bluuebunny/crossref_metadata_2025 huggingface dataset:
A Multiscale‐Model‐Based Near‐Term Prediction of Tropical Cyclone Genesis Frequency in the Northern Hemisphere
Authors: Zhao Jiuwei , Zhan Ruifen , Wang Yuqing , Jiang Leishan , Huang Xin
Published: November 2022

Near‐term prediction of tropical cyclone (TC) activity is of great importance to formulate the long‐term plans for mitigating the potential TC‐induced damages. Here, we introduce a multi‐timescale regression model of TC genesis frequency (TCGF), which includes contributions by three interannual modes (El Niño‐Southern Oscillation, sea surface temperature anomalies over the eastern Indian Ocean and tropical North Atlantic), two interdecadal modes (the Atlantic Multidecadal Oscillation and the Interdecadal Pacific Oscillation), and a global warming mode. The model is shown to be able to capture well the present‐day multi‐timescale changes in TCGF in the major TC basins in the Northern Hemisphere. By combining the model and 100‐member simulations by the Max Planck Institute Earth System Model, we predict a robust increase in TCGF over the eastern North Pacific, an insignificant increase over the western North Pacific, and little change over the North Atlantic during 2020–2030 relative to 2009–2019.
Developing the Maximum Incremental Reactivity for Volatile Organic Compounds in Major Cities of Central‐Eastern China
Authors: Zhang Yingnan , Xue Likun , Mu Jiangshan , Chen Tianshu , Li Hong , Gao Jian , Wang Wenxing
Published: November 2022

The Chinese government has identified volatile organic compounds (VOCs) management as a key priority in the fourteenth Five‐Year Plan (2021–2025) to alleviate ground‐level ozone (O3) air pollution. To provide scientific support for VOCs management, we developed the localized maximum incremental reactivity (MIR) for 57 VOCs species (prescribed by the Photochemical Assessment Monitoring Stations (PAMS)) in eight representative cities and averaged urban conditions over Central‐Eastern China, with application of the Master Chemical Mechanism box model coupled with solid observational constraints. Though the exact environmental conditions differ among cities, all of them are in VOCs‐limited O3 formation regime, underlining the importance of VOCs to O3 formation. The MIRs constructed based on regional average scenarios are well representative of those constructed based on individual cities, with Guangzhou as an exception due to its vast variance in chemical environments. The localized MIRs displayed the same overall pattern as the U.S. MIRs, but differed largely with respect to a few species (especially alkenes), owing to a combined influence of many factors. We applied the localized MIRs to quantify the concentration‐weighted ozone formation potential (OFP), which elucidate the importance of aromatics to O3 formation in the Chinese metropolitan areas. The top 10 key VOC species together with their explicitly tracked emission sources were determined, which could offer references for the formulation of effective control policies. The localized MIRs developed in this study can be applied to quantify OFPs for VOCs in Chinese cities, which has a great significance to VOCs management and O3 pollution control.
A Numerical Investigation of Hurricane Florence‐Induced Compound Flooding in the Cape Fear Estuary Using a Dynamically Coupled Hydrological‐Ocean Model
Authors: Bao Daoyang , Xue Z. George , Warner John C. , Moulton Melissa , Yin Dongxiao , Hegermiller Christie A. , Zambon Joseph B. , He Ruoying
Published: November 2022

Hurricane‐induced compound flooding is a combined result of multiple processes, including overland runoff, precipitation, and storm surge. This study presents a dynamical coupling method applied at the boundary of a processes‐based hydrological model (the hydrological modeling extension package of the Weather Research and Forecasting model) and the two‐dimensional Regional Ocean Modeling System on the platform of the Coupled‐Ocean‐Atmosphere‐Wave‐Sediment Transport Modeling System. The coupled model was adapted to the Cape Fear River Basin and adjacent coastal ocean in North Carolina, United States, which suffered severe losses due to the compound flood induced by Hurricane Florence in 2018. The model's robustness was evaluated via comparison against observed water levels in the watershed, estuary, and along the coast. With a series of sensitivity experiments, the contributions from different processes to the water level variations in the estuary were untangled and quantified. Based on the temporal evolution of wind, water flux, water level, and water‐level gradient, compound flooding in the estuary was categorized into four stages: (I) swelling, (II) local‐wind‐dominated, (III) transition, and (IV) overland‐runoff‐dominated. A nonlinear effect was identified between overland runoff and water level in the estuary, which indicated the estuary could serve as a buffer for surges from the ocean side by reducing the maximum surge height. Water budget analysis indicated that water in the estuary was flushed 10 times by overland runoff within 23 days after Florence's landfall.
“It’s on Me”: Perspectives of College Students Without Complex Medical Needs Learning to Manage Their Health Care
Authors: Rea Kelly E. , Armah Annabelle E. , Eaton Cyd K. , Suveg Cynthia , Davis Molly
Published: November 2022

Objective:

Most of the transition literature has examined adolescents and young adults with special health care needs, though many youth will eventually transition to adult health care providers, regardless of medical complexity. This study addressed this gap by examining transition needs and experiences specifically within a college student sample of emerging adults without complex medical needs.

Methods:

One hundred eight college students ( Mage = 20.93 years, SD = 1.14) completed interviews and questionnaires regarding transition. The most difficult and easiest aspects of health care self-management were thematically coded. Differences in questionnaires were assessed across sources of transition education.

Results:

Fifty-two percent of college students reported receiving education about managing health care from medical providers versus 95% from caregivers. Notably, 57% desired more support. Those receiving medical provider education reported higher responsibility. Students reported most difficulty managing health insurance. Results were similar across racial and ethnic groups and genders.

Conclusions:

Gaps in transition preparation include low rates of medical provider education and support regarding health insurance. College students receiving education from medical providers reported greater health care responsibility. Provider-led transition education is needed for college students without complex medical needs.

Implications for Impact Statement

This study suggests that college students without complex medical conditions experience gaps in transition preparation. Although half reported talking to their medical provider about transitioning to adult care, many desired more support, with the greatest difficulty reported in learning to manage health insurance.
Child and adult adiposity and subtype-specific endometrial cancer risk: a multivariable Mendelian randomisation study
Authors: Kennedy Oliver J. , Bafligil Cemsel , O’Mara Tracy A. , Wang Xuemin , Evans D. Gareth , Kar Siddhartha , Crosbie Emma J.
Published: November 2022

Increased adiposity is a known risk factor for endometrial cancer (EC). This study aimed to disentangle the separate causal roles of child and adult adiposity on EC risk in adults, including endometrioid and non-endometrioid histological subtypes using multivariable Mendelian randomisation. These analyses employed genetic associations derived from UK Biobank as proxies for child and adult body size in 12,906 cases and 108,979 controls that participated in the Endometrial Cancer Association Consortium. In multivariable analyses, adult body size increased overall EC (OR 2.30, 95% CI 1.73–3.06) and endometrioid EC risk (OR 2.28, 95% CI 1.65–3.16), while child body size had minimal effect. In contrast, child body size (OR 2.26, 95% CI 1.03–4.99) but not adult body size increased non-endometrioid EC risk. As such, child adiposity has an indirect effect on endometrioid EC risk that is mediated by adult adiposity but has a direct effect on non-endometrioid EC risk that is independent of adult adiposity. These novel findings indicate that interventions targeting adiposity during distinct periods in life have a critical role in preventing subtype-specific EC.
Muscular Swedish mutant APP-to-Brain axis in the development of Alzheimer’s disease
Authors: Pan Jin-Xiu , Lee Daehoon , Sun Dong , Zhao Kai , Xiong Lei , Guo Hao-Han , Ren Xiao , Chen Peng , Lopez de Boer Raquel , Lu Yuyi , Lin Helena , Mei Lin , Xiong Wen-Cheng
Published: November 2022

Alzheimer’s disease (AD) is the most common form of dementia. Notably, patients with AD often suffer from severe sarcopenia. However, their direct link and relationship remain poorly understood. Here, we generated a mouse line, TgAPPsweHSA, by crossing LSL (LoxP-STOP-LoxP)-APPswe with HSA-Cre mice, which express APPswe (Swedish mutant APP) selectively in skeletal muscles. Examining phenotypes in TgAPPsweHSA mice showed not only sarcopenia-like deficit, but also AD-relevant hippocampal inflammation, impairments in adult hippocampal neurogenesis and blood brain barrier (BBB), and depression-like behaviors. Further studies suggest that APPswe expression in skeletal muscles induces senescence and expressions of senescence-associated secretory phenotypes (SASPs), which include inflammatory cytokines and chemokines; but decreases growth factors, such as PDGF-BB and BDNF. These changes likely contribute to the systemic and hippocampal inflammation, deficits in neurogenesis and BBB, and depression-like behaviors, revealing a link of sarcopenia with AD, and uncovering an axis of muscular APPswe to brain in AD development.
A variant-proof SARS-CoV-2 vaccine targeting HR1 domain in S2 subunit of spike protein
Authors: Pang Wei , Lu Ying , Zhao Yan-Bo , Shen Fan , Fan Chang-Fa , Wang Qian , He Wen-Qiang , He Xiao-Yan , Li Ze-Kai , Chen Tao-Tao , Yang Cui-Xian , Li You-Zhi , Xiao Si-Xuan , Zhao Zu-Jiang , Huang Xu-Sheng , Luo Rong-Hua , Yang Liu-Meng , Zhang Mi , Dong Xing-Qi , Li Ming-Hua , Feng Xiao-Li , Zhou Qing-Cui , Qu Wang , Jiang Shibo , Ouyang Songying , Zheng Yong-Tang
Published: November 2022

The emerging SARS-CoV-2 variants, commonly with many mutations in S1 subunit of spike (S) protein are weakening the efficacy of the current vaccines and antibody therapeutics. This calls for the variant-proof SARS-CoV-2 vaccines targeting the more conserved regions in S protein. Here, we designed a recombinant subunit vaccine, HR121, targeting the conserved HR1 domain in S2 subunit of S protein. HR121 consisting of HR1–linker1–HR2–linker2–HR1, is conformationally and functionally analogous to the HR1 domain present in the fusion intermediate conformation of S2 subunit. Immunization with HR121 in rabbits and rhesus macaques elicited highly potent cross-neutralizing antibodies against SARS-CoV-2 and its variants, particularly Omicron sublineages. Vaccination with HR121 achieved near-full protections against prototype SARS-CoV-2 infection in hACE2 transgenic mice, Syrian golden hamsters and rhesus macaques, and effective protection against Omicron BA.2 infection in Syrian golden hamsters. This study demonstrates that HR121 is a promising candidate of variant-proof SARS-CoV-2 vaccine with a novel conserved target in the S2 subunit for application against current and future SARS-CoV-2 variants.
Distal 2q duplication in a patient with intellectual disability
Authors: Suzuki Toshifumi , Osaka Hitoshi , Miyake Noriko , Fujita Atsushi , Uchiyama Yuri , Seyama Rie , Koshimizu Eriko , Miyatake Satoko , Mizuguchi Takeshi , Takeda Satoru , Matsumoto Naomichi
Published: November 2022

We report on a patient with a distal 16.4-Mb duplication at 2q36.3-qter, who presented with severe intellectual disability, microcephaly, brachycephaly, prominent forehead, hypertelorism, prominent eyes, thin upper lip, and progenia. Copy number analysis using whole exome data detected a distal 2q duplication. This is the first report describing a distal 2q duplication at the molecular level.
A conserved megaprotein-based molecular bridge critical for lipid trafficking and cold resilience
Authors: Wang Changnan , Wang Bingying , Pandey Taruna , Long Yong , Zhang Jianxiu , Oh Fiona , Sima Jessica , Guo Ruyin , Liu Yun , Zhang Chao , Mukherjee Shaeri , Bassik Michael , Lin Weichun , Deng Huichao , Vale Goncalo , McDonald Jeffrey G. , Shen Kang , Ma Dengke K.
Published: November 2022

Cells adapt to cold by increasing levels of unsaturated phospholipids and membrane fluidity through conserved homeostatic mechanisms. Here we report an exceptionally large and evolutionarily conserved protein LPD-3 in C. elegans that mediates lipid trafficking to confer cold resilience. We identify lpd-3 mutants in a mutagenesis screen for genetic suppressors of the lipid desaturase FAT-7. LPD-3 bridges the endoplasmic reticulum (ER) and plasma membranes (PM), forming a structurally predicted hydrophobic tunnel for lipid trafficking. lpd-3 mutants exhibit abnormal phospholipid distribution, diminished FAT-7 abundance, organismic vulnerability to cold, and are rescued by Lecithin comprising unsaturated phospholipids. Deficient lpd-3 homologues in Zebrafish and mammalian cells cause defects similar to those observed in C. elegans. As mutations in BLTP1, the human orthologue of lpd-3, cause Alkuraya-Kucinskas syndrome, LPD-3 family proteins may serve as evolutionarily conserved highway bridges critical for ER-associated non-vesicular lipid trafficking and resilience to cold stress in eukaryotic cells.
Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome
Authors: Liu Qin , Su Qi , Zhang Fen , Tun Hein M. , Mak Joyce Wing Yan , Lui Grace Chung-Yan , Ng Susanna So Shan , Ching Jessica Y. L. , Li Amy , Lu Wenqi , Liu Chenyu , Cheung Chun Pan , Hui David S. C. , Chan Paul K. S. , Chan Francis Ka Leung , Ng Siew C.
Published: November 2022

Our knowledge of the role of the gut microbiome in acute coronavirus disease 2019 (COVID-19) and post-acute COVID-19 is rapidly increasing, whereas little is known regarding the contribution of multi-kingdom microbiota and host-microbial interactions to COVID-19 severity and consequences. Herein, we perform an integrated analysis using 296 fecal metagenomes, 79 fecal metabolomics, viral load in 1378 respiratory tract samples, and clinical features of 133 COVID-19 patients prospectively followed for up to 6 months. Metagenomic-based clustering identifies two robust ecological clusters (hereafter referred to as Clusters 1 and 2), of which Cluster 1 is significantly associated with severe COVID-19 and the development of post-acute COVID-19 syndrome. Significant differences between clusters could be explained by both multi-kingdom ecological drivers (bacteria, fungi, and viruses) and host factors with a good predictive value and an area under the curve (AUC) of 0.98. A model combining host and microbial factors could predict the duration of respiratory viral shedding with 82.1% accuracy (error ± 3 days). These results highlight the potential utility of host phenotype and multi-kingdom microbiota profiling as a prognostic tool for patients with COVID-19.
Intranasal delivery of a rationally attenuated SARS-CoV-2 is immunogenic and protective in Syrian hamsters
Authors: Liu Shufeng , Stauft Charles B. , Selvaraj Prabhuanand , Chandrasekaran Prabha , D’Agnillo Felice , Chou Chao-Kai , Wu Wells W. , Lien Christopher Z. , Meseda Clement A. , Pedro Cyntia L. , Starost Matthew F. , Weir Jerry P. , Wang Tony T.
Published: November 2022

Few live attenuated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are in pre-clinical or clinical development. We seek to attenuate SARS-CoV-2 (isolate WA1/2020) by removing the polybasic insert within the spike protein and the open reading frames (ORFs) 6–8, and by introducing mutations that abolish non-structural protein 1 (Nsp1)-mediated toxicity. The derived virus (WA1-ΔPRRA-ΔORF6-8-Nsp1K164A/H165A) replicates to 100- to 1000-fold-lower titers than the ancestral virus and induces little lung pathology in both K18-human ACE2 (hACE2) transgenic mice and Syrian hamsters. Immunofluorescence and transcriptomic analyses of infected hamsters confirm that three-pronged genetic modifications attenuate the proinflammatory pathways more than the removal of the polybasic cleavage site alone. Finally, intranasal administration of just 100 PFU of the WA1-ΔPRRA-ΔORF6-8-Nsp1K164A/H165A elicits robust antibody responses in Syrian hamsters and protects against SARS-CoV-2-induced weight loss and pneumonia. As a proof-of-concept study, we demonstrate that live but sufficiently attenuated SARS-CoV-2 vaccines may be attainable by rational design.
Wireless theranostic smart contact lens for monitoring and control of intraocular pressure in glaucoma
Authors: Kim Tae Yeon , Mok Jee Won , Hong Sang Hoon , Jeong Sang Hoon , Choi Hyunsik , Shin Sangbaie , Joo Choun-Ki , Hahn Sei Kwang
Published: November 2022

Glaucoma is one of the irreversible ocular diseases that can cause vision loss in some serious cases. Although Triggerfish has been commercialized for monitoring intraocular pressure in glaucoma, there is no smart contact lens to monitor intraocular pressure and take appropriate drug treatment in response to the intraocular pressure levels. Here, we report a precisely integrated theranostic smart contact lens with a sensitive gold hollow nanowire based intraocular pressure sensor, a flexible drug delivery system, wireless power and communication systems and an application specific integrated circuit chip for both monitoring and control of intraocular pressure in glaucoma. The gold hollow nanowire based intraocular pressure sensor shows high ocular strain sensitivity, chemical stability and biocompatibility. Furthermore, the flexible drug delivery system can be used for on-demand delivery of timolol for intraocular pressure control. Taken together, the intraocular pressure levels can be successfully monitored and controlled by the theranostic smart contact lens in glaucoma induced rabbits. This theranostic smart contact lens would be harnessed as a futuristic personal healthcare platform for glaucoma and other ocular diseases.
Formation of synthetic RNA protein granules using engineered phage-coat-protein -RNA complexes
Authors: Granik Naor , Katz Noa , Willinger Or , Goldberg Sarah , Amit Roee
Published: November 2022

Liquid-solid transition, also known as gelation, is a specific form of phase separation in which molecules cross-link to form a highly interconnected compartment with solid – like dynamical properties. Here, we utilize RNA hairpin coat-protein binding sites to form synthetic RNA based gel-like granules via liquid-solid phase transition. We show both in-vitro and in-vivo that hairpin containing synthetic long non-coding RNA (slncRNA) molecules granulate into bright localized puncta. We further demonstrate that upon introduction of the coat-proteins, less-condensed gel-like granules form with the RNA creating an outer shell with the proteins mostly present inside the granule. Moreover, by tracking puncta fluorescence signals over time, we detected addition or shedding events of slncRNA-CP nucleoprotein complexes. Consequently, our granules constitute a genetically encoded storage compartment for protein and RNA with a programmable controlled release profile that is determined by the number of hairpins encoded into the RNA. Our findings have important implications for the potential regulatory role of naturally occurring granules and for the broader biotechnology field.
Charge carrier mobilities of organic semiconductors: ab initio simulations with mode-specific treatment of molecular vibrations
Authors: Hutsch Sebastian , Panhans Michel , Ortmann Frank
Published: November 2022

The modeling of charge transport in organic semiconductors usually relies on the treatment of molecular vibrations by assuming a certain limiting case for all vibration modes, such as the dynamic limit in polaron theory or the quasi-static limit in transient localization theory. These opposite limits are each suitable for only a subset of modes. Here, we present a model that combines these different approaches. It is based on a separation of the vibrational spectrum and a quantum-mechanical treatment in which the slow modes generate a disorder landscape, while the fast modes generate polaron band narrowing. We apply the combined method to 20 organic crystals, including prototypical acenes, thiophenes, benzothiophenes, and their derivatives. Their mobilities span several orders of magnitude and we find a close agreement to the experimental mobilities. Further analysis reveals clear correlations to simple mobility predictors and a combination of them can be used to identify high-mobility materials.
Mass spectrometry captures biased signalling and allosteric modulation of a G-protein-coupled receptor
Authors: Yen Hsin-Yung , Liko Idlir , Song Wanling , Kapoor Parth , Almeida Fernando , Toporowska Joanna , Gherbi Karolina , Hopper Jonathan T. S. , Charlton Steven J. , Politis Argyris , Sansom Mark S. P. , Jazayeri Ali , Robinson Carol V.
Published: November 2022

G-protein-coupled receptors signal through cognate G proteins. Despite the widespread importance of these receptors, their regulatory mechanisms for G-protein selectivity are not fully understood. Here we present a native mass spectrometry-based approach to interrogate both biased signalling and allosteric modulation of the β1-adrenergic receptor in response to various ligands. By simultaneously capturing the effects of ligand binding and receptor coupling to different G proteins, we probed the relative importance of specific interactions with the receptor through systematic changes in 14 ligands, including isoprenaline derivatives, full and partial agonists, and antagonists. We observed enhanced dynamics of the intracellular loop 3 in the presence of isoprenaline, which is capable of acting as a biased agonist. We also show here that endogenous zinc ions augment the binding in receptor–Gs complexes and propose a zinc ion-binding hotspot at the TM5/TM6 intracellular interface of the receptor–Gs complex. Further interrogation led us to propose a mechanism in which zinc ions facilitate a structural transition of the intermediate complex towards the stable state.
Perovskite phase heterojunction solar cells
Authors: Ji Ran , Zhang Zongbao , Hofstetter Yvonne J. , Buschbeck Robin , Hänisch Christian , Paulus Fabian , Vaynzof Yana
Published: November 2022

Modern photovoltaic devices are often based on a heterojunction structure where two components with different optoelectronic properties are interfaced. The properties of each side of the junction can be tuned by either utilizing different materials (for example, donor/acceptor) or doping (for example, p–n junction) or even varying their dimensionality (for example, 3D/2D). Here we demonstrate the concept of phase heterojunction (PHJ) solar cells by utilizing two polymorphs of the same material. We demonstrate the approach by forming γ-CsPbI3/β-CsPbI3 perovskite PHJ solar cells. We find that all of the photovoltaic parameters of the PHJ device significantly surpass those of each of the single-phase devices, resulting in a maximum power conversion efficiency of 20.1%. These improvements originate from the efficient passivation of the β-CsPbI3 by the larger bandgap γ-CsPbI3, the increase in the built-in potential of the PHJ devices enabled by the energetic alignment between the two phases and the enhanced absorption of light by the PHJ structure. The approach demonstrated here offers new possibilities for the development of photovoltaic devices based on polymorphic materials.
Rethinking clinical study data: why we should respect analysis results as data
Authors: Barros Joana M. , Widmer Lukas A. , Baillie Mark , Wandel Simon
Published: November 2022

The development and approval of new treatments generates large volumes of results, such as summaries of efficacy and safety. However, it is commonly overlooked that analyzing clinical study data also produces data in the form of results. For example, descriptive statistics and model predictions are data. Although integrating and putting findings into context is a cornerstone of scientific work, analysis results are often neglected as a data source. Results end up stored as “data products” such as PDF documents that are not machine readable or amenable to future analyses. We propose a solution to “calculate once, use many times” by combining analysis results standards with a common data model. This analysis results data model re-frames the target of analyses from static representations of the results (e.g., tables and figures) to a data model with applications in various contexts, including knowledge discovery. Further, we provide a working proof of concept detailing how to approach standardization and construct a schema to store and query analysis results.
Assessing data bias in visual surveys from a cetacean monitoring programme
Authors: Oliveira-Rodrigues Cláudia , Correia Ana M. , Valente Raul , Gil Ágatha , Gandra Miguel , Liberal Marcos , Rosso Massimiliano , Pierce Graham , Sousa-Pinto Isabel
Published: November 2022

Long-term monitoring datasets are fundamental to understand physical and ecological responses to environmental changes, supporting management and conservation. The data should be reliable, with the sources of bias identified and quantified. CETUS Project is a cetacean monitoring programme in the Eastern North Atlantic, based on visual methods of data collection. This study aims to assess data quality and bias in the CETUS dataset, by 1) applying validation methods, through photographic confirmation of species identification; 2) creating data quality criteria to evaluate the observer’s experience; and 3) assessing bias to the number of sightings collected and to the success in species identification. Through photographic validation, the species identification of 10 sightings was corrected and a new species was added to the CETUS dataset. The number of sightings collected was biased by external factors, mostly by sampling effort but also by weather conditions. Ultimately, results highlight the importance of identifying and quantifying data bias, while also yielding guidelines for data collection and processing, relevant for species monitoring programmes based on visual methods.
pISA-tree - a data management framework for life science research projects using a standardised directory tree
Authors: Petek Marko , Zagorščak Maja , Blejec Andrej , Ramšak Živa , Coll Anna , Baebler Špela , Gruden Kristina
Published: November 2022

We developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. pISA-tree was initiated by end-user requirements thus its strong points are practicality and low maintenance cost. It enables on-the-fly creation of enriched directory tree structure (project/Investigation/Study/Assay) based on the ISA model, in a standardised manner via consecutive batch files. Templates-based metadata is generated in parallel at each level enabling guided submission of experiment metadata. pISA-tree is complemented by two R packages, pisar and seekr. pisar facilitates integration of pISA-tree datasets into bioinformatic pipelines and generation of ISA-Tab exports. seekr enables synchronisation with the FAIRDOMHub repository. Applicability of pISA-tree was demonstrated in several national and international multi-partner projects. The system thus supports findable, accessible, interoperable and reusable (FAIR) research and is in accordance with the Open Science initiative. Source code and documentation of pISA-tree are available at https://github.com/NIB-SI/pISA-tree.
Analysing functional implications of differences in left ventricular morphology using statistical shape modelling
Authors: Sophocleous Froso , Standen Lucy , Doolub Gemina , Laymouna Reem , Bucciarelli-Ducci Chiara , Caputo Massimo , Manghat Nathan , Hamilton Mark , Curtis Stephanie , Biglino Giovanni
Published: November 2022

Functional implications of left ventricular (LV) morphological characterization in congenital heart disease are not widely explored. This study qualitatively and quantitatively assessed LV shape associations with a) LV function and b) thoracic aortic morphology in patients with aortic coarctation (CoA) with/without bicuspid aortic valve (BAV), and healthy controls. A statistical shape modelling framework was employed to analyse three-dimensional (3D) LV shapes from cardiac magnetic resonance (CMR) data in isolated CoA (n = 25), CoA + BAV (n = 30), isolated BAV (n = 30), and healthy controls (n = 25). Average 3D templates and deformations were computed. Correlations between shape data and CMR-derived morphometric parameters (i.e., sphericity, conicity) or global and apical strain values were assessed to elucidate possible functional implications. The relationship between LV shape features and arch architecture was also explored. The LV template was shorter and more spherical in CoA patients. Sphericity was overall associated with global and apical radial (p = 0.001, R2 = 0.09; p < 0.0001, R2 = 0.17) and circumferential strain (p = 0.001, R2 = 0.10; p = 0.04, R2 = 0.04), irrespective of the presence of aortic stenosis and/or regurgitation and controlling for age and hypertension status. LV strain was not associated with arch architecture. Differences in LV morphology were observed between CoA and BAV patients. Increasing LV sphericity was associated with reduced strain, independent of aortic arch architecture and functional aortic valve disease.
Synthesis of CoFe2O4 magnetic nanoparticles for application in photocatalytic removal of azithromycin from wastewater
Authors: Modabberasl Ali , Pirhoushyaran Tahereh , Esmaeili-Faraj Seyyed Hamid
Published: November 2022

Azithromycin is one of the most widely used antibiotics in medicine prescribed for various infectious diseases such as COVID-19. A significant amount of this drug is always disposed of in hospital effluents. In this study, the removal of azithromycin using Cobalt-Ferrite magnetic nanoparticles (MNP) is investigated in the presence of UV light. For this purpose, magnetic nanoparticles are synthesized and added to the test samples as a catalyst in specific proportions. To determine the structural and morphological properties of nanoparticles, characterization tests including scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), vibrating-sample magnetometer (VSM), and Energy-dispersive X-ray spectroscopy (EDX) are performed. 27 runs have been implemented based on the design of experiments using the Box-Behnken Design (BBD) method. Parameters are the initial concentration of azithromycin (20–60 mg/L), contact time (30–90 min), pH (6–10), and the dose of magnetic nanoparticles (20–60 mg/L). The obtained model interprets test results with high accuracy (R2 = 0.9531). Also, optimization results by the software show that the contact time of 90 min, MNP dosage of 60 mg/L, pH value of 6.67, and azithromycin initial concentration of 20 mg/L leads to the highest removal efficiency of 89.71%. These numbers are in the range of other studies in this regard.
Development of an anti-oxidative intraocular irrigating solution based on reactive persulfides
Authors: Kunikata Hiroshi , Tawarayama Hiroshi , Tsuda Satoru , Akaike Takaaki , Nakazawa Toru
Published: November 2022

Anti-oxidative intraocular irrigating solutions (IISs) based on reactive persulfides, such as oxidized glutathione disulfide (GSSG), are commonly used worldwide. However, even with GSSG-based IISs, it has been shown that oxidative stress can occur during surgery, posing a risk to intraocular tissues. This study compared two IISs: one containing GSSG and one containing an oxidized glutathione trisulfide (GSSSG). Experimental in vivo irrigation with the IISs in rabbits showed that there was less leakage into the anterior chamber of rabbit serum albumin during perfusion with a 300-μM GSSSG IIS than with a 300-μM GSSG IIS. Experimental in vivo cataract surgery in rabbits showed that aqueous flare was suppressed 3 days after surgery with a 600-μM GSSSG IIS, but not with a 300-μM GSSSG or 300-μM GSSG IIS. Furthermore, an in vitro experiment, without any live tissue, showed that reactive oxygen species were suppressed more strongly with a 600-μM GSSSG IIS than with a 300-μM GSSG IIS. Thus, this study found that novel IISs based on GSSSG had anti-inflammatory and anti-oxidative effects during and after intraocular surgery and may decrease the rate of complications after surgery.
Simulating anti-skyrmions on a lattice
Authors: Criado Juan C. , Schenk Sebastian , Spannowsky Michael , Hatton Peter D. , Turnbull L. A.
Published: November 2022

Magnetic skyrmions are meta-stable spin structures that naturally emerge in magnetic materials. While a vast amount of effort has gone into the study of their properties, their counterpart of opposite topological charge, the anti-skyrmion, has not received as much attention. We aim to close this gap by deploying Monte Carlo simulations of spin-lattice systems in order to investigate which interactions support anti-skyrmions, as well as skyrmions of Bloch and Néel type. We find that the combination of ferromagnetic exchange and Dzyaloshinskii–Moriya (DM) interactions is able to stabilize each of the three types, depending on the specific structure of the DM interactions. Considering a three-dimensional spin lattice model, we provide a finite-temperature phase diagram featuring a stable anti-skyrmion lattice phase for a large range of temperatures. In addition, we also shed light on the creation and annihilation processes of these anti-skyrmion tubes and study the effects of the DM interaction strength on their typical size.
Grouting slurry diffusion range based on active heating fiber optics monitoring
Authors: Zhu Lei , Gu Wenzhe , Qiu Fengqi , Ouyang Yibo
Published: November 2022

To quantify the diffusion range of slurry in grouting engineering, an active heating optical fiber (AHFO) monitoring method is proposed. The AHFO is arranged on the coal seam floor. The temperature is taken as the monitoring parameter to monitor the diffusion range and state of slurry in the injected medium. Considering the time-varying characteristics of slurry rheological parameters, the theoretical calculation formula of spherical diffusion radius based on the power-law fluid is deduced. The relationship between the void ratio and grouting diffusion radius is discussed. Considering the influence of the seepage effect, the "water cement ratio change matrix" in the process of mud seepage is derived, and the influence of the space–time change of the slurry water cement ratio on the temperature gradient of the injected medium is studied. According to the factors affecting grouting diffusion, four groups of small three-dimensional simulation tests and one large three-dimensional grouting test are designed to verify the feasibility of the proposed method. The results show that the relative error of the AHFO monitoring radius is between 3.00 and 14.67%, based on the actual diffusion radius. In the large-scale three-dimensional grouting test, the data from AHFO is used to generate the two-dimensional surface of the grouting diffusion form, and the grouting diffusion range is asymmetric oval. Compared with the theoretical calculation results, the maximum relative error of grouting diffusion radius is 9.6%, and AHFO shows prediction accuracy. With the decrease in the water-cement ratio of slurry, the temperature gradient of the injection medium monitored by AHFO increases, showing an obvious space–time effect. The application of AHFO in the grouting simulation test can effectively analyze slurry diffusion in the injected medium.
Cardiorespiratory fitness decreases the odds for subclinical carotid plaques in apolipoprotein e4 homozygotes
Authors: Perez-Lasierra Jose Luis , Casajús José A. , Gonzalez-Agüero Alejandro , Arbones-Mainar José Miguel , Casasnovas José A. , Laclaustra Martin , Moreno-Franco Belén
Published: November 2022

Some studies suggest that being an apolipoprotein e4 (APOE e4) carrier increases the risk of atherosclerosis, and others suggest that cardiorespiratory fitness (CRF) could play a key role in atherosclerotic prevention. Our aim was to analyze the association ofAPOE e4with carotid atherosclerosis and the association of CRF with atherosclerosis inAPOE e4carriers. A cross-sectional analysis based on a subsample of 90 participants in the Aragon Workers’ Health Study was carried out. Ultrasonography was used to assess the presence of plaques in carotid territory; the submaximal Chester Step Test was used to assess CRF; and behavioral, demographic, anthropometric, and clinical data were obtained by trained personnel during annual medical examinations.APOE e4e4participants were categorized into Low-CRF (VO2max < 35 mL/kg/min) and High-CRF (VO2max ≥ 35 mL/kg/min) groups. After adjusting for several confounders, compared withAPOE e3e3, those participants genotyped asAPOE e3e4andAPOE e4e4showed an OR = 1.60 (95% CI 0.45, 5.71) and OR = 4.29 (95% CI 1.16, 15.91), respectively, for carotid atherosclerosis. Compared to Low-CRFAPOE e4e4carriers, the odds of carotid plaque detection were 0.09 (95% CI 0.008, 0.98) times lower among High-CRFAPOE e4e4carriers. TheAPOE e4e4genotype was associated with increased carotid atherosclerosis. However, CRF is a modifiable factor that may be targeted byAPOE e4e4to decrease the elevation of atherosclerotic risk due to this genetic condition.
Isolongifolene-loaded chitosan nanoparticles synthesis and characterization for cancer treatment
Authors: Manimaran Dharmar , Elangovan Namasivayam , Mani Panagal , Subramanian Kumaran , Ali Daoud , Alarifi Saud , Palanisamy Chella Perumal , Zhang Hongxia , Rangasamy Kowsalya , Palanisamy Vasan , Mani Renuka , Govarthanan Kavitha , Aruni Wilson , Shanmugam Rajeshkumar , Srinivasan Guru Prasad , Kalirajan Aruncahllam
Published: November 2022

Recent breakthroughs in the field of nanoparticle-based therapeutic delivery methods have changed the standpoint of cancer therapy by effectively delaying the process of disease development. Nanoparticles have a unique capacity of good penetrating ability than other therapeutic leads used in traditional therapeutics, and also, they have the highest impact on disease management. In the current study isolongifolene-loaded Chitosan nanoparticles have been formulated, synthesized and then characterized by the use of Fourier Transform Infrared Spectroscopy, X-ray Diffraction, Scanning Electron Microscopy and Transmission Electron Microscopy. Further, the characterized chitosan nano formulation was evaluated for hemocompatibility, plasma stability, and in-vitro release. Isolongifolene-loaded chitosan nanoparticles were found to be compatible with plasma and also, they exhibited a constant release pattern. Hence, chitosan-loaded nanoparticles could be employed as an excellent adjuvant in cancer therapeutic, to combat the multi-drug resistance in solid tumors.
Generative adversarial network based data augmentation for CNN based detection of Covid-19
Authors: Gulakala Rutwik , Markert Bernd , Stoffel Marcus
Published: November 2022

Covid-19 has been a global concern since 2019, crippling the world economy and health. Biological diagnostic tools have since been developed to identify the virus from bodily fluids and since the virus causes pneumonia, which results in lung inflammation, the presence of the virus can also be detected using medical imaging by expert radiologists. The success of each diagnostic method is measured by the hit rate for identifying Covid infections. However, the access for people to each diagnosis tool can be limited, depending on the geographic region and, since Covid treatment denotes a race against time, the diagnosis duration plays an important role. Hospitals with X-ray opportunities are widely distributed all over the world, so a method investigating lung X-ray images for possible Covid-19 infections would offer itself. Promising results have been achieved in the literature in automatically detecting the virus using medical images like CT scans and X-rays using supervised artificial neural network algorithms. One of the major drawbacks of supervised learning models is that they require enormous amounts of data to train, and generalize on new data. In this study, we develop a Swish activated, Instance and Batch normalized Residual U-Net GAN with dense blocks and skip connections to create synthetic and augmented data for training. The proposed GAN architecture, due to the presence of instance normalization and swish activation, can deal with the randomness of luminosity, that arises due to different sources of X-ray images better than the classical architecture and generate realistic-looking synthetic data. Also, the radiology equipment is not generally computationally efficient. They cannot efficiently run state-of-the-art deep neural networks such as DenseNet and ResNet effectively. Hence, we propose a novel CNN architecture that is 40% lighter and more accurate than state-of-the-art CNN networks. Multi-class classification of the three classes of chest X-rays (CXR), ie Covid-19, healthy and Pneumonia, is performed using the proposed model which had an extremely high test accuracy of 99.2% which has not been achieved in any previous studies in the literature. Based on the mentioned criteria for developing Corona infection diagnosis, in the present study, an Artificial Intelligence based method is proposed, resulting in a rapid diagnostic tool for Covid infections based on generative adversarial and convolutional neural networks. The benefit will be a high accuracy of lung infection identification with 99% accuracy. This could lead to a support tool that helps in rapid diagnosis, and an accessible Covid identification method using CXR images.
Aberrant expression of KDM1A inhibits ferroptosis of lung cancer cells through up-regulating c-Myc
Authors: Lu Can , Cai Yuan , Liu Wei , Peng Bi , Liang Qiuju , Yan Yuanliang , Liang Desheng , Xu Zhijie
Published: November 2022

Ferroptosis is a cell death process caused by metabolic dysfunction with the feature of aberrant iron accumulation. Emerging studies have identified that ferroptosis is an important biological function involving in the tumorigenesis, and targeting ferroptosis could provide promising therapeutic targets for lung cancer. However, such therapeutic strategies show limited therapeutic effect owing to drug resistance and other unknown underlying mechanisms. In this study, lysine-specific demethylase 1 (LSD1/KDM1A) was found to be significantly upregulated in lung cancer cells and tissues. The patients with KDM1A downregulation displayed the good prognosis. Using gene set enrichment analysis (GSEA), we demonstrated that KDM1A-associated genes might participate in the regulation of cell ferroptosis and Myc signaling in lung cancer. Knockdown of KDM1A inhibited the level of c-Myc and increased the concentration of malondialdehyde (MDA) and irons in human lung cancer cells H1299 and A549. Downregulation of c-Myc could facilitate KDM1A knockdown-mediated ferroptosis. Our study has elucidated the effect of KDM1A/c-Myc regulatory axis in the ferroptosis resistance of lung cancer cells.
DNA stable isotope probing on soil treated by plant biostimulation and flooding revealed the bacterial communities involved in PCB degradation
Authors: Vergani Lorenzo , Mapelli Francesca , Folkmanova Magdalena , Papik Jakub , Jansa Jan , Uhlik Ondrej , Borin Sara
Published: November 2022

Polychlorinated biphenyl (PCB)-contaminated soils represent a major treat for ecosystems health. Plant biostimulation of autochthonous microbial PCB degraders is a way to restore polluted sites where traditional remediation techniques are not sustainable, though its success requires the understanding of site-specific plant–microbe interactions. In an historical PCB contaminated soil, we applied DNA stable isotope probing (SIP) using 13C-labeled 4-chlorobiphenyl (4-CB) and 16S rRNA MiSeq amplicon sequencing to determine how the structure of total and PCB-degrading bacterial populations were affected by different treatments: biostimulation with Phalaris arundinacea subjected (PhalRed) or not (Phal) to a redox cycle and the non-planted controls (Bulk and BulkRed). Phal soils hosted the most diverse community and plant biostimulation induced an enrichment of Actinobacteria. Mineralization of 4-CB in SIP microcosms varied between 10% in Bulk and 39% in PhalRed soil. The most abundant taxa deriving carbon from PCB were Betaproteobacteria and Actinobacteria. Comamonadaceae was the family most represented in Phal soils, Rhodocyclaceae and Nocardiaceae in non-planted soils. Planted soils subjected to redox cycle enriched PCB degraders affiliated to Pseudonocardiaceae, Micromonosporaceae and Nocardioidaceae. Overall, we demonstrated different responses of soil bacterial taxa to specific rhizoremediation treatments and we provided new insights into the populations active in PCB biodegradation.
Reduction of glutamatergic activity through cholinergic dysfunction in the hippocampus of hippocampal cholinergic neurostimulating peptide precursor protein knockout mice
Authors: Suzuki Kengo , Ohi Yoshiaki , Sato Toyohiro , Tsuda Yo , Madokoro Yuta , Mizuno Masayuki , Adachi Kenichi , Uchida Yuto , Haji Akira , Ojika Kosei , Matsukawa Noriyuki
Published: November 2022

Cholinergic activation can enhance glutamatergic activity in the hippocampus under pathologic conditions, such as Alzheimer’s disease. The aim of the present study was to elucidate the relationship between glutamatergic neural functional decline and cholinergic neural dysfunction in the hippocampus. We report the importance of hippocampal cholinergic neurostimulating peptide (HCNP) in inducing acetylcholine synthesis in the medial septal nucleus. Here, we demonstrate that HCNP-precursor protein (pp) knockout (KO) mice electrophysiologically presented with glutamatergic dysfunction in the hippocampus with age. The impairment of cholinergic function via a decrease in vesicular acetylcholine transporter in the pre-synapse with reactive upregulation of the muscarinic M1 receptor may be partly involved in glutamatergic dysfunction in the hippocampus of HCNP-pp KO mice. The results, in combination with our previous reports that show the reduction of hippocampal theta power through a decrease of a region-specific choline acetyltransferase in the stratum oriens of CA1 and the decrease of acetylcholine concentration in the hippocampus, may indicate the defined cholinergic dysfunction in HCNP-pp KO mice. This may also support that HCNP-pp KO mice are appropriate genetic models for cholinergic functional impairment in septo-hippocampal interactions. Therefore, according to the cholinergic hypothesis, the model mice might are potential partial pathological animal models for Alzheimer’s disease.