic Study of Atherosclerosis (MESA)
Authors: Chehab Omar , Akl Elie , Abdollahi Ashkan , Zeitoun Ralph , Ambale-Venkatesh Bharath , Wu Colin , Tracy Russell , Blumenthal Roger S. , Post Wendy S. , Lima Joao A. C. , Rodriguez Annabelle 
Published: November 2023

AbstractEmerging research indicates that high HDL-C levels might not be cardioprotective, potentially worsening cardiovascular disease (CVD) outcomes. Yet, there is no data on HDL-C's association with other CVD risk factors like myocardial fibrosis, a key aspect of cardiac remodeling predicting negative outcomes. We therefore aimed to study the association between HDL-C levels with interstitial myocardial fibrosis (IMF) and myocardial scar measured by CMR T1-mapping and late-gadolinium enhancement (LGE), respectively. There were 1863 participants (mean age of 69 years) who had both serum HDL-C measurements and underwent CMR. Analysis was done among those with available indices of interstitial fibrosis (extracellular volume fraction [ECV]; N = 1172 and native-T1; N = 1863) and replacement fibrosis by LGE (N = 1172). HDL-C was analyzed as both logarithmically-transformed and categorized into < 40 (low),40–59 (normal), and ≥ 60mg/dL (high). Multivariable linear and logistic regression models were constructed to assess the associations of HDL-C with CMR-obtained measures of IMF, ECV% and native-T1 time, and myocardial scar, respectively. In the fully adjusted model, each 1-SD increment of log HDL-C was associated with a 1% increment in ECV% (p = 0.01) and an 18-ms increment in native-T1 (p < 0.001). When stratified by HDL-C categories, those with high HDL-C (≥ 60mg/dL) had significantly higher ECV (β = 0.5%, p = 0.01) and native-T1 (β = 7 ms, p = 0.01) compared with those with normal HDL-C levels. Those with low HDL-C were not associated with IMF. Results remained unchanged after excluding individuals with a history of myocardial infarction. Neither increasing levels of HDL-C nor any HDL-C category was associated with the prevalence of myocardial scar. Increasing levels of HDL-C were associated with increased markers of IMF, with those with high levels of HDL-C being linked to subclinical fibrosis in a community-based setting.
Evaluating the effects of brain injury, disease and tasks on cognitive fatigue
Authors: Wylie Glenn R. , Genova Helen M. , Yao Bing , Chiaravalloti Nancy , Román Cristina A. F. , Sandroff Brian M. , DeLuca John 
Published: November 2023

AbstractBecause cognitive fatigue (CF) is common and debilitating following brain injury or disease we investigated the relationships among CF, behavioral performance, and cerebral activation within and across populations by combining the data from two cross-sectional studies. Individuals with multiple sclerosis (MS) were included to model CF resulting from neurological disease; individuals who had sustained a traumatic brain injury (TBI) were included to model CF resulting from neurological insult; both groups were compared with a control group (Controls). CF was induced while neuroimaging data was acquired using two different tasks. CF significantly differed between the groups, with the clinical groups reporting more CF than Controls—a difference that was statistically significant for the TBI group and trended towards significance for the MS group. The accrual of CF did not differ across the three groups; and CF ratings were consistent across tasks. Increasing CF was associated with longer response time for all groups. The brain activation in the caudate nucleus and the thalamus was consistently correlated with CF in all three groups, while more dorsally in the caudate, activation differed across the groups. These results suggest the caudate and thalamus to be central to CF while more dorsal aspects of the caudate may be sensitive to damage associated with particular types of insult.
Dynamics of CWD prion detection in feces and blood from naturally infected white-tailed deer
Authors: Bravo‐Risi Francisca , Soto Paulina , Benavente Rebeca , Nichols Tracy A. , Morales Rodrigo 
Published: November 2023

AbstractChronic wasting disease (CWD) is a prion disease affecting cervids. Confirmatory testing of CWD is currently performed postmortem in obex and lymphoid tissues. Extensive evidence demonstrates the presence of infectious prions in feces of CWD-infected deer using in vitro prion-amplification techniques and bioassays. In experimental conditions, this has been achieved as soon as 6-month post-inoculation, suggesting this sample type is a candidate for antemortem diagnosis. In the present study, we optimized the detection of CWD-prions in fecal samples from naturally infected, pre-clinical white-tailed deer by comparing protocols aiming to concentrate CWD-prions with direct spiking of the sample into the PMCA reactions. Results of this screening were compared with similar analyses made in blood. Our data shows that CWD-prion detection in feces using PMCA is best in the absence of sample pre-treatments. We performed a screening of 169 fecal samples, detecting CWD-prions with diagnostic sensitivity and specificity of 54.81% and 98.46%, respectively. In addition, the PMCA seeding activity of 76 fecal samples was compared with that on blood of matched deer. Our findings, demonstrate that CWD-prions in feces and blood are increased at late pre-clinical stages, exhibiting similar detection in both sample types (> 90% sensitivity) when PrP96GG animals are tested. Our findings contribute to understand prion distribution across different biological samples and polymorphic variants in white-tailed deer. This information is also relevant for the current efforts to identify platforms to diagnose CWD.
Validity and reliability of “My Jump app” to assess vertical jump performance: a meta-analytic review
Authors: Gençoğlu Cebrail , Ulupınar Süleyman , Özbay Serhat , Turan Murat , Savaş Buğra Çağatay , Asan Selim , İnce İzzet 
Published: November 2023

AbstractThis systematic review and meta-analysis aims to investigate the validity and reliability of the My Jump smartphone application in measuring vertical jump height, specifically using flight-time-based measures. To identify potential studies for inclusion, a comprehensive search strategy was employed in PubMed, Web of Science, Scopus, and EBSCO host databases. Validity was assessed in two ways: (1) mean and standard deviations of My Jump measurements were compared to criterion methods to assess the agreement of raw scores; (2) correlation coefficients evaluated the within-group consistency of rankings between My Jump and criterion methods. Reliability was assessed using intraclass correlation coefficients (ICC). Heterogeneity was evaluated via Cochrane’s Q statistic, its p-value, I2 value, and tau2 value. Publication bias was explored through funnel plot symmetry and confirmed with extended Egger’s test. Following the search, 21 studies met the inclusion criteria. Results showed no significant difference in raw scores between My Jump and criterion methods, indicating high agreement. High correlation was also found for within-group rankings, suggesting consistency. The My Jump application demonstrated nearly perfect reliability scores. The My Jump application appears to be a valid and reliable tool for sports scientists and strength and conditioning practitioners, offering a cost-effective and accessible means for accurately assessing vertical jump performance in various settings. However, it should be noted that these results are specific to flight-time-based measures, and further research is needed to validate these findings against gold-standard take-off velocity methods.