bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic surveillance and evolutionary dynamics of influenza a virus in Sri Lanka
Authors: Jayadas Tibutius Thanesh Pramanayagam , Jeewandara Chandima , Senadheera Bhagya , Kuruppu Heshan , Wickramanayake Rivindu , Chathurangika Padukkage Harshani , Senatilleke Nushara , Warnakulasuriya Navanjana , Bary Farha , Wijewickrama Ananda , Manilgama Suranga , Gamage Manouri , Perera Nilanka , Ogg Graham S. , Malavige Gathsaurie Neelika 
Published: November 2024

Abstract
Background
Influenza A has been named as a priority pathogen by the WHO due to the potential to cause pandemics. Genomic sequencing of influenza strains is important to understand the evolution of the influenza strains and also to select the appropriate influenza vaccines to be used in the different influenza seasons in Sri Lanka. Therefore, we sought to understand the molecular epidemiology of the influenza viruses in the Western Province of Sri Lanka, including mutational analysis to investigate the evolutionary dynamics.

Methodology
A total of 349 individuals presenting with fever and respiratory symptoms were enrolled in this study from November 2022 to May 2024. Nasopharyngeal and oropharyngeal specimens were collected and screened using quantitative PCR to detect Influenza A, Influenza B, and SARS-CoV-2. Subtyping and genomic sequencing was carried out on influenza A strains using Oxford Nanopore Technology.

Results
Influenza A was detected in 49 (14%) patients, influenza B in 20 (5.7%) and SARS-CoV-2 in 41 (11.7%). Co-infections were observed in five participants. The phylogenetic analysis assigned the H1N1 HA gene sequences within the 6B.1 A.5a.2a clade. The HA gene of the H1N1 sequences in 2023 were assigned as belonging to the subclades C.1, C.1.2, and C.1.8, while the 2024 sequences were assigned to subclades C.1.8 and C.1.9. The H3N2 sequences from 2023 were assigned to the 3 C.2a1b.2a.2a.1b clade and subclade G.1.1.2, while the 2024 sequences were assigned to the 3 C.2a1b.2a.2a.3a.1 clade and subclade J.2. The K54Q, A186T, Q189E, E224A, R259K, K308R, I418V, and X215A amino acid substitutions were seen in the H1N1 in the 2023 and 2024 sequences. The 2024 H1N1 sequences additionally exhibited further substitutions, such as V47I, I96T, T120A, A139D, G339X, K156X, and T278S.

Conclusion
In this first study using genomic sequencing to characterize the influenza A strains in Sri Lanka, which showed different influenza A viruses circulating in an 18-month period. As the Sri Lankan strains also had certain mutations of unknown significance, it would be important to continue detailed surveillance of the influenza strains in Sri Lanka to choose the most suitable vaccines for the population and the timing of vaccine administration.
The renin–angiotensin–aldosterone-system in sepsis and its clinical modulation with exogenous angiotensin II
Authors: Legrand Matthieu , Khanna Ashish K. , Ostermann Marlies , Kotani Yuki , Ferrer Ricard , Girardis Massimo , Leone Marc , DePascale Gennaro , Pickkers Peter , Tissieres Pierre , Annoni Filippo , Kotfis Katarzyna , Landoni Giovanni , Zarbock Alexander , Wieruszewski Patrick M. , De Backer Daniel , Vincent Jean-Louis , Bellomo Rinaldo 
Published: November 2024

AbstractDysregulation of the renin–angiotensin–aldosterone-system (RAAS) in sepsis is a complex and early phenomenon with a likely significant contribution to organ failure and patient outcomes. A better understanding of the pathophysiology and intricacies of the RAAS in septic shock has led to the use of exogenous angiotensin II as a new therapeutic agent. In this review, we report a multinational and multi-disciplinary expert panel discussion on the role and implications of RAAS modulation in sepsis and the use of exogenous angiotensin II. The panel proposed guidance regarding patient selection and treatment options with exogenous angiotensin II which should trigger further research.
High-concentrated platelet-rich plasma (PRP) versus placebo in osteoarthritis in the thumb base: study protocol for an assessor-blinded randomized controlled trial
Authors: von Kieseritzky Johanna , Wilcke Maria 
Published: November 2024

Abstract
Background
Osteoarthritis in the thumb base (trapeziometacarpal joint, CMC-1 joint) is prevalent, particularly among middle-aged and elderly women, causing significant disability. Conservative treatments, including steroid injections, have been questioned for their efficacy, prompting exploration into alternative therapies such as platelet-rich plasma (PRP) injections. This randomized, double-blinded, controlled trial aims to evaluate the effectiveness of high-concentration PRP (platelet-rich plasma) injection compared to saline (placebo) in reducing pain and disability in patients with thumb base osteoarthritis.

Methods
Patients meeting inclusion criteria will be randomized and blinded, with injections administered under sterile conditions and radiological guidance.
With a planned sample size of 90 patients recruited from the Department of Hand Surgery at Södersjukhuset, Stockholm, the study will assess pain relief and functional improvement at 3, 6, and 12 months post-injection. The primary outcome measure is pain on load (numerical rating scale) at 6 months, with secondary outcomes including patient-reported outcomes, key pinch, grip strength, abduction of the thumb, and time to intervention within 1 year.
Statistical analyses will employ non-parametric tests, chi-square tests, and generalized estimating equations to compare outcomes between the PRP and placebo groups.

Discussion
The study aims to provide evidence regarding the efficacy of high-concentration PRP injections for thumb base osteoarthritis. If PRP proves superior to saline in reducing pain and improving function, it could offer a promising alternative treatment. Conversely, if PRP does not demonstrate significant benefits over placebo, its use for this condition is not justified. This study seeks to address the current gap in evidence regarding the efficacy of PRP injections for thumb base osteoarthritis.

Trial registration
The study has been approved by the Swedish Ethical Review Authority (2023–06860-01 and 2024–01238-02) and is registered on ClinicalTrials.gov (NCT06193499) 2024–01-04.
Methylation changes and INS-IGF2 expression predict progression in early-stage Wilms tumor
Authors: Jalal Deena , Ali Mohamed Y. , Elkinaai Naglaa , Abdelaziz Abdelaziz S. , Zekri Wael , Sayed Ahmed A. 
Published: November 2024

AbstractWilms tumor, the most common pediatric kidney cancer, accounts for 5% of childhood cancers and is classified by stage and histological subtype. Despite high survival rates (80–85%), approximately 15% of patients experience relapse, reducing survival to around 50%. Epigenetic changes, particularly DNA methylation, play a critical role in Wilms tumor pathogenesis. This study investigates the prognostic potential of DNA methylation in stage I and II patients with favorable histology, aiming to identify early relapse biomarkers. Genome-wide methylation was assessed using methylation microarrays in tumor tissues from relapsed patients (n = 9) and those with complete responses (n = 9), alongside normal tissues (n = 3 each). Differentially methylated probes and regions were analyzed, with additional ROC and survival analyses. Real-time PCR was used to measure IGF2 and INS-IGF2 gene expression. The analysis revealed hypomethylation in intergenic regions in remission patients, identifying 14 differentially methylated positions as potential biomarkers. Increased INS-IGF2 expression was associated with relapse, suggesting its role in disease progression. While the study concentrated on stages I and II patients, where relapse rates are lower, this focus inherently led to a smaller sample size. Despite this, the findings provide valuable insights into the potential role of DNA methylation markers for monitoring disease progression and guiding personalized treatment in Wilms tumor patients.
Graphical abstract

Genome methylation analysis of WT tumor and normal tissues from complete remission and relapse patients revealed 14 differentially methylated probes (DMPs) and three differentially methylated regions (DMRs) in tumor samples between both groups. Most DMPs demonstrated strong predictive performance for overall and event-free survival. RNA expression analysis showed elevated INS-IGF2 levels in relapse tumor tissue, highlighting its role in WT progression.
Adequacy of histopathology request forms and specimens sent to two histopathology centers in Khartoum, Sudan
Authors: Elhassan Eman Abdel Azim Elsadek , Khalifa Mohanad Saeed Ahmed , Ibrahim Faisal , Mohammed Sawsan Abdil Rahim 
Published: November 2024

Abstract
Background
Every branch of surgery relies in some way on histology to obtain a conclusive diagnosis. Since precise and comprehensive information on the request form is crucial to the correct analysis and interpretation of test results, it is anticipated that all patient data and information for any requested test be provided. One of the most significant duties of the peri-operative team is the care and handling of intraoperative surgical specimens. Poor labeling and handling of surgical specimens can lead to unfavorable consequences such as misdiagnosis, incorrect or delayed therapy, and even the need for repeat surgery. The study’s. objective is to highlight the primary mistakes that occur in the pre analytical stage of histopathology request forms and specimens at two Khartoum-based histopathological institutions.

Methods
A prospective descriptive laboratory based cross-sectional study was carried out on 528 request forms and specimens sent to two histopathology centers between the period of May to August 2019 having gotten Ethical clearance from SMSB.

Results
A total of 528 laboratory request forms and specimens, Age was written in 75.6% (n 399), while the gender only was written only in 46.2% (n 244). No clinical history in 48.3% (n 255). The differential diagnosis found only in 29.5% (n156) of request forms. Regarding specimen 15.7% (83) were inadequate relative to the size of the container and only 5.3% (28) were not labeled with any information. 17.4% (92) were not sent in formalin but in normal saline. Marking of the specimen was not needed in 60% (317) and among the rest cases; 34.2% was not marked.

Conclusion
The study shows that laboratory request forms were not properly and thoroughly completed. Most of the specimens sent for histology had inadequate fixative and unsuitable containers, or they were mislabeled and not properly tagged. This for sure will have a detrimental effect on the quality of care.
Handoff Mnemonics Used in Perioperative Handoff Intervention Studies: A Systematic Review
Authors: Patel Sabina M. , Fuller Sarah , Michael Meghan M. , O’Hagan Emma C. , Lazzara Elizabeth H. , Riesenberg Lee Ann 
Published: November 2024

BACKGROUND:
Perioperative handoffs are known to present unique challenges to safe and effective patient care. Numerous national accrediting bodies have called for standardized, structured handoff processes. Handoff mnemonics provide a memory aid and standardized structure, as well as promote a shared mental model. We set out to identify perioperative handoff intervention studies that included a handoff mnemonic; critically assess process and patient outcome improvements that support specific mnemonics; and propose future recommendations.

METHODS:
We conducted a systematic review of the English language perioperative handoff intervention literature designed to identify handoff mnemonic interventions. A comprehensive protocol was developed and registered (CRD42022363615). Searches were conducted using PubMed, Scopus, ERIC (EBSCO), Education Full Text (EBSCO), EMBASE (Elsevier), and Cochrane (January 1, 2010 to May 31, 2022). Pairs of trained reviewers were involved in all phases of the search and extraction process.

RESULTS:
Thirty-seven articles with 23 unique mnemonics met the inclusion criteria. Most articles were published after 2015 (29/37; 78%). Situation, Background, Assessment, Recommendation (SBAR), and SBAR variants were used in over half of all studies (22/37; 59%), with 45% (10/22) reporting at least 1 statistically significant process improvement. Seventy percent of handoff mnemonics (26/37) were expanded into lists or checklists. Fifty-seven percent of studies (21/37) reported using an interdisciplinary/interprofessional team to develop the intervention. In 49% of all studies (18/37) at least 1 measurement tool was either previously published or the authors conducting some form of measurement tool validation. Forty-one percent of process measurement tools (11/27) had some form of validation. Although most studies used training/education as an implementation strategy (36/37; 97%), descriptions tended to be brief with few details and no study used interprofessional education. Twenty-seven percent of the identified studies (10/37) measured perception alone and 11% (4/37) measured patient outcomes.

CONCLUSIONS:
While the evidence supporting one handoff mnemonic over others is weak, SBAR/SBAR variants have been studied more often in the perioperative environment demonstrating some process improvements. A key finding is that 70% of included studies converted their handoff mnemonic to a list or checklist. Finally, given the essential nature of effective handoffs to perioperative patient safety, it is crucial that handoff interventions are well developed, implemented, and evaluated. We propose 8 recommendations for future perioperative handoff mnemonic clinical interventions and research.
The Resurgence of a Tibetan Medical Hauntology
Authors: van der Valk Jan M. A. 
Published: November 2024

Abstract
During the first wave of COVID-19 and the ensuing “anthropause” enforced by lockdown policies, Tibetan medicine (Sowa Rigpa) rapidly emerged as a key interface through which Tibetan, Himalayan, and online communities responded to the spread of the virus. Apart from a host of preventative, protective, and curative measures—ranging from pills to amulets and mantras—the root causes for the pandemic’s appearance and spread were framed through the interrelated lenses of Tibetan medical etiology and morally infused cosmologies. This digital anthropological study is based on an unprecedented flurry of English-language media interviews, webinars, blog posts, and articles by Sowa Rigpa physician-scholars in 2020–21. It builds on a thematic overview of the integrative ways in which they approached COVID-19, further analyzing the highly distinctive more-than-human ecological perspective through a hauntological lens of spectral justice. The essay unpacks how practitioners drew on textual idioms of contagion, spirit provocation, karmic retribution, and Buddhist prophecies of a degenerate age (Sanskrit, kaliyuga) to invoke a particular kind of revenge of nature: mediated by angered earth protectors and mother beings, yet influenced by contemporary environmentalism. Recognizing the emancipatory potential of revenge, I interpret this resurgent kaliyuga as a Tibetan medico-religious critique and refiguration of the Anthropocene.
Seeing the Anthropocene through Montage
Authors: Arends Bergit 
Published: November 2024

Abstract
Environmental changes and the age of the Anthropocene demand new ways of seeing. This article contends that montage serves both as form and as argument in representing the modern Western experience of human-nature relations in the supposed Anthropocene. It suggests that montage resists a single narrative of the Anthropocene and allows for modified readings to address race and capital through alternative notions such as the Capitalocene and Black Anthropocenes. Montage in relation to the Anthropocene is exemplified through two works by contemporary British artists that visualize agencies and legacies of human interventions into fluvial geographies, the sea, and whales: the touring film installation Vertigo Sea (2015) by John Akomfrah, and the site-specific intervention BERLINWAL (Berlin Whale) (2018) by Elizabeth Price at the Museum für Naturkunde in Berlin, Germany. Both works, though differing in medium, use montage as a structure to hold different materialities and multiple spatial and temporal scales, affording integration as well as confrontation. Their multifocal perceptions and multiple perspectives challenge ontologies and afford a decentering of the viewer toward de-exceptionalizing the human.
Tuberous Heroes, Partial Examples, and the Making of Ethical Companions in Agricultural Collectives
Authors: Angé Olivia 
Published: November 2024

Abstract
The history of capitalism features a number of glorified characters, such as Frederick the Great and Antoine Parmentier, lauded for contributing to national prosperity by purportedly introducing the prolific potato to the masses. This article redirects our attention toward vaunted varieties in the tuber population itself, which here are called tuberous heroes. While popularly dismissed as a humble crop, the potato has also been acknowledged as having changed world history for both the better and the worse. An analysis of these antagonistic evaluations reveals how struggles for the advent of tuberous heroism were also political campaigns for worlds to come. The concept of a partial example is introduced to account for the fragmented and situated tuber appreciation found at the center of potato domestication in Peru and is held in contrast to the agro-industrial search for supercrops. This exploration of shifting vegetal virtuosity highlights the ecological attunement of partial exemplarity when compared with the expected ubiquity of heroic and villainous crops. The contrast between heroic and partial exemplarity highlights how a plant becomes an ethical companion offering propositions for entangled flourishing.
Ghostly Entanglements and Ruptures
Authors: Drew John 
Published: November 2024

Abstract
This analysis considers how education positioned at the intersections of literature and nature can help expose and confront the violence of animal agriculture. To do so, it extends from field research in London, Canada, with children who discursively and materially engaged with the story Charlotte’s Web through guided walks in an altered landscape. Once farmland and now a rapidly declining forest behind their school, this sociohistorical space is home to lingering remnants of an animal agricultural past that evoke the pastoral imagery of the novel. In combination with a place-based lens that recognizes settler-colonial agrarian legacies, the animals and interspecies relations of Charlotte’s Web offer an invitation into seeing and empathizing with farmed animals, both past and present. This analysis traces theoretical and pedagogical pathways that challenge embedded anthropocentrism and promote diverse subjective engagements with the multispecies world. Together, Indigenous ways of knowing, relational ontologies, and Derrida’s notion of hauntology can help illuminate an ethically and environmentally engaged literacy education within the Anthropocene.
Spot the Difference
Authors: Laird Tessa , Goodman Andrew 
Published: November 2024

Abstract
How and why is pattern undervalued in Western thought? Pattern’s narrative is checkered: historically banned from respectable clothing for its transgressive power; in the sciences relegated to survivalist function; in the arts tamed as decoration. This article advocates for pattern’s radical provocation to think outside cultural conventions and neo-Darwinist constraints. Pattern connects with vitality rather than utility; its radical excess overruns proprietorial boundaries. Pattern blurs delineations of figure and field, operating as a decolonial force, queering the separability of phyla, and unsettling the false binary between nature and culture. Drawing on process philosophy, art, literature, histories of fabrics, Black studies, queered biology, ecofeminism, and the continuum of naturecultures, this article experiments with the playful patterning of writing and voices and follows wild and impersonal tendencies, creating space for collective individuation, more-than-human joy, and beauty.
Beyond Heroes and Villains
Authors: Rudge Alice 
Published: November 2024

Abstract
Oil palm plantations often produce figurations of heroism and villainy attributed to human and nonhuman actors. Yet these categories may mask the subtleties of local experiences. Indigenous Batek people in Malaysia highly value the autonomy of both plants and people, but with forests disappearing, many who turn to labor on plantations find themselves struggling for autonomy. At the same time, they do not extend autonomous personhood to the oil palms with which they labor. This article explores the degrees of personhood attributed to botanical persons and the entangled human and botanical autonomies thus produced. It demonstrates the ambivalences of multispecies relationships in plantation frontier contexts and argues that by attending more closely to Batek theories and enactments of autonomy, categories of heroism and villainy are destabilized. This might offer alternative modalities for grasping the ambivalent nature of life on the edges of a plantation.
Power and the River Lords
Authors: Johnson Andrew Alan 
Published: November 2024

Abstract
The Mekong River is experiencing a crisis, with water flows and flood cycles rendered unstable owing to large-scale hydropower development in China and Laos. As communities face the radical decline of fisheries and unexpected floods and ebbs, residents and regional NGOs alike turn toward voices of moral authority and power to seek to mitigate these losses. But the kinds of authority sought out by fishers on the river are not the same as those identified by environmental groups; “spirit lords” and other divine figures enter into the conversation just as much as activists and lobbyists. In addition, these religious figures present multiple perspectives on how to live in a changed world and a model of resistance that challenges how we might see political power and its heroes.
PIKFYVE inhibition induces endosome- and lysosome-derived vacuole enlargement via ammonium accumulation
Authors: Uwada Junsuke , Nakazawa Hitomi , Kiyoi Takeshi , Yazawa Takashi , Muramatsu Ikunobu , Masuoka Takayoshi 
Published: November 2024

ABSTRACT
FYVE-type zinc finger-containing phosphoinositide kinase (PIKFYVE), which is essential for phosphatidylinositol 3,5-bisphosphate [PtdIns(3,5)P2] production, is an important regulator of lysosomal homeostasis. PIKFYVE dysfunction leads to cytoplasmic vacuolization; however, the underlying mechanism remains unknown. In this study, we explored the cause of vacuole enlargement upon PIKFYVE inhibition in DU145 prostate cancer cells. Enlargement of vacuoles upon PIKFYVE inhibition required glutamine and its metabolism by glutaminases. Addition of ammonia, a metabolite of glutamine, was sufficient to enlarge vacuoles via PIKFYVE inhibition. Moreover, PIKFYVE inhibition led to intracellular ammonium accumulation. Endosome–lysosome permeabilization resulted in ammonium leakage from the cells, indicating ammonium accumulation in the endosomes and lysosomes. Ammonium accumulation and vacuole expansion were suppressed by the lysosomal lumen neutralization. It is therefore assumed that PIKFYVE inhibition interferes with the efflux of NH4+, which formed through protonation of NH3 in the lysosomal lumen, leading to osmotic swelling of vacuoles. Notably, glutamine or ammonium is required for PIKFYVE inhibition-induced suppression of lysosomal function and autophagic flux. In conclusion, this study shows that PIKFYVE inhibition disrupts lysosomal homeostasis via ammonium accumulation.