bluuebunny/crossref_metadata_2025 huggingface dataset:
A fuzzy rough approach to analyze the significance of semantic levels for building tags in OpenStreetMap
Authors: Ahmadian Somayeh , Pahlavani Parham
Published: July 2024

In the realm of volunteered geographic information (VGI), the existence of comparable tags, attributes, and values across diverse categories of geographic objects gives rise to major categorization challenges such as conceptual overlap and indiscernibility. Enhancing the semantic data retrieval of VGI relies on the semantic quality of descriptive content annotated for tagging geographic objects. The main focus of this study is analyzing the descriptive content of OpenStreetMap to assess the significance of semantic levels. The proposed methodology relies on fuzzy rough set calculations to determine the degrees of dependency and significance of semantic levels. Three indicators, namely, the significance of semantic levels, decreasing the heterogeneity of attributes, and replicability were defined and assessed for a subset of building‐related tags. Analyzing building‐related tags in OpenStreetMap unveiled the higher significance for simple object, similarity, purpose, and function levels. The value of decreasing the heterogeneity of attributes was calculated at 63%, and the average replicability indicator of important attributes was doubled. Based on the results, the significance of semantic levels was deemed fit to enhance semantic homogeneity and replicability.
Negative politeness and no worries in Australian English
Authors: Peters Pam , Burke Isabelle
Published: July 2024

This paper explores how a distinctive politeness token can establish itself in a variety of world English by virtue of its pragmatics. It examines the usage of no worries as a negative politeness thanking response in a large multigenerational corpus of informal dialogues by men and women recorded at the University of Western Australia (UWA). Data from this UWA corpus reflect the steady evolution of no worries, from its indexical association with Australian men's talk to be taken up by younger Australian women. Though rooted in laconic spoken exchanges, the data also show extended uses of no worries in quoted speech as well as narrative reconstructions of spoken encounters to highlight their outcomes. In its further linguistic evolution, it works as a stance adverbial in dramatized interior monologues. It thus acquires new functions in various discourse contexts where a modicum of negative politeness adds value to the narrative or argument.
Hybrid subconvexity bound for GL(3)×GL(2)L$GL(3)\times GL(2) \ L$‐functions: t$t$ and level aspect
Authors: Harun Mohd , Kumar Sumit , Singh Saurabh Kumar
Published: July 2024

In this article, we will get nontrivial estimates for the central values of degree six Rankin–Selberg ‐functions associated with a form and a form using the delta symbol approach in the hybrid level and ‐aspect.
Japanese encephalitis virus NS5 protein interacts with nucleolin to enhance the virus replication
Authors: Deb Arundhati , Nagpal Shilpi , Yadav Rajnesh Kumari , Thakur Harsh , Nair Deepak , Krishnan Vengadesan , Vrati Sudhanshu
Published: July 2024

Japanese encephalitis virus (JEV) is an arthropod-borne, plus-strand flavivirus causing viral encephalitis in humans with a high case fatality rate. The JEV non-structural protein 5 (NS5) with the RNA-dependent RNA polymerase activity interacts with the viral and host proteins to constitute the replication complex. We have identified the multifunctional protein Nucleolin (NCL) as one of the several NS5-interacting host proteins. We demonstrate the interaction and colocalization of JEV NS5 with NCL in the virus-infected HeLa cells. The siRNA-mediated knockdown of NCL indicated that it was required for efficient viral replication. Importantly, JEV grew to higher titers in cells over-expressing exogenous NCL, demonstrating its pro-viral role. We demonstrated that NS5 interacted with the RRM and GAR domains of NCL. We show that the NCL-binding aptamer AS1411 containing the G-quadruplex (GQ) structure and the GQ ligand BRACO-19 caused significant inhibition of JEV replication. The antiviral effect of AS1411 and BRACO-19 could be overcome in HeLa cells by the overexpression of exogenous NCL. We demonstrated that the synthetic RNAs derived from the 3′-NCR of JEV genomic RNA containing the GQ sequence could bind NCL
in vitro
. The replication complex binding to the 3′-NCR is required for the viral RNA synthesis. It is likely that NCL present in the replication complex destabilizes the GQ structures in the genomic RNA, thus facilitating the movement of the replication complex resulting in efficient virus replication.

IMPORTANCE

Japanese encephalitis virus (JEV) is endemic in most parts of South-East Asia and the Western Pacific region, causing epidemics of encephalitis with a high case fatality rate. While a tissue culture-derived JEV vaccine is available, no antiviral therapy exists. The JEV NS5 protein has RNA-dependent RNA polymerase activity. Together with several host and viral proteins, it constitutes the replication complex necessary for virus replication. Understanding the interaction of NS5 with the host proteins could help design novel antivirals. We identified Nucleolin (NCL) as a crucial host protein interactor of JEV NS5 having a pro-viral role in virus replication. The NS5-interacting NCL binds to the G-quadruplex (GQ) structure sequence in the 3′-NCR of JEV RNA. This may smoothen the movement of the replication complex along the genomic RNA, thereby facilitating the virus replication. This study is the first report on how NCL, a host protein, helps in JEV replication through GQ-binding.
Cell-surface
d
-glucuronyl C5-epimerase binds to porcine deltacoronavirus spike protein facilitating viral entry
Authors: Xiao Wenwen , Chen Chaoqun , Xia Sijin , Li Zhuang , Ding Tong , Zhou Junwei , Fang Liurong , Fang Puxian , Xiao Shaobo
Published: July 2024

Porcine deltacoronavirus (PDCoV) is an emerging swine enteric coronavirus with zoonotic potential. The coronavirus spike (S) glycoprotein, especially the S1 subunit, mediates viral entry by binding to cellular receptors. However, the functional receptor of PDCoV remains poorly understood. In this study, we used the soluble PDCoV S1 protein as bait to capture the S1-binding cellular transmembrane proteins in combined immunoprecipitation and mass spectrometry analyses. A single guide RNA screen identified
d
-glucuronyl C5-epimerase (GLCE), a heparan sulfate-modifying enzyme, as a proviral host factor for PDCoV infection. GLCE knockout significantly inhibited the attachment and internalization stages of PDCoV infection. We also demonstrated the interaction between GLCE and PDCoV S with coimmunoprecipitation in both an overexpression system and PDCoV-infected cells. GLCE could be localized to the cell membrane, and an anti-GLCE antibody suppressed PDCoV infection. Although GLCE expression alone did not render nonpermissive cells susceptible to PDCoV infection, GLCE promoted the binding of PDCoV S to porcine amino peptidase N (pAPN), acting synergistically with pAPN to enhance PDCoV infection. In conclusion, our results demonstrate that GLCE is a novel cell-surface factor facilitating PDCoV entry and provide new insights into PDCoV infection.

IMPORTANCE

The identification of viral receptors is of great significance, potentially extending our understanding of viral infection and pathogenesis. Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus with the potential for cross-species transmission. However, the receptors or coreceptors of PDCoV are still poorly understood. The present study confirms that
d
-glucuronyl C5-epimerase (GLCE) is a positive regulator of PDCoV infection, promoting viral attachment and internalization. The anti-GLCE antibody suppressed PDCoV infection. Mechanically, GLCE interacts with PDCoV S and promotes the binding of PDCoV S to porcine amino peptidase N (pAPN), acting synergistically with pAPN to enhance PDCoV infection. This work identifies GLCE as a novel cell-surface factor facilitating PDCoV entry and paves the way for further insights into the mechanisms of PDCoV infection.
Molecular insight into the neutralization mechanism of human-origin monoclonal antibody AH100 against Hantaan virus
Authors: Wang Feiran , Liu Tiezhu , Liao Liying , Chai Yan , Qi Jianxun , Gao Feng , Liang Mifang , Gao George Fu , Wu Yan
Published: July 2024

Both Old World and New World hantaviruses are transmitted through rodents and can lead to hemorrhagic fever with renal syndrome or hantavirus cardiopulmonary syndrome in humans without the availability of specific therapeutics. The square-shaped surface spikes of hantaviruses consist of four Gn-Gc heterodimers that are pivotal for viral entry into host cells and serve as targets for the immune system. Previously, a human-derived neutralizing monoclonal antibody, AH100, demonstrated specific neutralization against the Old World hantavirus, Hantaan virus. However, the precise mode binding of this neutralizing monoclonal antibody remains unclear. In the present study, we determined the structure of the Hantaan virus Gn-AH100 antigen-binding fragment complex and identified its epitope. Crystallography revealed that AH100 targeted the epitopes on domain A and b-ribbon and E3-like domain. Epitope mapping onto a model of the higher order (Gn-Gc)
4
spike revealed its localization between neighboring Gn protomers, distinguishing this epitope as a unique site compared to the previously reported monoclonal antibodies. This study provides crucial insights into the structural basis of hantavirus neutralizing antibody epitopes, thereby facilitating the development of therapeutic antibodies.

IMPORTANCE

Hantaan virus (HTNV) poses a significant threat to humans by causing hemorrhagic fever with renal syndrome with high mortality rates. In the absence of FDA-approved drugs or vaccines, it is urgent to develop specific therapeutics. Here, we elucidated the epitope of a human-derived neutralizing antibody, AH100, by determining the HTNV glycoprotein Gn-AH100 antigen-binding fragment (Fab) complex structure. Our findings revealed that the epitopes situated on the domain A and b-ribbon and E3-like domain of the HTNV Gn head. By modeling the complex structure in the viral lattice, we propose that AH100 neutralizes the virus by impeding conformational changes of Gn protomer, which is crucial for viral entry. Additionally, sequence analysis of all reported natural isolates indicated the absence of mutations in epitope residues, suggesting the potential neutralization ability of AH100 in diverse isolates. Therefore, our results provide novel insights into the epitope and the molecular basis of AH100 neutralization.
Conserved cysteine residues in Kaposi’s sarcoma herpesvirus ORF34 are necessary for viral production and viral pre-initiation complex formation
Authors: Watanabe Tadashi , McGraw Aidan , Narayan Kedhar , Tibebe Hasset , Kuriyama Kazushi , Nishimura Mayu , Izumi Taisuke , Fujimuro Masahiro , Ohno Shinji
Published: July 2024

Kaposi’s sarcoma herpesvirus (KSHV) ORF34 plays a significant role as a component of the viral pre-initiation complex (vPIC), which is indispensable for late gene expression across beta- and gammaherpesviruses. Although the key role of ORF34 within the vPIC and its function as a hub protein have been recognized, further clarification regarding its specific contribution to vPIC functionality and interactions with other components is required. This study employed a deep learning algorithm-assisted structural model of ORF34, revealing highly conserved amino acid residues across human beta- and gammaherpesviruses localized in structured domains. Thus, we engineered ORF34 alanine-scanning mutants by substituting conserved residues with alanine. These mutants were evaluated for their ability to interact with other vPIC factors and restore viral production in cells harboring the ORF34-deficient KSHV-BAC. Our experimental results highlight the crucial role of the four cysteine residues conserved in ORF34: a tetrahedral arrangement consisting of a pair of C-X
n
-C consensus motifs. This suggests the potential incorporation of metal cations in interacting with ORF24 and ORF66 vPIC components, facilitating late gene transcription, and promoting overall virus production by capturing metal cations. In summary, our findings underline the essential role of conserved cysteines in KSHV ORF34 for effective vPIC assembly and viral replication, thereby enhancing our understanding of the complex interplay between the vPIC components.

IMPORTANCE

The initiation of late gene transcription is universally conserved across the beta- and gammaherpesvirus families. This process employs a viral pre-initiation complex (vPIC), which is analogous to a cellular PIC. Although KSHV ORF34 is a critical factor for viral replication and is a component of the vPIC, the specifics of vPIC formation and the essential domains crucial for its function remain unclear. Structural predictions suggest that the four conserved cysteines (C170, C175, C256, and C259) form a tetrahedron that coordinates the metal cation. We investigated the role of these conserved amino acids in interactions with other vPIC components, late gene expression, and virus production to demonstrate for the first time that these cysteines are pivotal for such functions. This discovery not only deepens our comprehensive understanding of ORF34 and vPIC dynamics but also lays the groundwork for more detailed studies on herpesvirus replication mechanisms in future research.
Neoproterozoic tectonic shift along the western margin of the Yangtze block, South China craton: Implications for its paleogeographic position during the Rodinia–Gondwana transition
Authors: Qi Liang , Hou Mingcai , Cawood Peter A. , Xiong Fuhao , Peng Touping , Huang Hu
Published: July 2024

Neoproterozoic igneous rocks in the Panxi region from the western margin of the Yangtze block, South China craton, record major changes in tectonic evolution and crustal thickness, and provide important constraints on the paleogeographic position and climate changes of the block in Rodinia and Gondwana reconstructions. Our new dating results show that the Pengguan complex from the Panxi region comprises ca. 743 Ma adakitic granodiorites and ca. 741 Ma A-type granites. The former is plagioclase-rich and has relatively low SiO2 content (65.22–67.36 wt%), high Mg# values (44.40–52.33), Sr/Y (23.22–61.94) and (La/Yb)N ratios (normalized to chondritic values; 13.41–24.00), with positive whole-rock εNd(t) values (+1.17 to +5.15), and high zircon εHf(t) (+5.53 to +8.83) and low zircon δ18O (4.21‰ to 5.51‰) values, indicating derivation from the partial melting of thickened juvenile mafic lower crust. By contrast, the granites are rich in K-feldspar and have high SiO2 contents (78.71–84.62 wt%), 10,000 × Ga/Al ratios (>2.6), and Fe/Mg ratios, with negative εNd(t) values (−1.47 to −0.02), high zircon εHf(t) (+2.94 to +9.77), and high saturation temperatures (828–920 °C). These features indicate fractional crystallization and partial melting of continental crust in a low-pressure, high-temperature, extensional environment. Integrated with the zircon Eu anomalies (Eu/Eu*) data and Hf-O isotopic data on pre-740 Ma magmatism in the Panxi region, we find that a rapid increase of crustal thickening (820–740 Ma) was synchronous with a gradual decrease of zircon δ18O and an increase of zircon εHf(t) values. These variations indicate an increase in the degree of hybridization between mantle sources and subducting slab-derived materials, thus generating a great number of low-δ18O melts, and continuous crustal thickening through the underplating of juvenile magmas. In addition, thinning of the crust since ca. 740 Ma, along with the gradual increase in zircon δ18O and εHf(t), suggests a shift from regional compression to extension. This documented shift, together with regional data from along the western margin of the Yangtze block, indicates a change from the well-developed and long-established Panxi convergent plate margin arc system (at least ca. 870–750 Ma) to passive-margin development and Cryogenian (720–635 Ma) glaciation. The long-lived subduction zone requires a peripheral location of South China that was linked to northern India during the Rodinia breakup. The subsequent and contemporaneous passive-margin development of the Yangtze block and India, along with the similar tectonic affinities of the Cathaysia block with India, indicate that South China lay outboard of the northern Gondwana margin during the assembly of this supercontinent.
Volcanic and orbitally forced carbon release during the Middle Eocene Climatic Optimum
Authors: Ma Yiquan , Fan Majie , Zhang Chen , Grasby Stephen E. , Yin Runsheng , Lu Yangbo , Zhang Bolin , Jin Xin , Ma Chao , Lu Yongchao , Sluijs Appy
Published: July 2024

The drivers of the Middle Eocene Climatic Optimum (MECO) remain enigmatic. Here we report a high-resolution terrestrial MECO record from the Bohai Bay Basin, eastern China. The record shows episodic Hg enrichments and a volcanogenic Δ199Hg signature during the MECO, and an abrupt chemical weathering enhancement and negative δ13Corg excursion (CIE) during the MECO peak warmth. A high-resolution age model constrains the MECO to ca. 40.59–40.18 Ma with the onset in the first ~320 k.y. Peak warmth and the CIE initiated at 40.27 Ma, corresponding to 405 k.y. and 100 k.y. eccentricity maxima, and lasted for ~90 k.y., reminiscent of the early Eocene hyperthermals. Our findings suggest that episodic volcanism contributed to gradual atmospheric pCO2 rise, leading to the long duration of the MECO onset. Orbital forcing at 40.27 Ma, on top of CO2 forcing, caused the peak warmth and a positive carbon cycle feedback. The regional increase in weathering is inconsistent with evidence for weakened global continental weathering, suggesting strong spatial heterogeneity in the weathering response to MECO warming.
Economic evaluation of the hospitalist care model in an acute medical unit: a benefit–cost analysis
Authors: Kim Hyun Jeong , Kim Jinhyun , Ohn Jung Hun , Kim Nak-Hyun
Published: July 2024

Objective

This study aimed to assess the economic efficiency of the acute medical unit (AMU) hospitalist care model, utilising patient outcomes (length of hospital stay, emergency department (ED)-length of hospital stay, in-hospital mortality) from a previous investigation.

Design

A retrospective cohort study was conducted using benefit–cost analysis from a societal perspective. Data relating to clinical factors, outcomes and medical costs were obtained from the electronic medical record database at our institution. Literature-based costing was applied to determine direct non-medical costs and indirect costs that could not be obtained directly.

Setting

A tertiary care hospital in the Republic of Korea.

Participants

We evaluated 6391 medical inpatients admitted through the ED from 1 June 2016 to 31 May 2017.

Interventions

The study compared multiple types of costs and benefits among inpatients from the ED between a non-hospitalist group and an AMU hospitalist group.

Results

This investigation found a significant reduction in medical costs and total costs in the AMU hospitalist group compared to the non-hospitalist group (30% reduction, 95% CI: 27.6–32.1%,P=0.000; 29.3% reduction, 95% CI: 27.0–31.5%,P=0.000; respectively). Furthermore, significant reductions in direct and indirect costs were found in the AMU hospitalist group compared to the non-hospitalist group (28.6% reduction, 95% CI: 26.6–30.5%,P=0.000; 23.3% reduction, 95% CI: 20.9–25.5%,P=0.000; respectively). The net-benefit and benefit-cost ratio (BCR) of the AMU hospitalist care group were US $6846 and 1.33 per patient admission, respectively.

Conclusions

The AMU hospitalist care model was associated with remarkable reductions in multiple costs. The results of the sensitivity analysis indicated that the net-benefit estimates of AMU hospitalist care were similar to the baseline estimates. Thus, the overall net-benefit of AMU hospitalist care was found to be largely positive.
Characteristics of mental skills interventions in dance: a mixed methods systematic review protocol
Authors: Dwarika Michelle Schachtler , Quinton Mary L , Nordin-Bates Sanna , Cumming Jennifer
Published: July 2024

Introduction

Dancers are expected to navigate major challenges in their careers that might take a toll on their physical and mental health. To address underlying factors that might increase dancers’ mental and physical health difficulties, research suggests the systematic use of techniques to build mental skills that can reduce risk factors and enhance protective factors against the challenges dancers encounter. However, existing mental skills training interventions in dance present a lack of consistency in design, content and duration, making it difficult to provide evidence-based recommendations. Hence, dance researchers and practitioners would benefit from a mixed methods systematic review (MMSR) of the why, what and how of these interventions. Adopting tools such as the Template for Intervention Description and Replication (TIDieR) can aid this endeavour by describing replicable aspects of interventions, thus offering dance researchers suggestions on how to understand, appraise and report intervention characteristics and processes in dance. Therefore, this protocol outlines a MMSR that will employ TIDieR to identify and assess characteristics of mental skills interventions in dance.

Methods and analysis

A systematic search will be undertaken in Psycinfo, Medline, Embase, Sportdiscus, Web of Science and the first 30 pages of GoogleScholar. Following the search, two reviewers will independently screen identified studies in Covidence. One reviewer will extract data using the TIDieR framework and the Mixed Methods Appraisal Tool (MMAT) for quality appraisal, while a second reviewer will check a sample of extracted studies for accuracy. A convergent integrated synthesis will be conducted where quantitative and qualitative evidence will be integrated by qualitising the quantitative data into textual descriptions.

Ethics and dissemination

There is no requirement for ethical approval for this systematic review as no empirical data will be collected. The findings will be disseminated through a peer-reviewed publication in a scientific journal and presentations in several different forums (eg, a dance psychology network, at scientific and applied conferences).

Prospero registration number

CRD42024537249.
It’s about the long game, not epic workouts: unpacking HIIT for endurance athletes
Authors: Seiler Stephen
Published: July 2024

High-intensity interval training (HIIT) prescriptions manipulate intensity, duration, and recovery variables in multiple combinations. Researchers often compare different HIIT variable combinations and treat HIIT prescription as a “maximization problem”, seeking to identify the prescription(s) that induce the largest acute VO2/HR/RPE response. However, studies connecting the magnitude of specific acute HIIT response variables like work time >90% of VO2max and resulting cellular signalling and/or translation to protein upregulation and performance enhancement are lacking. This is also not how successful endurance athletes train. First, HIIT training cannot be seen in isolation. Successful endurance athletes perform most of their training volume below the first lactate turn point (<LT1), with “threshold training” and HIIT as integrated parts of a synergistic combination of training intensities and durations. Second, molecular signalling research reveals multiple, “overlapping” signalling pathways driving peripheral adaptations, with those pathways most sensitive to work intensity showing substantial feedback inhibition. This makes current training content and longer-term training history critical modulators of HIIT adaptive responses. Third, long term maximization of endurance capacity extends over years. Successful endurance athletes balance low-intensity and high-intensity, low systemic stress, and high systemic stress training sessions over time. The endurance training process is therefore an “optimization problem”. Effective HIIT sessions generate both cellular signal and systemic stress that each individual athlete responds to and recovers from over weeks, months, and even years of training. It is not “epic” HIIT sessions but effective integration of intensity, duration, and frequency of all training stimuli over time that drives endurance performance success.
A quasi-experimental study on the energy expenditure, exercise intensity, and rating of perceived exertion of a male bodybuilding posing training
Authors: Peixoto Douglas Leão , Nacimento Dahan da Cunha , Moura Ronaldo Ferreira , de Moraes Wilson Max Almeida Monteiro , Magalhães Bruno , de Sousa Leandro Lima , Rolnick Nicholas , Prestes Jonato
Published: July 2024

This study aimed to evaluate the intensity of posing training in male bodybuilders by comparing it to vigorous intensity parameters and examining the effects of stimulant usage and preparation phases. Specifically, this study compared posing training to established vigorous intensity benchmarks using metabolic equivalents (METs) and heart rate (HR) responses and assessed differences between athletes using stimulants versus those not using stimulants, as well as during peak week versus other preparation phases. Fifteen male bodybuilding athletes (mean age: 32.07 ± 7.82 years; mean body mass: 92.89 ± 9.06 kg; mean height: 1.76 ± 0.05 m; mean body mass index: 29.78 ± 2.24 kg/m²) completed four compulsory posing sets. Findings demonstrated that posing training can be classified as vigorous training intensity using METs (mean difference of −0.50 METs, p = 0.067, ES = −0.51) and maximum HR (mean difference of 14.55 bpm, p = 0.009, ES = 0.79) compared to the established values of 6.0 METs and 77% vigorous intensity of %HRmax, respectively. Additionally, athletes using stimulants exhibited higher ratings of perceived exertion (RPE) of 2.20 arbitrary units ( p = 0.008) and maximum HR (mean difference of 24.37 bpm, p = 0.005, ES = 0.79) compared to those not using stimulants. During peak week, athletes showed higher RPE of 2.38 arbitrary units ( p = 0.004) and maximum HR (mean difference of 14.55 bpm, p = 0.009, ES = 0.79) compared to other preparation phases. These results indicate that bodybuilding posing training meets the criteria for vigorous exercise intensity and that stimulant use and peak week significantly affect physiological responses and perceived exertion.

Novelty

This study is novel in classifying bodybuilding posing training as vigorous intensity exercise using metabolic equivalents (METs) and heart rate (HR) responses. It provides empirical evidence showing that posing training meets the vigorous intensity benchmarks, with METs and %HRmax values comparable to established vigorous exercise standards. The research highlights the novel finding that stimulant usage and the peak week phase of preparation significantly influence physiological responses and perceived exertion in bodybuilders. Specifically, athletes using stimulants and those in peak week displayed higher ratings of perceived exertion (RPE) and maximum heart rates, indicating that these factors notably affect the intensity and perceived difficulty of posing training.
Risk-informed design of debris-flow mitigation at Cheekeye Fan
Authors: LeSueur Philip , Strouth Alex , Mark Emily , Collier-Pandya Beatrice , Zubrycky Sophia
Published: July 2024

The Cheekeye Fan, located within the District of Squamish, is prone to debris-flow hazards that pose unacceptable risk to development. This article describes how a debris-flow barrier that would protect existing and proposed development was designed to achieve locally adopted risk tolerance criteria. A risk assessment showed that the barrier should manage debris flows with volumes up to 2.8 Mm3 (1:10 000-year return-period events) to achieve tolerable risk, and that debris flows with volumes below 0.2 Mm3 (10–30-year events) can pass the barrier through an outlet without exceeding risk tolerance thresholds. The local government specifies that tolerable debris-flow risks be reduced “as low as reasonably practicable” (ALARP), defined in this project as the point where the cost of additional mitigation measures is grossly disproportionate to the benefits gained. By estimating the disproportionality ratio for potential auxiliary measures, this study shows that the barrier reduces risk ALARP without additional measures in place. The authors believe that new development approval on Cheekeye fan would not be possible without the risk-informed decision-making process described in this article.
Identification of key drivers of antimicrobial resistance in Enterococcus using machine learning
Authors: Kim Jee In , Manuele Alexander , Maguire Finlay , Zaheer Rahat , McAllister Tim A. , Beiko Robert G.
Published: July 2024

With antimicrobial resistance (AMR) rapidly evolving in pathogens, quick and accurate identification of genetic determinants of phenotypic resistance is essential for improving surveillance, stewardship, and clinical mitigation. Machine learning (ML) models show promise for AMR prediction in diagnostics but require a deep understanding of internal processes to use effectively. Our study utilised AMR gene, pangenomic, and predicted plasmid features from 647 Enterococcus faecium and Enterococcus faecalis genomes across the One Health continuum, along with corresponding resistance phenotypes, to develop interpretive ML classifiers. Vancomycin resistance could be predicted with 99% accuracy with AMR gene features, 98% with pangenome features, and 96% with plasmid clusters. Top pangenome features overlapped with the resistance genes of the vanA operon, which are often laterally transmitted via plasmids. Doxycycline resistance prediction achieved approximately 92% accuracy with pangenome features, with the top feature being elements of Tn 916 conjugative transposon, a tet(M) carrier. Erythromycin resistance prediction models achieved about 90% accuracy, but top features were negatively correlated with resistance due to the confounding effect of population structure. This work demonstrates the importance of reviewing ML models’ features to discern biological relevance even when achieving high-performance metrics. Our workflow offers the potential to propose hypotheses for experimental testing, enhancing the understanding of AMR mechanisms, which are crucial for combating the AMR crisis.
Catalpol from Rehmannia glutinosa Targets Nrf2/NF-κB Signaling Pathway to Improve Renal Anemia and Fibrosis
Authors: Liu Zhi-Hui , Xu Qing-Yang , Wang Yu , Gao Hong-Xin , Min Ya-Hong , Jiang Xiao-Wen , Yu Wen-Hui
Published: July 2024

Rehmannia glutinosa is widely recognized as a prominent medicinal herb employed by practitioners across various generations for the purpose of fortifying kidney yin. Within Rehmannia glutinosa, the compound known as catalpol (CAT) holds significant importance as a bioactive constituent. However, the protective effects of CAT on kidneys, including ameliorative effects on chronic kidney disease — most prominently renal anemia and renal fibrosis — have not been clearly defined. In this study, the kidney injury model of NRK-52E cells and C57BL/6N male mice was prepared by exposure to aristolochic acid I (AA-I), and it was discovered that CAT could ameliorate oxidative stress injury, inflammatory injury, apoptosis, renal anemia, renal fibrosis, and other renal injuries both in vivo and in vitro. Further treatment of NRK-52E cells with Nrf2 inhibitors (ML385) and activators (ML334), as well as NF-κB inhibitors (PDTC), validated CAT’s ability to target Nrf2 activation. Furthermore, the expression of phosphorylated NF-κB p65, IL-6, and Cleaved-Caspase3 protein was inhibited. CAT also inhibited NF-κB, and then inhibited the expression of IL-6, p-STAS3, TGF-β1 protein. Therefore, CAT can regulate Nrf2/NF-κB signaling pathway, significantly correct renal anemia and renal fibrosis, and is conducive to the preservation of renal structure and function, thus achieving a protective effect on the kidneys.
Generalized slip impact of Casson nanofluid through cylinder implanted in swimming gyrotactic microorganisms
Authors: Gangadhar Kotha , Sujana Sree T. , Wakif Abderrahim
Published: July 2024

In this paper, the self-propelled movement on gyrotactic swimming microorganisms into this generalized slip flow by nanoliquid over the stretching cylinder with strong magnetic field is discussed. Constant wall temperature was pretended as well as the Nield conditions of boundary. The intuitive non-Newtonian particulate suspension was included into applying Casson fluid by the base liquid and nanoparticles. This formation on the bio-mathematical model gives the boundary value problem by the nonlinear partial differential equations. Primly, modeled numerical system was converted to nondimensional against this help on acceptable scaling variables and the bvp4c technique was used to acquire the mathematical outcomes on the governing system. This graphical description by significant parameters and their physical performance was widely studied. The Prandtl number has the maximum contribution (112.595%) along the selected physical parameters, whereas the Brownian motion has the least (0.00165%) heat transfer rate. Anyhow, Casson fluid was established for much helpful suspension of this method on fabrication and coatings, etc. Therefore, this magnetic field performs like the resistive force of that fluid motion, and higher energy was enlarged into the structure exhibiting strong thermal radiation.
Blockchain Technology and Smart Contract Application in Security Management of Intelligent Chemical Plants
Authors: Wang Changwen , Su Junde , Liu Hang
Published: July 2024

As blockchain technology and smart contracts develop, computer technology is constantly integrating with smart chemical plants. Due to the continuous development of intelligent chemical plants, their systems have gradually become large and dispersed, posing a threat to safety management. In order to improve the performance of intelligent security management systems, the study first explores the principles of blockchain and smart contract technology, and then combined with the requirements of intelligent chemical plant security management systems, designs an intelligent security management system based on blockchain and smart contract technology. The experimental results showed that compared to systems without smart contract support, the communication success rate between nodes was lower. The error rates of blockchain-based encryption systems, deep learning-based encryption systems and improved data encryption systems proposed in the study were 0.22, 0.07 and 0.09, respectively. The packet loss rates were 0.13, 0.04 and 0.05, respectively. The lower the bit error rate and packet loss rate of the encryption system, the clearer the illegal eavesdropping information. The experimental results indicate that the intelligent security management system designed in this study has good encryption performance and a higher communication success rate. The results have certain reference value in security management application in intelligent chemical plants.
Hybrid PDES Simulation of HPC Networks Using Zombie Packets
Authors: Cruz-Camacho Elkin , Brown Kevin , Wang Xin , Xu Xiongxiao , Shu Kai , Lan Zhiling , Ross Bob , Carothers Christopher
Published: July 2024

Although high-fidelity network simulations have proven to be reliable and cost-effective tools to peer into architectural questions for high-performance computing (HPC) networks, they incur a high resource cost. The time spent in simulating a single millisecond of network traffic in the highest detail can take hours, even for static, well-behaved traffic patterns such as uniform random. Surrogate models offer a significant reduction in runtime, yet they cannot serve as complete replacements and should only be used when appropriate. Thus, there is a need for hybrid modeling, where high-fidelity simulation and surrogates run side-by-side. We present a surrogate model for HPC networks in which: packets bypass the network, while the network state is left untouched,
i.e
, suspended. To bypass the network, we use historical data to estimate the arrival time at which every packet should be scheduled at; to suspend the network, all in-flight packets are scheduled to arrive at their destinations, and are kept in the system to awaken as zombies when switching back to high-fidelity. Speedup for a hybrid model is relative to the proportion of surrogate to high-fidelity. This light-weight surrogate obtained up to 76 × speedup. Keeping the zombies in the network showed an increase in the accuracy of the high-fidelity simulation on restart when compared to restarting the network from an empty state.
Designing with Data: An Annotated Portfolio
Authors: Gaver William , Boucher Andy
Published: July 2024

This article presents an account of the Interaction Research Studio’s distinctive approach to incorporating data into design, unpacking a vital but previously unexamined facet of our two-decade-long research programme. We demonstrate how data have served as a pragmatic tool in creating and engaging contextually aware computational products that provide alternatives to dominant task-oriented and consumerist narratives by promoting interpretation, imagination, spirituality and socio-cultural reflection. Leveraging an annotated portfolio approach, we revisit our diverse portfolio of designs, starting from individual reflections before surfacing overarching themes. This article foregrounds our strategies for utilising data, the associated labour and the challenges that have arisen throughout our design process. This emergent and empirical account may complement more theoretical treatments of designing with data and provide valuable insights for researchers, designers and practitioners navigating the complexities of data-integrated design in the contemporary technological landscape.
Parameter Estimation for Gibbs Distributions
Authors: Harris David G. , Kolmogorov Vladimir
Published: July 2024

A central problem in computational statistics is to convert a procedure for
sampling
combinatorial objects into a procedure for
counting
those objects, and vice versa. We consider sampling problems coming from
Gibbs distributions
, which are families of probability distributions over a discrete space

\(\Omega\)

with probability mass function of the form

\(\mu^{\Omega}_{\beta}(\omega)\propto e^{\beta H(\omega)}\)

for

\(\beta\)

in an interval

\([\beta_{\min},\beta_{\max}]\)

and

\(H(\omega)\in\{0\}\cup[1,n]\)

. Two important parameters are the
partition function
, which is the normalization factor

\(Z(\beta)=\sum_{\omega\in\Omega}e^{\beta H(\omega)}\)

and the vector of pre-image

counts

\(c_{x}=|H^{-1}(x)|\)

.

We develop black-box sampling algorithms to estimate the counts using roughly

\(\tilde{O}(\frac{n^{2}}{\varepsilon^{2}})\)

samples for integer-valued distributions and

\(\tilde{O}(\frac{q}{\varepsilon^{2}})\)

samples for general distributions, where

\(q=\log\frac{Z(\beta_{\max})}{Z(\beta_{\min})}\)

(ignoring some second-order terms and parameters). We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs, independent sets, and perfect matchings. As a key subroutine, we estimate all values of the partition function using

\(\tilde{O}(\frac{n^{2}}{\varepsilon^{2}})\)

samples for integer-valued distributions and

\(\tilde{O}(\frac{q}{\varepsilon^{2}})\)

samples for general distributions. This improves over a prior algorithm of Huber (2015) which computes a single point estimate

\(Z(\beta_{\max})\)

and which uses a slightly larger amount of samples. We show matching lower bounds, demonstrating this complexity is optimal as a function of

\(n\)

and

\(q\)

up to logarithmic terms.
Longitudinal importance of the soluble receptor for advanced glycation end-products in nonintubated hospitalized patients with COVID-19 pneumonia
Authors: Wick Katherine D. , Siegel Lianne , Oldmixon Cathryn , Lundgren Jens D. , Thompson B. Taylor , Jones Chayse , Leroux Carolyn , Matthay Michael A. ,   ACTIV-3/TICO Study Group
Published: July 2024

The soluble receptor for advanced glycation end-products (sRAGE) is a marker of alveolar type I epithelial cell injury associated with clinical outcomes in acute respiratory distress syndrome and, more recently, in hospitalized subjects with COVID-19. How plasma sRAGE changes over time and whether plasma sRAGE remains associated with long-term clinical outcomes beyond a single baseline measurement in patients with COVID-19 have not been well studied.
Liver Transplantation: A Test of Cellular Physiology, Preservation, and Injury
Authors: Martins B. , Mossemann J. , Aguilar F. , Zhao S. , Bilan P. J. , Sayed B. A.
Published: July 2024

Liver transplantation has evolved into a mature clinical field, but scarcity of usable organs poses a unique challenge. Expanding the donor pool requires novel approaches for protecting hepatic physiology and cellular homeostasis. Here we define hepatocellular injury during transplantation, with an emphasis on modifiable cell death pathways as future therapeutics.
Low-Grade Chronic Inflammation: a Shared Mechanism for Chronic Diseases
Authors: Cifuentes Mariana , Verdejo Hugo E. , Castro Pablo F. , Corvalan Alejandro H. , Ferreccio Catterina , Quest Andrew F. G. , Kogan Marcelo J. , Lavandero Sergio
Published: July 2024

Inflammation is an important physiological response of the organism to restore homeostasis upon pathogenic or damaging stimuli. However, the persistence of the harmful trigger or a deficient resolution of the process can evolve into a state of low-grade, chronic inflammation. This condition is strongly associated with the development of several increasingly prevalent and serious chronic conditions, such as obesity, cancer, and cardiovascular diseases, elevating overall morbidity and mortality worldwide. The current pandemic of chronic diseases underscores the need to address chronic inflammation, its pathogenic mechanisms, and potential preventive measures to limit its current widespread impact. The present review discusses the current knowledge and research gaps regarding the association between low-grade chronic inflammation and chronic diseases, focusing on obesity, cardiovascular diseases, digestive diseases, and cancer. We examine the state of the art in selected aspects of the topic and propose future directions and approaches for the field.
Exploring Thoracic Aortic Graft Infection: A Comprehensive Review of Diagnosis and Treatment Options with a Management Strategy Algorithm
Authors: O’ Sullivan Katie E. , Casey Laura , Sidhu Pushpinder , Graham Alastair , Austin Christopher , Hunter Michael
Published: July 2024

As surveillance and the diagnosis of pathology grow, increasing numbers of patients are undergoing major aortic interventions globally. As a result, surgeons and physicians will encounter thoracic aortic graft infections with increasing frequency. These infections are extremely challenging, high‐risk problems to deal with. This article provides a comprehensive overview of the pathogenesis, diagnosis, and management both medical and surgical of this high‐risk complication. We provide proposed diagnostic criteria and suggested algorithm for the management of this important group of patients.
An Extensive Review of the Literature Using the Diophantine Equations to Study Fuzzy Set Theory
Authors: Abirami K. M. , Veena Narayanan , Srikanth R. , Dhanasekaran P.
Published: July 2024

Every field in mathematics has made significant progress in research with fuzzy sets. Numerous application fields were discovered in both empirical and theoretical investigations, ranging from information technology to medical technology, from the natural sciences to the physical sciences, and from technical education to fine arts education. However, it has limitations of its own and has not been able to function in real‐world situations. An interdisciplinary approach of fuzzy theory with number theory, especially Diophantine equations, needs to be accomplished to overcome this problem. A thorough literature study of the Diophantine equations, fuzzy sets, and the combination known as the linear Diophantine fuzzy set (LDFS) is accomplished in the present study. New forms of LDFSs have been added recently, and these additions have found use in a variety of fields, including the disciplines of pharmacology, power, healthcare, goods, and finance. The genesis of these expansions is also examined in this study of the literature. Hence, in the present work, some applications of LDFS are described in detail. Further in the present study, the existing primary constraints in the research on LDFS are highlighted. Also, the last section of the review is dedicated to outlining some future directions for the study of LDFS.
Unveiling Social Belonging: Exploring the Narratives of Immigrant Muslim Older Women
Authors: Au Alesia , Hilario Carla , Meherali Salima , Salma Jordana
Published: July 2024

Background and Objectives. Older adults who lack a secure sense of social belonging may report loneliness, isolation, and ostracization in their communities. Little attention has been paid to the perceptions of social belonging among immigrant Muslim older (IMO) women. This study aimed to address this gap by exploring IMO women’s experiences of social belonging. Research Design and Methods. This qualitative descriptive study used photo elicitation and narrative interviewing to draw on the experiences of 14 IMO women living in Edmonton, Canada. An integrative framework of social belonging was used to guide theoretical conceptualizations of what comprises belonging, and a thematic analysis approach was used to highlight factors and influences that shape how participants have constructed their experiences of belonging. Results. The findings suggest that a sense of belonging is influenced by feelings of loneliness and loss, opportunities for community engagement, and social competencies related to maintaining family relationships. Additionally, the findings indicate the importance of IMO women’s perceptions and reflections on aging as these shape their sense of belonging. These findings not only provide insight into the intricate and shifting nature of belonging but also emphasize the need for structural support to benefit both IMO women and the communities they reside in. Discussion and Implications. Cultivating belonging is a collective responsibility involving older women, their social networks, and society at large, including government and public services. A sense of belonging is crucial to counter ageism and promote positive self‐perceptions of aging, particularly within ethnocultural communities.