bluuebunny/crossref_metadata_2025_split huggingface dataset:
A retrospective analysis of haemolytic reactions to intravenous immunoglobulin using data from the Transfusion‐Transmitted Injuries Surveillance System (Ontario)
Authors: Batarfi Khalid , Liu Yang , Nixon Joanne , Webert Kathryn E. , John Melanie St. , Karunakaran Meera , Alhomsi Nour , Park Jane J. , Heddle Nancy M. 
Published: August 2023

AbstractBackground and ObjectivesHaemolysis can occur following intravenous immunoglobulin (IVIG) infusion. Haemovigilance data were analysed using a novel approach for including two control groups with no haemolysis to IVIG. Objectives included a summary of all reactions to IVIG, rate estimates and analysis of haemolytic reactions including risk factors.Materials and MethodsCanadian haemovigilance data from Ontario (2013–2021), IVIG distribution and transfusion data from the blood supplier, and data from a large local transfusion registry were used. An ‘other‐reactions’ control group included patients with IVIG reactions that were not haemolytic, and registry patients with no‐reaction were the ‘no‐reaction controls’. Descriptive analysis and two logistic regression models for the different control groups were performed.ResultsOne thousand one hundred and seventy reactions were included. Most common were febrile non haemolytic (26.1%), minor allergic (24.5%) and IVIG headache (15.3%) followed by haemolytic 10.9% (128/1170). Haemolytic reaction rates decreased over time: rates since 2020 estimated between 1.5 and 2.9/1000 kg IVIG used. The regression model for other‐reaction controls identified two risk factors for haemolysis: non‐O blood group recipients compared with group O recipients (p value = 0.0106) and IVIG dose per 10 g increase (OR 1.359; 95% CI 1.225–1.506). The model using no‐reaction controls gave similar results and also showed no pre‐medication was associated with a higher risk of haemolysis (OR 29.084; 95% CI 1.989–425.312).ConclusionThe frequency of haemolytic reactions has decreased over time. We confirmed non‐O blood group recipients and IVIG dose as risk factors for haemolysis and raise the hypothesis that no pre‐medication may increase the risk of haemolysis.
Molecular phylogeny of the marine snail genus Haminoea (Gastropoda, Cephalaspidea): A framework to study marine diversity and speciation
Authors: Turani Martina , Valdés Ángel , Malaquias Manuel António E. 
Published: August 2023

AbstractHaminoea are herbivorous, coastal snails occurring in temperate and tropical waters of the Atlantic and Eastern Pacific oceans, with one species present in temperate South Africa (Indian Ocean). The genus is taxonomically difficult as several available nominal species were introduced based on shell descriptions alone, or described based on subtle differences in morpho‐anatomical features, without a phylogenetic molecular framework. Fifteen species are currently accepted as valid in recent scientific literature and field guides (eight Eastern Atlantic, one temperate Indian Ocean, four Western Atlantic and three Eastern Pacific). Here we generate the first complete phylogeny (Bayesian and Maximum Likelihood) of this genus based on multilocus molecular data (COI, 12S rRNA, 16S rRNA, 28S rRNA) using a taxon set accumulated over a period of 15 years, coupled with species delimitation analyses methods (ABGD, ASAP, bPTP) and morpho‐anatomical studies. The goal of this study is to provide insights into the taxonomy, phylogenetic relationships and geographical distributions of species while generating a framework for future systematic reviews of the genus, as well as to study speciation and historical biogeography. Our results rendered four possible hypotheses of species diversity: with 14, 15, 19 and 20 candidate species and point to the fact that several taxa presently regarded as valid might be conspecific (e.g. H. orteai–H. templadoi–H. exigua; and H. alfredensis–H. antillarum–H. orbignyana), while highlighting the existence of a complex of four or five species often identified as H. elegans. Pervasive nomenclatural problems in the genus, including with the type species H. hydatis, are highlighted and discussed.
Proteolytic markers associated with a gain and loss of leg muscle mass with resistance training followed by high‐intensity interval training
Authors: Michel J. Max , Godwin Joshua S. , Plotkin Daniel L. , Mesquita Paulo H. C. , McIntosh Mason C. , Ruple Bradley A. , Libardi Cleiton A. , Mobley C. Brooks , Kavazis Andreas N. , Roberts Michael D. 
Published: August 2023

AbstractWe recently reported that vastus lateralis (VL) cross‐sectional area (CSA) increases after 7 weeks of resistance training (RT, 2 days/week), with declines occurring following 7 weeks of subsequent treadmill high‐intensity interval training (HIIT) (3 days/week). Herein, we examined the effects of this training paradigm on skeletal muscle proteolytic markers. VL biopsies were obtained from 11 untrained college‐aged males at baseline (PRE), after 7 weeks of RT (MID), and after 7 weeks of HIIT (POST). Tissues were analysed for proteolysis markers, and in vitro experiments were performed to provide additional insights. Atrogene mRNAs (TRIM63, FBXO32, FOXO3A) were upregulated at POST versus both PRE and MID (P < 0.05). 20S proteasome core protein abundance increased at POST versus PRE (P = 0.031) and MID (P = 0.049). 20S proteasome activity, and protein levels for calpain‐2 and Beclin‐1 increased at MID and POST versus PRE (P < 0.05). Ubiquitinated proteins showed model significance (P = 0.019) with non‐significant increases at MID and POST (P > 0.05). in vitro experiments recapitulated the training phenotype when stimulated with a hypertrophic stimulus (insulin‐like growth factor 1; IGF1) followed by a subsequent AMP‐activated protein kinase activator (5‐aminoimidazole‐4‐carboxamide ribonucleotide; AICAR), as demonstrated by larger myotube diameter in IGF1‐treated cells versus IGF1 followed by AICAR treatments (I+A; P = 0.017). Muscle protein synthesis (MPS) levels were also greater in IGF1‐treated versus I+A myotubes (P < 0.001). In summary, the loss in RT‐induced VL CSA with HIIT coincided with increases in several proteolytic markers, and sustained proteolysis may have driven this response. Moreover, while not measured in humans, we interpret our in vitro data to suggest that (unlike RT) HIIT does not stimulate MPS.
Complete genome sequence of the
Microbacterium
sp. strain BDGP8
Authors: Wan Kenneth H. , Park Soo , Booth Benjamin W. , Brydon Ella C. , Eichenberger Joanne , Inman Jamie L. , Mao Jian-Hua , Snijders Antoine M. , Celniker Susan E. 
Published: August 2023

ABSTRACT

Microbacterium
sp. BDGP8 is a species of facultative anaerobic gram-positive bacterium of the family Microbacteriaceae. The complete genome consists of a single circular chromosome of 3,293,567 bp with a G + C content of 69.84% and two plasmids of 49,365 bp and 32,884 bp.
Phyllosphere microbial diversity and specific taxa mediate within-cultivar resistance to
Phytophthora palmivora
in cacao
Authors: Schmidt Jennifer E. , Puig Alina S. , DuVal Ashley E. , Pfeufer Emily E. 
Published: August 2023

ABSTRACT

The oomycete pathogen
Phytophthora palmivora
, which causes black pod rot (BPR) on cacao (
Theobroma cacao
L.), is responsible for devastating yield losses worldwide. Genetic variation in resistance to
Phytophthora
spp. is well documented among cacao cultivars, but variation has also been observed in the incidence of BPR even among trees of the same cultivar. In light of evidence that the naturally occurring phyllosphere microbiome can influence foliar disease resistance in other host-pathogen systems, it was hypothesized that differences in the phyllosphere microbiome between two field accessions of the cultivar Gainesville II 164 could be responsible for their contrasting resistance to
P. palmivora
. Bacterial alpha diversity was higher but fungal alpha diversity was lower in the more resistant accession MITC-331, and the accessions harbored phyllosphere microbiomes with distinct community compositions. Six bacterial and 82 fungal amplicon sequence variants (ASVs) differed in relative abundance between MITC-333 and MITC-331, including bacterial putative biocontrol agents and a high proportion of fungal pathogens, and nine fungal ASVs were correlated with increased lesion development. The roles of contrasting light availability and host mineral nutrition, particularly potassium, are also discussed. Results of this preliminary study can be used to guide research into microbiome-informed integrated pest management strategies effective against
Phytophthora
spp. in cacao.

IMPORTANCE

Up to 40% of the world’s cacao is lost each year to diseases, the most devastating of which is black pod rot, caused by
Phytophthora palmivora
. Though disease resistance is often attributed to cacao genotypes (i.e., disease-resistant rootstocks), this study highlights the role of the microbiome in contributing to differences in resistance even among accessions of the same cacao cultivar. Future studies of plant-pathogen interactions may need to account for variation in the host microbiome, and optimizing the cacao phyllosphere microbiome could be a promising new direction for
P. palmivora
resistance research.
Catalase produced by
Candida albicans
protects
Streptococcus mutans
from H
2
O
2
stress—one more piece in the cross-kingdom synergism puzzle
Authors: Katrak Callahan , Garcia Bruna A. , Dornelas-Figueira Louise M. , Nguyen Mary , Williams Robert B. , Lorenz Michael C. , Abranches Jacqueline 
Published: August 2023

ABSTRACT

Co-infection with
Streptococcus mutans
and
Candida albicans
is associated with dental caries, and their co-cultivation results in enhanced biofilm matrix production that contributes to increased virulence and caries risk. Moreover, the catalase-negative
S. mutans
demonstrates increased oxidative stress tolerance when co-cultivated in biofilms with
C. albicans,
a catalase-producing yeast. Here, we sought to obtain mechanistic insights into the increased H
2
O
2
tolerance of
S. mutans
when co-cultivated with clinical isolates of
Candida glabrata
,
Candida tropicalis,
and
C. albicans
. Additionally, the
C. albicans
SC5314 laboratory strain, its catalase mutant (SC5314
Δcat1
), and
S. mutans
UA159 and its glucosyltransferase B/C mutant (UA159
ΔgtfB/C
) were grown as single- and dual-species biofilms. Time-kill assays revealed that upon acute H
2
O
2
challenge, the survival rates of
S. mutans
in dual-species biofilms with the clinical isolates and
C. albicans
SC5314 were greater than when paired with SC5314
Δcat1
or as a single-species biofilm. Importantly, this protection was independent of glucan production through
S. mutans
GtfB/C. Transwell assays and treatment with H
2
O
2
-pre-stimulated
C. albicans
SC5314 supernatant revealed that this protection is contact-dependent. Biofilm stability assays with sublethal H
2
O
2
or peroxigenic
Streptococcus
A12 challenge resulted in biomass reduction of single-species
S. mutans
UA159 and dual-species with SC5314
Δcat1
biofilms compared to UA159 biofilms co-cultured with
C. albicans
SC5314.
S. mutans
oxidative stress genes were upregulated in single-species biofilms when exposed to H
2
O
2,
but not when
S. mutans
was co-cultivated with
C. albicans
SC5314. Here, we uncovered a novel, contact-dependent, synergistic interaction in which the catalase of
C. albicans
protects
S. mutans
against H
2
O
2
.

IMPORTANCE

It is well established that co-infection with the gram-positive caries-associated bacterium
Streptococcus mutans
and the yeast pathobiont
Candida albicans
results in aggressive forms of caries in humans and animal models. Together, these microorganisms form robust biofilms through enhanced production of extracellular polysaccharide matrix. Further, co-habitation in a biofilm community appears to enhance these microbes’ tolerance to environmental stressors. Here, we show that catalase produced by
C. albicans
protects
S. mutans
from H
2
O
2
stress in a biofilm matrix-independent manner. Our findings uncovered a novel synergistic trait between these two microorganisms that could be further exploited for dental caries prevention and control.
Tezacaftor/Ivacaftor therapy has negligible effects on the cystic fibrosis gut microbiome
Authors: Marsh Ryan , Dos Santos Claudio , Hanson Liam , Ng Christabella , Major Giles , Smyth Alan R. , Rivett Damian , van der Gast Christopher 
Published: August 2023

ABSTRACT
People with cystic fibrosis (pwCF) experience a range of persistent gastrointestinal symptoms throughout life. There is evidence indicating interaction between the microbiota and gut pathophysiology in CF. However, there is a paucity of knowledge on the potential effects of CF transmembrane conductance regulator (CFTR) modulator therapies on the gut microbiome. In a pilot study, we investigated the impact of Tezacaftor/Ivacaftor dual combination CFTR modulator therapy on the gut microbiota and metabolomic functioning in pwCF. Fecal samples from 12 pwCF taken at baseline and following placebo or Tezacaftor/Ivacaftor administration were subjected to microbiota sequencing and to targeted metabolomics to assess the short-chain fatty acid (SCFA) composition. Ten healthy matched controls were included as a comparison. Inflammatory calprotectin levels and patient symptoms were also investigated. No significant differences were observed in overall gut microbiota characteristics between any of the study stages, extended also across intestinal inflammation, gut symptoms, and SCFA-targeted metabolomics. However, microbiota and SCFA metabolomic compositions, in pwCF, were significantly different from controls in all study treatment stages. CFTR modulator therapy with Tezacaftor/Ivacaftor had negligible effects on both the gut microbiota and SCFA composition across the course of the study and did not alter toward compositions observed in healthy controls. Future longitudinal CFTR modulator studies will investigate more effective CFTR modulators and should use prolonged sampling periods, to determine whether longer-term changes occur in the CF gut microbiome.

IMPORTANCE
People with cystic fibrosis (pwCF) experience persistent gastrointestinal (GI) symptoms throughout life. The research question “how can we relieve gastrointestinal symptoms, such as stomach pain, bloating, and nausea?” remains a top priority for clinical research in CF. While CF transmembrane conductance regulator (CFTR) modulator therapies are understood to correct underlying issues of CF disease and increasing the numbers of pwCF are now receiving some form of CFTR modulator treatment. It is not known how these therapies affect the gut microbiome or GI system. In this pilot study, we investigated, for the first time, effects of the dual combination CFTR modulator medicine, Tezacaftor/Ivacaftor. We found it had negligible effects on patient GI symptoms, intestinal inflammation, or gut microbiome composition and functioning. Our findings are important as they fill important knowledge gaps on the relative effectiveness of these widely used treatments. We are now investigating triple combination CFTR modulators with prolonged sampling periods.
Genomic diversity and biogeographic distributions of a novel lineage of bacteriophages that infect marine OM43 bacteria
Authors: Yang Mingyu , Du Sen , Zhang Zefeng , Xia Qian , Liu He , Qin Fang , Wu Zuqing , Ying Hanqi , Wu Yin , Shao Jiabing , Zhao Yanlin 
Published: August 2023

ABSTRACT

The marine methylotrophic OM43 clade is considered an important bacterial group in coastal microbial communities. OM43 bacteria, which are closely related to phytoplankton blooms, have small cell sizes and streamlined genomes. Bacteriophages profoundly shape the evolutionary trajectories, population dynamics, and physiology of microbes. The prevalence and diversity of several phages that infect OM43 bacteria have been reported. In this study, we isolated and sequenced two novel OM43 phages, MEP401 and MEP402. These phages share 90% of their open reading frames (ORFs) and are distinct from other known phage isolates. Furthermore, a total of 99 metagenomic viral genomes (MVGs) closely related to MEP401 and MEP402 were identified. Phylogenomic analyses suggest that MEP401, MEP402, and these identified MVGs belong to a novel subfamily in the family
Zobellviridae
and that they can be separated into two groups. Group I MVGs show conserved whole-genome synteny with MEP401, while group II MVGs possess the MEP401-type DNA replication module and a distinct type of morphogenesis and packaging module, suggesting that genomic recombination occurred between phages. Most members in these two groups were predicted to infect OM43 bacteria. Metagenomic read-mapping analysis revealed that the phages in these two groups are globally ubiquitous and display distinct biogeographic distributions, with some phages being predominant in cold regions, some exclusively detected in estuarine stations, and others displaying wider distributions. This study expands our knowledge of the diversity and ecology of a novel phage lineage that infects OM43 bacteria by describing their genomic diversity and global distribution patterns.

IMPORTANCE

OM43 phages that infect marine OM43 bacteria are important for host mortality, community structure, and physiological functions. In this study, two OM43 phages were isolated and characterized. Metagenomic viral genome (MVG) retrieval using these two OM43 phages as baits led to the identification of two phage groups of a new subfamily in the family
Zobellviridae
. We found that group I MVGs share similar genomic content and arrangement with MEP401 and MEP402, whereas group II MVGs only possess the MEP401-type DNA replication module. Metagenomic mapping analysis suggests that members in these two groups are globally ubiquitous with distinct distribution patterns. This study provides important insights into the genomic diversity and biogeography of the OM43 phages in the global ocean.
He Isotopic Composition of Alkaline Intrusions of the Hovsgol Area, Northwestern Mongolia
Authors: Vrublevskii V. V. , Petlina A. A. , Gudkov A. V. , Sidorov M. Yu. , Semiryuakov A. S. , Shelepaev R. A. , Vishnevskii A. V. , Gertner I. F. , Fomina E. N. , Kozlov E. N. , Udoratina O. V. 
Published: August 2023

Abstract
The He isotopic composition of fluid inclusions in magnetite of alkaline and subalkaline intrusion of the Hovsgol region, Northwestern Mongolia, is studied. The measured 4He content varies from 6.6 × 10–7 to 114 × 10–7 cm3/g. The 3He/4He isotope ratio of most samples is 0.23–0.59 Ra indicating the presence of He from different sources in magmatic fluid. The maximum of mantle He (2.51 Ra) is observed in magnetite of subalkali gabbro. The mantle He component was ~40–60% during the generation of parental magma with possible involvement of subcontinental lithospheric mantle material or a plume-like reservoir less enriched in 3He. The mantle He component did not exceed 10–15% during the evolution of the foidoitic and alkali-syenitic melts because of mixing with crustal radiogenic He. We suggest the interaction of intrusions with fragments of the Precambrian accretionary–collision complexes of the Tuva–Mongolian Terrane. This mixing of He isotopes in melts and fluids can serve as indirect evidence of the development of mantle magmatism at the active continental margin.
Possibility of Using Zoning of Fallow Vegetation by Vegetation Indices to Assess Organic Matter Accumulation in Postagrogenic Soils
Authors: Giniyatullin K. G. , Sahabiev I. A. , Ryazanov S. S. , Smirnova E. V. , Tishin D. V. , Latypova L. I. 
Published: August 2023

Abstract
Light gray forest soils (Eutric Retisols (Loamic, Cutanic, Ochric)) were studied under a 20–25-yr-old fallow at the stage of overgrowing by meadow vegetation, pine, and birch. The studied area plot was confined to one element of topography, without morphological evidences of erosion processes, and with relatively homogenous soil texture. To assess the influence of fallow vegetation on the formation of soil organic matter (SOM), the plant cover was zoned according to vegetation indices calculated on the basis of remote sensing data. The k-means algorithms and the Random Forest method were used for this purpose. It was shown that there were statistically significant differences between the types of land cover in terms of the SOM stocks in the upper layer of the old-arable horizon with the specification of three and four clusters. The specification of three classes of vegetation on the fallow—coniferous woody vegetation, deciduous woody vegetation, and herbaceous vegetation—proved to be the most expedient; the correctness of their allocation was confirmed by the geobotanical survey of the territory. The results of a pairwise comparison of sites occupied by different types of fallow vegetation indicated that they significantly differ in the SOM stocks only in the uppermost 5-cm-thick layer of the old-arable horizon and only for the pair of coniferous woody and herbaceous vegetation. Differences in the accumulated humus stocks in the layer of 0–10 cm were statistically significant for the soils under deciduous and coniferous woody vegetation and under herbaceous and coniferous woody vegetation. There was no significant difference in this indicator between the soils under deciduous woody vegetation and herbaceous vegetation.
Implementation of the HepClinktest-and-treat community strategy targeting Pakistani migrants with hepatitis C living in Catalonia (Spain) compared with the current practice of the Catalan health system: budget impact analysis
Authors: Reyes-Urueña Juliana , Costell-González Francisco , Egea-Cortés Laia , Ouaarab Hakima , Saludes Veronica , Buti Maria , Majó Xavier , Colom Joan , Gómez i Prat Jordi , Casabona Jordi , Martró Elisa 
Published: August 2023

ObjectivesTo perform a budget impact analysis of the HepClinktest-and-treat strategy in which community health agents offer hepatitis C virus (HCV) testing, diagnosis and treatment to the Pakistani population living in Catalonia compared with the current practice of the Catalan health system (without targeted screening programmes).MethodsWe estimated the population of adult Pakistani migrants registered at the primary care centres in Catalonia by means of the Information System for the Development of Research in Primary Care (n=37 972 in 2019, Barcelona health area). This cohort was followed for a time period of 10 years after HCV diagnosis (2019–2028). The statistical significance of the differences observed in the anti-HCV positivity rate between screened and non-screened was confirmed (α=0.05). The budget impact was calculated from the perspective of the Catalan Department of Health. Sensitivity analyses included different levels of participation in HepClink: pessimistic, optimistic and maximum.ResultsThe HepClinkscenario screened a higher percentage of individuals (69.8%) compared with the current scenario of HCV care (39.7%). Viraemia was lower in the HepClinkscenario compared with the current scenario (1.7% vs 2.5%, respectively). The budget impact of the HepClinkscenario was €884 244.42 in 10 years.ConclusionsScaling up the HepClinkstrategy to the whole Catalan territory infers a high budget impact for the Department of Health and allows increasing the detection of viraemia (+17.8%) among Pakistani migrants ≥18 years. To achieve a sustainable elimination of HCV by improving screening and treatment rates, there is room for improvement at two levels. First, taking advantage of the fact that 68.08% of the Pakistani population had visited their primary care physicians to reinforce targeted screening in primary care. Second, to use HepClinkat the community level to reach individuals with reluctance to use healthcare services.