bluuebunny/crossref_metadata_2025 huggingface dataset:
Models of palliative care for under-served populations in high-income countries: a scoping review protocol
Authors: Dadich Ann , van der Kruk Shannen , Cornell Victoria , Nobes Karen , Gunn Kate , Eliott Jaklin , Laurence Caroline
Published: September 2023

Objective:

The objective of this scoping review is to describe models of palliative care for under-served populations in high-income countries, defined as adults of culturally and linguistically diverse communities, low socioeconomic status, and/or residing in rural areas.

Introduction:

Models of palliative care are processual, referring to the way palliative care services are delivered as people experience a condition, injury, or event. The aim of these models is to ensure people get the right care, at the right time, by the right team, in the right place. Evidence suggests there is a wide variety of models of palliative care, but what is not known is how these models can vary to meet the needs of under-served populations.

Inclusion criteria:

This scoping review will consider articles that focus on models of palliative care for under-served populations, irrespective of sex, age, or primary diagnosis.

Methods:

MEDLINE (Ovid), Embase (Ovid), PsycINFO (Ovid), Emcare (Ovid), CINAHL (EBSCOhost), and Scopus will be searched for articles, irrespective of language, published from 2014. Two independent reviewers will screen titles and abstracts, followed by a full-text review of potentially relevant articles. Discrepancies will be reconciled with another reviewer. Two independent reviewers will extract data from included articles using a data extraction tool developed for this review. Results will be tabulated and/or presented diagrammatically, as well as summarized to explicitly address the objective of the review.

Review registration:

Open Science Framework osf.io/x4ky3
Influence of external circuitry on CF4 breakdown process in capacitively coupled plasma
Authors: Chen Zhaoyu , Xu Jingwen , Wang Hongyu , Wu Hao , Jiang Wei , Zhang Ya
Published: September 2023

Capacitively coupled plasma (CCP) tools are crucial for etching, deposition, and cleaning processes in the semiconductor industry. A comprehensive understanding of their discharge characteristics is vital for the advancement of chip processing technology. In this study, the influence of external circuitry on the breakdown process was investigated under the CF4 discharge system, with a particular focus on challenges presented by the nonlinear nature of the plasma. The results demonstrated that the external circuit significantly affects the discharge process by altering the electric field distribution as well as modifying the electron density and temperature of the plasma. By incorporating the matching circuit, stable discharge was achieved at reduced voltage levels. During breakdown, a substantial increase in the capacitance of the discharge chamber is induced by the formation of the sheath, which alters the amplitude of the electrical signal within the external circuit. The breakdown characteristics are significantly influenced by the capacitance of the matching network. Breakdowns with distinctive characteristics can be achieved by selectively choosing different capacitors. Furthermore, a shift in the CF4 discharge mode at different pressures under the external circuit model and the alteration in the discharge mode affect the electrical properties of the plasma in the matched circuit. These findings could be used to optimize the discharge of CCP and its applications, including surface treatment, material synthesis, and environmental remediation.
Plasma functionalization mechanism to modify isocyanate groups on multiwalled carbon nanotubes
Authors: Ogawa Daisuke , Nakamura Keiji
Published: September 2023

This article reports a possible functionalization mechanism of isocyanate (NCO) groups on multiwalled carbon nanotubes (CNTs) with low-temperature plasma. The mechanism was clarified according to the analysis with two plasmas generated with the gas mixture of (1) nitrogen and carbon dioxide and (2) nitrogen and oxygen. We analyzed the mechanism through optical emission spectroscopy from these plasmas and the NCO functionalization ratio measured with the fluorescent method after plasma exposure over CNTs. The optical emission gave us information on the quantitative analysis of the gas species of atomic nitrogen (N), atomic oxygen (O), and carbon monoxide (CO) and the qualitative analysis of carbon nitride (CN) species in the plasma. Compared with our results from the gas species in the plasma and the NCO functionalization ratio on CNTs, CO and CN species in the gas phase in plasma are less likely to contribute to forming NCO groups on CNTs. Rather, the equal densities of atomic nitrogen and oxygen species in the plasma could be effective in forming NCO groups on the CNT surface: the NCO groups should form by N, O, and carbon (C) species on the CNT surface. The groups likely build up gradually by N, O, and C individually reaching a CNT surface, or the NCO radicals form in the gas phase and then attach to the CNT surface.
Enhancing biocompatibility, mechanical properties, and corrosion resistance of laser cladding β-TiNb coatings
Authors: Zheng Yu , Xu Peng , Li Long , Liu Qibin , Guo Shanzhu
Published: September 2023

β-type TiNb biomedical alloys have received quite significant attention rooted in their excellent comprehensive performance. Nevertheless, their practical application is hampered by relatively poor performance and biological toxicity. Herein, TixNb alloy coatings were fabricated on the surface of Ti6Al4V (TC4) by laser cladding to evade the property-toxicity trade-off. Biocompatibility and mechanical properties, as well as the corrosion resistance of the TixNb alloy coatings, were discussed. The results show that the microstructure is composed of β grains and a small amount of the α″ martensite phase uniformly precipitated around them. The rapid melting process of laser cladding promotes the formation of the β phase, which improves the microhardness and wear resistance of the coating. However, the corrosion resistance was significantly improved due to the formation of the densification and stabilization of the passive films formed on the coating’s surface. Benefiting from the superior wettability and the biologically active sites of Ti and Nb on the alloy surface, MG-63 cells adhered to the coating’s surfaces in spindle shape and proliferated rapidly in cell experiments, denoting that the coatings have better biocompatibility than TC4. Hereby, the obtained TixNb laser cladding coatings with excellent mechanical properties and biocompatibility have extensive application prospects in the field of orthopedic biomaterials.
Lumped element models of sound conduction in the human ear: A systematic review
Authors: Wils Irina , Geerardyn Alexander , Putzeys Tristan , Denis Kathleen , Verhaert Nicolas
Published: September 2023

Lumped element models facilitate investigating the fundamental mechanisms of human ear sound conduction. This systematic review aims to guide researchers to the optimal model for the investigated parameters. For this purpose, the literature was reviewed up to 12 July 2023, according to the PRISMA guidelines. Seven models are included via database searching, and another 19 via cross-referencing. The quality of the models is assessed by comparing the predicted middle ear transfer function, the tympanic membrane impedance, the energy reflectance, and the intracochlear pressures (ICPs) (scala vestibuli, scala tympani, and differential) with experimental data. Regarding air conduction (AC), the models characterize the pathway from the outer to the inner ear and accurately predict all six aforementioned parameters. This contrasts with the few existing bone conduction (BC) models that simulate only a part of the ear. In addition, these models excel at predicting one observable parameter, namely, ICP. Thus, a model that simulates BC from the coupling site to the inner ear is still lacking and would increase insights into the human ear sound conduction. Last, this review provides insights and recommendations to determine the appropriate model for AC and BC implants, which is highly relevant for future clinical applications.
Auditory masking in odobenid and otariid carnivores
Authors: Jones Ryan A. , Sills Jillian M. , Synnott Mitzi , Mulsow Jason , Williams Rob , Reichmuth Colleen
Published: September 2023

As the only living species within the odobenid lineage of carnivores, walruses (Odobenus rosmarus) have no close relatives from which auditory information can be extrapolated. Sea lions and fur seals in the otariid lineage are the nearest evolutionary outgroup. To advance understanding of odobenid and otariid hearing, we conducted behavioral testing with two walruses and one California sea lion (Zalophus californianus). Detection thresholds for airborne sounds were measured from 0.08 to at least 16 kHz in ambient noise conditions and then re-measured in the presence of octave-band white masking noise. Walruses were more sensitive than the sea lion at lower frequencies and less sensitive at higher frequencies. Critical ratios for the walruses ranged from 20 dB at 0.2 kHz to 32 dB at 10 kHz, while critical ratios for the sea lion ranged from 16 dB at 0.2 kHz to 35 dB at 32 kHz. The masking values for these species are comparable to one another and to those of terrestrial carnivores, increasing by about 3 dB per octave with increasing frequency. Despite apparent differences in hearing range and sensitivity, odobenids and otariids have a similar ability to hear signals in noisy conditions.
Efficient design of neural networks for the classification of acoustic spectra
Authors: Paul Vlad S. , Nelson Philip A.
Published: September 2023

A previous paper by Paul and Nelson [(2021). J. Acoust. Soc. Am. 149(6), 4119–4133] presented the application of the singular value decomposition (SVD) to the weight matrices of multilayer perceptron (MLP) networks as a pruning strategy to remove weight parameters. This work builds on the previous technique and presents a method of reducing the size of a hidden layer by applying a similar SVD algorithm. Results show that by reducing the neurons in the hidden layer, a significant amount of training time is saved compared to the algorithm presented in the previous paper while no or little accuracy is being lost compared to the original MLP model.
B-CLEAN-SC: CLEAN-SC for broadband sources
Authors: Goudarzi Armin
Published: September 2023

This paper presents B-CLEAN-SC, a variation of CLEAN-SC for broadband sources. In contrast to CLEAN-SC, which “deconvolves” the beamforming map for each frequency individually, B-CLEAN-SC processes frequency intervals. Instead of performing a deconvolution iteration at the location of the maximum level, B-CLEAN-SC performs it at the location of the over-frequency-averaged maximum to improve the location estimation. The method is validated and compared to standard CLEAN-SC on synthetic cases and real-world experiments for broad- and narrowband sources. It improves the source reconstruction at low and high frequencies and suppresses noise, while it only increases the need for memory and not computational effort.
Misoriented high-entropy iridium ruthenium oxide for acidic water splitting
Authors: Hu Chun , Yue Kaihang , Han Jiajia , Liu Xiaozhi , Liu Lijia , Liu Qiunan , Kong Qingyu , Pao Chih-Wen , Hu Zhiwei , Suenaga Kazu , Su Dong , Zhang Qiaobao , Wang Xianying , Tan Yuanzhi , Huang Xiaoqing
Published: September 2023

Designing an efficient catalyst for acidic oxygen evolution reaction (OER) is of critical importance in manipulating proton exchange membrane water electrolyzer (PEMWE) for hydrogen production. Here, we report a fast, nonequilibrium strategy to synthesize quinary high-entropy ruthenium iridium-based oxide (M-RuIrFeCoNiO
2
) with abundant grain boundaries (GB), which exhibits a low overpotential of 189 millivolts at 10 milliamperes per square centimeter for OER in 0.5 M H
2
SO
4
. Microstructural analyses, density functional calculations, and isotope-labeled differential electrochemical mass spectroscopy measurements collectively reveal that the integration of foreign metal elements and GB is responsible for the enhancement of activity and stability of RuO
2
toward OER. A PEMWE using M-RuIrFeCoNiO
2
catalyst can steadily operate at a large current density of 1 ampere per square centimeter for over 500 hours. This work demonstrates a pathway to design high-performance OER electrocatalysts by integrating the advantages of various components and GB, which breaks the limits of thermodynamic solubility for different metal elements.
Bioaerosols are the dominant source of warm-temperature immersion-mode INPs and drive uncertainties in INP predictability
Authors: Cornwell Gavin C. , McCluskey Christina S. , Hill Thomas C. J. , Levin Ezra T. , Rothfuss Nicholas E. , Tai Sheng-Lun , Petters Markus D. , DeMott Paul J. , Kreidenweis Sonia , Prather Kimberly A. , Burrows Susannah M.
Published: September 2023

Ice-nucleating particles (INPs) are rare atmospheric aerosols that initiate primary ice formation, but accurately simulating their concentrations and variability in large-scale climate models remains a challenge. Doing so requires both simulating major particle sources and parameterizing their ice nucleation (IN) efficiency. Validating and improving model predictions of INP concentrations requires measuring their concentrations delineated by particle type. We present a method to speciate INP concentrations into contributions from dust, sea spray aerosol (SSA), and bioaerosol. Field campaign data from Bodega Bay, California, showed that bioaerosols were the primary source of INPs between −12° and −20°C, while dust was a minor source and SSA had little impact. We found that recent parameterizations for dust and SSA accurately predicted ambient INP concentrations. However, the model did not skillfully simulate bioaerosol INPs, suggesting a need for further research to identify major factors controlling their emissions and INP efficiency for improved representation in models.
The efficacy of Facebook’s vaccine misinformation policies and architecture during the COVID-19 pandemic
Authors: Broniatowski David A. , Simons Joseph R. , Gu Jiayan , Jamison Amelia M. , Abroms Lorien C.
Published: September 2023

Online misinformation promotes distrust in science, undermines public health, and may drive civil unrest. During the coronavirus disease 2019 pandemic, Facebook—the world’s largest social media company—began to remove vaccine misinformation as a matter of policy. We evaluated the efficacy of these policies using a comparative interrupted time-series design. We found that Facebook removed some antivaccine content, but we did not observe decreases in overall engagement with antivaccine content. Provaccine content was also removed, and antivaccine content became more misinformative, more politically polarized, and more likely to be seen in users’ newsfeeds. We explain these findings as a consequence of Facebook’s system architecture, which provides substantial flexibility to motivated users who wish to disseminate misinformation through multiple channels. Facebook’s architecture may therefore afford antivaccine content producers several means to circumvent the intent of misinformation removal policies.
Toward an increased reliability of chemical bonding assignment in insulating samples by x-ray photoelectron spectroscopy
Authors: Greczynski Grzegorz , Pshyk Oleksandr , Hultman Lars
Published: September 2023

X-ray photoelectron spectroscopy (XPS) spectra from solid samples are conventionally referenced to the spectrometer Fermi level (FL). While, in the case of metallic samples, alignment of the sample and the spectrometer FLs can be directly verified from the measured Fermi edge position, thus allowing to assess the surface electrical potential, this is not a workable option for insulators. When applied, it generates a large spread in reported binding energy values that often exceed involved chemical shifts. By depositing insulating amorphous alumina thin films on a variety of conducting substrates with different work functions, we show not only that FL referencing fails but also that the Al
2
O
3
energy levels align instead to the vacuum level, as postulated in the early days of XPS. Based on these model experiments that can be repeated for all sorts of thin-film insulators, a solution to the binding energy reference problem is proposed for reliable assessment of chemical bonding.
ATP1A3 as a target for isolating neuron-specific extracellular vesicles from human brain and biofluids
Authors: You Yang , Zhang Zhengrong , Sultana Nadia , Ericsson Maria , Martens Yuka A. , Sun Min , Kanekiyo Takahisa , Ikezu Seiko , Shaffer Scott A. , Ikezu Tsuneya
Published: September 2023

Neuron-derived extracellular vesicles (NDEVs) are potential biomarkers of neurological diseases although their reliable molecular target is not well established. Here, we demonstrate that ATPase Na
+
/K
+
transporting subunit alpha 3 (ATP1A3) is abundantly expressed in extracellular vesicles (EVs) isolated from induced human neuron, brain, cerebrospinal fluid, and plasma in comparison with the presumed NDEV markers NCAM1 and L1CAM by using super-resolution microscopy and biochemical assessments. Proteomic analysis of immunoprecipitated ATP1A3
+
brain-derived EVs shows higher enrichment of synaptic markers and cargo proteins relevant to Alzheimer’s disease (AD) compared to NCAM1
+
or LICAM
+
EVs. Single particle analysis shows the elevated amyloid-β positivity in ATP1A3
+
EVs from AD plasma, providing better diagnostic prediction of AD over other plasma biomarkers. Thus, ATP1A3 is a reliable target to isolate NDEV from biofluids for diagnostic research.
Integrated BATF transcriptional network regulates suppressive intratumoral regulatory T cells
Authors: Shan Feng , Cillo Anthony R. , Cardello Carly , Yuan Daniel Y. , Kunning Sheryl R. , Cui Jian , Lampenfeld Caleb , Williams Asia M. , McDonough Alexandra P. , Pennathur Arjun , Luketich James D. , Kirkwood John M. , Ferris Robert L. , Bruno Tullia C. , Workman Creg J. , Benos Panayiotis V. , Vignali Dario A. A.
Published: September 2023

Human regulatory T cells (Tregs) are crucial regulators of tissue repair, autoimmune diseases, and cancer. However, it is challenging to inhibit the suppressive function of Tregsfor cancer therapy without affecting immune homeostasis. Identifying pathways that may distinguish tumor-restricted Tregsis important, yet the transcriptional programs that control intratumoral Treggene expression, and that are distinct from Tregsin healthy tissues, remain largely unknown. We profiled single-cell transcriptomes of CD4+T cells in tumors and peripheral blood from patients with head and neck squamous cell carcinomas (HNSCC) and those in nontumor tonsil tissues and peripheral blood from healthy donors. We identified a subpopulation of activated Tregsexpressing multiple tumor necrosis factor receptor (TNFR) genes (TNFR+Tregs) that is highly enriched in the tumor microenvironment (TME) compared with nontumor tissue and the periphery. TNFR+Tregsare associated with worse prognosis in HNSCC and across multiple solid tumor types. Mechanistically, the transcription factor BATF is a central component of a gene regulatory network that governs key aspects of TNFR+Tregs. CRISPR-Cas9–mediatedBATFknockout in human activated Tregsin conjunction with bulk RNA sequencing, immunophenotyping, and in vitro functional assays corroborated the central role of BATF in limiting excessive activation and promoting the survival of human activated Tregs. Last, we identified a suite of surface molecules reflective of the BATF-driven transcriptional network on intratumoral Tregsin patients with HNSCC. These findings uncover a primary transcriptional regulator of highly suppressive intratumoral Tregs, highlighting potential opportunities for therapeutic intervention in cancer without affecting immune homeostasis.
The matrix protein of respiratory syncytial virus suppresses interferon signaling via RACK1 association
Authors: Cao Jingjing , Shi Menghan , Zhu Lina , Li Xiangzhi , Li Aiying , Wu Shwu-Yuan , Chiang Cheng-Ming , Zhang Youming
Published: September 2023

Respiratory syncytial virus (RSV) is a frequent cause of respiratory illness among pediatric and elderly populations. The severity of the respiratory disease is determined, in part, by RSV virulence and the host immune response, especially type I interferon (IFN) production. Using proteomics for the identification of partner proteins associated with RSV-encoded matrix (M) protein in transiently M-expressed and RSV-infected cells, we identified many M-interacting proteins involved in diverse biological processes including cell stress and innate immune response, highlighting M protein as a novel antagonist of IFN-β potentially accounting for limited IFN production in RSV-infected epithelial cells. To clarify the M antagonistic mechanism, we focused on M-interacting receptor of activated C kinase 1 (RACK1), which is an adaptor protein and a negative regulator of IRF3/7. Knockdown of RACK1 with small-interfering RNA attenuated the M-suppressed IFN-β response leading to increased IFN-β production and reduced RSV genome replication, confirming RACK1 as a critical host factor for efficient RSV infection. Our finding unravels an immune-intervening effect of RSV M protein on IFN response and further identifies RACK1 as a promising target for antiviral therapy.

IMPORTANCE

Respiratory syncytial virus (RSV) matrix (M) protein is indispensable for virion assembly and release. It is localized to the nucleus during early infection to perturb host transcription. However, the function of RSV M protein in other cellular activities remains poorly understood. In this study, several interferon response-associated host factors, including RACK1, were identified by proteomic analysis as RSV M interactors. Knockdown of RACK1 attenuates RSV-restricted IFN signaling leading to enhanced host defense against RSV infection, unraveling a role of M protein in antagonizing IFN response via association with RACK1. Our study uncovers a previously unrecognized mechanism of immune evasion by RSV M protein and identifies RACK1 as a novel host factor recruited by RSV, highlighting RACK1 as a potential new target for RSV therapeutics development.
Effects on exocytosis by two HSV-1 mutants unable to block autophagy
Authors: Waisner Hope , Lasnier Sarah , Suma Sreenath Muraleedharan , Kalamvoki Maria
Published: September 2023

Herpes simplex virus 1 (HSV-1) is a prominent human pathogen that manipulates host responses to support the infection. HSV-1 infection triggers an increased release of extracellular vesicles (EVs) through the CD63 biogenesis pathway that contains the DNA sensor STING and exerts an antiviral effect on recipient cells. However, it is currently unknown how different viral proteins influence EV production. The viral proteins ICP0 and ICP34.5 are important for blocking host responses, including autophagy. Considering that autophagy and exocytosis are interwoven processes regulating intercellular communication, we sought to determine changes in EV biogenesis after infection with a ΔICP0 and a ΔICP34.5 virus that displayed defects in blocking autophagy compared with wild-type virus. ΔICP34.5 virus induced a greater release of EVs as compared to HSV-1(F), whereas ΔICP0 virus did not. EVs released by ΔICP34.5-infected cells differ in origin from those released by HSV-1(F)-infected cells as they contained markers of microvesicles and apoptotic bodies, but lacked major tetraspanins (CD63 or CD81) or lysosomal membrane proteins. EVs released by ΔICP0-infected cells are generated through the CD63 biogenesis pathway activated by HSV-1(F) but displayed reduced amounts of cargo. EVs released by these mutant viruses triggered robust innate immunity gene expression in uninfected recipient cells that exceeded host responses due to infection by these viruses. Overall, we have characterized how infection with viruses unable to block autophagy affects EV biogenesis, and their effect on recipient cells.

IMPORTANCE

Pathogens often hijack extracellular vesicle (EV) biogenesis pathways for assembly, egress, and cell-to-cell spread. Herpes simplex virus 1 (HSV-1) infection stimulated EV biogenesis through a CD63 tetraspanin biogenesis pathway and these EVs activated antiviral responses in recipient cells restricting the infection. HSV-1 inhibits autophagy to evade the host, and increased CD63 exocytosis could be a coping mechanism, as CD63 is involved in both cargo delivery to lysosomes during autophagy and exocytosis. We analyzed exocytosis after infection with two HSV-1 mutants, a ΔICP34.5 and a ΔICP0, that could not inhibit autophagy. Unlike HSV-1(F), neither of these viruses stimulated increased EV biogenesis through the CD63 pathway. ΔICP34.5 stimulated production of microvesicles and apoptotic bodies that were CD63-negative, while ΔICP0 displayed an overall reduced production of EVs. These EVs activated innate immunity gene expression in recipient cells. Given the potential use of these mutants for therapeutic purposes, the immunomodulatory properties of EVs associated with them may be beneficial.
Direct interaction with the BRD4 carboxyl-terminal motif (CTM) and TopBP1 is required for human papillomavirus 16 E2 association with mitotic chromatin and plasmid segregation function
Authors: Prabhakar Apurva T. , James Claire D. , Fontan Christian T. , Otoa Raymonde , Wang Xu , Bristol Molly L. , Yeager Calvin , Hill Ronald D. , Dubey Aanchal , Wu Shwu-Yuan , Chiang Cheng-Ming , Morgan Iain M.
Published: September 2023

During the human papillomavirus 16 (HPV16) life cycle, the E2 protein binds simultaneously to the viral genome and host chromatin throughout mitosis, ensuring viral genomes reside in daughter cell nuclei following cell division. Previously, we demonstrated that CK2 phosphorylation of E2 on serine 23 promotes interaction with TopBP1, and that this interaction is required for optimum E2 mitotic chromatin association and plasmid segregation function. Others have implicated BRD4 in mediating the plasmid segregation function of E2 and we have demonstrated that there is a TopBP1-BRD4 complex in the cell. We therefore further investigated the role of the E2-BRD4 interaction in mediating E2 association with mitotic chromatin and plasmid segregation function. Using a combination of immunofluorescence and our novel plasmid segregation assay in U2OS and N/Tert-1 cells stably expressing a variety of E2 mutants, we report that direct interaction with the BRD4 carboxyl-terminal motif (CTM) and TopBP1 is required for E2 association with mitotic chromatin and plasmid segregation. We also identify a novel TopBP1-mediated interaction between E2 and the BRD4 extra-terminal domain
in vivo
. In addition, we demonstrate for the first time that E2 plasmid segregation function occurs in human foreskin keratinocytes immortalized by HPV16. Overall, the results demonstrate that direct interaction with TopBP1 and the BRD4 CTM is required for E2 mitotic chromatin association and plasmid segregation function. Disruption of this complex offers therapeutic options for targeting segregation of viral genomes into daughter cells, potentially combating HPV16 infections and cancers that retain episomal genomes.

Importance

Human papillomavirus 16 (HPV16) is a causative agent in around 3%–4% of all human cancers, and currently, there are no anti-viral therapeutics available for combating this disease burden. In order to identify new therapeutic targets, we must increase our understanding of the HPV16 life cycle. Previously, we demonstrated that an interaction between E2 and the cellular protein TopBP1 mediates the plasmid segregation function of E2, allowing distribution of viral genomes into daughter nuclei following cell division. Here, we demonstrate that E2 interaction with an additional host protein, BRD4, is also essential for E2 segregation function, and that BRD4 exists in a complex with TopBP1. Overall, these results enhance our understanding of a critical part of the HPV16 life cycle and presents several therapeutic targets for disruption of the viral life cycle.
Independent loss events of a functional
tetherin
gene in galliform birds
Authors: Krchlíková Veronika , Lotke Rishikesh , Haußmann Isabell , Reinišová Markéta , Kučerová Dana , Pecnová Ľubomíra , Ungrová Lenka , Hejnar Jiří , Sauter Daniel , Elleder Daniel
Published: September 2023

The restriction factor tetherin (bone marrow stromal cell antigen 2) is an interferon-inducible protein preventing the release of newly formed viral particles from infected cells. Tetherin displays antiviral activity against a broad range of enveloped viruses, including retroviruses. While tetherin orthologs have been identified in several mammalian species, little is known about its expression and activity in non-mammalian vertebrates, including birds. We have previously described antiviral activity of chicken (
Gallus gallus
) tetherin against the prototypical avian retrovirus avian sarcoma and leukosis virus (ASLV). Here, we report the loss of functional tetherin orthologs in several galliform birds, including turkey (
Meleagris gallopavo
) and Mikado pheasant (
Syrmaticus mikado
). In both species, the
tetherin
coding sequence acquired inactivating mutations, including an in-frame stop codon and frameshifting deletions. Similar to the chicken tetherin ortholog, reconstituted turkey and Mikado pheasant tetherins restricted ASLV and HIV-1 indicating antiviral activity of the ancestor protein. Previous work revealed the presence of the
TMCC(aT
) gene in close proximity to tetherin, encoding a protein with tetherin-like structure in multiple vertebrates. Intriguingly, ectopic overexpression of chicken and turkey TMCC(aT) proteins in human cells decreased total HIV-1 yield. In contrast to tetherin, however, TMCC(aT) did not specifically restrict virion release, suggesting distinct antiviral mechanisms. In line with this, IFNα stimulation did not reduce the release of ASLV particles from infected turkey cells. Overall, our data describe the loss of functional
tetherin
genes in several galliform species and identify an antiviral activity of the related TMCC(aT) protein that is mechanistically different from that of tetherin.

IMPORTANCE

Birds represent important hosts for numerous viruses, including zoonotic viruses and pathogens with the potential to cause major economic losses to the poultry industry. Viral replication and transmission can be inhibited or blocked by the action of antiviral restriction factors (RFs) encoded by the host. One well-characterized RF is tetherin, a protein that directly blocks the release of newly formed viral particles from infected cells. Here, we describe the evolutionary loss of a functional tetherin gene in two galliform birds, turkey (
Meleagris gallopavo
) and Mikado pheasant (
Syrmaticus mikado
). Moreover, we demonstrate that the structurally related protein TMCC(aT) exerts antiviral activity in several birds, albeit by a mechanism different from that of tetherin. The evolutionary scenario described here represents the first documented loss-of-tetherin cases in vertebrates.
A disintegrin and metalloproteinase domain 9 facilitates SARS-CoV-2 entry into cells with low ACE2 expression
Authors: Melano Ivonne , Cheng Wei-Chung , Kuo Li-Lan , Liu Yuag-Meng , Chou Yu Chi , Hung Mien-Chie , Lai Michael M. C. , Sher Yuh-Pyng , Su Wen-Chi
Published: September 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the Coronavirus disease-19 (COVID-19) pandemic, utilizes angiotensin-converting enzyme 2 (ACE2) as a receptor for virus infection. However, the expression pattern of ACE2 does not coincide with the tissue tropism of SARS-CoV-2, hinting that other host proteins might be involved in facilitating SARS-CoV-2 entry. To explore potential host factors for SARS-CoV-2 entry, we performed an arrayed shRNA screen in H1650 and HEK293T cells. Here, we identified a disintegrin and a metalloproteinase domain 9 (ADAM9) protein as an important host factor for SARS-CoV-2 entry. Our data showed that silencing ADAM9 reduced virus entry, while its overexpression promoted infection. The knockdown of ADAM9 decreased the infectivity of the variants of concern tested—B.1.1.7 (alpha), B.1.617.2 (delta), and B.1.1.529 (omicron). Furthermore, mechanistic studies indicated that ADAM9 is involved in the binding and endocytosis stages of SARS-CoV-2 entry. Through immunoprecipitation experiments, we demonstrated that ADAM9 binds to the S1 subunit of the SARS-CoV-2 Spike. Additionally, ADAM9 can interact with ACE2, and co-expression of both proteins markedly enhances virus infection. Moreover, the enzymatic activity of ADAM9 facilitates virus entry. Our study reveals an insight into the mechanism of SARS-CoV-2 virus entry and elucidates the role of ADAM9 in virus infection.

IMPORTANCE

COVID-19, an infectious respiratory disease caused by SARS-CoV-2, has greatly impacted global public health and the economy. Extensive vaccination efforts have been launched worldwide over the last couple of years. However, several variants of concern that reduce the efficacy of vaccines have kept emerging. Thereby, further understanding of the mechanism of SARS-CoV-2 entry is indispensable, which will allow the development of an effective antiviral strategy. Here, we identify a disintegrin and metalloproteinase domain 9 (ADAM9) protein as a co-factor of ACE2 important for SARS-CoV-2 entry, even for the variants of concern, and show that ADAM9 interacts with Spike to aid virus entry. This virus-host interaction could be exploited to develop novel therapeutics against COVID-19.
Nanotopography by chromatic confocal microscopy of the endothelium in Fuchs endothelial corneal dystrophy, pseudophakic bullous keratopathy and healthy corneas
Authors: Vaitinadapoulé Hanielle , Poinard Sylvain , He Zhiguo , Pascale-Hamri Alina , Thomas Justin , Gain Philippe , Thuret Jean-Yves , Mascarelli Frédéric , Thuret Gilles
Published: September 2023

Aim

To investigate the interest of chromatic confocal microscopy (CCM) to characterise guttae in Fuchs endothelial corneal dystrophy (FECD).

Methods

Descemet’s membranes (DM) were obtained during endothelial keratoplasty in patients with FECD and pseudophakic bullous keratopathy (PBK). They were compared with healthy samples obtained from body donation to science. Samples were fixed in 0.5% paraformaldehyde and flat mounted. Surface roughness of DMs was quantified using CCM and the AltiMap software that provided the maximum peak (Sp) and valley (Sv) heights, the mean square roughness (Rq) and the asymmetry coefficient (Ssk).

Results

The physiological roughness of healthy samples was characterised by an Rqof 0.12±0.05 µm, which was two times rougher than in PBK (Rq=0.06±0.03 µm), but both were still flat with a symmetrical distribution between peaks and valleys (Sskclose to 0, npeaks=nvalleys), smaller than 1 µm. In FECD, the maximum peak height was 5.10±2.40 µm, up to 5.8 and 8.3 times higher than the control and PBK, respectively. The maximum valley depth was half than the peak (2.28±0.89 µm). The surface with guttae was very rough (Rq=0.45±0.14 µm) and the Ssk=1.84± 0.43 µm, greater than 0, confirms an asymmetric surface with high peaks and low valleys (npeaks>nvalleys). Moreover, the CCM provided quantitative parameters allowing to distinguish different types of guttae from different patients.

Conclusions

CCM is an innovative approach to describe and quantify different morphologies of guttae. It could be useful to analyse the different stages of FECD and define subgroups of patients.
Effectiveness of thoracic spine manipulation for upper quadrant musculoskeletal disorders: protocol for a systematic review
Authors: Thoomes Erik , Tilborghs Gus , Heneghan Nicola R , Falla Deborah , de Graaf Marloes
Published: September 2023

Introduction

Upper quadrant musculoskeletal disorders (UQMD), comprising of cranial, cervical, shoulder and upper extremity disorders, are among the most frequently reported disorders in clinical practice. Thoracic high velocity low amplitude thrust (Tx-HVLAT) manipulation is a form of conservative management recommended in systematic reviews as an effective treatment option for aspects of UQMD disorders such headache, shoulder pain and lateral elbow pain. However, no recent systematic reviews have assessed the effectiveness across UQMD. Therefore, this systematic review aims to update the current evidence on the effectiveness of Tx-HVLAT for patients with UQMD on (1) patient-reported outcomes, (2) performance measures or (3) psychosocial outcomes.

Methods and analysis

The Cochrane Controlled Trials Register, MEDLINE, EMBASE, CINAHL, PEDro and Index to Chiropractic Literature will be searched from inception using Medical Subject Headings (MeSH), Thesaurus and/or free-text words. Combinations will be made based on localisation, disorder, intervention and design. Following guidelines as advised by the Cochrane Back Review Group, published randomised controlled trials will be included. Two review authors will independently assess the risk of bias (ROB) using the Cochrane Back Review Group’s recommended ROB2 tool and will independently extract the data using a standardised data extraction form. Overall quality of the evidence will be evaluated using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) method. For continuous data, we will calculate standardised mean differences with 95% CIs. For dichotomous outcomes, relative risks and 95% CIs will be calculated. Where possible we will present a subgroup analysis by disorder. For pooling, a random-effects model will be used.

Ethics and dissemination

Ethics approval is not required for this systematic review. The study findings will be submitted to a relevant peer-reviewed journal for dissemination and presented at relevant conferences.

PROSPERO registration number

CRD42023429996.
Pain catastrophising in Chinese patients with breast cancer during postoperative chemotherapy: a qualitative study
Authors: Zhang Yanting , Long Wenjia , Wang Hongying , Wang Jingyi , Tang Chen , Ma Jing , Zhong Jun
Published: September 2023

Objective

To investigate the pain catastrophising in patients with breast cancer during postoperative chemotherapy.

Methods

Objective sampling method was used to select patients with breast cancer who underwent breast surgery and received chemotherapy in a third-class hospital of Wuhan from October to December 2022 through semi-structured interview. The interview data were sorted out and analysed by content analysis method.

Results

A total of 11 patients were interviewed and five categories were summarised: (1) Physical memory of pain; (2) the special meaning of time; (3) disease treatment and prognosis; (4) interpersonal communication and coping; (5) personal behaviour and growth.

Conclusion

Patients with breast cancer have adverse pain experience during postoperative chemotherapy. The evaluation and screening of psychological variables such as pain catastrophising should be strengthened to provide new ideas for pain management.
Potential benefits of therapeutic drug monitoring for beta-lactam antibiotics in augmented renal clearance patients: a case report
Authors: El-Haffaf Ibrahim , Laverdière Jean , Albert Martin , Marsot Amélie , Williamson David
Published: September 2023

Augmented renal clearance (ARC) is commonly described in critically ill patients, making drug pharmacokinetics even harder to predict in this population. This case report displays the value of therapeutic drug monitoring (TDM) of piperacillin/tazobactam (PTZ) in this population. We identified two patients with ARC and intermittent administration of PTZ who took part in a prospective, descriptive study conducted at Hôpital du Sacré-Cœur de Montréal. Both had plasma samples drawn at peak, middle, and end of their dosing intervals of PTZ. Minimal inhibitory concentrations (MICs) of 4 and 8 mg/L were chosen to evaluate therapeutic target attainment at middle and end of dosing interval. The first patient was a 52-year-old male with a renal clearance rate estimated at 147 mL/min who received 3.375 g PTZ every 6 h. The second patient, a 49-year-old male, had an estimated renal clearance rate of 163 mL/min and received the same regimen. Both patients had piperacillin concentrations above the target MICs at middle of the dosing interval, but they failed to reach a trough concentration above 8 mg/L. The present case report showcases two patients with subtherapeutic PTZ concentrations despite strict following of local administration protocols. This suboptimal administration could not only lead to treatment failure, but also to the selection and growth of resistant pathogens. Implementing TDM would offer the possibility to adjust drug regimens in real-time and prevent situations like these from occurring.
Bell inequalities and quantum entanglement in weak gauge boson production at the LHC and future colliders
Authors: Fabbrichesi Marco , Floreanini Roberto , Gabrielli Emidio , Marzola Luca
Published: September 2023

Quantum entanglement of weak interaction gauge bosons produced at colliders can be explored by computing the corresponding polarization density matrix. To this end, we consider the Higgs boson decays $$H\rightarrow W W^*$$

H
→
W

W
∗

and $$H\rightarrow Z Z^*$$

H
→
Z

Z
∗

, in which $$W^*$$

W
∗

and $$Z^*$$

Z
∗

are off-shell states, and the WW, WZ and ZZ di-boson production in proton collisions. The polarization density matrix of the di-boson state is determined by the amplitude of the production process and can be experimentally reconstructed from the angular distribution of the momenta of the final states into which the gauge bosons decay. We show that a suitable instance of the Bell inequality is violated in $$H\rightarrow Z Z^*$$

H
→
Z

Z
∗

to a degree that can be tested at the LHC with future data. The same Bell inequality is violated in the production of WW and ZZ boson pairs for invariant masses above 900 GeV and scattering angles close to $$\pi /2$$

π
/
2

in the center of mass frame. LHC data in this case are not sufficient to establish the violation of the Bell inequality. We also analyze the prospects for detecting Bell inequality violations in di-boson final states at future $$e^+e^-$$

e
+

e
-

and muon colliders. A further observable that provides a lower bound on the amount of polarization entanglement in the di-boson system is computed for each of the examined processes. The analytic expressions for the polarization density matrices are presented in full in an Appendix. We also provide the unitary matrices required in the optimization procedure necessary in testing the Bell inequalities.
VisActive: Visual-concept-based Active Learning for Image Classification under Class Imbalance
Authors: Khaleel Mohammed , Idris Azeez , Tavanapong Wallapak , Pratt Jacob R. , Oh Junghwan , C. de Groen Piet
Published: September 2023

Active learning methods recommend the most informative images from a large unlabeled dataset for manual labeling. These methods improve the performance of an image classifier while minimizing manual labeling efforts. We propose VisActive, a visual-concept-based active learning method for image classification under class imbalance. VisActive learns a visual concept, a generalized representation that holds the most important image characteristics for class prediction, and then recommends for each class four sets of unlabeled images with different visual concepts to increase the diversity and enlarge the training dataset. Experimental results on four datasets show that VisActive outperforms the state-of-the-art deep active learning methods.
A Review of Stability in Topic Modeling: Metrics for Assessing and Techniques for Improving Stability
Authors: Hosseiny Marani Amin , Baumer Eric P. S.
Published: September 2023

Topic modeling includes a variety of machine learning techniques for identifying latent themes in a corpus of documents. Generating an exact solution (i.e., finding global optimum) is often computationally intractable. Various optimization techniques (e.g., Variational Bayes or Gibbs Sampling) are employed to generate topic solutions approximately by finding local optima. Such an approximation often begins with a random initialization, which leads to different results with different initializations. The term “stability” refers to a topic model’s ability to produce solutions that are partially or completely identical across multiple runs with different random initializations. Although a variety of work has been done analyzing, measuring, or improving stability, no single paper has provided a thorough review of different stability metrics nor of various techniques that improved the stability of a topic model. This paper fills that gap and provides a systematic review of different approaches to measure stability and of various techniques that are intended to improve stability. It also describes differences and similarities between stability measures and other metrics (e.g., generality, coherence). Finally, the paper discusses the importance of analyzing both stability and quality metrics to assess and to compare topic models.
A Survey of Privacy Attacks in Machine Learning
Authors: Rigaki Maria , Garcia Sebastian
Published: September 2023

As machine learning becomes more widely used, the need to study its implications in security and privacy becomes more urgent. Although the body of work in privacy has been steadily growing over the past few years, research on the privacy aspects of machine learning has received less focus than the security aspects. Our contribution in this research is an analysis of more than 45 papers related to privacy attacks against machine learning that have been published during the past seven years. We propose an attack taxonomy, together with a threat model that allows the categorization of different attacks based on the adversarial knowledge, and the assets under attack. An initial exploration of the causes of privacy leaks is presented, as well as a detailed analysis of the different attacks. Finally, we present an overview of the most commonly proposed defenses and a discussion of the open problems and future directions identified during our analysis.
Electrodeposition of Carbon from CO2 in Room-Temperature Ionic Liquid Triethylpentylphosphonium Bis(trifluoromethanesulfonyl)imide
Authors: Tchorap-Yamamoto Shoma , Suzuki Yuta , Tanaka Seiya , Kobatake Hidekazu , Goto Takuya
Published: September 2023

The conversion of CO2 to solid carbon by the electrochemical method is an attractive process as a CO2 recycling technology, but the electrolyte has been limited to high-temperature molten salts. In this study, the electrodeposition of solid carbon from CO2 on an Ag substrate in triethylpentylphosphonium bis(trifluoromethanesulfonyl)imide at room temperature and 1 atm CO2 atmosphere was investigated. Cyclic voltammetry with multiple cycles revealed that the three potential steps causing reduction, oxidation, and reduction current are important for the carbon electrodeposition from CO2. Based on the cyclic voltammogram, potentiostatic electrolysis was performed in the three potential steps. Consequently, the Ag substrate was covered with a black film because of the electrodeposited solid carbon. Raman spectroscopy, scanning electron microscopy, and transmission electron microscopy revealed that the deposits were composed of the electrodeposited solid carbon and nanometer-size silver particles coming from the Ag substrate. From the experimental results, we propose a model of the electrochemical formation mechanism of solid carbon from CO2 on the Ag substrate. This study shows that the electrochemical method has the potential to convert CO2 into valuable carbonaceous materials with optimized electrochemical parameters, even at room temperature, and that this technique will contribute to developing a carbon-circulation society.