bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of host species on assembly, composition, and functional profiles of phycosphere microbiomes
Authors: Roager Line , Kempen Paul J. , Bentzon-Tilia Mikkel , Sonnenschein Eva C. , Gram Lone 
Published: November 2023

AbstractMicroalgal microbiomes play vital roles in the growth and health of their host, however, their composition and functions remain only partially characterized, especially across microalgal phyla. In this study, a natural seawater microbiome was introduced to three distinct, axenic species of microalgae, the haptophyteIsochrysis galbana,the chlorophyteTetraselmis suecica,and the diatomConticribra weissflogii(previouslyThalassiosira), and its divergence and assembly was monitored over 49 days using 16S rRNA amplicon and metagenomic analyses. The microbiomes had a high degree of host specificity in terms of taxonomic composition and potential functions, including CAZymes profiles. Rhodobacteraceae and Flavobacteriaceae families were abundant across all microalgal hosts, butI .galbanamicrobiomes diverged further fromT. suecicaandC. weissflogiimicrobiomes.I .galbanamicrobiomes had a much higher relative abundance of Flavobacteriaceae, whereas the two other algal microbiomes had higher relative abundances of Rhodobacteraceae. This could be due to the mixotrophic nature ofI. galbanaaffecting the carbohydrate composition available to the microbiomes, which was supported by the CAZymes profile ofI. galbanamicrobiomes diverging further from those ofT. suecicaandC. weissflogiimicrobiomes. Finally, the presence of denitrification and other anaerobic pathways was found exclusively in microbiomes ofC. weissflogiipotentially resulting from anoxic microenvironments in aggregates formed by this diatom during the experiment. These results underline the deterministic role of the microalgal host species on microbiome composition and functional profiles along with other factors, such as trophic mode of the microalgal host.ImportanceAs the main primary producers of the oceans, microalgae serve as cornerstones of the ecosystems they are part of. Additionally, they are increasingly used for biotechnological purposes such as the production of nutraceuticals, pigments, and antioxidants. Since the bacterial microbiomes of microalgae can affect their hosts in beneficial and detrimental ways, understanding these microbiomes is crucial to both ecological and applied roles of microalgae. The present study advances the understanding of microalgal microbiome assembly, composition, and functionality across microalgal phyla, which may inform modeling and engineering of microalgal microbiomes for biotechnological purposes.
Transglobal spread of an ecologically significant sea urchin parasite
Authors: Ritchie Isabella T. , Vilanova-Cuevas Brayan , Altera Ashley , Cornfield Kaileigh , Evans Ceri , Evans James S. , Hopson-Fernandes Maria , Kellogg Christina A. , Looker Elayne , Taylor Oliver , Hewson Ian , Breitbart Mya 
Published: November 2023

AbstractMass mortality of the dominant coral reef herbivoreDiadema antillarumin the Caribbean in the early 1980s led to a persistent phase shift from coral-to algal-dominated reefs. In 2022, a scuticociliate most closely related toPhilaster apodigitiformiscaused further mass mortality ofD. antillarumacross the Caribbean, leading to >95% mortality at affected sites. Mortality was also reported in the related speciesDiadema setosumin the Mediterranean in 2022, where urchins experienced gross signs compatible with scuticociliatosis. However, the causative agent of the Mediterranean outbreak has not yet been determined. In April 2023, mass mortality ofD. setosumoccurred along the Sultanate of Oman’s coastline. Urchins displayed signs compatible with scuticociliatosis including abnormal behavior, drooping and loss of spines, followed by tissue necrosis and death. Here we report the detection of an 18S rRNA gene sequence in abnormal urchins from Muscat, Oman that is identical to thePhilasterstrain responsible forD. antillarummass mortality in the Caribbean. We also show that scuticociliatosis signs can be elicited inD. setosumby experimental challenge with the cultivatedPhilasterstrain associated with Caribbean scuticociliatosis. These results demonstrate thePhilastersp. associated withD. antillarummass mortality has rapidly spread to geographically distant coral reefs, compelling global-scale awareness and monitoring for this devastating condition through field surveys, microscopy, and molecular microbiological approaches, and prompting investigation of long-range transmission mechanisms.
Phenotypic heterogeneity drives phage-bacteria coevolution in the intestinal tract
Authors: Wenner Nicolas , Bertola Anouk , Larsson Louise , Rocker Andrea , Bekele Nahimi Amare , Sauerbeck Chris , Rocha Leonardo F. Lemos , Druelle Valentin , Harms Alexander , Diard Médéric 
Published: November 2023

AbstractPhenotypic heterogeneity in bacteria can generate reversible resistance against various stressors, including predation by phages. This allows mixed populations of phenotypically resistant and sensitive bacteria to coexist with virulent phages. However, it remains unclear if these dynamics prevent the evolution of genetic resistance in bacteria and how they affect the evolution of phages. In this work, we focus on bistable alterations of the O-antigen (known as phase variation) inSalmonellaTyphimurium (S.Tm) to study how heterogeneous phenotypic resistance affects phage-bacteria coevolution. Our findings reveal that phase variation allows a stable coexistence ofS.Tm with a virulent T5-like phagein vitro. This coexistence is nevertheless short-lived whenS.Tm and the phage interact within the intestinal tract of mice. In this context, the phage evolves to also infect phenotypically resistantS.Tm cells, incidentally altering infectivity on otherSalmonellaserovars. In return, the broader host range of the evolved phages drives the evolution of genetic resistance inS.Tm, which results in phage extinction. This work demonstrates that phenotypic heterogeneity profoundly influences the antagonistic coevolution of phages and bacteria, with outcomes intricately tied to the ecological context.
Design of a symmetry-broken tetrahedral protein cage by a method of internal steric occlusion
Authors: Gladkov Nika , Scott Elena A. , Meador Kyle , Lee Eric J. , Laganowsky Arthur D. , Yeates Todd O. , Castells-Graells Roger 
Published: November 2023

ABSTRACTMethods in protein design have made it possible to create large and complex, self-assembling protein cages with diverse applications. These have largely been based on highly symmetric forms exemplified by the Platonic solids. Prospective applications of protein cages would be expanded by strategies for breaking the designed symmetry,e.g., so that only one or a few (instead of many) copies of an exterior domain or motif might be displayed on their surfaces. Here we demonstrate a straightforward design approach for creating symmetry-broken protein cages able to display singular copies of outward-facing domains. We modify the subunit of an otherwise symmetric protein cage through fusion to a small inward-facing domain, only one copy of which can be accommodated in the cage interior. Using biochemical methods and native mass spectrometry, we show that co-expression of the original subunit and the modified subunit, which is further fused to an outward-facing anti-GFP DARPin domain, leads to self-assembly of a protein cage presenting just one copy of the DARPin protein on its exterior. This strategy of designed occlusion provides a facile route for creating new types of protein cages with unique properties.
Diagnostic accuracy of a remote eye exam in measuring refractive errors and detecting cataract, glaucoma, and diabetic retinopathy
Authors: Moreira Taís de Campos , Pagano Cassia Garcia Moraes , Chagas Maria Eulália Vinadé , Falavigna Maicon , Rados Dimitris Rucks Varvaki , Silva Rodolfo Souza da , Harzheim Erno , Gonçalves Marcelo Rodrigues , Umpierre Roberto Nunes , de Azevedo Pietro Baptista , Waquil Alice Paul , Fabris Caroline , Lang Martha Pereira Lima , Szortika Adriana , Szortyka Anelise , de Araujo Aline Lutz , Cabral Felipe Cezar 
Published: November 2023

AbstractPorpuseApproximately 2.2 billion people worldwide have some type of visual impairment and among these, many could have been avoided or solved if adequate care had been provided in a timely manner. In these cases, telemedicine can assist in solving the problems of many ophthalmological conditions by providing support, performing screening, telediagnosis or supervision of distant appointments. The use of telemedicine for eye health is well established for some eye diseases, such as diabetic retinopathy, macular diseases and strabismus, however, there is a lack of information on diagnostic accuracy for other ophthalmological pathologies prevalent in the world population, such as refractive errors. To evaluate the reliability of the diagnosis made through teleophthalmology, using the ophthalmologist’s face-to-face diagnosis as the gold standard.MethodsA diagnostic accuracy study was carried out, with 216 patients assessed by the TeleOftalmo project who underwent eye examinations both on-site and through telemedicine. The patients underwent refraction tests, intraocular pressure measurement, photodocumentation in the slit-lamp and subjective refraction using the visual acuity screen and the digital refractor.ResultsThe conditions evaluated were refractive errors, cataracts, diabetic retinopathy and suspected glaucoma. Kappa values, sensitivity, specificity, positive predictive value and negative predictive value were calculated. Approximately, 61.6% of the sample were women, with mean age of 47 years old. Kappa values show strong reliability regarding the diagnosis of cataracts (k = 0.86) and diabetic retinopathy (k = 0.79). Regarding refractive errors and suspected glaucoma, the kappa values were considered moderate (k = 0.598 and 0.478, respectively).ConclusionThe use of telemedicine has shown favorable results regarding the diagnosis of refractive errors, cataracts and diabetic retinopathy, as well as moderate reliability for suspected glaucoma.
Elevated Pre-Treatment Systemic Immuno-Inflammatory Indices, Triple-Negative Breast Cancer, and p53 Mutation are Associated with Early-Onset Breast Cancer in Southern Nigeria
Authors: Okoye Jude Ogechukwu , Samuel Dorcas Onyeka , Ezidiegwu Kosisochukwu Stephanie , Chiemeka Michael Emeka 
Published: November 2023

AbstractBackgroundIn West Africa, breast cancer (BC) patients have a mortality rate that is three times higher than those in North America and Northwestern Europe. This study aimed to identify high-risk patients by evaluating the pre-treatment systemic inflammatory indices, p53, and BRCA2 expressions in molecular sub-types of BC in West Africa.MethodsThis retrospective cohort study included 152 BC tissues, diagnosed between January 2017 and December 2022. The tissue sections were immunohistochemically stained for p53, BRCA2, hormone receptors, and human epidermal growth factor receptor 2 (HER2), scored, and analyzed accordingly. Statistical significance was set at p≤ 0.05.ResultsThe frequency of early-onset BC (≤ 49 years) was 58.6% while the frequency of early-onset BC among patients with a family history of cancer was 76.5%. The frequency of late-stage BC was 84.9%. The frequency of luminal A and triple-negative BC (TNBC) was 1.7 times higher in early-onset BC. In comparison, the frequency of Luminal B/B-like and HER2-enriched BC was 1.9 times higher in late-onset BC (p= 0.022). The frequency of p53 and BRCA2 mutation was 1.6 times and 1.2 times higher in early-onset BC than in late-onset BC (p= 0.003 and p= 0.843, respectively). Significant differences in pre-treatment systemic inflammatory index were observed between patients with early-onset and late-onset BC, and ≤ 6 months survival and > 12 months survival (p< 0.05).ConclusionThis study found a high incidence of early-onset BC, p53 mutation, and TNBC. Additionally, it suggests that pre-treatment systemic inflammatory indices can identify high-mortality-risk patients and early-onset BC.
Associations between D3Cr muscle mass and MR thigh muscle volume with strength, power, physical performance, fitness, and limitations in older adults in the SOMMA study
Authors: Cawthon Peggy M. , Blackwell Terri L. , Kritchevsky Stephen B. , Newman Anne B. , Hepple Russell T. , Coen Paul M. , Goodpaster Bret H. , Duchowny Kate , Hetherington-Rauth Megan , Mau Theresa , Shankaran Mahalakshmi , Hellerstein Marc , Evans William J. , Cummings Steven R. 
Published: November 2023

AbstractBackgroundDifferent measures to assess muscle size - magnetic resonance (MR) derived thigh muscle volume and d3-creatine dilution derived muscle mass (D3Cr muscle mass) – may have similar associations with strength, power, physical performance, fitness, and functional limitations in older adults.MethodsMen (N=345) and women (N=482) aged ≥70 years from the Study of Muscle, Mobility and Aging completed exams including leg extension strength (1-repetition max) and cardiopulmonary exercise testing to assess fitness (VO2peak). Correlations and adjusted regression models stratified by sex were used to assess the association between muscle size measures and study outcomes; we tested for sex interactions.ResultsD3Cr muscle mass and MR thigh muscle volume were correlated (men: r=0.62, women: r=0.51, p<.001). Lower D3Cr muscle mass and lower MR thigh muscle volume were associated with lower strength and lower VO2peak in both men and women; D3Cr muscle mass was more strongly associated with strength in men than in women (p-int<0.05). There were correlations, though less consistent, between muscle size or mass with physical performance and function. Associations between the muscle size measures and the study outcomes occasionally varied by sex, and associations of MR thigh muscle volume were, at times, slightly more strongly associated with the study outcomes than was D3Cr muscle mass.ConclusionsLess muscle –measured by either D3Cr muscle mass or MR thigh muscle volume - was associated with lower strength and worse performance. Varied associations by sex and assessment method suggest consideration be given to which measurement to use in future studies.
Chymase in Plasma and Urine Extracellular Vesicles: Novel Biomarkers for Primary Hypertension
Authors: Ahmad Sarfaraz , Deep Gagan , Punzi Henry A , Su Yixin , Singh Sangeeta , Kumar Ashish , Mishra Shalini , Saha Amit K , Wright Kendra N , VonCannon Jessica L , Dell’Italia Louis J , Meredith Wayne J , Ferrario Carlos M 
Published: November 2023

ABSTRACTBACKGROUNDExtracellular vesicles (EVs) have emerged as a promising liquid biopsy for various diseases. For the first time, using plasma and urinary EVs, we assessed the activity of renin-angiotensin system (RAS), a central regulator of renal, cardiac, and vascular physiology, in patients with control (Group I) or uncontrolled (Group II) primary hypertension.METHODSEVs were isolated from 34 patients with history of hypertension, and characterized for size and concentration by nanoparticle tracking analyses, exosomal biomarkers by immunogold labeling coupled with transmission electron microscopy, flow cytometry and immunoblotting. EVs were analyzed for the hydrolytic activity of chymase, angiotensin converting enzyme (ACE), ACE2, and neprilysin (NEP) by HPLC.RESULTSPlasma and urinary EVs were enriched for small EVs and expressed exosomal markers (CD63, CD9, and CD81). The size of urinary EVs (but not plasma EVs) was significantly larger in Group II compared to Group I. Differential activity of RAS enzymes was observed, with significantly higher chymase activity compared to ACE, ACE2, and NEP in plasma EVs. Similarly, urinary EVs exhibited higher chymase and NEP activity compared to ACE and ACE2 activity. Importantly, compared to Group I, significantly higher chymase activity was observed in urinary EVs (p = 0.03) from Group II, while no significant difference in activity was observed for other RAS enzymes.CONCLUSIONSBioactive RAS enzymes are present in plasma and urinary EVs. Detecting chymase in plasma and urinary EVs uncovers a novel mechanism of angiotensin II-forming enzyme and could also mediate cell-cell communication and modulate signaling pathways in recipient cells.GRAPHICAL ABSTRACT
Boston criteria v2.0 for cerebral amyloid angiopathy without hemorrhage: An MRI-neuropathological validation study
Authors: Switzer Aaron , Charidimou Antreas , McCarter Stuart J. , Vemuri Prashanthi , Nguyen Aivi , Przybelski Scott A. , Lesnick Timothy G. , Rabinstein Alejandro A. , Brown Robert D. , Knopman David S. , Petersen Ronald C. , Jack Clifford R. , Reichard R. Ross , Graff-Radford Jonathan 
Published: November 2023

AbstractBACKGROUNDUpdated criteria for the clinical-MRI diagnosis of cerebral amyloid angiopathy (CAA) have recently been proposed. However, their performance in individuals without intracerebral hemorrhage (ICH) or transient focal neurological episodes (TFNE) is unknown. We assessed the diagnostic performance of the Boston criteria version 2.0 for CAA diagnosis in a cohort of individuals presenting without symptomatic ICH.METHODSFifty-four participants from the Mayo Clinic Study of Aging or Alzheimer’s Disease Research Center were included if they had an antemortem MRI with gradient-recall echo sequences and a brain autopsy with CAA evaluation. Performance of the Boston criteria v2.0 was compared to v1.5 using histopathologically verified CAA as the reference standard.RESULTSMedian age at MRI was 75 years (IQR 65-80) with 28/54 participants having histopathologically verified CAA (i.e., moderate-to-severe CAA in at least 1 lobar region). The sensitivity and specificity of the Boston criteria v2.0 were 28.6% (95%CI: 13.2-48.7%) and 65.3% (95%CI: 44.3-82.8%) for probable CAA diagnosis (AUC 0.47) and 75.0% (55.1-89.3) and 38.5% (20.2-59.4) for any CAA diagnosis (possible + probable; AUC: 0.57), respectively. The v2.0 Boston criteria was not superior in performance compared to the prior v1.5 criteria for either CAA diagnostic category.CONCLUSIONSThe Boston criteria v2.0 have low accuracy in patients who are asymptomatic or only have cognitive symptoms.. Additional biomarkers need to be explored to optimize CAA diagnosis in this population.
Ecological interactions between host, commensal and pathogenic bacteria in models for the intestinal epithelium
Authors: Nanlohy Nening M. , Johannesson Nina , Wijnands Lucas , Arroyo Laura , de Wit Jelle , den Hartog Gerco , Wolthers Katja C. , Sridhar Adithya , Fuentes Susana 
Published: November 2023

AbstractGut host physiology and the microbiome intricately interact in the complex ecosystem of the human digestive tract, playing a crucial role in maintaining overall health. In recent decades, the role of the gut microbiota in the defence against pathogens and modulating local and distal immunity has been well-established. The interactions between commensal and potential pathogenic bacteria with the intestinal epithelium can initiate immune responses in the epithelial cells, which, in turn, activate downstream immune responses in other immune cells. These intricate processes involved, especially when multiple microorganisms are present as seen in the intestinal microbiome, remain only partially understood. Previously, it was observed that in adults aged 60 years or older, the commensalRuminococcus torques(Rt) andEscherichia coliwere associated with influenza-like illness and a heightened pro-inflammatory immune profile. In this study, we used a CaCo-2 cell-based model and a human intestinal enteroid (HIE) model to explore epithelial responses to Rt and an adherent invasiveE. coli(AIEC) both individually and in co-cultures under anaerobic conditions. Additionally, CaCo-2 cells were co-cultured with peripheral blood mononuclear cells, revealing downstream activation of immune cells. While both systems showed comparable cytokine profiles, they differed in their responses to the different bacteria, with the organoid system being more representative for intestinal epithelial cells in humans. We provide mechanistic evidence of the pro-inflammatory responses associated with these bacteria in the intestinal ecosystem. These models, particularly in the context of combined infections, represent a valuable and promising avenue for future research. They contribute to a deeper understanding of the complex interactions between the gut microbiota, epithelial intestinal cells and immune cells in the gut ecosystem, thereby promoting advances in the field of gut health and host response.
Global distribution and diversity of marine Parmales
Authors: Ban Hiroki , Endo Hisashi ,   The EukBank Team, Kuwata Akira , Ogata Hiroyuki 
Published: November 2023

AbstractParmales (Bolidophyceae) is a minor eukaryotic phytoplankton group, sister to diatoms, that exists as two distinct forms of unicellular organisms: silicified cells and naked flagellates. Since their discovery, many field studies of Parmales have been performed, but their global distribution remains under-investigated. Here, we compile over 3,000 marine DNA metabarcoding datasets targeting the V4 region of the 18S rRNA gene from the EukBank database. By linking this large dataset with the latest morphological and genetic information, we provide updated estimates on the diversity and distribution of Parmales in the global ocean at a fine taxonomic resolution. Parmalean amplicon sequence variants (ASVs) were detected in nearly 90% of the analyzed samples. However, the relative abundance of parmaleans in the eukaryotic community is less than 0.2% on average, and the estimated true richness of parmalean ASVs is about 316 ASVs, confirming their low abundance and low diversity. Phylogenetic analysis clearly divides these algae into four clades, and three known morphotypes of silicified cells were classified into three different clades. The abundance of Parmales is generally high in the pole and decreases toward the tropics, and individual clades/subclades show further distinctions in distributions. Overall, our results suggest their clade/subclade-specific adaptation to different ecological niches.
Dynamics ofTrypanosoma cruziinfection in hamsters and novel association with progressive motor dysfunction
Authors: Langston Harry , Francisco Amanda Fortes , Doidge Ciaran , Roberts Chrissy H. , Khan Archie A. , Jayawardhana Shiromani , Taylor Martin C. , Kelly John M. , Lewis Michael D. 
Published: November 2023

AbstractChagas disease is a zoonosis caused by the protozoan parasiteTrypanosoma cruzi.Clinical outcomes range from long-term asymptomatic carriage to cardiac, digestive, neurological and composite presentations that can be fatal in both acute and chronic stages of the disease. Studies ofT. cruziin animal models, principally mice, have informed our understanding of the biological basis of this variability and its relationship to infection and host response dynamics. Hamsters have higher translational value for many human infectious diseases, but they have not been well developed as models of Chagas disease. We transposed a real-time bioluminescence imaging system forT. cruziinfection from mice into female Syrian hamsters (Mesocricetus auratus). This enabled us to study chronic tissue pathology in the context of spatiotemporal infection dynamics. Acute infections were widely disseminated, whereas chronic infections were almost entirely restricted to the skin and subcutaneous adipose tissue. Neither cardiac nor digestive tract disease were reproducible features of the model. Skeletal muscle had only sporadic parasitism in the chronic phase, but nevertheless displayed significant inflammation and fibrosis, features also seen in mouse models. Whereas mice had normal locomotion, all chronically infected hamsters developed hindlimb muscle hypertonia and a gait dysfunction resembling spastic diplegia. With further development, this model may therefore prove valuable in studies of peripheral nervous system involvement in Chagas disease.