bluuebunny/crossref_metadata_2025_split huggingface dataset:
Securing the Self, Embracing Anxiety, or Nurturing Growth? How the Pragmatism of Dewey, James, and Mead Speaks to Ontological Security Studies
Authors: Ralph Jason 
Published: May 2024

AbstractA Pragmatist form of Constructivism speaks to, and encourages, an ethical/normative turn in Ontological Security Studies (OSS). Recognition that Self-securing routines are sometimes “unhealthy” implies that the subject of security is human experience and that social identities or social roles are means to that end. This resonates with John Dewey's Pragmatist focus on the practical task of ameliorating experience in environments constantly in the process of becoming. Normative value is not ontological, i.e., found in a fixed identity; it is processural, i.e., found in the practice of “learning” and the process of “growth.” A Pragmatist narrative of learning and growth offers OSS a normative focus that is more compelling than the recent calls to “embrace anxiety,” although it is important to acknowledge that even these narratives can induce anxiety. OSS can, in this instance, turn to the Pragmatist William James and his focus on the role that “faith” plays in encouraging the Self to adopt new identities. Building on this, Dewey formulated a “civic faith” to defend democratic routines (and the democratic identity) as a useful method of (social) learning. Finally, the Pragmatism of George Herbert Mead demonstrates how this democratic commitment to include “the Other” in the processes that secure the Self helps restructure an environment that otherwise demands dangerous routines. The article draws on Cold War history to demonstrate how such practices can and should be part of the “cultural repertoire” informing ontological security-seeking practices in contemporary Europe.
Macroalgal virosphere assists with host–microbiome equilibrium regulation and affects prokaryotes in surrounding marine environments
Authors: Zhao Jiulong , Nair Shailesh , Zhang Zenghu , Wang Zengmeng , Jiao Nianzhi , Zhang Yongyu 
Published: May 2024

Abstract
The microbiomes in macroalgal holobionts play vital roles in regulating macroalgal growth and ocean carbon cycling. However, the virospheres in macroalgal holobionts remain largely underexplored, representing a critical knowledge gap. Here we unveil that the holobiont of kelp (Saccharina japonica) harbors highly specific and unique epiphytic/endophytic viral species, with novelty (99.7% unknown) surpassing even extreme marine habitats (e.g. deep-sea and hadal zones), indicating that macroalgal virospheres, despite being closest to us, are among the least understood. These viruses potentially maintain microbiome equilibrium critical for kelp health via lytic-lysogenic infections and the expression of folate biosynthesis genes. In-situ kelp mesocosm cultivation and metagenomic mining revealed that kelp holobiont profoundly reshaped surrounding seawater and sediment virus–prokaryote pairings through changing surrounding environmental conditions and virus–host migrations. Some kelp epiphytic viruses could even infect sediment autochthonous bacteria after deposition. Moreover, the presence of ample viral auxiliary metabolic genes for kelp polysaccharide (e.g. laminarin) degradation underscores the underappreciated viral metabolic influence on macroalgal carbon cycling. This study provides key insights into understanding the previously overlooked ecological significance of viruses within macroalgal holobionts and the macroalgae–prokaryotes–virus tripartite relationship.
Enantioselective transformation of phytoplankton-derived dihydroxypropanesulfonate by marine bacteria
Authors: Liu Le , Gao Xiang , Dong Changjie , Wang Huanyu , Chen Xiaofeng , Ma Xiaoyi , Liu Shujing , Chen Quanrui , Lin Dan , Jiao Nianzhi , Tang Kai 
Published: May 2024

Abstract
Chirality, a fundamental property of matter, is often overlooked in the studies of marine organic matter cycles. Dihydroxypropanesulfonate (DHPS), a globally abundant organosulfur compound, serves as an ecologically important currency for nutrient and energy transfer from phytoplankton to bacteria in the ocean. However, the chirality of DHPS in nature and its transformation remain unclear. Here, we developed a novel approach using chiral phosphorus-reagent labeling to separate DHPS enantiomers. Our findings demonstrated that at least one enantiomer of DHPS is present in marine diatoms and coccolithophores, and that both enantiomers are widespread in marine environments. A novel chiral-selective DHPS catabolic pathway was identified in marine Roseobacteraceae strains, where HpsO and HpsP dehydrogenases at the gateway to DHPS catabolism act specifically on R-DHPS and S-DHPS, respectively. R-DHPS is also a substrate for the dehydrogenase HpsN. All three dehydrogenases generate stable hydrogen bonds between the chirality-center hydroxyls of DHPS and highly conserved residues, and HpsP also form coordinate–covalent bonds between the chirality-center hydroxyls and Zn2+, which determines the mechanistic basis of strict stereoselectivity. We further illustrated the role of enzymatic promiscuity in the evolution of DHPS metabolism in Roseobacteraceae and SAR11. This study provides the first evidence of chirality’s involvement in phytoplankton-bacteria metabolic currencies, opening a new avenue for understanding the ocean organosulfur cycle.
Three-years of dalbavancin use at a UK tertiary referral hospital serving a population with high numbers of people who inject drugs
Authors: Bresges Carolin , Bresges Kristina , Hewitt Claudette , Sharma Sunil , Davies Bethany 
Published: May 2024

Abstract

Background
Dalbavancin’s unique properties have led to an increase in its off-licence use in complex infection and in vulnerable populations including people who inject drugs (PWID), but data remain limited. In this retrospective cohort study, we describe the characteristics, treatment rationale and outcomes for all adult inpatients treated with dalbavancin at a UK tertiary hospital.

Results
Fifty-eight inpatients were treated with dalbavancin between 1 January 2018 and 1 January 2021, 98.3% for off-licence diagnoses. Acute bacterial skin and skin structure infection, infective endocarditis and endovascular infections were each diagnosed in 22.4% of patients. Bone and joint infections were diagnosed in 18.9%, discitis in 12.1% and central line-associated bloodstream infections in 5.2%. Sixty-nine percent of patients were bacteraemic; 52.5% Staphylococcus aureus, 5.0% MRSA. Two mild adverse reactions were attributed to dalbavancin. Treatment was successful in 43 (75.4%) patients, and failed in seven (12.3%). Seven (12.3%) were lost to follow-up.
Thirty-five patients (60.3%) were PWID, with low median age (41.0 years) and Charlson Comorbidity scores (0). Self-discharge was taken by 17.1% of PWID, and 20.6% were lost to follow-up. At 90 days, three (8.6%) PWID were deceased.

Conclusions
In this first UK cohort, dalbavancin was used off licence and in persons facing barriers to conventional therapies. Where data is available, it was safe and effective. Dalbavancin appears a potentially valuable tool in improving outcomes for PWID.
Antimicrobial resistance and ESBL production in uropathogenic Escherichia coli: a systematic review and meta-analysis in Ethiopia
Authors: Asmare Zelalem , Erkihun Mulat , Abebe Wagaw , Tamrat Ephrem 
Published: May 2024

Abstract

Background
Antimicrobial resistance (AMR) is a serious threat to global health systems. Escherichia coli is a major cause of urinary tract infections (UTIs). Understanding the AMR patterns of uropathogenic E. coli (UPEC) is crucial for effective public health interventions worldwide.

Objectives
This systematic review and meta-analysis aimed to consolidate existing research and provide a comprehensive information on AMR UPEC in Ethiopia.

Methods
We systematically searched databases such as PubMed, Web of Science, and Science Direct, along with including articles from Google Scholar. Data were extracted into Microsoft Excel and analysed using STATA 17.0. Cohen’s kappa was computed to assess reviewer agreement, while the I2 statistic evaluated heterogeneity. Egger’s tests were conducted to detect publication bias, and random-effects models were utilized to estimate the pooled resistance, with AMR rates for each antibiotic pooled separately.

Results
UPEC showed resistance rates, ranging from 3.64% (95% CI: −4.38% to 11.67%) for amikacin to 85.32% (95% CI: 78.6%–92.04%) for ampicillin. Highest resistance was to ampicillin (85.32%), followed by amoxicillin at 82.52% (95% CI: 74.3%–90.74%), tetracycline at 60.67% (95% CI: 51.53%–69.81%) and trimethoprim/sulfamethoxazole at 57.17% (95% CI: 49.93%–64.42%). Conversely, resistance rates were lower for amikacin at 3.64% and meropenem at 5.26% (95% CI: 2.64%–7.88%). UPEC demonstrated a pooled MDR rate of 79.17% (95% CI: 70.32%–88.01%) and a pooled ESBL production rate of 29.16% (95% CI: 22.36%–38.55%).

Conclusions
High levels of AMR were observed in UPEC strains, highlighting a critical public health issue requiring urgent action through robust antimicrobial stewardship and surveillance to preserve effective UTI treatment options.
Connected fragments: an early Hong Kong archaeological collection
Authors: Fraser Tullia C , Sung Agnes P Y , Chiesa Benjamin 
Published: May 2024

Abstract
During a refurbishment project at the University Museum and Art Gallery of the University of Hong Kong in 2018, a large collection of uncatalogued artefacts was discovered. Between February and September 2021 an internal project team conducted a preliminary review of this material, identifying it as an orphaned collection of bulk archaeological finds, largely from Hong Kong, collected in various excavations from the 1920s to 1967. This article offers an account of this reviewing exercise and provides insights into the histories of the formation and deposition of the collection. By identifying key individuals and the excavations involved, we situate the artefacts within the broader study of the development of archaeology in Hong Kong, and show that they constitute one of the earliest composite archaeological legacy collections in the city.
Rapid molecular species identification of mammalian scat samples using nanopore adaptive sampling
Authors: Frank Lexi E , Lindsey Laramie L , Kipp Evan J , Faulk Christopher , Stone Suzanne , Roerick Tanya M , Moore Seth A , Wolf Tiffany M , Larsen Peter A 
Published: May 2024

Abstract
Accurate taxonomic species identification is essential to the study of mammals. Despite this necessity, rapid and accurate identification of cryptic, understudied, and elusive mammals remains challenging. Traditional barcoding of mitochondrial genes is standard for molecular identification but requires time-consuming wet-lab methodologies. Recent bioinformatic advancements for nanopore sequencing data offer exciting opportunities for noninvasive and field-based identification of mammals. Nanopore adaptive sampling (NAS), a polymerase chain reaction (PCR)-free method, selectively sequences regions of DNA according to user-specified reference databases. Here, we utilized NAS to enrich mammalian mitochondrial genome sequencing to identify species. Fecal DNA extractions were sequenced from 9 mammals, several collected in collaboration with Minnesota Tribal Nations, to demonstrate utility for NAS barcoding of noninvasive samples. By mapping to the entire National Center for Biotechnology Information mammalian mitochondrial reference genome database and bioinformatically analyzing highly similar matches, we successfully produced species identifications for all fecal samples. Eight of 9 species identifications matched previous PCR or animal/fecal appearance-based identifications. For the ninth species, our genetic data indicate a misidentification stemming from the original study. Our approach has a range of applications—particularly in field-based wildlife research, conservation, disease surveillance, and monitoring of wildlife trade. Of importance to Minnesota tribes is invasive species monitoring, detections, and confirmation as climate impacts cause changes in biodiversity and shifts in species distributions. The rapid assessment techniques described here will be useful as new introductions and range expansions of native and invasive species may first be detected by the presence of signs such as scat rather than direct observations and will be helpful for chronically understaffed tribal natural resources agencies.
Negative strengthening: The interplay of evaluative polarity and scale structure
Authors: Gotzner Nicole , Mazzarella Diana 
Published: May 2024

Abstract
This work investigates absolute adjectives in the not very construction and how their pragmatic interpretation depends on the evaluative polarity and the scale structure of their antonymic pairs. Our experimental study reveals that evaluatively positive adjectives (clean) are more likely to be strengthened than evaluatively negative ones (dirty), and that maximum standard adjectives (clean or closed) are more likely to be strengthened than minimum standard ones (dirty or open). Our findings suggest that both evaluative polarity and scale structure drive the asymmetric interpretation of gradable adjectives under negation. Overall, our work adds to the growing literature on the interplay between pragmatic inference, valence and semantic meaning.
A peculiar presentation of tamponade: pericardial mesothelioma
Authors: Syed Ahmad Syed Danial , Kirk Frazer , Wijesinghe Wisalya , He Cheng , Stroebel Andrie 
Published: May 2024

Abstract
Pericardial mesothelioma (PM) is rare with only 200 cases recorded, and a post-mortem prevalence of &lt;0.0022%. It is the third most common cardiac/pericardial tumour, behind angiosarcoma and rhabdomyosarcoma. PM incidence increases with age, typically incidentally diagnosed between 50 and 70 years, with a 3:1 male predominance. Occasional PM can cause chest pain, dyspnoea, cough and even dysphagia. PMs are often misdiagnosed with only 25% of cases being antemortem diagnoses. Unlike pleural mesothelioma, the link between asbestos exposure and malignancy is less convincing, with only 20% of cases having known exposure. 6 There are three histological types: epithelioid, fibrous (spindle cell), and biphasic (mixed). The average life-expectancy post diagnosis is 3–10 months. Due to the heterogeneity of the presentation and rarity there is no standardized management algorithm, and the diagnostic imaging or laboratory investigations are scarcely described. We are presenting one of the cases diagnosed in our unit here in the Gold Coast.
Salvage surgery for recurrent transdiaphragmatic thymoma in a patient not eligible for chemotherapy
Authors: Fabbri Giulia , Berjaoui Nabih , Lampridis Savvas , Bilkhu Rajdeep , Chauhan Ishaan , Kew Ee Phui , Patel Akshay , Bille Andrea 
Published: May 2024

Abstract
The recurrence rate following thymoma surgery has been reported to be as high as 29%. In cases of localized recurrence, complete resection can result in prolonged patient survival. However, surgery is rarely considered in cases of invasive recurrent thymomas with high disease burden. Here, we present the case of a woman with type B2 thymoma (Masaoka–Koga stage IVa) treated with surgery, chemotherapy, and radiotherapy. The disease recurred 6 years later, with invasion of the left lung and the 12th thoracic vertebra, as well as extension into the retroperitoneum. Due to the development of chemotherapy-associated toxicity, she underwent surgery with complete tumor resection and has remained free of disease at a 12-months follow-up. Radical surgery for recurrent invasive thymoma extending through the diaphragm is a feasible and safe therapeutic option in highly selected patients who are not eligible for systemic treatments.
Robotic-assisted partial nephrectomy for a neuroendocrine tumor in a horseshoe kidney: a case report
Authors: Kikkawa Kazuro , Maruno Kouhei , Hazama Tatsuya , Takahashi Toshifumi , Yamada Yuya , Nakashima Masakazu , Tamaki Masahiro , Ito Noriyuki 
Published: May 2024

Abstract
Neuroendocrine tumors of the kidney are exceedingly rare. We report the first case of robotic-assisted partial nephrectomy for such tumors in horseshoe kidneys. A 65-year-old woman was incidentally found to have a 27 mm renal mass in the isthmus of her horseshoe kidney during computed tomography. Based on contrast-enhanced computed tomography results, we initially suspected renal cell carcinoma originating from the horseshoe kidney. Subsequently, robotic-assisted partial nephrectomy with isthmus transection was performed. Intraoperatively, we adjusted the port position for camera insertion and the patient’s positioning to facilitate better visualization for dorsal isthmus and vessel dissection. Pathological examination and immunohistochemical analysis revealed a well-differentiated neuroendocrine tumor. Therefore, robotic-assisted partial nephrectomy is a safe and effective approach for managing neuroendocrine tumors in the isthmus of horseshoe kidneys. Given the nonspecific clinical presentation of renal neuroendocrine tumors and their rarity, the optimal management of these tumors remains controversial.
Malat1 affects transcription and splicing through distinct pathways in mouse embryonic stem cells
Authors: Aslanzadeh Morteza , Stanicek Laura , Tarbier Marcel , Mármol-Sánchez Emilio , Biryukova Inna , Friedländer Marc R 
Published: May 2024

Abstract
Malat1 is a long-noncoding RNA with critical roles in gene regulation and cancer metastasis, however its functional role in stem cells is largely unexplored. We here perform a nuclear knockdown of Malat1 in mouse embryonic stem cells, causing the de-regulation of 320 genes and aberrant splicing of 90 transcripts, some of which potentially affecting the translated protein sequence. We find evidence that Malat1 directly interacts with gene bodies and aberrantly spliced transcripts, and that it locates upstream of down-regulated genes at their putative enhancer regions, in agreement with functional genomics data. Consistent with this, we find these genes affected at both exon and intron levels, suggesting that they are transcriptionally regulated by Malat1. Besides, the down-regulated genes are regulated by specific transcription factors and bear both activating and repressive chromatin marks, suggesting that some of them might be regulated by bivalent promoters. We propose a model in which Malat1 facilitates the transcription of genes involved in chromatid dynamics and mitosis in one pathway, and affects the splicing of transcripts that are themselves involved in RNA processing in a distinct pathway. Lastly, we compare our findings with Malat1 perturbation studies performed in other cell systems and in vivo.
Immunogenicity of Current and Next-Generation Pneumococcal Conjugate Vaccines in Children: Current Challenges and Upcoming Opportunities
Authors: Feemster Kristen , Buchwald Ulrike K , Banniettis Natalie , Joyce Joseph G , Velentgas Priscilla , Chapman Timothy J , Yildirim Inci 
Published: May 2024

Abstract
Global use of pneumococcal conjugate vaccines (PCVs) with increasingly broader serotype coverage has helped to reduce the burden of pneumococcal disease in children and adults. In clinical studies comparing PCVs, higher-valency PCVs have met noninferiority criteria (based on immunoglobulin G geometric mean concentrations and response rates) for most shared serotypes. A numeric trend of declining immunogenicity against shared serotypes with higher-valency PCVs has also been observed; however, the clinical relevance is uncertain, warranting additional research to evaluate the effectiveness of new vaccines. Novel conjugation processes, carriers, adjuvants, and vaccine platforms are approaches that could help maintain or improve immunogenicity and subsequent vaccine effectiveness while achieving broader protection with increasing valency in pneumococcal vaccines.
Strain Differences in Bloodstream and Skin Infection: Methicillin-Resistant Staphylococcus aureus Isolated in 2018–2021 in a Single Health System
Authors: Hofstetter Katrina S , Jacko Natasia F , Shumaker Margot J , Talbot Brooke M , Petit Robert A , Read Timothy D , David Michael Z 
Published: May 2024

Abstract
Staphylococcus aureus is a common cause of skin and soft-tissue infections (SSTIs) and has become the most common cause of bloodstream infections (BSIs) in recent years, but whether the strains causing these two clinical syndromes overlap has not been studied adequately. USA300/500 (clonal complex [CC] 8–sequence type [ST] 8) and USA100 (CC5-ST5) have dominated among methicillin-resistant S aureus (MRSA) strains in the United States since the early 2000s. We compared the genomes of unselected MRSA isolates from 131 SSTIs with those from 145 BSIs at a single US center in overlapping periods in 2018–2021. CC8 MRSA was more common among SSTIs, and CC5 was more common among BSIs, consistent with prior literature. Based on clustering genomes with a threshold of 15 single-nucleotide polymorphisms, we identified clusters limited to patients with SSTI and separate clusters exclusively comprising patients with BSIs. However, we also identified eight clusters that included at least one SSTI and one BSI isolate. This suggests that virulent MRSA strains are transmitted from person to person locally in the healthcare setting or the community and that single lineages are often capable of causing both SSTIs and BSIs.
Nocardia Infection in Patients With Anti–Granulocyte-Macrophage Colony-Stimulating Factor Autoantibodies: A Prospective Multicenter French Study
Authors: Kerdiles Thibault , Lejeune Sophie , Portais Antoine , Bourgeois Gaelle , Lefevre Benjamin , Charmillon Alexandre , Sixt Thibault , Moretto Florian , Cornille Cyril , Vidal Magali , Coustillères François , Martellosio Jean-Philippe , Quenet Marion , Belan Martin , Andry Fanny , Jaffal Karim , Pinazo-Melia Angela , Rondeau Paul , Luque Paz David , Jouneau Stephane , Borie Raphael , Monnier Delphine , Lebeaux David ,   GM-Noc Study Group, Bergeron-Lafaurie Anne , Carpentier-Blanc Gabrielle , Cottin Vincent , Froidure Marie , Duverge Alice Hadchouel , Jouneau Stéphane , Laurent Frédéric , Lepeule Raphael , Lortholary Olivier , Mahévas Matthieu , Ménard Cédric , Rodriguez-Nava Véronica , Traclet Julie 
Published: May 2024

Abstract

Background
Nocardiosis, a bacterial opportunistic infection caused by Nocardia spp, has recently been reported in patients with anti–granulocyte-macrophage colony-stimulating factor (GM-CSF) autoantibodies, but insufficient data are available about disease presentation, outcomes, and occurrence of autoimmune pulmonary alveolar proteinosis (aPAP) in this population.

Methods
We performed a prospective, multicenter, nationwide study in France and included patients with a Nocardia infection who had anti-GM-CSF autoantibodies. We describe their clinical, microbiological, and radiological characteristics, and their outcome at 1 year of follow-up.

Results
Twenty patients (18 [90%] male) were included, with a median age of 69 (interquartile range, 44–75) years. The organs most frequently involved were the brain (14/20 [70%]) and the lung (12/20 [60%]). Half of the infections were disseminated (10/20 [50%]). Nocardia identification was predominantly made in abscess fluid (17/20 [85%]), among which 10 (59%) were brain abscesses. The 1-year all-cause mortality was 5% (1/20), and only 1 case of aPAP (1/20 [5%]) occurred during the follow-up period.

Conclusions
Nocardiosis with anti-GM-CSF autoantibodies is associated with a low mortality rate despite a high incidence of brain involvement. Although the occurrence of aPAP was infrequent during the 1-year follow-up period, long-term clinical data are needed to fully understand the potential relationship between nocardiosis, anti-GM-CSF autoantibodies, and aPAP.