bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimized estimation of marine deflection of the vertical from multibeam laser altimeter data of ICESat-2
Authors: Peng Huihui , Liu Xin , Li Zhen , Wei Xuyang , Fan Xin , Guo Jinyun 
Published: August 2024

SUMMARY
Satellite altimetry data, with its increasing density and quality, has become the primary source for marine deflection of the vertical (DOV) and gravity anomaly modelling. Limited by orbital inclinations, the precision of the meridian component of the gridded deflection of the vertical (GDOV) calculated by traditional altimetry satellites is significantly better than that of the prime vertical component, and the excessive precision difference between these two components restricts the inversion precision of marine gravity anomaly model. The study of cross-track deflection of the vertical (CTDOV) is enabled by the multibeam synchronous observation mode of the new laser altimetry satellite, Ice, Cloud and Land Elevation Satellite-2 (ICESat-2). Based on the remove-restore method, residual geoid gradients are first calculated in this paper using three approaches: along-track (A-T), cross-track (C-T) and an integration of along-track and cross-track. Vertical deflections are then computed on a 1′ × 1′ grid using the least squares collocation (LSC) method, and the precision is verified against the SIO V32.1_DOV model. An optimized combination is proposed to address the issue of precision differences between the meridian and prime vertical components, and to enhance the precision of DOV inversion. A new DOV combination is formed by combining the meridian component from along-track deflection of the vertical (ATDOV) with the prime vertical component from cross-track deflection of the vertical (CTDOV) based on the remove-restore method. The Philippine Sea (0°–35°N, 120°–150°E) is selected as the test area to verify the feasibility of the optimized combination. The results indicate that the optimized combination of the meridian and prime vertical components achieved test precision of 2.63 and 3.33 μrad, respectively, when compared against the SIO V32.1_DOV model. The precision gap between the components is effectively narrowed by this approach, which maintains the precision of the meridian component and enhances that of the prime vertical component, thereby achieving optimal inversion precision for gravity anomalies.
Impact of glycan depletion, glycan debranching and increased glycan charge on HIV-1 neutralization sensitivity and immunogenicity
Authors: D’Addabbo Alessio , Tong Tommy , Crooks Emma T , Osawa Keiko , Xu Jiamin , Thomas Alyssa , Allen Joel D , Crispin Max , Binley James M 
Published: August 2024

Abstract
Broadly neutralizing antibodies (bNAbs) isolated from HIV-1 infected donors are vaccine paradigms. These bNAbs recognize envelope glycoprotein trimers that carry 75–90 oligomannose and complex-type glycans. Although bNAbs and their precursors must navigate past glycans, they usually also make some glycan contacts. Glycan-modified vaccines may therefore be useful to initiate and guide bNAb development. Here, we describe two ways to modify Env glycans for possible vaccine use: 1) using a cocktail of glycosidases (termed “NGAF3” (Neuraminidase, β-Galactosidase, N-Acetylglucosaminidase, endoglycosidase F3 (endo F3)) to deplete complex glycans to try to minimize bNAb-glycan clashes and 2) co-expressing β-1,4-galactosyltransferase 1 (B4G) and β-galactoside α-2,6 sialyltransferase 1 (ST6) during Env biosynthesis, creating bNAb-preferred glycan structures. Mass spectrometry revealed that NGAF3 removed glycan heads at 3/7 sites occupied by complex glycans. B4G overexpression resulted in hybrid glycan development whenever complex glycans were closely spaced. The glycan at position 611 in of Env’s gp41 transmembrane subunit was uniquely isolated from the effects of both endo F3 and B4G. B4G and ST6 co-expression increased hybrid and sialylated glycan abundance, reducing glycan complexity. In rabbit vaccinations, B4G + ST6 virus-like particles (VLPs) induced less frequent, weaker titer NAbs, implying that ST6-mediated increased Env charge dampens vaccine antibodies. In some cases, vaccine sera preferentially neutralized B4G + ST6-modified pseudovirus. HIV-1+ donor plasma NAbs were generally more effective against B4G + ST6 modified pseudovirus, suggesting a preference for less complex and/or α-2,6 sialylated Env trimers. Collectively, our data suggest that B4G and ST6 Env modifications are best suited for intermediate or late vaccine shots.
Advancing the future of equitable access to health care: recommendations from international health care leaders
Authors: Boyer Beth , Huber Katie , Zimlichman Eyal , Saunders Robert , McClellan Mark , Kahn Charles , Noach Ryan , Salzberg Claudia 
Published: August 2024

Abstract
Disparities in access to health care are persistent and contribute to poor health outcomes for many populations around the world. Barriers to access are often similar across countries, despite differences in how health systems are structured. Health care leaders can work to address these barriers through bold, evidence-based actions. The Future of Health (FOH), an international community of senior health leaders, collaborated with the Duke-Margolis Institute for Health Policy to identify priority organizational and policy actions needed to improve equitable access to health care through a consensus-building exercise, a targeted literature review, and an expert discussion group. This paper describes four key action areas for health care leaders that FOH members identified as critical to enabling the future of equitable access to health care: ensuring prioritization of and accountability for equitable access to care; establishing comprehensive, organization-wide strategies to address barriers to access; clearly defining and incentivizing improvement on key measures related to reducing disparities in access; and establishing cross-sector partnerships to improve equitable access.
Production of structurally diverse sphingolipids by anaerobic marine bacteria in the euxinic Black Sea water column
Authors: Ding Su , von Meijenfeldt F A Bastiaan , Bale Nicole J , Sinninghe Damsté Jaap S , Villanueva Laura 
Published: August 2024

Abstract
Microbial lipids, used as taxonomic markers and physiological indicators, have mainly been studied through cultivation. However, this approach is limited due to the scarcity of cultures of environmental microbes, thereby restricting insights into the diversity of lipids and their ecological roles. Addressing this limitation, here we apply metalipidomics combined with metagenomics in the Black Sea, classifying and tentatively identifying 1623 lipid-like species across 18 lipid classes. We discovered over 200 novel, abundant, and structurally diverse sphingolipids in euxinic waters, including unique 1-deoxysphingolipids with long-chain fatty acids and sulfur-containing groups. Sphingolipids were thought to be rare in bacteria and their molecular and ecological functions in bacterial membranes remain elusive. However, genomic analysis focused on sphingolipid biosynthesis genes revealed that members of 38 bacterial phyla in the Black Sea can synthesize sphingolipids, representing a 4-fold increase from previously known capabilities and accounting for up to 25% of the microbial community. These sphingolipids appear to be involved in oxidative stress response, cell wall remodeling, and are associated with the metabolism of nitrogen-containing molecules. Our findings underscore the effectiveness of multi-omics approaches in exploring microbial chemical ecology.
Patient and public understanding of antimicrobial resistance: a systematic review and meta-ethnography
Authors: Wojcik Gosha , Afseth Janyne , Fagan Ross , Thomson Fiona , Ring Nicola 
Published: August 2024

Abstract

Objectives
To further develop an understanding of laypeople’s (adult patients and public) beliefs and attitudes toward antimicrobial resistance (AMR) by developing a conceptual model derived from identifying and synthesizing primary qualitative research.

Methods
A systematic search of 12 electronic databases, including CINAHL, MEDLINE, PsycINFO, PubMed and Web of Science to identify qualitative primary studies exploring patient and public understanding of AMR published between 2012 and 2022. Included studies were quality appraised and synthesized using Noblit and Hare’s meta-ethnographic approach and reported using eMERGe guidance.

Results
Thirteen papers reporting 12 qualitative studies were synthesized. Studies reported data from 466 participants aged 18–90 years. Five themes were identified from these original studies: the responsible patient; when words become meaningless; patient–prescriber relationship; past experience drives antibiotic use; and reframing public perception. These themes supported the development of a conceptual model that illustrates the tension between two different assumptions, that is, how can antibiotics be used for the collective good whilst balancing the immediate needs of individual patients.

Conclusions
Findings suggest that AMR is a distinct ethical issue and should not be viewed purely as a prescribing problem. The meta-ethnography-generated conceptual model illustrates many factors affecting the public’s perception of AMR. These include laypeople’s own knowledge, beliefs and attitudes around antibiotic use, the relationship with the healthcare provider and the wider context, including the overwhelming influence of the media and public health campaigns. Future research is needed to explore effective health messaging strategies to increase laypeople’s baseline awareness of AMR as a public threat.
Genomic characterization of carbapenemase-producing Enterobacterales from Dhaka food markets unveils the spread of high-risk antimicrobial-resistant clones and plasmids co-carrying blaNDM and mcr-1.1
Authors: Nisa Tania Tabassum , Sugawara Yo , Hamaguchi Shigeto , Takeuchi Dan , Abe Ryuichiro , Kuroda Eisuke , Morita Masatomo , Zuo Hui , Ueda Akiko , Nishi Isao , Hossain Nowrin , Hasan Md Mahmudul , Siddiqee Mahbubul H , Nakatani Daisaku , Nakata Ken , Akeda Yukihiro 
Published: August 2024

Abstract

Background
The transmission of carbapenemase-producing Enterobacterales (CPE) in the external environment, especially through food, presents a significant public health risk.

Objectives
To investigate the prevalence and genetic characteristics of CPE in food markets of Dhaka, Bangladesh, using WGS.

Methods
CPE isolates were obtained from different food and water samples collected from food markets in the southern part of Dhaka, Bangladesh. The isolates subsequently underwent molecular typing, WGS employing both short- and long-read sequencers, and plasmid analysis.

Results
This study unveiled an extensive spread of CPE, with no significant difference in contamination rates observed in samples (N = 136), including meat (n = 8), fish (n = 5), vegetables (n = 36) or various food-washed water (n = 65) from markets near hospitals or residential areas. Thirty-eight Enterobacterales from 33 samples carried carbapenemase genes (blaNDM-1, -4, -7, blaKPC-2, blaOXA-181 or blaIMI-1). Among these, the high-risk Escherichia coli ST410 clone was the most prevalent and distributed across various locations. Furthermore, the identification of IncHI2 plasmids co-harbouring resistance genes like blaNDM-5 and mcr-1.1, without discernible epidemiological connections, is a unique finding, suggesting their widespread dissemination.

Conclusions
The analysis unveils a dynamic landscape of CPE dissemination in food markets, underscored by the proliferation of novel IncHI2 hybrid plasmids carrying both colistin- and carbapenem-resistance genes. This illuminates the ever-evolving landscape of antimicrobial resistance in Dhaka, urging us to confront its emergent challenges.
IFN-α2 Autoantibody Screening and Functional Evaluation in Viral and Bacterial Infections
Authors: Cockx Maaike , Steels Sophie , Michiels Birthe , Van Elslande Jan , Vermeersch Pieter , Frans Glynis , Claeys Kristl G , Desmet Stefanie , De Munter Paul , Bossuyt Xavier 
Published: August 2024

Abstract

Background
The presence of anti-interferon (IFN)-α2 autoantibodies is a strong indicator of severe disease course during viral infections and is observed in autoimmune diseases (e.g., myasthenia gravis). Detection of these autoantibodies during severe bacterial infections is understudied. Multiple anti-IFN-α2 autoantibody screening assays are available. However, the results do not always correlate with the neutralizing capacity of the autoantibodies.

Methods
Anti-IFN-α2 antibodies were measured by a Luminex-based assay in serum samples from individuals admitted to the intensive care unit infected with influenza (n = 38), invasive bacteria (n = 152), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (n = 52). Anti-IFN-α2 antibodies were also studied in individuals with myasthenia gravis (n = 22) and in healthy individuals (n = 37). Individuals testing positive by Luminex were subsequently tested by enzyme-linked immunosorbent assay (ELISA) and tested for nonspecific reactivity and neutralization.

Results
Three of 16 Luminex-positive samples had nonspecific reactivity, 11/16 were positive by ELISA, and 10/16 had neutralizing activity. Anti-IFN-α2 antibodies were found in individuals infected with SARS-CoV-2 (7/52), influenza (3/38), invasive bacteria [2/152, of which 1 was Legionella pneumophilia and was 1 Escherichia coli (E. coli) (out of 39 E. coli infections)], and in individuals with myasthenia gravis (2/22).

Conclusions
Anti-IFN-α2 autoantibodies were detected in viral infections, myasthenia gravis, and rarely in bacterial infections. ELISA and Luminex screening assays do not give similar results. Nonspecific reactivity and functional assays are necessary to validate the screening test result.
Molecular characterization, antimicrobial resistance and invasion of epithelial cells by Streptococcus agalactiae strains isolated from colonized pregnant women and newborns in Rio de Janeiro, Brazil
Authors: Pimentel Bruna Alves da Silva , Lannes-Costa Pamella Silva , Viana Alice Slotfeldt , Santos Gabriela da Silva , Leobons Maria Beatriz Gerardin Poirot , Ferreira-Carvalho Bernadete Teixeira , Nagao Prescilla Emy 
Published: August 2024

Abstract

Aims
To evaluate the prevalence, molecular characteristics, antimicrobial susceptibility, and epithelial invasion of Streptococcus agalactiae strains isolated from pregnant women and newborns in Rio de Janeiro, Brazil.

Methods and results
A total of 67 S. agalactiae isolates, 48 isolates from pregnant women and 19 from neonates, were analyzed. Capsular type Ia and V were predominant (35.8%/each). The multilocus sequence typing analysis revealed the presence of 19 STs grouped into 6 clonal complexes with prevalence of CC17/40.3% and CC23/34.3%. The lmb and iag virulence genes were found in 100% of isolates. Four S. agalactiae strains, belonging to CC17/ST1249 and CC23/ST23, were able to adhere to A549 respiratory epithelial cells. Antimicrobial resistance was verified mainly to tetracycline (85%), erythromycin (70.8%), and clindamycin (58.3%). Four S. agalactiae isolates were multidrug resistant. The resistance genes tested were found in 92.5% of isolates for tetM, 58.2% for ermB, 28.4% for mefAE, and 10.4% for tetO.

Conclusion
The study showed a high prevalence of virulence and antimicrobial genes in S. agalactiae strains isolated from pregnant women and newborns, supporting the idea that continued surveillance is necessary to identify risk factors and perform long-term follow-up in pregnant women and neonates in Rio de Janeiro.
Data sharing considerations to maximize the use of pathogen biological and genomics resources data for public health
Authors: Holden Nicola J 
Published: August 2024

Abstract
Public sector data associated with health are a highly valuable resource with multiple potential end-users, from health practitioners, researchers, public bodies, policy makers, and industry. Data for infectious disease agents are used for epidemiological investigations, disease tracking and assessing emerging biological threats. Yet, there are challenges in collating and re-using it. Data may be derived from multiple sources, generated and collected for different purposes. While public sector data should be open access, providers from public health settings or from agriculture, food, or environment sources have sensitivity criteria to meet with ethical restrictions in how the data can be reused. Yet, sharable datasets need to describe the pathogens with sufficient contextual metadata for maximal utility, e.g. associated disease or disease potential and the pathogen source. As data comprise the physical resources of pathogen collections and potentially associated sequences, there is an added emerging technical issue of integration of omics ‘big data’. Thus, there is a need to identify suitable means to integrate and safely access diverse data for pathogens. Established genomics alliances and platforms interpret and meet the challenges in different ways depending on their own context. Nonetheless, their templates and frameworks provide a solution for adaption to pathogen datasets.
Precision feeding as a tool to reduce the environmental footprint of pig production systems: a life-cycle assessment
Authors: Llorens Berta , Pomar Candido , Goyette Bernard , Rajagopal Rajinikanth , Andretta Ines , Latorre Maria Angeles , Remus Aline 
Published: August 2024

Abstract
Nitrogen and phosphorus excretion are major sources of environmental contamination in growing–finishing pig operations. Nutrient excretion can be reduced by feeding pigs daily-tailored diets to their estimated nutrient requirements using individual precision feeding (IPF) techniques. This study modeled and evaluated the environmental impact of moving from conventional group 3-phase feeding (CGF) to IPF systems in Quebec, Canada, using life-cycle assessment with SimaPro software. The cradle-to-farm model included inputs and outputs of each subphase: raw materials/feedstuffs production, feed mill processing, transport, animal rearing, and manure management. The model was identical for both treatments in all aspects except for the production of feeds and barn and manure emissions in the growing–finishing phases. All feed ingredients originated from Quebec, simulating agricultural practices using real management data from an average farm in Quebec. Based on observed pig growth data, the CGF and IPF systems were compared in the growing–finishing phase. IPF diets were modeled as the blend of 2 feeds (i.e., A and B), while CGF diets were stablished according to the industry. The evaluated impact categories were global warming potential (GWP), eutrophication potential (EP), and acidification potential (AP). The functional unit was 1 t of feed at the feed mill gate and 1 t of finished pig live weight at the farm gate. A Monte Carlo analysis determined the uncertainty of the growth performance results. Feeding programs were compared using analysis of variance. Corn was associated with elevated GWP and AP impacts, leading to higher impacts for diets with higher corn content. Feed B, which contained 83% corn, resulted in impacts of 645 kg of CO2-eq., 8.53 kg SO2-eq., and 4.89 kg PO4-eq. Diets with higher EP impact had a higher percentage of soybean meal. Feed A contained 25% of this ingredient and had an impact of 608 kg CO2-eq., 6.98 kg SO2-eq., and 5.57 kg PO4-eq. CGF diets had environmental impacts between those of feeds A and B. Compared to CGF, applying IPF programs during the growing–finishing phase decreased GWP by 7.6%, AP by 16.2% and EP by 13.0%. IPF significantly reduced the environmental impact in all categories through the more efficient use of nutritional resources by pigs. IPF could help to improve the sustainability of growing–finishing pig operations in Quebec and likely other regions using corn and soybean-based diets.
Identification of APBB1 as a substrate for anaplastic lymphoma kinase
Authors: Suzuki Yuji , Tsubota Shoma , Kadomatsu Kenji , Sakamoto Kazuma 
Published: August 2024

Abstract
Anaplastic lymphoma kinase (ALK) is a well-known oncogene involved in various malignancies such as anaplastic large cell lymphoma, lung cancer and neuroblastoma. Several substrates for fused ALK have been identified and their biological functions have been described. However, the lack of a comprehensive identification of ALK substrates limits our understanding of the biological roles of receptor ALK. Thus, this study aimed to identify novel ALK substrates and characterize their biological functions. We screened the interactors of the kinase domain of receptor ALK using proximity-dependent biotin identification and identified 43 interactors. We narrowed down the candidates by evaluating whether these interactors were downstream of ALK in a neuroblastoma cell line, NB-1. Amongst these, we identified amyloid beta precursor protein-binding family B member 1 (APBB1) as an ALK downstream molecule involved in NB-1 cell viability. Finally, we assessed the kinase-substrate relationship between ALK and APBB1 and found that ALK phosphorylated multiple tyrosine residues in APBB1 both in-cell and in-tube assays, with tyrosine 269 as a major target. In conclusion, we successfully identified a new substrate for receptor ALK. Our results may help further elucidate the molecular mechanism of ALK downstream signalling in neuroblastoma.
Contributions of T Cell Signaling for Wound Healing
Authors: Meng Lingzhang , Tang Qiang , Zhou Wei , Wei Dalong , Zhao Jingjie , Shen Jiajia , Yang Mingyue , He Siyuan , Huang Shaoang , Qin Yujuan , Song Jian , Luo Liangping , Tang Qianli 
Published: August 2024

Abstract
It has long been known that T cells participate in wound healing; however, the landscape of the signaling derived from T cells in the process of wound healing is still enigmatic. With the advantages of scRNA-seq, in combination with immunofluorescent imaging, we identified activated T cells, cytotoxic T cells (CTLs), exhausting T cells, and Tregs existing in the inflammation phase of wound healing. Further analysis revealed each T cell population possess distinguished signals contributed to wound healing, some are critical for improving the wound healing quality. Besides, this study discovered and validated the existence of exhausting T cells among the T cells accumulated in the skin during wound healing, and the molecular mechanism(s) and contribution of exhausting T cells to wound healing deserve extensive studies in the future.