bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved Simulation of the Polar Atmospheric Boundary Layer by Accounting for Aerodynamic Roughness in the Parameterization of Surface Scalar Exchange Over Sea Ice
Authors: Elvidge A. D. , Renfrew I. A. , Edwards J. M. , Brooks I. M. , Srivastava P. , Weiss A. I. 
Published: March 2023

AbstractA new, simple parameterization scheme for scalar (heat and moisture) exchange over sea ice and the marginal ice zone is tested in a numerical weather and climate prediction model. This new “Blended A87” scheme accounts for the influence of aerodynamic roughness on the relationship between momentum and scalar exchange over consolidated sea ice, in line with long‐standing theory and recent field observations, and in contrast to the crude schemes currently operational in most models. Using aircraft observations and Met Office Unified Model simulations of cold‐air outbreak (CAO) conditions over aerodynamically rough sea ice, we demonstrate striking improvements in model performance when the Blended A87 scheme replaces the model's operational treatment for surface scalar exchange, provided that the aerodynamic roughness over consolidated ice is appropriately prescribed. The mean biases in surface sensible heat flux, surface latent heat flux, near‐surface air temperature, and surface temperature reduce from 25 to 11 W m−2, 22 to 12 W m−2, 0.8 to 0.0 K, and 1.4 to 0.8 K, respectively. We demonstrate that such impacts on surface exchange over sea ice can have a marked impact on the evolution of the atmospheric boundary layer across hundreds of kilometres downwind of the sea ice during CAO conditions in the model. Our results highlight the importance of spatiotemporal variability in the topography of consolidated sea ice for both momentum and scalar exchange over sea ice; accounting for which remains a key challenge for modeling polar weather and climate.
Framework for an Ocean‐Connected Supermodel of the Earth System
Authors: Counillon François , Keenlyside Noel , Wang Shuo , Devilliers Marion , Gupta Alok , Koseki Shunya , Shen Mao‐Lin 
Published: March 2023

AbstractA supermodel connects different models interactively so that their systematic errors compensate and achieve a model with superior performance. It differs from the standard non‐interactive multi‐model ensembles (NI), which combines model outputs a‐posteriori. Supermodels with Earth system models (ESMs) has not been developed because it is technically challenging to combine models with different state space. Here, we formulate the first supermodel framework for ESMs and use data assimilation to synchronise models. The ocean of three ESMs is synchronised every month by assimilating pseudo sea surface temperature (SST) observations generated by them on a common grid to handle discrepancies in grid and resolution. We compare the performance of two supermodel approaches to that of the NI. In the first (EW), the models are connected to the equal‐weight multi‐model mean, while in the second (SINGLE), they are connected to a single model. Both versions achieve synchronisation in the ocean and in the atmosphere, where the ocean drives the variability. The time variability of the supermodel multi‐model mean SST is reduced compared to observations, most where synchronisation is not achieved and is lower‐bounded by NI. The damping is larger in EW, for which variability in the individual models is also damped. Hence, under partial synchronisation, the unsynchronized variability gets damped in the multi‐model average pseudo‐observations, causing a deflation during the assimilation. The SST bias in individual models of EW is reduced compared to that of NI, and so is its multi‐model mean in the synchronised regions. A trained supermodel remains to be tested.
Benchmarking of survival outcomes following Haematopoietic Stem Cell Transplantation (HSCT): an update of the ongoing project of the European Society for Blood and Marrow Transplantation (EBMT) and Joint Accreditation Committee of ISCT and EBMT (JACIE)
Authors: Saccardi Riccardo , Putter Hein , Eikema Dirk-Jan , Busto María Paula , McGrath Eoin , Middelkoop Bas , Adams Gillian , Atlija Marina , Ayuk Francis Ayuketang , Baldomero Helen , Beguin Yves , de la Cámara Rafael , Cedillo Ángel , Balari Anna María Sureda , Chabannon Christian , Corbacioglu Selim , Dolstra Harry , Duarte Rafael F. , Dulery Rémy , Greco Raffaella , Gusi Andreu , Hamad Nada , Kenyon Michelle , Kröger Nicolaus , Labopin Myriam , Lee Julia , Ljungman Per , Manson Lynn , Mensil Florence , Milpied Noel , Mohty Mohamad , Oldani Elena , Orchard Kim , Passweg Jakob , Pearce Rachel , de Latour Régis Peffault , Poirel Hélène A. , Rintala Tuula , Rizzo J. Douglas , Ruggeri Annalisa , Sanchez-Martinez Carla , Sanchez-Guijo Fermin , Sánchez-Ortega Isabel , Trnková Marie , Ferreiras David Valcárcel , Wilcox Leonie , de Wreede Liesbeth C. , Snowden John A. 
Published: March 2023

AbstractFrom 2016 EBMT and JACIE developed an international risk-adapted benchmarking program of haematopoietic stem cell transplant (HSCT) outcome to provide individual EBMT Centers with a means of quality-assuring the HSCT process and meeting FACT-JACIE accreditation requirements relating to 1-year survival outcomes. Informed by previous experience from Europe, North America and Australasia, the Clinical Outcomes Group (COG) established criteria for patient and Center selection, and a set of key clinical variables within a dedicated statistical model adapted to the capabilities of the EBMT Registry. The first phase of the project was launched in 2019 to test the acceptability of the benchmarking model through assessment of Centers’ performance for 1-year data completeness and survival outcomes of autologous and allogeneic HSCT covering 2013–2016. A second phase was delivered in July 2021 covering 2015–2019 and including survival outcomes. Reports of individual Center performance were shared directly with local principal investigators and their responses were assimilated. The experience thus far has supported the feasibility, acceptability and reliability of the system as well as identifying its limitations. We provide a summary of experience and learning so far in this ‘work in progress’, as well as highlighting future challenges of delivering a modern, robust, data-complete, risk-adapted benchmarking program across new EBMT Registry systems.
State-dependent evolutionary models reveal modes of solid tumour growth
Authors: Lewinsohn Maya A. , Bedford Trevor , Müller Nicola F. , Feder Alison F. 
Published: March 2023

AbstractSpatial properties of tumour growth have profound implications for cancer progression, therapeutic resistance and metastasis. Yet, how spatial position governs tumour cell division remains difficult to evaluate in clinical tumours. Here, we demonstrate that faster division on the tumour periphery leaves characteristic genetic patterns, which become evident when a phylogenetic tree is reconstructed from spatially sampled cells. Namely, rapidly dividing peripheral lineages branch more extensively and acquire more mutations than slower-dividing centre lineages. We develop a Bayesian state-dependent evolutionary phylodynamic model (SDevo) that quantifies these patterns to infer the differential division rates between peripheral and central cells. We demonstrate that this approach accurately infers spatially varying birth rates of simulated tumours across a range of growth conditions and sampling strategies. We then show that SDevo outperforms state-of-the-art, non-cancer multi-state phylodynamic methods that ignore differential sequence evolution. Finally, we apply SDevo to single-time-point, multi-region sequencing data from clinical hepatocellular carcinomas and find evidence of a three- to six-times-higher division rate on the tumour edge. With the increasing availability of high-resolution, multi-region sequencing, we anticipate that SDevo will be useful in interrogating spatial growth restrictions and could be extended to model non-spatial factors that influence tumour progression.
Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection
Authors: Wei Jin , Patil Ajinkya , Collings Clayton K. , Alfajaro Mia Madel , Liang Yu , Cai Wesley L. , Strine Madison S. , Filler Renata B. , DeWeirdt Peter C. , Hanna Ruth E. , Menasche Bridget L. , Ökten Arya , Peña-Hernández Mario A. , Klein Jon , McNamara Andrew , Rosales Romel , McGovern Briana L. , Luis Rodriguez M. , García-Sastre Adolfo , White Kris M. , Qin Yiren , Doench John G. , Yan Qin , Iwasaki Akiko , Zwaka Thomas P. , Qi Jun , Kadoch Cigall , Wilen Craig B. 
Published: March 2023

AbstractIdentification of host determinants of coronavirus infection informs mechanisms of viral pathogenesis and can provide new drug targets. Here we demonstrate that mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) chromatin remodeling complexes, specifically canonical BRG1/BRM-associated factor (cBAF) complexes, promote severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and represent host-directed therapeutic targets. The catalytic activity of SMARCA4 is required for mSWI/SNF-driven chromatin accessibility at the ACE2 locus, ACE2 expression and virus susceptibility. The transcription factors HNF1A/B interact with and recruit mSWI/SNF complexes to ACE2 enhancers, which contain high HNF1A motif density. Notably, small-molecule mSWI/SNF ATPase inhibitors or degraders abrogate angiotensin-converting enzyme 2 (ACE2) expression and confer resistance to SARS-CoV-2 variants and a remdesivir-resistant virus in three cell lines and three primary human cell types, including airway epithelial cells, by up to 5 logs. These data highlight the role of mSWI/SNF complex activities in conferring SARS-CoV-2 susceptibility and identify a potential class of broad-acting antivirals to combat emerging coronaviruses and drug-resistant variants.
EEG resting-state networks in Alzheimer’s disease associated with clinical symptoms
Authors: Aoki Yasunori , Takahashi Rei , Suzuki Yuki , Pascual-Marqui Roberto D. , Kito Yumiko , Hikida Sakura , Maruyama Kana , Hata Masahiro , Ishii Ryouhei , Iwase Masao , Mori Etsuro , Ikeda Manabu 
Published: March 2023

AbstractAlzheimer’s disease (AD) is a progressive neuropsychiatric disease affecting many elderly people and is characterized by progressive cognitive impairment of memory, visuospatial, and executive functions. As the elderly population is growing, the number of AD patients is increasing considerably. There is currently growing interest in determining AD’s cognitive dysfunction markers. We used exact low-resolution-brain-electromagnetic-tomography independent-component-analysis (eLORETA-ICA) to assess activities of five electroencephalography resting-state-networks (EEG-RSNs) in 90 drug-free AD patients and 11 drug-free patients with mild-cognitive-impairment due to AD (ADMCI). Compared to 147 healthy subjects, the AD/ADMCI patients showed significantly decreased activities in the memory network and occipital alpha activity, where the age difference between the AD/ADMCI and healthy groups was corrected by linear regression analysis. Furthermore, the age-corrected EEG-RSN activities showed correlations with cognitive function test scores in AD/ADMCI. In particular, decreased memory network activity showed correlations with worse total cognitive scores for both Mini-Mental-State-Examination (MMSE) and Alzheimer’s Disease-Assessment-Scale-cognitive-component-Japanese version (ADAS-J cog) including worse sub-scores for orientation, registration, repetition, word recognition and ideational praxis. Our results indicate that AD affects specific EEG-RSNs and deteriorated network activity causes symptoms. Overall, eLORETA-ICA is a useful, non-invasive tool for assessing EEG-functional-network activities and provides better understanding of the neurophysiological mechanisms underlying the disease.
Modulating heart rate oscillation affects plasma amyloid beta and tau levels in younger and older adults
Authors: Min Jungwon , Rouanet Jeremy , Martini Alessandra Cadete , Nashiro Kaoru , Yoo Hyun Joo , Porat Shai , Cho Christine , Wan Junxiang , Cole Steve W. , Head Elizabeth , Nation Daniel A. , Thayer Julian F. , Mather Mara 
Published: March 2023

AbstractSlow paced breathing via heart rate variability (HRV) biofeedback stimulates vagus-nerve pathways that counter noradrenergic stress and arousal pathways that can influence production and clearance of Alzheimer's disease (AD)-related proteins. Thus, we examined whether HRV biofeedback intervention affects plasma Αβ40, Αβ42, total tau (tTau), and phosphorylated tau-181 (pTau-181) levels. We randomized healthy adults (N = 108) to use slow-paced breathing with HRV biofeedback to increase heart rate oscillations (Osc+) or to use personalized strategies with HRV biofeedback to decrease heart rate oscillations (Osc−). They practiced 20–40 min daily. Four weeks of practicing the Osc+ and Osc− conditions produced large effect size differences in change in plasma Aβ40 and Aβ42 levels. The Osc+ condition decreased plasma Αβ while the Osc− condition increased Αβ. Decreases in Αβ were associated with decreases in gene transcription indicators of β-adrenergic signaling, linking effects to the noradrenergic system. There were also opposing effects of the Osc+ and Osc− interventions on tTau for younger adults and pTau-181 for older adults. These results provide novel data supporting a causal role of autonomic activity in modulating plasma AD-related biomarkers.Trial registration: NCT03458910 (ClinicalTrials.gov); first posted on 03/08/2018.
Determining the most accurate 16S rRNA hypervariable region for taxonomic identification from respiratory samples
Authors: López-Aladid Ruben , Fernández-Barat Laia , Alcaraz-Serrano Victoria , Bueno-Freire Leticia , Vázquez Nil , Pastor-Ibáñez Roque , Palomeque Andrea , Oscanoa Patricia , Torres Antoni 
Published: March 2023

Abstract16S rRNA gene profiling, which contains nine hypervariable regions (V1–V9), is the gold standard for identifying taxonomic units by high-throughput sequencing. Microbiome studies combine two or more region sequences (usually V3–V4) to increase the resolving power for identifying bacterial taxa. We compare the resolving powers of V1–V2, V3–V4, V5–V7, and V7–V9 to improve microbiome analyses in sputum samples from patients with chronic respiratory diseases. DNA were isolated from 33 human sputum samples, and libraries were created using a QIASeq screening panel intended for Illumina platforms (16S/ITS; Qiagen Hilden, Germany). The analysis included a mock community as a microbial standard control (ZymoBIOMICS). We used the Deblur algorithm to identify bacterial amplicon sequence variants (ASVs) at the genus level. Alpha diversity was significantly higher for V1–V2, V3–V4, and V5–V7 compared with V7–V9, and significant compositional dissimilarities in the V1–V2 and V7–V9 analyses versus the V3–V4 and V5–V7 analyses. A cladogram confirmed these compositional differences, with the latter two being very similar in composition. The combined hypervariable regions showed significant differences when discriminating between the relative abundances of bacterial genera. The area under the curve revealed that V1–V2 had the highest resolving power for accurately identifying respiratory bacterial taxa from sputum samples. Our study confirms that 16S rRNA hypervariable regions provide significant differences for taxonomic identification in sputum. Comparing the taxa of microbial community standard control with the taxa samples, V1–V2 combination exhibits the most sensitivity and specificity. Thus, while third generation full-length 16S rRNA sequencing platforms become more available, the V1–V2 hypervariable regions can be used for taxonomic identification in sputum.
Estimation of interface frictional anisotropy between sand and snakeskin-inspired surfaces
Authors: Lee Seung-Hun , Nawaz Muhammad Naqeeb , Chong Song-Hun 
Published: March 2023

AbstractThe transmission of loads across the soil-structure mobilizes direction-dependent shear resistance, which can be selectively used to design geo-structures. A previous study confirmed the frictional anisotropy induced by the interface between the soil and snakeskin-inspired surfaces. However, it is necessary to estimate the interface friction angle quantitatively. In this study, a conventional direct shear apparatus is modified, and 45 cases are performed in two-way shearing directions between bio-inspired surfaces and Jumunjin standard sand under three vertical stresses (50, 100, and 200 kPa). The results show that: (1) shearing against the scales (cranial shearing) mobilizes larger shear resistance and produces a dilative response than shearing along the scales (caudal shearing) and (2) higher scale height or shorter scale length exhibits dilative tendency and produces higher interface friction angle. Further analysis is conducted to capture the frictional anisotropy as a function of the scale geometry ratio, which reveals that the interface anisotropy response is more pronounced during cranial shearing in all the cases, and the difference in the interface friction angle for the caudal → cranial test is higher than that for the cranial → caudal test at the given scale ratio.
Population trends of striped hyena (Hyaena hyaena) in Israel for the past five decades
Authors: Hadad Ezra , Kosicki Jakub Z. , Yosef Reuven 
Published: March 2023

AbstractThe striped hyena (Hyaena hyaena) is considered “Near Threatened” globally and “Vulnerable” in the Middle East. In Israel, the species has experienced extreme population fluctuations owing to poisoning campaigns during the British Mandate (1918–1948) which were also further exacerbated by the Israeli authorities in the mid-twentieth century. We collated data from the archives of the Israel Nature and Parks Authority for the past 47 years to elucidate the temporal and geographic trends of this species. During this period we found a 68% increase in population and the estimated density is at present 2.1 individuals/100km2. This is significantly higher than all previous estimates for Israel. It appears that the major factors contributing to their phenomenal increase in number are the increase in prey availability because of the intensification of human development, preying on Bedouin livestock, the extinction of the leopard (Panthera pardus nimr), and the hunting of wild boars (Sus scorfa) and other agricultural pests in some parts of the country. Reasons should also be sought in increasing people's awareness as well as in advanced technological capabilities that have allowed an improved observation and reporting system. Future studies need to understand the effects of the large concentrations of striped hyenas on the spatial distribution and temporal activity of other sympatric wildlife to ensure the continued persistence of the wildlife guilds in the Israeli nature.
Novel method of differentiating human induced pluripotent stem cells to mature cardiomyocytes via Sfrp2
Authors: Hsueh Ying-Chang , Pratt Richard E. , Dzau Victor J. , Hodgkinson Conrad P. 
Published: March 2023

AbstractCurrent methods to generate cardiomyocytes from induced pluripotent stem cells (iPSc) utilize broad-spectrum pharmacological inhibitors. These methods give rise to cardiomyocytes which are typically immature. Since we have recently demonstrated that cardiomyogenesis in vitro and in vivo requires Sfrp2, we asked if Sfrp2 would drive differentiation of human iPSc into cardiomyocytes. Indeed, we found that Sfrp2 induced robust cardiac differentiation. Importantly, replacement of broad spectrum pharmacological inhibitors with Sfrp2 gave rise to mature cardiomyocytes as evidenced by their sarcomere structure, electrophysiological profiles, and ability to form gap junctions.
Effect of Limosilactobacillus fermentum 332 on physicochemical characteristics, volatile flavor components, and Quorum sensing in fermented sausage
Authors: Gu Yue , Qiao Ruifang , Jin Bo , He Yinfeng , Tian Jianjun 
Published: March 2023

AbstractThe effects of Limosilactobacillusfermentum 332 on quality characteristics in fermented sausage were explored in terms of physicochemical characteristics, volatile flavor components, and Quorum sensing (QS). The results showed that the pH of fermented sausage decreased from 5.20 to 4.54 within 24 h with the inoculation of L.fermentum 332. Lightness and redness were significantly improved, and hardness and chewiness were significantly increased after the addition of L.fermentum 332. With the inoculation of L.fermentum 332, the thiobarbituric acid reactive substance content decreased from 0.26 to 0.19 mg/100 g and total volatile basic nitrogen content decreased from 2.16 to 1.61 mg/100 g. In total, 95 and 104 types of volatile flavor components were detected in the control and fermented sausage inoculated with starter culture, respectively. The AI-2 activity of fermented sausage inoculated with L.fermentum 332 was significantly higher than that of the control and positively correlated with viable count and quality characteristics. These results provide support for further research on the effect of microorganisms on the quality of fermented food.
Optimum frequency response with decentralized drivers in power system
Authors: Maldonado Diego , Cepeda Jaime , Gamboa Silvana , Torres Jackeline Abad , Cruz Patricio J. 
Published: March 2023

AbstractThis document presents a novel methodology to optimize the power system frequency response based on the implementation of decentralized controllers. The proposed method focuses on the control of the internal rotor angle in the selected generator, which allows its governor to act as a decentralized controller that requires as input local measurements. Through a proposed optimization process, it is first possible to establish a set of optimal parameters for each controller and, second, to determine the required phasor measurement units (PMUs) and their locations that are necessary to be installed in a power system. This comprehensive proposal is based on the time domain evaluation of the frequency response when multiple scenarios of deviations between demand and generation occur. Finally, the new proposal is applied to the IEEE 39‐bus test system to validate its advantages; for this, the test power system as well as the proposed controllers are implemented in DIgSILENT PowerFactory, along with Python to manage the optimization process.