bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic performance of host protein signatures as a triage test for active pulmonary TB
Authors: Koeppel Lisa , Denkinger Claudia M. , Wyss Romain , Broger Tobias , Chegou Novel N. , Dunty Jill M. , Scott Kerry , Cáceres Tatiana , Dutoit Elloise , Ugarte-Gil Cesar , Nicol Mark , Gotuzzo Eduardo , Corstjens Paul L. A. M. , Geluk Annemieke , Sutherland Jayne , Sigal George B. , Moreau Emmanuel , Albertini Audrey , Mantsoki Anna , Ongarello Stefano , Walzl Gerhard , Fernandez Suarez Marta 
Published: September 2023

ABSTRACT
The current four-symptom screen recommended by the World Health Organization (WHO) is widely used as screen to initiate diagnostic testing for active pulmonary tuberculosis (TB), yet the performance is poor especially when TB prevalence is low. In contrast, more sensitive molecular tests are less suitable for placement at primary care level in low-resource settings. In order to meet the WHO End TB targets, new diagnostic approaches are urgently needed to find the missing undiagnosed cases. Proteomics-derived blood host biomarkers have been explored because protein detection technologies are suitable for the point-of-care setting and could meet cost targets. This study aimed to find a biomarker signature that fulfills WHO’s target product profile (TPP) for a TB screening. Twelve blood-based protein biomarkers from three sample populations (Vietnam, Peru, and South Africa) were analyzed individually and in combinations via advanced statistical methods and machine learning algorithms. The combination of I-309, SYWC and kallistatin showed the most promising results to discern active TB throughout the data sets meeting the TPP for a triage test in adults from two countries (Peru and South Africa). The top-performing individual markers identified at the global level (I-309 and SYWC) were also among the best-performing markers at country level in South Africa and Vietnam. This analysis clearly shows that a host protein biomarker assay is feasible in adults for certain geographical regions based on one or two biomarkers with a performance that meets minimal WHO TPP criteria.
Evolution of the T4 phage virion is driven by selection pressure from non-bacterial factors
Authors: Majewska Joanna , Miernikiewicz Paulina , Szymczak Aleksander , Kaźmierczak Zuzanna , Goszczyński Tomasz M. , Owczarek Barbara , Rybicka Izabela , Ciekot Jarosław , Dąbrowska Krystyna 
Published: September 2023

ABSTRACT

Bacteriophages colonize animal and human bodies, propagating on sensitive bacteria that are symbionts, commensals, or pathogens of animals and humans. T4-like phages are dependent on abundant symbionts such as
Escherichia coli
, commonly present in animal and human gastrointestinal (GI) tracts. Bacteriophage T4 is one of the most complex viruses, and its intricate structure, particularly the capsid head protecting the phage genome, likely contributes substantially to the overall phage fitness in diverse environments. We investigated how individual head proteins—gp24, Hoc, and Soc—affect T4 phage survival under pressure from non-bacterial factors. We constructed a panel of T4 phage variants defective in these structural proteins: T4∆Soc, T4∆24byp24, T4∆Hoc∆Soc, T4∆Hoc∆24byp24, T4∆Soc∆24byp24, and T4∆Hoc∆Soc∆24byp24 (byp = bypass). These variants were investigated for their sensitivity to selected environmental conditions relevant to the microenvironment of the GI tract, including pH, temperature, and digestive enzymes. The simple and “primitive” structure of the phage capsid (∆24byp24) was significantly less stable at low pH and more sensitive to inactivation by digestive enzymes, and the simultaneous lack of gp24 and Soc resulted in a notable decrease in phage activity at 37°C. Gp24 was also found to be highly resistant to thermal and chemical denaturation. Thus, gp24, which was acquired relatively late in evolution, seems to play a key role in T4 withstanding environmental conditions, including those related to the animal/human GI tract, and Soc is a molecular glue that enhances this protective effect.

IMPORTANCE
Bacteriophages are important components of animal and human microbiota, particularly in the gastrointestinal tract, where they dominate the viral community and contribute to shaping microbial balance. However, interactions with bacterial hosts are not the only element of the equation in phage survival—phages inhabiting the GI tract are constantly exposed to increased temperature, pH fluctuations, or digestive enzymes, which raises the question of whether and how the complex structure of phage capsids contributes to their persistence in the specific microenvironment of human/animal bodies. Here we address this phage-centric perspective, identifying the role of individual head proteins in T4 phage survival in GI tract conditions. The selection pressure driving the evolution of T4-like phages could have come from the external environment that affects phage virions with increased temperature and variable pH; it is possible that in the local microenvironment along the GI tract, the phage benefits from stability-protecting proteins.
Interferon-independent processes constrain measles virus cell-to-cell spread in primary human airway epithelial cells
Authors: Durnell Lorellin A. , Hippee Camilla E. , Cattaneo Roberto , Bartlett Jennifer A. , Singh Brajesh K. , Sinn Patrick L. 
Published: September 2023

ABSTRACT

Amplification of measles virus (MeV) in human airway epithelia may contribute to its extremely high contagious nature. We use well-differentiated primary cultures of human airway epithelial cells (HAE) to model
ex vivo
how MeV spreads in human airways. In HAE, MeV spreads cell-to-cell for 3–5 days, but then, infectious center growth is arrested. What stops MeV spread in HAE is not understood, but interferon (IFN) is known to slow MeV spread in other
in vitro
and
in vivo
models. Here, we assessed the role of type I and type III IFN in arresting MeV spread in HAE. The addition of IFN-β or IFN-λ1 to the medium of infected HAE slowed MeV infectious center growth, but when IFN receptor signaling was blocked, infectious center size was not affected. In contrast, blocking type-I IFN receptor signaling enhanced respiratory syncytial virus spread. HAE were also infected with MeV mutants defective for the V protein. The V protein has been demonstrated to interact with both MDA5 and STAT2 to inhibit activation of innate immunity; however, innate immune reactions were unexpectedly muted against the V-defective MeV in HAE. Minimal innate immunity activation was confirmed by deep sequencing, quantitative RT-PCR, and single-cell RNA-seq analyses of the transcription of IFN and IFN-stimulated genes. We conclude that in HAE, IFN-signaling can contribute to slowing infectious center growth; however, IFN-independent processes are most important for limiting cell-to-cell spread.

Importance
Fundamental biological questions remain about the highly contagious measles virus (MeV). MeV amplifies within airway epithelial cells before spreading to the next host. This final step likely contributes to the ability of MeV to spread host-to-host. Over the course of 3–5 days post-infection of airway epithelial cells, MeV spreads directly cell-to-cell and forms infectious centers. Infectious center formation is unique to MeV. In this study, we show that interferon (IFN) signaling does not explain why MeV cell-to-cell spread is ultimately impeded within the cell layer. The ability of MeV to spread cell-to-cell in airway cells without appreciable IFN induction may contribute to its highly contagious nature. This study contributes to the understanding of a significant global health concern by demonstrating that infectious center formation occurs independent of the simplest explanation for limiting viral transmission within a host.
Age variability and decadal time-averaging in oyster reef death assemblages
Authors: Durham Stephen R. , Dietl Gregory P. , Hua Quan , Handley John C. , Kaufman Darrell , Clark Cheryl P. 
Published: September 2023

Abstract
Using paleoecological data to inform resource management decisions is challenging without an understanding of the ages and degrees of time-averaging in molluscan death assemblage (DA) samples. We illustrate this challenge by documenting the spatial and stratigraphic variability in age and time-averaging of oyster reef DAs. By radiocarbon dating a total of 630 oyster shells from samples at two burial depths on 31 oyster reefs around Florida, southeastern United States, we found that (1) spatial and stratigraphic variability in DA sample ages and time-averaging is of similar magnitude, and (2) the shallow oyster reef DAs are among the youngest and highest-resolution molluscan DAs documented to date, with most having decadal-scale time-averaging estimates, and sometimes less. This information increases the potential utility of the DAs for habitat management because DA data can be placed in a more specific temporal context relative to real-time monitoring data. More broadly, the results highlight the potential to obtain decadal-scale resolution from oyster bioherms in the fossil record.
Frequency of postoperative cognitive dysfunction after non-cardiac surgery and its impact on functional outcomes: protocol for a systematic review
Authors: Roldan Yetiani , Khattak Shahzaib , Samari Saif , Chan Olsen , Pancucci Meghan , Sritharan Praveen , Jamil Yasser , Marcucci Maura 
Published: September 2023

IntroductionOlder surgical candidates are at increased risk of a phenomenon known as postoperative cognitive dysfunction (POCD). Several studies have looked at the incidence of POCD at different time points following surgery, using different study methods. Fewer have assessed whether changes in cognition after surgery are attributable to surgery and how they impact patient function and quality of life. The aim of this systematic review is to summarise and appraise studies addressing any of the following research questions (RQs): (RQ1) what is the frequency of POCD after non-cardiac surgery?; (RQ2) is non-cardiac surgery associated with an increased risk of cognitive decline?; (RQ3) is POCD after non-cardiac surgery associated with patient-important outcomes?Methods and analysisThis protocol adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols guidelines. Three electronic databases (MEDLINE, PsycINFO and EMBASE) will be systematically searched from their inception date. Identified studies will be screened by two reviewers for eligibility using Covidence, and data will be extracted into a standardised electronic form. We will evaluate methodological quality of included studies using the Quality In Prognosis Studies and its adaptation to the overall prognosis question, and the CLARITY risk of bias for cohort and case–control studies. For RQ1, we will estimate an average POCD frequency at different time points by performing a meta-analysis of included studies when appropriate. For RQ2 and RQ3, we will extract and meta-analyse the effect measures for the association of surgery with cognitive decline when compared with the non-surgical comparator, and association of cognitive changes with functional changes, quality of life and other patient-important outcomes based on available evidence. We will narratively summarise and discuss the different methods implemented in the existing studies to answer the three RQs, and when meta-analysis is deemed infeasible, we will qualitatively report the results of the included studies.Ethics and disseminationThis project involves the collection and analysis of data from previously published studies and therefore does not require ethics approval. We plan to present the findings of this research project at peer-reviewed conferences and publish the results in peer-reviewed journals.PROSPERO registration numberCRD42022370674.
Social isolation, depression, nutritional status and quality of life during COVID-19 among Chinese community-dwelling older adults: a cross-sectional study
Authors: Wang Xinxin , Zhang Chengrui , Luan Wei 
Published: September 2023

ObjectiveThis survey investigated the relationship between social isolation, depression, nutritional status and quality of life among community-dwelling older adults during COVID-19.DesignThis was a cross-sectional survey study.SettingCommunities in Pudong New Area, Shanghai, China that have contracted with Renji Hospital, affiliated with Shanghai Jiao Tong University School of Medicine.ParticipantsFrom May to July 2022, 406 community-dwelling older adults were selected by convenience sampling in Shanghai, China.Primary and secondary outcome measuresThe Lubben Social Network Scale, Geriatric Depression Scale, 36-item Short Form Health Survey Scale and risk assessment of malnutrition were used in older adults. Mediation models were constructed to determine the mediating role of depression and nutritional status on social isolation and quality of life among older adults.ResultsThe prevalence of social isolation among older adults in the community was 44.3%. The total social isolation score in community-dwelling older adults was positively associated with the total malnutrition risk and quality of life scores, and negatively associated with depression (p<0.01). Logistic regression demonstrated that living alone, loss of families or friends during COVID-19 and depression were risk factors for social isolation among community-dwelling older adults (p<0.05). Social isolation could directly affect the quality of life (β=0.306). In addition, depression (β=0.334) and nutritional status (β=0.058) had a significant mediating effect on the relationship between social isolation and quality of life.ConclusionsOur findings showed that the prevalence of social isolation among older adults increased during COVID-19. Depression and nutritional status played parallel mediating roles on the effect of social isolation on quality of life. Community workers and healthcare providers should develop intervention plans to improve the status of social isolation in older adults, eliminating existing and ongoing adverse effects.
A closer look at Toronto's water quality control design criteria for bioretention cells
Authors: Rowe Elizabeth , Guo Yiping , Li Zhong 
Published: September 2023

Bioretention cells in the Toronto region are usually sized to accommodate runoff from the 90th percentile storm, which has a depth of about 25 mm. This research examines the water quality control performance and cost of bioretention cells sized to satisfy alternative design criteria ranging from 5 to 50 mm. The long-term average runoff-capture efficiencies provided by representative bioretention cells are determined, and their capital as well as operation and maintenance costs are estimated. Results indicate that the current design criterion of 25 mm is probably too high and not cost-efficient. In fact, above some threshold levels, little improvement in runoff-capture and pollutant removal performances may be achieved if the design criterion is increased further, but cost would still linearly increase. Presented here is a methodology that can be used to properly consider both the performance and cost of bioretention cells for establishing a more cost-efficient design criterion. It is shown that a more cost-efficient design criterion for Toronto could be lower than the current one, and significant cost savings can be realized if a lower design criterion is implemented. Some inappropriate ways of quantifying the effective volume of storage provided by bioretention cells are also identified in this paper.
Assembly and Characterization of Length-Sorted, Aligned Boron Nitride/Carbon Nanotube Thin Film Composites Via Slow Vacuum Filtration
Authors: Shapturenka Pavel , Fagan Jeffrey 
Published: September 2023

Globally aligned single-wall carbon nanotubes (SWCNTs) are a promising, scalable platform for studying fundamental physical phenomena and an important vehicle for optoelectronic device applications. Recent work by Rust et al. [1] has identified nanotube length as an important mediating factor in the degree and scale of SWCNT alignment via slow vacuum filtration (SVF).
Building on this work and that of Walker et al. [2,3], we explore the co-assembly of length-sorted SWCNTs and boron nitride nanotubes (BNNTs) atop polycarbonate track-etched membranes. BNNTs have recently gained interest as a chirality-agnostic, wide-bandgap material for encapsulation, insulation, thermal/mechanical robustness, and visible-light transparency, while also having a similar high aspect ratio morphology, making them an exceptional and alignable host matrix for individualized CNT species. To prepare such hybrid assemblies, a polymer-assisted, depletion-based method was first used to length-sort different diameter SWCNT (alkane filled electric-arc, CoMoCAT, metallic-sorted Tuball), and BNNT nanotube populations. Thereafter, we investigated the impacts of tube lengths, relative BN/C fraction, mass loading, and presence of a global director force on the multi-scale assembly behavior. A combination of birefringence microscopy and polarized Raman spectroscopy probed and identified trends in global and local ordering under these conditions.
[1] Rust, C., Shapturenka, P., Spari, M., Jin, Q., Li, H., Bacher, A., Guttmann, M., Zheng, M., Adel, T., Hight Walker, A. R., Fagan, J. A., & Flavel, B. S. (2022). The Impact of Carbon Nanotube Length and Diameter on their Global Alignment by Dead-End Filtration. Small (forthcoming).
[2] Walker, J. S., Fagan, J. A., Biacchi, A. J., Kuehl, V. A., Searles, T. A., Hight Walker, A. R., & Rice, W. D. (2019). Global Alignment of Solution-Based Single-Wall Carbon Nanotube Films via Machine-Vision Controlled Filtration. Nano Letters, 19(10), 7256–7264.
[3] Walker, J. S., Macdermid, Z. J., Fagan, J. A., Kolmakov, A., Biacchi, A. J., Searles, T. A., Walker, A. R. H., & Rice, W. D. (2022). Dependence of Single‐Wall Carbon Nanotube Alignment on the Filter Membrane Interface in Slow Vacuum Filtration. Small, 18, 2105619.
(Invited) Microenvironment Responsiveness of Defect Photoluminescence of Locally Functionalized Single-Walled Carbon Nanotubes and Its Sensing Applications
Authors: Shiraki Tomohiro , Niidome Yoshiaki , Fujigaya Tsuyohiko 
Published: September 2023

Photoluminescence (PL) of single-walled carbon nanotubes (SWCNTs) in the near infrared (NIR) region is applicable to advanced optical applications such as bio-imaging and sensing. Local chemical functionalization (slight amount of chemical modification) of SWCNTs has been developed to introduce sp3 carbon defects in the sp2 carbon network of the tube walls for the luminescent defect formation.[1-3] The resultant locally functionalized SWCNTs (lf-SWCNTs) show defect PL (E
11* PL) with red-shifted wavelengths and increased quantum yields compared to original E
11 PL of pristine SWCNTs. For lf-SWCNTs, molecularly designed modifier molecules have enabled the defect PL wavelength modulation[4] and the sensing function creation.[5,6]
Recently, we have reported the unique microenvironment responsiveness of defect PL of lf-SWCNTs; namely, the greater wavelength shifts of E
11* PL than E
11 PL by dielectric effects[7] and the PL shifting behavior modulation based on the chemical structure difference of the functionalized sites and the exciton localization effects[8] were observed. The microenvironment responsiveness of the defect PL was applied to the biological sensing application development.[9] To investigate protein detection/recognition functions of lf-SWCNTs, we introduced an avidin-biotin interaction with a selective and strong binding fashion at the functionalized sites of lf-SWCNTs. The lf-SWCNTs tethering biotin groups (lf-SWCNTs-b) were synthesized through diazonium chemistry, followed by its subsequent-modification. When neutravidin was mixed with a lf-SWCNTs-b solution, E
11* PL peak was red-shifted, indicating the higher polarity environment formation by the neutravidin adsorption on lf-SWCNTs-b. When avidin or streptavidin was used, wavelength shifting behaviors of E
11* PL of lf-SWCNTs-b were clearly changed depending on the used avidin derivatives. The results indicate the different polarity environment formation deriving from structural differences of each avidin derivative. Moreover, the detection signal enhancement was observed in a film device using lf-SWCNTs-b. Therefore, lf-SWCNTs have a high potential for development of advanced protein detection/recognition systems using NIR PL.
[1] T. Shiraki et al. Acc. Chem. Res., 53, 1846 (2020). [2] S. Tretiak et al., Acc. Chem. Res., 53, 1791(2020) [3] Y. Wang et al. Nat. Rev. Chem., 3, 375 (2019). [4] T. Shiraki et al. ACS Nano, DOI: 10.1021/acsnano.2c09897 (2022). [5] T. Shiraki et al. Chem. Commun., 52, 12972 (2016). [6] S. Kruss et al, Angew. Chem. Int. Ed., 59, 17732 (2020). [7] T. Shiraki et al. Chem. Commun., 55, 3662 (2019). [8] T. Shiraki et al. J. Phys. Chem. C, 125, 12758 (2021). [9] T. Shiraki et al. Nanoscale, 14, 13090 (2022).

Figure 1
(Invited) Mechanically Interlocked Derivatives of SWNTs: What, Why, How, and What for?
Authors: Perez Emilio M 
Published: September 2023

In the last few years, the mechanical bond has been added to the chemistry toolbox for SWNT modification.[1] In this presentation, I will first discuss the characteristics of the mechanical bond that make it appealing for SWNTs. I will then describe the potential advantages of making mechanically-interlocked derivatives of SWNTs (MINTs), as compared to covalent or classic supramolecular derivatives of SWNTs, and go on to explain our approach for the synthesis of MINTs.[2,3] Finally, I will illustrate with examples how the making of MINTs can contribute to modifying the surface properties of SWNTs,[4] modulating their electronic properties,[5] and linking them to functional molecular fragments.[6,7]
References
[1] A. López-Moreno, J. Villalva, E. M. Pérez, “Mechanically interlocked derivatives of carbon nanotubes: synthesis and potential applications” Chem. Soc. Rev. 2022, 51, 9433-9444.
[2] A. de Juan, Y. Pouillon, L. Ruiz-González, A. Torres-Pardo, S. Casado, N. Martín, A. Rubio, E. M. Pérez, Angew. Chem., Int. Ed. 2014, 53, 5394-5400.
[3] E. M. Pérez, Chem. Eur. J. 2017, 23, 12681-12689.
[4] A. López-Moreno, B. Nieto-Ortega, M. Moffa, A. de Juan, M. M. Bernal, J. P. Fernández-Blázquez, J. J. Vilatela, D. Pisignano, E. M. Pérez, ACS Nano 2016, 10, 8012-8018.
[5] M. Blanco, B. Nieto-Ortega, A. de Juan, M. Vera-Hidalgo, A. López-Moreno, S. Casado, L. R. González, H. Sawada, J. M. González-Calbet, and E. M. Pérez, Nat. Commun. 2018, 9, 2671.
[6] S. Moreno-Da Silva, J. I. Martínez, A. Develioglu, B. Nieto-Ortega, L. de Juan-Fernández, L. Ruiz-Gonzalez, A. Picón, S. Oberli, P. J. Alonso, D. Moonshiram, E. M. Pérez, E. Burzurí, J. Am. Chem. Soc. 2021, 143, 21286-21293.
[7] W. Zhang, M. Guillén-Soler, S. Moreno-Da Silva, A. López-Moreno, M. L. Ruiz-González, M. Giménez, E. M. Pérez Chem. Sci., 2022, 13, 9706-9712.

Figure 1