bluuebunny/crossref_metadata_2025 huggingface dataset:
Speciation and species: a process perspective
Authors: Dupré John
Published: August 2024

This perspective article proposes that we should think of speciation in the context of a general processual ontology, in which organisms and lineages are seen as central, interdependent processes. It explains what is implied by process ontology with the example of the organism, to illustrate that processes can be persistent individuals, though generally requiring active stabilization. It then explores the idea that speciation should be seen as a bifurcation of a lineage. The relevant notion of species, as a temporal part of an evolving lineage, is narrower than the most inclusive basal taxonomic unit, so speciation in this sense is not applicable to all organisms. The lineage as concrete process is an evolved entity, and hence organisms pre-existed lineages and may still exist outside them.
Transitioning an In-Person Survey of Older Adults to Multimode Data Collection
Authors: Wiencrot Anna , O’Doherty Katie , Lawrence Daniel , Walsh Sara , Satorius Jennifer , Sedlak Lauren , Pudelek Kelly , O’Keefe Kaitlyn , Zepeda Evelyn , Park Hanvit , Hoffmann Joscelyn , You Hannah , McClintock Martha , Smith Stephen
Published: August 2024

Objectives

The first 3 rounds of the National Social Life, Health, and Aging Project (NSHAP) were in-person. Preparing for Round Four (R4), NSHAP began developing ways to collect complex questionnaire and biomeasure data remotely. R4 was scheduled to begin in 2020, but due to the coronavirus pandemic, NSHAP delayed R4 data collection and instead conducted a study on respondents’ experiences during the pandemic, as well as pretests to strengthen NSHAP’s remote data collection capability. This paper describes the methodology, results, and lessons learned from these efforts, which were undertaken as a bridge between NSHAP’s all-in-person past and multimode future.

Methods

The coronavirus disease 2019 (COVID-19) Study was a multimode survey of NSHAP respondents to assess the impact of the pandemic. The multimode approach allowed evaluation of the feasibility of using different modes of data collection with older adults. NSHAP adapted its in-person questionnaire for phone and web administration and conducted pretests of the full phone questionnaire and sections of the web questionnaire. The project developed and tested a “BioBox,” a kit containing all the supplies and instructions for respondents to self-collect biomeasures remotely. The BioBox was tested through an in-lab and in-home pilot, followed by 2 larger-scale pretests.

Results

The COVID-19 Study and pretests achieved NSHAP respondent participation in remote questionnaire and biomeasure collection, despite being accustomed to fully in-person data collection.

Discussion

Our findings and experiences will inform the collection of NSHAP data in future rounds and could inform other panel studies of older adults considering multimode data collection.
Capturing Successful Aging in Daily Life: Exploring the Intensive Longitudinal Findings from a US National Sample
Authors: Tse Dwight C K , Finley Kelsey P , Crawford Linzi F , Nakamura Jeanne
Published: August 2024

Background and Objectives

Thus far, successful aging has been conceptualized and operationalized as a relatively static construct. Investigating daily successful aging provides a dynamic approach highlighting how successful aging can be achieved through everyday actions, giving older adults a stronger sense of control over their lives.

Research Design and Methods

We used 8-day diary data from MIDUS 2’s US national sample of older adults (N=716, Mage[SD]=68.80[6.45]). Participants reported daily physical symptoms, functioning, and engagement in life (collectively, successful aging indicators), alongside daily stressors and positive events. We also correlated personal mean and standard deviation of the indicators with one-time measures of health and well-being.

Results

Intra-class correlation revealed substantial within-person variability in successful aging indicators. These indicators were associated with daily stressors and positive events. One-time health and well-being indicators were positively associated with personal mean levels of successful aging, although their correlations with personal standard deviations were less consistent.

Discussion and Implications

Intra-individual variations in successful aging as everyday symptoms, functioning, and engagement with life are observable among a national sample of older adults, challenging the static view of successful aging and, instead, emphasizing the need to understand “micro-level” contributors of successful aging.
A new automated procedure to obtain reliable moment tensor solutions of small to moderate earthquakes (3.0 ≤ M ≤ 5.5) in the Bayesian framework
Authors: Halauwet Yehezkiel , Afnimar  , Triyoso Wahyu , Vackář Jiří , Daryono Daryono , Supendi Pepen , Daniarsyad Gatut , Simanjuntak Andrean V H , Pranata Bayu , Narwadan Herlina A A M , Hakim Muhammad L
Published: August 2024

The complete catalogue of moment tensor (MT) solutions is essential for a wide range of research in solid earth science. However, the number of reliable MT solutions for small to moderate earthquakes (3.0 ≤ M ≤ 5.5) is limited due to uncertainties arising from data and theoretical errors. In this study, we develop a new procedure to enhance the resolvability of MT solutions and provide more reliable uncertainty estimates for these smaller to moderate earthquakes. This procedure is fully automatic and efficiently accounts for both data and theoretical errors through two sets of hybrid linear–non-linear Bayesian inversions. In the inversion process, the covariance matrix is estimated using an empirical approach: the data covariance matrix is derived from the pre-event noise and the theoretical covariance matrix is derived from the residuals of the initial solution. We conducted tests using synthetic data generated from the 3-D velocity model and interference from background seismic noise. The tests found that using a combination of the non-Toeplitz data covariance matrix and the Toeplitz theoretical covariance matrix improves the solution and its uncertainties. Test results also suggest that including a theoretical covariance matrix when analysing MT in complex tectonic regions is essential, even if we have the best 1D velocity model. The application to earthquakes in the northern region of the Banda Arc resulted in the first published Regional Moment Tensor (RMT) catalogue, containing more than three times the number of trusted solutions compared to the Global Centroid Moment Tensor (GCMT) and the Indonesian Agency for Meteorology Climatology and Geophysics Moment Tensor (BMKG-MT) catalogue. The comparison shows that the trusted solutions align well with the focal mechanism of the GCMT and BMKG-MT, as well as with the maximum horizontal stress of the World Stress Map, and tectonic conditions in the study area. The newly obtained focal mechanisms provide several key findings: (i) they confirm that the deformation in the northern and eastern parts of Seram Island is influenced by oblique intraplate convergence rather than by the subduction process; (ii) they validate the newly identified Amahai Fault with a greater number of focal mechanisms and (iii) they reveal an earthquake Mw 4.7 with the same location and source mechanism 6 yr before the 2019 Ambon-Kairatu earthquake (Mw 6.5) which occurred on a previously unidentified fault.
How loss of nature through clear-cutting forestry affects well-being
Authors: Nesbakken Solvor , Rønningen Grete Eide , Torp Steffen
Published: August 2024

The United Nations declares that the global degradation of ecosystems represents a danger to human health. Deterioration of forests is one of several threats against the natural systems. The aim of this exploratory study was to investigate people’s experiences with clear-cutting and how it had affected their health and well-being. Qualitative data from six people who valued forest ecosystems were collected through semi-structured interviews and analyzed in accordance with Graneheim and Lundman’s qualitative content analysis (Graneheim, U. H. and Lundman, B. (2004) Qualitative content analysis in nursing research: concepts, procedures and measures to achieve trustworthiness. Nurse Education Today, 24, 105–112). Clear-cutting was not regarded as an environment-friendly forestry method. The interviewees described emotional reactions such as grief and poor mental well-being when beloved forests were clear-felled. The grief was partly because of a personal loss of place and recreation area that was important for their physical and emotional well-being. Another part was grief on behalf of nature itself, that is, the loss of habitats of animals and plants and a worsening of the global climate. The interviewees held that emotions related to loss of nature were insufficiently communicated in public discourse. They felt powerless and unable to influence forestry because of what they experienced as an impenetrable industry. Clear-cutting of forests may result in poor well-being among people who value forest ecosystems. More focus on planetary health is needed, including healthy public policy promoting forest management that considers people’s need for nature experiences and possible ecological grief when forests are totally and abruptly cleared.
Endoscopic Skipping, Stricturing, and Penetrating Complications in Crohn’s Disease on Tandem Ileo-colonoscopy and Cross-sectional Imaging: A Retrospective Cohort Study
Authors: Solitano Virginia , Vuyyuru Sudheer Kumar , Aruljothy Achuthan , Alkhattabi Maan , Zou Joshua , Beaton Melanie , Gregor Jamie , Kassam Zahra , Sedano Rocio , Marshall Harry , Ramsewak Darryl , Sey Michael , Jairath Vipul
Published: August 2024

Background

Crohn’s disease (CD) is characterized by discontinuous inflammation. Failure to identify skipping lesions of the terminal ileum (TI) or transmural changes can lead to incorrect management.

Methods

Eligible adult patients with CD undergoing ileo-colonoscopy and computed tomography enterography or magnetic resonance enterography within 6 months. We determined the prevalence of endoscopic skipping (normal ileum on colonoscopy but proximal small bowel inflammation on cross-sectional imaging), skip lesions (discontinuous inflammation along the gastrointestinal tract identified on cross-sectional imaging), stricturing, and penetrating complications.

Results

Among 202 patients, 45 (22.3%) had endoscopic skipping proximal to TI intubation. Fifty patients (24.5%) had small bowel skip lesions, primarily in the ileum. Strictures were identified in 34 patients (16.8%) through both imaging and ileo-colonoscopy, in 21 patients (10.4%) solely through cross-sectional imaging, and in 3 patients (1.5%) solely through ileo-colonoscopy. Approximately 36.2% of stricturing cases would be missed without cross-sectional imaging. Penetrating complications, including abscesses (2.5%) and various fistula types (4.9%), were detected in 15 (7.4%) patients.

Conclusions

Ileo-colonoscopy missed detection of active CD in approximately one-fifth of cases due to more proximal disease location. Stricturing disease might be missed in more than a third of cases if cross-sectional imaging is not performed.
Enhancing Sensitivity in Detecting Severe Fever With Thrombocytopenia Syndrome Virus: Development of a Reverse Transcription–Droplet Digital Polymerase Chain Reaction
Authors: Zhang Yuanyuan , Tian Wen , Zhang Shuai , Lin Ling , Song Chuan , Liu Yuanni , Xu Yanli , Zhang Ligang , Geng Shuying , Li Xin , Wang Xi , Chen Zhihai , Zhang Wei
Published: August 2024

Severe fever with thrombocytopenia syndrome (SFTS) is a highly fatal disease. Droplet digital polymerase chain reaction (ddPCR) presents unparalleled sensitivity and enables absolute quantification of viral load. In this prospective study, we enrolled 111 patients with SFTS and collected 259 continuous samples. Our findings unveil a robust reverse transcription (RT)–ddPCR method for SFTS with a limit of detection of 2.46 copies/µL (95% CI, 1.50–11.05), surpassing the sensitivity of RT–quantitative polymerase chain reaction at 103.29 copies/µL (95% CI, 79.69–216.35). Longitudinal cohort analysis revealed significantly higher RT-ddPCR detection rates at days 10 to 11, 13 to 14, and ≥15 of the disease course as compared with RT–quantitative polymerase chain reaction (P < .05). Positive RT-ddPCR results were associated with declined platelet and elevated aspartate aminotransferase and lactate dehydrogenase on the same day vs negative RT-ddPCR samples. RT-ddPCR exhibits commendable diagnostic efficacy in SFTS, and it remains detectable in blood samples from patients with an extended disease course. Furthermore, RT-ddPCR correlates with clinical laboratory tests, furnishing valuable reference data for clinical diagnosis.
Healing sequelae following tooth extraction and dental implant placement in an aged, ovariectomy model
Authors: Latimer Jessica M , Maekawa Shogo , Shiba Takahiko , Fretwurst Tobias , Chen Michael , Larsson Lena , Sugai James V , Kostenuik Paul , Mitlak Bruce , Lanske Beate , Giannobile William V
Published: August 2024

At present, a lack of consensus exists regarding the clinical impact of osteoporosis on alveolar bone metabolism during implant osseointegration. While limited preclinical and clinical evidence demonstrates a negative influence of osteoporosis on dental extraction socket healing, no preclinical studies offer data on the results of implant placement in 6-mo-old, ovariectomized (OVX) Sprague–Dawley rats. This study aimed to investigate the outcomes of dental tooth extraction socket healing and implant placement in a rodent model of osteoporosis following daily vehicle (VEH) or abaloparatide (ABL) administration. Micro-CT and histologic analysis demonstrated signs of delayed wound healing, consistent with alveolar osteitis in extraction sockets following 42 d of healing in both the VEH and ABL groups. In a semiquantitative histological analysis, the OVX-ABL group demonstrated a tendency for improved socket regeneration with a 3-fold greater rate for moderate socket healing when compared to the OVX-VEH group (43% vs 14%), however, this finding was not statistically significant (p=.11). No significant differences were observed between vehicle and test groups in terms of implant outcomes (BMD and bone volume/total volume) at 14- and 21-d post-implant placement. Abaloparatide (ABL) significantly increased BMD of the femoral shaft and intact maxillary alveolar bone sites in OVX animals, demonstrating the therapeutic potential for oral hard tissue regeneration. The present model involving estrogen-deficiency-induced bone loss demonstrated an impaired healing response to dental extraction and implant installation.
The role of the pharmacist during the first year of the COVID-19 pandemic: an updated scoping review
Authors: Lima Tácio de Mendonça , Rotta Inajara , Figueiredo Isabel Vitória , Visacri Marília Berlofa
Published: August 2024

Objective

To identify new articles that describe services provided by pharmacists during the first year of the COVID-19 pandemic.

Methods

An update scoping review was conducted in MEDLINE, Embase, Scopus, LILACS, and Google Scholar between 21 May 2020 and 31 May 2021. Study selection and data extraction were performed by two independent authors. DEPICT v. 2 was used to characterize the components of pharmacists’ interventions. It was also verified whether the articles evaluated outcomes of care.

Key findings

A total of 8983 records were identified, of which 120 met the inclusion criteria. The hospital was the workplace of the pharmacist most often described (55%). The majority of articles (73.3%) described the main domains of DEPICT v.2. Pharmacists provided interventions for patients (27.5%), healthcare professionals (25.8%), both (34.2%), individually (84.2%), through face-to-face contact (44.2%), and followed by telephone (41.7%). The main actions included patient counseling (56.7%), drug supply management (42.5%), and drug information for healthcare professionals (40.8%). Less than half of the articles (36.6%) evaluated the dimension “outcomes of care” of the study population.

Conclusion

Although most of the articles reported the pharmacists’ interventions, the description is still not satisfactory. In addition, the majority of articles focused solely on the dimension “process of care”. Future research should provide more detailed descriptions of the pharmacists’ interventions and assess the effectiveness of their interventions.
Evaluation of a Modified Vesikari Severity Score as a Research Tool for Assessing Pediatric Acute Gastroenteritis
Authors: Wikswo Mary E , Weinberg Geoffrey A , Szilagyi Peter G , Selvarangan Rangaraj , Harrison Christopher J , Klein Eileen J , Englund Janet A , Sahni Leila C , Boom Julie A , Halasa Natasha B , Stewart Laura S , Staat Mary Allen , Schlaudecker Elizabeth P , Azimi Parvin H , Johnston Samantha H , Mirza Sara A
Published: August 2024

A modified Vesikari severity score (MVSS) is a useful research tool for assessing severity of acute gastroenteritis. We present a MVSS for studies in which a follow-up assessment of symptoms cannot be obtained. The MVSS significantly correlated with other markers of severity, including illness duration and work and school absenteeism.
Transnational belonging and disrupted care relationships
Authors: Svensson Hanna
Published: August 2024

For refugees, forced displacement in combination with increasingly strict barriers to family reunification means that transnational care relationships are often their only way of caring for their families. These relationships are often complicated by the precarious living conditions of family members and are also more liable to disruptions through recurring instability as well as limitations to mobility or connectivity. In this article, I investigate the transnational experiences of refugees settled in New Zealand and Sweden, and particularly their experiences of disruptions to transnational care relationships. Using a dialogical lens, I consider how their sense of responsibility towards their transnational family impacts their lives when they are unable to provide sufficient responses to requests for care, and how this in turn impacts activities designed to promote settlement. I argue that it is essential for resettlement nations to consider how family separation and unfulfilled care responsibilities impact resettled refugees.
Probing the magnetized gas distribution in galaxy groups and the cosmic web with POSSUM Faraday rotation measures
Authors: Anderson Craig S , McClure-Griffiths N M , Rudnick L , Gaensler B M , O’Sullivan S P , Bradbury S , Akahori T , Baidoo L , Bruggen M , Carretti E , Duchesne S , Heald G , Jung S L , Kaczmarek J , Leahy D , Loi F , Ma Y K , Osinga E , Seta A , Stuardi C , Thomson A J M , Van Eck C , Vernstrom T , West J
Published: August 2024

We present initial results from the Polarization Sky Survey of the Universe’s Magnetism (POSSUM), analysing 22 817 Faraday rotation measures (RMs) with median uncertainties of 1.2 rad m$^{-2}$ across 1520 deg2 to study magnetized gas associated with 55 nearby galaxy groups ($z\lesssim 0.025$) with halo masses between $10^{12.5}$ and $10^{14.0}$ M$_\odot$. We identify two distinct gas phases: the intragroup medium (IGrM) within 0–2 splashback radii and the warm-hot intergalactic medium (WHIM) extending from 2 to 7 splashback radii. These phases enhance the standard deviation of residual (i.e. Galactic foreground RM-subtracted) RMs by $6.9\pm 1.8$ rad m$^{-2}$ and $4.2 \pm 1.2$ rad m$^{-2}$, respectively. Estimated magnetic field strengths are several μG within the IGrM and 0.1–1 μG in the WHIM. We estimate the plasma $\beta$ in both phases, and show that magnetic pressure might be more dynamically important than in the ICM of more massive clusters or sparse cosmic web filaments. Our findings indicate that ‘missing baryons’ in the WHIM likely extend beyond the gravitational radii of group-mass haloes to Mpc scales, consistent with large-scale, outflow-driven ‘magnetized bubbles’ seen in cosmological simulations. We demonstrate that RM grids are an effective method for detecting magnetized thermal gas at galaxy group interfaces and within the cosmic web. This approach complements X-ray and Sunyaev-Zel’dovich effect methods, and when combined with fast radio burst dispersion measures, data from the full POSSUM survey – comprising approximately a million RMs – will allow direct magnetic field measurements to further our understanding of baryon circulation in these environments and the magnetized universe.
Accurate simultaneous constraints on the dust mass, temperature, and emissivity index of a galaxy at redshift 7.31
Authors: Algera Hiddo S B , Inami Hanae , De Looze Ilse , Ferrara Andrea , Hirashita Hiroyuki , Aravena Manuel , Bakx Tom , Bouwens Rychard , Bowler Rebecca A A , Da Cunha Elisabete , Dayal Pratika , Fudamoto Yoshinobu , Hodge Jacqueline , Hygate Alexander , van Leeuwen Ivana , Nanayakkara Themiya , Palla Marco , Pallottini Andrea , Rowland Lucie , Smit Renske , Sommovigo Laura , Stefanon Mauro , Vijayan Aswin P , van der Werf Paul
Published: August 2024

We present new multifrequency Atacama Large Millimeter/submillimeter Array (ALMA) continuum observations of the massive [$\log _{10}(M_\star /\mathrm{M}_\odot) = 10.3_{-0.2}^{+0.1}$], UV-luminous [$M_\mathrm{UV} = -21.7 \pm 0.2$] $z=7.31$ galaxy REBELS-25 in Bands 3, 4, 5, and 9. Combining the new observations with previously taken data in Bands 6 and 8, we cover the dust continuum emission of the galaxy in six distinct bands – spanning rest-frame $50-350\, \mu$m – enabling simultaneous constraints on its dust mass ($M_\mathrm{dust}$), temperature ($T_\mathrm{dust}$), and emissivity index ($\beta _\mathrm{IR}$) via modified blackbody fitting. Given a fiducial model of optically thin emission, we infer a cold dust temperature of $T_\mathrm{dust} = 32_{-6}^{+9}\,$ K and a high dust mass of $\log _{10}(M_\mathrm{dust}/\mathrm{M}_\odot) = 8.2_{-0.4}^{+0.6}$, and moderately optically thick dust does not significantly alter these estimates. If we assume dust production is solely through supernovae (SNe), the inferred dust yield would be high, $y = 0.7_{-0.4}^{+2.3}\, \mathrm{M}_\odot$ per SN. Consequently, we argue grain growth in the interstellar medium of REBELS-25 also contributes to its dust build-up. This is supported by the steep dust emissivity index $\beta _\mathrm{IR} = 2.5 \pm 0.4$ we measure for REBELS-25, as well as by its high stellar mass, dense interstellar medium, and metal-rich nature. Our results suggest that constraining the dust emissivity indices of high-redshift galaxies is important not only to mitigate systematic uncertainties in their dust masses and obscured star formation rates, but also to assess if dust properties evolve across cosmic time. We present an efficient observing set-up to do so with ALMA, combining observations of the peak and Rayleigh–Jeans tail of the dust emission.
Relationship between MRI findings and renal histopathology in IgG4-related tubulointerstitial nephritis
Authors: Suenaga Atsuhiko , Oba Yuki , Ikuma Daisuke , Sekine Akinari , Yamanouchi Masayuki , Hasegawa Eiko , Mizuno Hiroki , Suwabe Tatsuya , Kono Kei , Kinowaki Keiichi , Ohashi Kenichi , Miyazono Motoaki , Yamaguchi Yutaka , Ubara Yoshifumi , Sawa Naoki
Published: August 2024

Objectives

Magnetic resonance imaging (MRI) is expected to be a valuable tool for evaluating disease activity in immunoglobulin G4 (IgG4)-related tubulointerstitial nephritis (IgG4-TIN). However, the correlation between MRI findings and renal histopathological findings remains to be elucidated. This study aimed to clarify the correlation.

Methods

This retrospective cross-sectional study investigated 26 patients with biopsy-proven IgG4-TIN who underwent simultaneous percutaneous kidney biopsies and abdominal MRI examinations. We reviewed kidney biopsy specimens and scored the degree of inflammatory cell infiltration and interstitial fibrosis. We assessed abdominal MRI, specifically examining T1-weighted imaging (T1WI), T2-weighted imaging (T2WI), and diffusion-weighted imaging (DWI), for the presence of abnormal signals in the inferior pole of the kidney. Spearman’s correlation coefficient test was conducted to examine the relationship between the images and histological findings.

Results

For T1WI, eight cases showed a positive low-intensity signal, and 18 cases were negative. For T2WI, 19 cases were positive for a low-intensity signal, and seven cases were negative. In DWI, 23 cases were positive for a high-intensity signal, and one was negative. T1WI low-intensity signal and T2WI low-intensity signal were significantly correlated with interstitial fibrosis score (correlation coefficients 0.52 and 0.64).

Conclusion

Low-intensity signal on T2WI is useful for predicting the degree of fibrosis in IgG4-TIN.
Activation of Wnt/β-catenin signaling is critical for the tumorigenesis of choroid plexus
Authors: Ho Kim Hoa , Trapp Marleen , Guida Catello , Ivanova Ekaterina L , De Jaime-Soguero Anchel , Jabali Ammar , Thomas Christian , Salasova Alena , Bernatík Ondřej , Salio Chiara , Horschitz Sandra , Hasselblatt Martin , Sassoè-Pognetto Marco , Čajánek Lukáš , Ishikawa Hiroshi , Schroten Horst , Schwerk Christian , Acebrón Sergio P , Angel Peter , Koch Philipp , Patrizi Annarita
Published: August 2024

Background

The choroid plexus (ChP) is the secretory epithelial structure located in the brain ventricles. Choroid plexus tumors (CPTs) are rare neoplasms predominantly occurring in young patients with intensified malignancy in children. CPT treatment is hindered by insufficient knowledge of tumor pathology and the limited availability of valid models.

Methods

Genomic and transcriptomic data from CPT patients were analyzed to identify the putative pathological pathway. Cellular and molecular techniques were employed to validate bioinformatic results in CPT patient samples. Pharmacologic inhibition of Wnt/β-catenin signaling was assessed in CPT cells. Cell-based assays of ChP cell lines were performed following CRISPR-Cas9-derived knockout and overexpression of Wnt/β-catenin pathway genes. A 3D CPT model was generated through CRISPR-Cas9-derived knockout of APC.

Results

We discovered that Wnt/β-catenin signaling is activated in human CPTs, likely as a consequence of large-scale chromosomal instability events of the CPT genomes. We demonstrated that CPT-derived cells depend on autocrine Wnt/β-catenin signaling for survival. Constitutive Wnt/β-catenin pathway activation, either through knockout of the negative regulator APC or overexpression of the ligand WNT3A, induced tumorigenic properties in ChP 2D in vitro models. Increased activation of the Wnt/β-catenin pathway in ChP organoids, through treatment with a potent GSK3β inhibitor, reduced the differentiation of mature ChP epithelial cells. Remarkably, the depletion of APC was sufficient to induce the oncogenic transformation of ChP organoids.

Conclusions

Our research identifies Wnt/β-catenin signaling as a critical driver of CPT tumorigenesis and provides the first 3D in vitro model for future pathological and therapeutic studies of CPT.
Radiocatalytic ammonia synthesis from nitrogen and water
Authors: Mu Bo-Shuai , Xu Yang , Tu Zhiyu , Zhang Yugang , Liang Weiqiu , Li Jiahao , Wang Xianglin , Shen Siyong , Chen Junyi , Liu Zhibo
Published: August 2024

The development of alternative methods to the Haber–Bosch process for ammonia (NH3) synthesis is a pressing and formidable challenge. Nuclear energy represents a low-carbon, efficient and stable source of power. The harnessing of nuclear energy to drive nitrogen (N2) reduction not only allows ‘green’ NH3 synthesis, but also offers the potential for the storage of nuclear energy as a readily transportable zero-carbon fuel. Herein, we explore radiocatalytic N2 fixation to NH3 induced by γ-ray radiation. Hydrated electrons (e−aq) that are generated from water radiolysis enable N2 reduction to produce NH3. Ru-based catalysts synthesized by using γ-ray radiation with excellent radiation stability substantially improve NH3 production in which the B5 sites of Ru particles may play an important role in the activation of N2. By benefitting from the remarkable penetrating power of γ-ray radiation, radiocatalytic NH3 synthesis can proceed in an autoclave under appropriate pressure conditions, resulting in an NH3 concentration of ≤5.1 mM. The energy conversion efficiency of the reaction is as high as 563.7 mgNH3·MJ−1. This radiocatalytic chemistry broadens the research scope of catalytic N2 fixation while offering promising opportunities for converting nuclear energy into chemical energy.
Heritable Tissue-Culture-Free Gene Editing in Nicotiana benthamiana through Viral Delivery of SpCas9 and sgRNA
Authors: Yoshida Tetsuya , Ishikawa Masayuki , Toki Seiichi , Ishibashi Kazuhiro
Published: August 2024

Conventional plant gene editing requires laborious tissue-culture-mediated transformation, which restricts the range of applicable plant species. In this study, we developed a heritable and tissue-culture-free gene editing method in Nicotiana benthamiana using tobacco ringspot virus (TRSV) as a vector for in planta delivery of Cas9 and single-guide RNA (sgRNA) to shoot apical meristems. Agrobacterium-mediated inoculation of the TRSV vector induced systemic and heritable gene editing in Nicotiana benthamiana PHYTOENE DESATURASE. Transient downregulation of RNA silencing enhanced gene editing efficiency, resulting in an order of magnitude increase (0.8–13.2%) in the frequency of transgenerational gene editing. While the TRSV system had a preference for certain sgRNA sequences, co-inoculation of a TRSV vector carrying only Cas9 and a tobacco rattle virus vector carrying sgRNA successfully introduced systemic mutations with all five tested sgRNAs. Extensively gene-edited lateral shoots occasionally grew from plants inoculated with the virus vectors, the transgenerational gene editing frequency of which ranged up to 100%. This virus-mediated heritable gene editing method makes plant gene editing easy, requiring only the inoculation of non-transgenic plants with a virus vector(s) to obtain gene-edited individuals.
Optimizing intervention dissemination at scale: A qualitative study of multi-sector partner organization experiences
Authors: Cassar Samuel , Salmon Jo , Timperio Anna , Powell Byron J , Della Gatta Jacqueline , Ma Jiani , Koorts Harriet
Published: August 2024

For population-wide impact of interventions, evidence-based programs must be successfully disseminated and adopted at scale. Research–practice partnerships can legitimize programs and support organizational adoption, however, ways of leveraging the contributions of partners during dissemination processes are less clear. TransformUs is a school-based physical activity and sedentary behaviour program, and since 2018, has been disseminated at scale to all primary schools in Victoria, Australia, in partnership with 16 state and national organizations. The study objective was to investigate the experiences of partner organizations disseminating TransformUs within their networks, and factors associated with awareness and adoption of the program in schools, from the perspective of partner organizations. Semi-structured interviews with representatives from 15 (out of 16) partner organizations in 2019 involved in disseminating TransformUs state-wide. An interview guide was informed by the RE-AIM framework. Interviews were audio-recorded, transcribed, and coded anonymously. Data were analysed thematically. Four themes (and 13 sub-themes) were identified: (i) organizational barriers and facilitators to dissemination; (ii) implementation support for partners; (iii) overall research experience; and (iv) dissemination strategy. Partners used multiple dissemination channels to increase adoption, and strong alignment between TransformUs and the partner organization’s goals appeared to enable dissemination. Partners outlined several local, regional, and state organizations to partner with, and offered suggestions regarding preferred content and timing of dissemination activities for their networks. Researchers planning research–practice partnerships should proactively consider organizational barriers partners may face during dissemination. Regular communication and feedback on dissemination outcomes may contribute to positive research–practice experiences and allow for tailored dissemination strategies.
Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia
Authors: Martínez David , Gómez Marcela , Hernández Carolina , Campo-Palacio Sandra , González-Robayo Marina , Montilla Marcela , Pavas-Escobar Norma , Tovar-Acero Catalina , Geovo-Arias Lillys , Valencia-Urrutia Esilda , Córdoba-Renteria Nayade , Carrillo-Hernandez Marlen Y , Ruiz-Saenz Julian , Martinez-Gutierrez Marlen , Paniz-Mondolfi Alberto , Patiño Luz H , Muñoz Marina , Ramírez Juan David
Published: August 2024

Dengue fever remains as a public health challenge in Colombia, standing as the most prevalent infectious disease in the country. The cyclic nature of dengue epidemics, occurring approximately every 3 years, is intricately linked to meteorological events like El Niño Southern Oscillation (ENSO). Therefore, the Colombian system faces challenges in genomic surveillance. This study aimed to evaluate local dengue virus (DENV) transmission and genetic diversity in four Colombian departments with heterogeneous incidence patterns (department is first-level territorial units in Colombia). For this study, we processed 266 serum samples to identify DENV. Subsequently, we obtained 118 genome sequences by sequencing DENV genomes from serum samples of 134 patients infected with DENV-1 and DENV-2 serotypes. The predominant serotype was DENV-2 (108/143), with the Asian-American (AA) genotype (91/118) being the most prevalent one. Phylogenetic analysis revealed concurrent circulation of two lineages of both DENV-2 AA and DENV-1 V, suggesting ongoing genetic exchange with sequences from Venezuela and Cuba. The continuous migration of Venezuelan citizens into Colombia can contribute to this exchange, emphasizing the need for strengthened prevention measures in border areas. Notably, the time to most recent common ancestor analysis identified cryptic transmission of DENV-2 AA since approximately 2015, leading to the recent epidemic. This challenges the notion that major outbreaks are solely triggered by recent virus introductions, emphasizing the importance of active genomic surveillance. The study also highlighted the contrasting selection pressures on DENV-1 V and DENV-2 AA, with the latter experiencing positive selection, possibly influencing its transmissibility. The presence of a cosmopolitan genotype in Colombia, previously reported in Brazil and Peru, raises concerns about transmission routes, emphasizing the necessity for thorough DENV evolution studies. Despite limitations, the study underscores genomic epidemiology’s crucial role in early detection and comprehension of DENV genotypes, recommending the use of advanced sequencing techniques as an early warning system to help prevent and control dengue outbreaks in Colombia and worldwide.
Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection
Authors: El Moussaoui Majdouline , Bontems Sebastien , Meex Cecile , Hayette Marie-Pierre , Lejeune Marie , Hong Samuel L , Dellicour Simon , Moutschen Michel , Cambisano Nadine , Renotte Nathalie , Bours Vincent , Darcis Gilles , Artesi Maria , Durkin Keith
Published: August 2024

Accumulating evidence points to persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunocompromised individuals as a source of novel lineages. While intrahost evolution of the virus in chronically infected patients has previously been reported, existing knowledge is primarily based on samples from the nasopharynx. In this study, we investigate the intrahost evolution and genetic diversity that accumulated during a prolonged SARS-CoV-2 infection with the Omicron BF.7 sublineage, which is estimated to have persisted for >1 year in an immunosuppressed patient. Based on the sequencing of eight samples collected at six time points, we identified 87 intrahost single-nucleotide variants, 2 indels, and a 362-bp deletion. Our analysis revealed distinct viral genotypes in the nasopharyngeal (NP), endotracheal aspirate, and bronchoalveolar lavage samples. This suggests that NP samples may not offer a comprehensive representation of the overall intrahost viral diversity. Our findings not only demonstrate that the Omicron BF.7 sublineage can further diverge from its already exceptionally mutated state but also highlight that patients chronically infected with SARS-CoV-2 can develop genetically specific viral populations across distinct anatomic compartments. This provides novel insights into the intricate nature of viral diversity and evolution dynamics in persistent infections.
Viromics Reveals Two Novel Viruses of the Family Closteroviridae in Codiaeum variegatum Plant with Leaf Variegation Symptoms
Authors: Che Haiyan , Gao Shengfeng , Lin Yating , Long Haibo , Li Ye , Cai Lulu , Li Shifang , Ma Yuxin
Published: August 2024

Codiaeum variegatum is a valuable ornamental plant with distinct bright yellowing and golden spots on dark green leaves, which resemble virus symptoms. To investigate the factors, especially viral agents, associated with the variegated leaf color of C. variegatum, we performed virome profiling of a single C. variegatum ‘Gold Dust’ leaf sample collected from Hainan, China, using ribosomal RNA-depleted total RNA sequencing on an Illumina NovaSeq 6000 platform. Two novel viruses, with two variants each, belonging to the family Closteroviridae, were detected and characterized: Croton golden spot-associated virus C variants 1 and 2 (CGSaVC-v1 and CGSaVC-v2) of the genus Crinivirus and Croton golden spot-associated virus A variants 1 and 2 (CGSaVA-v1 and CGSaVA-v2) of the genus Ampelovirus. Transmission electron microscopy showed long, flexuous, filamentous virus particles approximately 15 nm in diameter and 760 to 770 nm in length. Molecular screening of 97 variegated individual plant leaves showed a high prevalence of CGSaVA-v2 (90.7%), CGSaVA-v1 (75.3%), CGSaVC-v1 (70.1%), and CGSaVC-v2 (47.4%), while asymptomatic leaves near the meristem tip were mostly free of the target viruses. To our knowledge, this is the first study to demonstrate the significant association between closterovirids and the golden spots. The findings provide novel insights into the genetic diversity of the family Closteroviridae and inform future germplasm conservation and new cultivar development of C. variegatum.
Identification of Streptomycin-Resistant Erwinia amylovora in Iowa
Authors: Schmidt Sophia G. , Alstott Emma T. , Paulsen Ashley A. , Slack Suzanne M. , Yuan Xiaochen
Published: August 2024

Erwinia amylovora is a bacterial pathogen that causes fire blight, an important disease in apples and pears. Applying the antibiotic streptomycin during the phenological bloom stage is considered the most effective management tactic for fire blight. Although streptomycin-resistant (SmR) E. amylovora populations have emerged in major U.S. apple-producing regions, antibiotic resistance data for medium- to small-sized apple-producing regions such as the Midwest are still lacking. This Short Communication article collected symptomatic fire blight samples from Iowa apple orchards during 2022 and 2023, where recent fire blight outbreaks persisted despite streptomycin use. Among E. amylovora isolates from seven counties in Central and Eastern Iowa, approximately 90% of them were SmR. All SmR isolates exhibited a single base pair mutation in codon 43 of the rpsL gene, conferring resistance to streptomycin levels exceeding 1,000 μg/ml. Through clustered regularly interspaced short palindromic repeat (CRISPR) analysis, we characterized two E. amylovora genotypes unique to our region. Whole genome sequencing of one representative SmR isolate, IA01, confirmed its CRISPR genotype, and subsequent phylogenetic analysis suggested that IA01 is genetically similar to Michigan isolates and distinct from those in eastern and western regions of North America. Furthermore, the disease-causing ability of IA01 was comparable to that of the highly virulent Ea110 strain, a streptomycin-sensitive strain isolated from Michigan, in immature pears. Overall, this study underscores the urgent need for regional strategies to address antibiotic resistance and provides insights into its genetic basis and geographic distribution, which are crucial for sustainable orchard management.
Abundance and distribution of ringed and bearded seals in the Chukchi Sea: a reference for future trends
Authors: Boveng Peter L. , Chernook Vladimir I. , Moreland Erin E. , Conn Paul B. , Trukhanova Irina S. , Cameron Michael F. , Christman Cynthia L. , Crawford Justin A. , Harwood Lois , Hou Benjamin X. , Koslovsky Stacie M. , Lindsay Jessica M. , Litovka Denis I. , London Josh M. , McClintock Brett T. , Platonov Nikita , Quakenbush Lori , Richmond Erin L. , Vasiliev Alexander , Von Duyke Andrew L. , Willoughby Amy
Published: August 2024

Ringed (Pusa hispida) and bearded (Erignathus barbatus) seals are vulnerable to decreasing sea ice habitat in the rapidly warming Arctic. In April and May of 2016, we conducted an aerial survey over the ice-covered areas of the Chukchi Sea using thermal and color cameras to detect and count these seals on sea ice. We related the seal counts to environmental variables, and used the relationships to estimate the species’ distributions and abundance throughout the Chukchi Sea. We accounted for incomplete detection due to seals missed by sensors or image processing errors, behavioral responses to aircraft, or incomplete availability (i.e. seals that are in water or in snow dens on the ice, called lairs). For the latter, we used wet/dry records from satellite-linked bio-loggers, and remotely sensed snow melt dates to estimate the proportion of ringed seal individuals that were visible on ice for each day and location surveyed. To our knowledge, this is the first study where use of lairs by ringed seals has been formally addressed while estimating abundance from aerial surveys. Ringed seal abundance was estimated as= 592,577 (95% CI: 478,448–733,929), with highest densities near Kotzebue Sound, Alaska, USA. Bearded seal abundance was estimated as= 147,421 (95% CI: 114,155–190,380), with highest densities in broken pack ice near Bering Strait. The influence of environmental variables, such as snow depth and ice type, was consistent with prior studies of the species’ natural history, particularly ringed seals’ preference for snow of adequate depth for lairs. Our study provides the first comprehensive abundance estimates for ringed and bearded seals in the Chukchi Sea and establishes a reference for monitoring how their populations respond to Arctic warming.
Ubie Symptom Checker: A Clinical Vignette Simulation Study
Authors: Taylor N. Kenji , Nishibayashi Takashi
Published: August 2024

Background

AI-driven symptom checkers (SC) are increasingly adopted in healthcare for their potential to provide users with accessible and immediate preliminary health education. These tools, powered by advanced artificial intelligence algorithms, assist patients in quickly assessing their symptoms. Previous studies using clinical vignette approaches have evaluated SC accuracy, highlighting both strengths and areas for improvement.

Objective

This study aims to evaluate the performance of the Ubie Symptom Checker (Ubie SC) using an innovative large language model-assisted (LLM) simulation method.

Methods

The study employed a three-phase methodology: gathering 400 publicly available clinical vignettes, medical entity linking these vignettes to the Ubie SC using large language models and physician supervision, and evaluation of accuracy metrics. The analysis focused on 328 vignettes that were within the scope of the Ubie SC with accuracy measured by Top-5 hit rates.

Results

Ubie achieved a Top-5 hit accuracy of 63.4% and a Top-10 hit accuracy of 71.6%, indicating its effectiveness in providing relevant information based on symptom input. The system performed particularly well in domains such as the nervous system and respiratory conditions, though variability in accuracy was observed across different ICD groupings, highlighting areas for further refinement. When compared to physicians and comparator SC’s that used the same clinical vignettes set, Ubie compared favorably to the median physician hit accuracy.

Conclusions

The Ubie Symptom Checker shows considerable promise as a supportive education tool in healthcare. While the study highlights the system’s strengths, it also identifies areas for improvement suggesting continued refinement and real-world testing are essential to fully realize Ubie’s potential in AI-assisted healthcare.
Extracellular Vesicle-Mediated Delivery of HIF1α Reprograms Macrophages for resolutive response in Sepsis
Authors: Lee Yeji , Goo Jiyoung , Cho Seongeon , Kim Seong A , Nam Gi-Hoon , Kim Iljin , Park Jong-Wan , Jeong Cherlhyun , Kim In-San
Published: August 2024

In sepsis, the liver functions as a central filter organ, where hepatic macrophages form a primary antimicrobial defense layer by eliminating bacteria and regulating immune responses. Therefore, precise regulation of the immune response in hepatic macrophages is crucial for triggering effective defense mechanisms. We aim to modulate the defense immune response by delivering transcription factor HIF1α, a key regulator of monocyte/macrophage reprogramming in sepsis. Transcription factors are promising candidates because they dynamically modulate gene expression across diverse conditions, though delivering them remains challenging. In this study, we suggest a novel method for loading HIF1α into extracellular vesicles (EVs) to enhance immune defense and resolve sepsis. By delivering HIF1α to macrophages during sepsis, we promoted the differentiation of Nr1h3-dependent pro-efferocytic MoMFs and C/ebpβ-dependent pro-survival MoMFs. Pro-efferocytic MoMFs eliminate damaged hepatocytes and immune cells and pro-survival MoMFs withstand inflammatory conditions and trigger innate memory responses. Particularly, the zonation of these macrophages in the periportal region ensures effective pathogen clearance and minimizes tissue damage. These findings suggest that EV-mediated HIF1α delivery could be a promising therapeutic option for managing sepsis.
MorphoCellSorter: An Andrews plot-based sorting approach to rank microglia according to their morphological features
Authors: Benkeder Sarah , Dinh Son-Michel , Marchal Paul , Gea Priscille De , Thoby-Brisson Muriel , Hubert Violaine , Hristovska Ines , Pitollat Gabriel , Combet Kassandre , Cardoit Laura , Pillot Bruno , Léon Christelle , Wiart Marlène , Marty Serge , Honnorat Jérôme , Pascual Olivier , Comte Jean-Christophe
Published: August 2024

Microglia exhibit diverse morphologies reflecting environmental conditions, maturity or functional states. Thus, morphological characterization provides important information to understand microglial roles and functions. Most recent morphological analysis relies on classifying cells based on morphological parameters. However, this classification may lack biological relevance, as microglial morphologies represent a continuum rather than distinct, separate groups, and do not correspond to mathematically defined, clusters irrelevant of microglial cells function. Instead, we propose a new open-source tool, MorphoCellSorter, which assesses microglial morphology by automatically computing morphological criteria, using principal component analysis and Andrews plots to rank cells. MorphoCellSorter properly ranked cells from various microglia datasets in mice and rats of different age, fromin vivo,in vitroandex vivomodels, that were acquired using diverse imaging techniques. This approach allowed for the discrimination of cell populations in various pathophysiological conditions. Finally, MorphoCellSorter offers a versatile, easy and ready-to-use method to evaluate microglial morphological diversity that could easily be generalized to standardize practices across laboratories.