bluuebunny/crossref_metadata_2025_split huggingface dataset:
Marine phytoplankton impose strong selective pressures on in vitro microbiome assembly, but drift is the dominant process
Authors: Morales Sergio E , Tobias-Hünefeldt Sven P , Armstrong Evelyn , Pearman William S , Bogdanov Kirill 
Published: January 2025

Abstract
Phytoplankton are known ecosystem engineers that modulate ocean community assembly processes, but the universality and extent of their microbiome control remains unclear. We used in vitro incubations and 16S ribosomal RNA gene amplicon sequencing to test the influence of Southern and South Pacific oceans dominant phytoplankton on assembly processes and community successions in response to phytoplankton blooms. Phytoplankton grown with reduced-diversity cultures or supplemented with exogenously added microbiomes showed reduced diversity, suggesting environmental filtering. Community profiles were distinct under all culture conditions, further confirming strong selection for specific microbiomes based on phytoplankton. Analysis of core, abundant, and rare organisms in each culture condition showed a conserved response in which core organisms were enriched under conditions of exogenously added phytoplankton. Progression through phytoplankton growth phases selected first for rare and abundant organisms, with increased selection for core members during the exponential phase and relaxing of selection during the death phase, as seen throughout incubations for microbiome-only controls. Surprisingly, selection process quantification identified drift as the dominant process across all conditions and growth phases, with homogenous selection and dispersal limitation accounting for the remainder. Altogether, using Southern Ocean–derived model organisms we confirmed the role phytoplankton play in community assembly but also demonstrated that stochastic processes still predominately drive community selection.
Emergence of multi-drug-resistant, vancomycin-resistant, and multi-virulent Enterococcus species from chicken, dairy, and human samples in Egypt
Authors: Abd El-Hamid Marwa I , Abd El-Aziz Norhan K , Ammar Ahmed M , Gharib Ahlam A , Ibrahim Ghada A , Moawed Basma F M , Alshamy Hend , El-Malt Rania M S 
Published: January 2025

Abstract

Aims
The present study aimed to detect the frequency of vancomycin resistance and virulence genes’ profiles of multi-drug-resistant (MDR) enterococcal isolates from different sources and to investigate the sequence heterogeneity between the esp genes of MDR and vancomycin-resistant Enterococcus faecalis isolates from chicken and human sources.

Methods and results
Conventional phenotypic methods identified 91 isolates (60.7%) as Enterococcus species, and these isolates were retrieved from dairy (37/52), chicken (35/54), and human (19/44) origins. Enterococcal isolates were frequently resistant to rifampin (67%), and 38.5% of the isolates were MDR. Of the 22 vancomycin-resistant enterococci (VRE) detected isolates, 11 (50%), 9 (41%), 1 (4.5%), and 1 (4.5%) isolate were identified as E. faecium, E. faecalis, E. casseliflavus, and un-specified Enterococcus spp., respectively. Moreover, 22 (100%) and 19 (86.4%) isolates harbored vanA and vanB genes, respectively. Of note, gelE and asa1 genes were more prevalent among the tested isolates (95.5% each), and the multi-virulence criteria were detected among 68.2% of the examined isolates. The sequences of esp genes of E. faecalis from the chicken breast meat and human urine samples were 100% identical with other esp genes and pathogenicity islands on GeneBank, which is undesirable.

Conclusion
Our findings require strict hygienic measures during the processing of chickens and their by-products to minimize the possibility of transmission of virulent enterococcal strains. Furthermore, the use of antimicrobials in poultry and animal production in developing countries should be controlled to minimize the prevalence of MDR and VRE isolates in humans.
Multi-modal prediction of extracorporeal support—a resource intensive therapy, utilizing a large national database
Authors: Zhu Daoyi , Xue Bing , Shah Neel , Payne Philip Richard Orrin , Lu Chenyang , Said Ahmed Sameh 
Published: January 2025

Abstract

Objective
Extracorporeal membrane oxygenation (ECMO) is among the most resource-intensive therapies in critical care. The COVID-19 pandemic highlighted the lack of ECMO resource allocation tools. We aimed to develop a continuous ECMO risk prediction model to enhance patient triage and resource allocation.

Material and Methods
We leveraged multimodal data from the National COVID Cohort Collaborative (N3C) to develop a hierarchical deep learning model, labeled “PreEMPT-ECMO” (Prediction, Early Monitoring, and Proactive Triage for ECMO) which integrates static and multi-granularity time series features to generate continuous predictions of ECMO utilization. Model performance was assessed across time points ranging from 0 to 96 hours prior to ECMO initiation, using both accuracy and precision metrics.

Results
Between January 2020 and May 2023, 101 400 patients were included, with 1298 (1.28%) supported on ECMO. PreEMPT-ECMO outperformed established predictive models, including Logistic Regression, Support Vector Machine, Random Forest, and Extreme Gradient Boosting Tree, in both accuracy and precision at all time points. Model interpretation analysis also highlighted variations in feature contributions through each patient’s clinical course.

Discussion and Conclusions
We developed a hierarchical model for continuous ECMO use prediction, utilizing a large multicenter dataset incorporating both static and time series variables of various granularities. This novel approach reflects the nuanced decision-making process inherent in ECMO initiation and has the potential to be used as an early alert tool to guide patient triage and ECMO resource allocation. Future directions include prospective validation and generalizability on non-COVID-19 refractory respiratory failure, aiming to improve patient outcomes.
A review of the Quichua Porcupine Coendou quichua complex (Rodentia: Erethizontidae) with the description of a new species from Colombia
Authors: Ramírez-Chaves Héctor E , Mazepa Glib O , Morales-Martínez Darwin M , Suárez-Castro Andrés Felipe , Colmenares-Pinzón Javier E , Pulido-Santacruz Paola , Noguera-Urbano Elkin A 
Published: January 2025

Abstract
Coendou quichua is a widely distributed trans-Andean species in Colombia, Ecuador, and Panama. However, analysis of the cytochrome b (Cytb) gene suggests the presence of cryptic diversity. Recent reviews found that morphological variation within this taxon is mainly associated with elevation. Still, mitochondrial divergence values between some populations are similar to those reported between well-diagnosable sister species in the genus. Here, we provide new Cytb sequences from Colombian and Ecuadorian specimens and morphological observations from specimens collected in different natural regions to show that C. quichua is indeed a species complex. Coendou quichua complex contains 3 separate lineages: (i) the typical C. quichua from the Andes of Ecuador; (ii) a sister lineage from the Chocó-Darién ecoregion; and (iii) an undescribed new species from wet and dry forests of the Magdalena inter-Andean valley and the Caribbean regions of Colombia. Based on morphological, ecological niche modeling, and geographical analyses, the lineage from Chocó-Darién in Colombia and Ecuador is here treated as a different species for which the name C. rothschildi is available. The lineage involving samples from the wet and dry forests of the Magdalena inter-Andean Valley and the Caribbean regions represents an unnamed taxon described herein as Coendou vossi sp. nov., endemic to Colombia.
Are the protections offered by EU law adequate alternatives to those offered by international investment law?
Authors: Gáspár-Szilágyi Szilárd 
Published: January 2025

Abstract
This article, within the Special Issue’s ‘Justice beyond investor-state dispute settlement’ theme, looks at whether the protections offered by European Union (EU) law are adequate alternatives to those offered by international investment law (IIL) in the post-Achmea world of intra-EU investment protection. While EU law offers far-reaching protections to businesses operating in the EU, sometimes going beyond the protections offered by IIL, from an investment law perspective the article argues that not all the substantive and procedural protections offered by EU law are adequate for the purposes of IIL. This is because investment law has a narrower focus on protecting and promoting investments, which in turn influences how the legal provisions are interpreted. EU law, on the other hand, has the much broader and deeper purpose of creating an ‘ever-closer’ Union with an internal market, a ‘systemic’ purpose that permeates the Court of Justice of the European Union (CJEU)’s interpretation of EU law. Thus, the deeper we look, the more differences we find in the personal and material scope of the two systems, the substantive standards of treatment, the derogations from the substantive standards, and the procedural protections and remedies. Coming full circle, the different epistemic communities of adjudicators, just like the different purposes and objectives, result in similar or the same concepts being interpreted differently. It is quite unfortunate that the CJEU viewed these two systems as competitors, in which investor–State arbitration ‘removed’ cases from the jurisdiction of EU Member State courts, when in fact they are complementary systems of protection.
Different approaches to managing bilateral distal femur periprosthetic fractures in a single patient: case reports and review of the literature
Authors: Castagno Christopher , Klahs Kyle J , Adler Adam , Hosseini Mehrdad , Ofori Brendon , Abdelgawad Amr , Thabet Ahmed M 
Published: January 2025

Abstract
A 61-year-old female with a bilateral total knee arthroplasty (2010) and subsequent separate bilateral distal femur periprosthetic fractures (2020 and 2022) treated with distal femur replacement (left) and retrograde intramedullary nail fixation (right). Self-reported outcomes and knee injury and osteoarthritis outcome scores (KOOS) were compared. The patient reported higher pain and lower functionality with the left knee (overall KOOS of 50%) and no lasting impact or pain with the right knee (overall KOOS of 89%). When KOOS individual (P-value of &lt;0.0001) and categorical/overall (P-value of 0.0048) metrics were compared they demonstrated statistical significance. The report’s data, based solely on a one-sample-size data set, suggest that performing an intramedullary nail for distal femur periprosthetic fractures should be the preferred choice based on this patient’s improved pain, functionality, and overall satisfaction, even if anatomic alignment is difficult.
Perforated marginal ulceration in the setting of single anastomosis duodeno-ileal switch (SADI-S) with conversion to Roux-en-Y gastric bypass and literature review
Authors: Marcucci Vincent , Camarda Amanda R , Embel Veysel , Kipnis Seth 
Published: January 2025

Abstract
The single anastomosis duodenal-ileal switch (SADI-S) has become a safe alternative to Roux-en-Y gastric bypass (RYGB) in the treatment for morbid obesity. A known complication after bariatric surgery is the development of marginal ulceration. The current literature demonstrates an overwhelmingly low incidence of ulceration in patients who underwent SADI-S. The management and prevention is an ongoing subject of debate with no clear algorithm. The conversation of SADI-S to RYGB has been accomplished; however, this procedure has not been previously reported for marginal ulceration.
Essence Facts and the Source of Normativity
Authors: Baysan Umut 
Published: January 2025

Abstract
What is the source of normativity? According to Bengson, Cuneo and Shafer-Landau (2023), we can answer this question by identifying non-normative grounds of fundamental normative facts. To illustrate how this can be achieved, they argue that facts concerning essences of normative properties are non-normative facts, and such facts can be seen as non-normative grounds of fundamental normative facts. I argue that this strategy is misguided. First, explanations citing essence facts about normative properties are poor answers to the question of the source of normativity. Second, it is not clear if such facts are non-normative in the relevant sense. Along the way, I address questions about what it is to be a normative fact and relate the implications of this discussion to general issues about metaphysical explanation in meta-normativity.
Improved halo model calibrations for mixed dark matter models of ultralight axions
Authors: Dome Tibor , May Simon , Laguë Alex , Marsh David J E , Johnston Sarah , Bose Sownak , Tocher Alex , Fialkov Anastasia 
Published: January 2025

ABSTRACT
We study the implications of relaxing the requirement for ultralight axions to account for all dark matter in the Universe by examining mixed dark matter (MDM) cosmologies with axion fractions $f \le 0.3$ within the fuzzy dark matter window $10^{-25}$ eV $\lesssim m \lesssim 10^{-23}$ eV. Our simulations, using a new MDM gravity solver implemented in AxiREPO, capture wave dynamics across various scales with high accuracy down to redshifts $z\approx 1$. We identify haloes with Rockstar using the cold dark matter component and find good agreement of inferred halo mass functions and concentration–mass relations with theoretical models across redshifts $z=1{\!-\!}10$. This justifies our halo finder approach a posteriori as well as the assumptions underlying the MDM halo model AxionHMcode. Using the inferred axion halo mass–cold halo mass relation $M_{\text{a}}(M_{\text{c}})$ and calibrating a generalized smoothing parameter $\alpha$ to our MDM simulations, we present a new version of AxionHMcode. The code exhibits excellent agreement with simulations on scales $k\lt 20 \, h \, \text{cMpc}^{-1}$ at redshifts $z=1{\!-\!}3.5$ for $f\le 0.1$ around the fiducial axion mass $m = 10^{-24.5}\, \text{eV} = 3.16\times 10^{-25}\, \text{eV}$, with maximum deviations remaining below 10 per cent. For axion fractions $f\le 0.3$, the model maintains accuracy with deviations under 20 per cent at redshifts $z\approx 1$ and scales $k\lt 10 \, h \, \text{cMpc}^{-1}$, though deviations can reach up to 30 per cent for higher redshifts when $f=0.3$. Reducing the run-time for a single evaluation of AxionHMcode to below 1 min, these results highlight the potential of AxionHMcode to provide a robust framework for parameter sampling across MDM cosmologies in Bayesian constraint and forecast analyses.
The NAC transcription factor LpNAC48 promotes trichome formation in Lilium pumilum
Authors: Xin Yin , Pan Wenqiang , Zhao Yajie , Yang Chenglong , Li Jingru , Wang Shaokun , Wu Jingxiang , Zhang Mingfang , Shi Jinxin , Ma Yang , Fang Shaozhong , Liang Yuwei , Zaccai Michele , Zhang Xiuhai , Du Yunpeng , Wu Jian 
Published: January 2025

Abstract
Trichomes play a crucial role in plant resistance to abiotic and biotic stresses, and their development and characteristics vary across different species. This study demonstrates that trichomes of Lilium pumilum exhibit synchronized growth during flower bud differentiation and enhance the plant's adaptability to UV-B radiation and aphid infection. We identified LpNAC48, a NAC family transcription factor (TF), that interacted with the B-box (BBX) family TF LpBBX28 during trichome formation in L. pumilum. Silencing LpNAC48 or LpBBX28 impaired trichome development and reduced trichome density on the outer perianths. We demonstrated that the upstream regulators LpNAC48 and LpBBX28 directly bound to the promoter of the bHLH TF-encoding gene LpGL3-LIKE (LpGL3L) to activate its expression. Moreover, an ABA-responsive element within a 259-bp DNA variation in the LpNAC48 promoter was important for its expression and was bound by the bZIP TF LpbZIP29 during trichome development. This binding activated LpNAC48 expression and contributed to trichome formation. This study provides insights into the role of a small DNA sequence variation in gene expression and trichome traits.
Schizophrenia Following Early Adolescence Prodrome: A Neurodevelopmental Subtype With Autism-like Sensorimotor and Social Cognition Deficits
Authors: Iftimovici Anton , Martinez Gilles , Victor Julie , Bendjemaa Narjès , Jantac Célia , Danset-Alexandre Charlotte , Amado Isabelle , Pina-Camacho Laura , Chaumette Boris , Fatjó-Vilas Mar , Fañanás Lourdes , Duchesnay Edouard , Krebs Marie-Odile 
Published: January 2025

Abstract

Background and Hypothesis
While age at onset in schizophrenia (SCZ) is usually defined by age at onset of psychosis, the illness actually occurs earlier, with a prodrome often starting in childhood or adolescence. We postulated that SCZ with early-adolescence prodromes (SCZ-eaP) presents with social cognition deficits and sensorimotor impairments more similar to autism spectrum disorders (ASD) than SCZ with late-adolescence prodromes (SCZ-laP).

Study Design
The movie for the assessment of social cognition and neurological soft signs (NSS) were compared between four groups, ASD, SCZ-eaP (&lt;15 years), SCZ-laP (&gt;15 years), and controls (N = 119), while accounting for age, sex, intelligence quotient, education level, and medication effect. Mediation analyses tested the effect of NSS on social cognition, across groups, and local gyrification indices were used to test whether NSS reflected deviations in early neurodevelopmental trajectories.

Study Results
For social cognition and NSS, subjects with ASD were not different from SCZ-eaP, while they differed from SCZ-laP. Age at onset of prodrome correlated with NSS (r = −0.34, P = .018), and social cognition (r = 0.28, P = .048). Neurological soft signs mediated social cognition impairment across diagnoses (β = −1.24, P &lt; 1e−6), and was explained by hypergyrification in the right fusiform gyrus, right frontal pole gyrus, and left postcentral gyrus.

Conclusions
Earlier age of prodrome in SCZ is associated with impaired social cognition, mediated by neurodevelopmentally-related sensorimotor impairments along the ASD-SCZ spectrum. It suggests age of prodrome, rather than the age at psychosis onset, should be considered to define more homogeneous subgroups in SCZ.
‘We Need Time…’: An Expert Survey on Societal Acceptance of Urban Drones
Authors: Wang Ning , Mutzner Nico , Blanchet Karl 
Published: January 2025

Abstract
Drones are rapidly becoming integral components of urban air mobility. Their integration into urban environments hinges not just on broader public sentiments but also on the perceptions of experts who drive their development, deployment, and management. This study delves into experts’ perspectives on urban drones to supplement existing knowledge by improving the understanding of acceptance factors and associated challenges. The results indicate that themes of privacy, safety, and regulation are recurring. Notably, trust towards different institutions deploying drones varies, while the need for dedicated awareness and education efforts to inform public understanding is an emergent theme. Overall, the insights gained accentuate the importance of governance strategies that consider all stakeholders’ viewpoints and the intertwined nature of challenges they are faced with. This calls for the scientific community to support the development of effective framework conditions alongside enhanced stakeholder collaborations towards a smooth integration of urban drones in society.
HIV Vaccine Research Coordination by the World Health Organization Between 1990 and 1995: Negotiating the Access to Research Cohorts of Military Subjects
Authors: David Pierre-Marie 
Published: January 2025

Summary
This article presents how acquired immunodeficiency syndrome (AIDS) vaccine research was coordinated internationally between 1990 and 1995 by creating a special unit within the World Health Organization (WHO), the AIDS Vaccine Development (VAD) unit. This WHO’s international coordination constituted a paradoxical repoliticisation of international human immunodeficiency virus (HIV) research, as it centralised scattered, privatised and sometimes hidden research within a single international organisation, while also reinscribing research in southern countries into ambivalent, postcolonial power relations by means of humanist arguments and research cohorts of military subjects. This history is important because the WHO coordination appears to have unwillingly elided the sociopolitical conditions of possibility for experimentation that were also, in part, driving the explosion of HIV infection on the continent at that time. Finally, it helps reflect on how the current global health paradigm of accelerated research for innovations and vaccine development can institute uneven research infrastructures.
Understanding pediatric cervicofacial non-tuberculous mycobacterial infection
Authors: Im Eunice , Gawel Erin , Coppola Alyson , Carr Michele 
Published: January 2025

ABSTRACT
Cervicofacial non-tuberculous mycobacterial infection should be a part of the differential diagnosis for immunocompetent children ages 1 to 5 years who present with painless submandibular or preauricular lymphadenopathy. Although a benign and self-limiting disease, patients can develop a chronically draining fistula if not diagnosed and treated promptly. The diagnostic process can be managed with a combination of microbiological studies, cytology, laboratory tests, and imaging studies. Surgical excision is the most definitive curative measure. Incision and curettage, medical management with antibiotic therapy, or observation are other treatment strategies that may be considered. Frontline clinicians play a pivotal role in identifying which children may have this condition and can facilitate prompt diagnosis and treatment of this uncommon disease.
Chimeric antigen receptor therapy in hematologic malignancies
Authors: Brownlee Elizabeth , Turley Melissa , Nations Heather 
Published: January 2025

ABSTRACT
Chimeric antigen receptor (CAR) T-cell therapy has led to significant advances in the treatment of blood cancers such as leukemia, lymphoma, and multiple myeloma, and now shows promise for solid tumors. This type of immunotherapy can achieve high response rates in patients with hematologic malignancies, but carries serious adverse reactions, including cytokine release syndrome and immune-effector cell-associated neurotoxicity syndrome. This article describes CAR T-cell therapy, guidance for primary care providers caring for patients undergoing therapy, and the ongoing need for research to enhance CAR T-cell therapy's safety and effectiveness.