bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of cell‐free tumor DNA in cerebrospinal fluid as a diagnostic biomarker for leptomeningeal melanoma metastasis: A case series
Authors: Dirven Iris , Vounckx Manon , Kessels Jolien I. , Lauwyck Justine , Awada Gil , Vanbinst Anne‐Marie , Neyns Bart 
Published: July 2024

AbstractLeptomeningeal melanoma metastases (LMM) are associated with poor survival. Diagnosis is based on clinical presentation, brain MRI and cerebrospinal fluid (CSF) analysis. Inconclusive findings at initial presentation can delay treatment. In this single‐center case series, detection of BRAFV600‐ and NRASQ61‐mutant cell‐free tumor DNA (cfDNA) in CSF was evaluated as a complementary diagnostic biomarker. In 12 patients with clinical suspicion of LMM, a retrospective analysis of MRI, CSF cytology and cfDNA analysis on 1 mL of CSF using the Idylla® platform was carried out. Nine patients displayed MRI abnormalities suggesting LMM. CSF analysis identified malignant cells in three patients (including one without MRI abnormalities). BRAFV600‐ or NRASQ61‐mutant cfDNA was detected in CSF of nine patients (eight with and one without MRI abnormalities; all patients with positive CSF cytology). Subsequent follow‐up confirmed LMM in all patients with positive and in one patient with a negative CSF cfDNA analysis (sensitivity 81.8%; specificity 100%). Our findings suggest that analyzing BRAFV600‐ and NRASQ61‐mutant cfDNA in CSF using the Idylla® platform holds promise as a sensitive and specific complementary diagnostic biomarker for LMM, particularly in case of inconsistency between imaging and CSF cytology. The 110‐min analysis can facilitate urgent treatment decisions.
Characteristics of Bachaur bull semen
Authors: Azad C. S. , Prasad J. K. , Sengupta D. , Sheetal S. K. , Kumar Anil , Rana Tanmoy 
Published: July 2024

AbstractThe Bachaur is a mediumized draft purpose breed which has been recognized by ICAR‐National Bureau of Animal Genetic Resources (NBAGR) Karnal, India, and presently is on the verge of extinction. Since there are no data regarding the seminal parameters of this breed, this work was performed to evaluate seminal parameters of freshly ejaculated semen. A total of three healthy breeding Bachaur bulls aged 2.5–5 years were selected for the study which were maintained under identical managemental conditions. Semen parameters of these bulls were studied across 10 ejaculates. The average scrotal circumference and testicular weight of the three bulls were 27.78 ± 1.2 cm and 400.67 ± 26.6 g, respectively. The average overall volume (mL), pH, concentration (million/mL), liveability (%), abnormality (%), HOST (%) and acrosome integrity (%) were 2.20 ± 0.19, 6.86 ± 0.06, 1245.60 ± 23.49, 85.09 ± 0.91, 4.13 ± 0.06, 81.16 ± 1.18 and 83.54 ± 1.32, respectively. The average overall mass motility of three Bachaur bulls was 3.57 ± 0.06 in 0–5 scale and individual motility averaged 84.78 ± 1.70 per cent. The volume of ejaculates in Bachaur bull seemed to be lower as compared to other exotic and Indian breeds. However, the semen parameters with regard to mass motility, liveability, abnormalities, hypo‐osmotic swelling test (HOST) and acrosomal integrity seemed similar to other exotic and Indian breeds.
Delineating dengue risk zones in Jaipur: An interdisciplinary approach to inform public health strategies
Authors: Kanga Shruti , Roy Priyanka , Singh Suraj Kumar , Meraj Gowhar , Kumar Pankaj , Debnath Jatan 
Published: July 2024

AbstractDengue fever (DF) is a pervasive public health concern in tropical climates, with densely populated regions, such as India, disproportionately affected. Addressing this issue requires a multifaceted understanding of the environmental and sociocultural factors that contribute to the risk of dengue infection. This study aimed to identify high‐risk zones for DF in Jaipur, Rajasthan, India, by integrating physical, demographic, and epidemiological data in a comprehensive risk analysis framework. We investigated environmental variables, such as soil type and plant cover, to characterize the potential habitats of Aedes aegypti, the primary dengue vector. Concurrently, demographic metrics were evaluated to assess the population's susceptibility to dengue outbreaks. High‐risk areas were systematically identified through a comparative analysis that integrated population density and incidence rates per ward. The results revealed a significant correlation between high population density and an increased risk of dengue, predominantly facilitated by vertical transmission. Spatially, these high‐risk zones are concentrated in the northern and southern sectors of Jaipur, with the northern and southwestern wards exhibiting the most acute risk profiles. This study underscores the importance of targeted public health interventions and vaccination campaigns in vulnerable areas. It further lays the groundwork for future research to evaluate the effectiveness of such interventions, thereby contributing to the development of robust evidence‐based strategies for dengue risk mitigation.
The Life Attachment Scale (LAS‐R)
Authors: Bertelsen Preben , Ozer Simon 
Published: July 2024

IntroductionThe proposed concept of secure/insecure lifeattachment reflects the experience of the world and life as a good (or insecure/threatening) place to be. The present article describes the theoretical foundation, development, and validation of a revised measure that captures the phenomenon of secure/insecure life attachment. The revised scale consists of seven dimensions: (1) Coexistence, (2) Reliability, (3) Safetiness, (4) Integration, (5) Inclusion, (6) Participation, and (7) Deliberation.MethodsIn three studies (N = 1,059), we examined the factor structure and the convergent and predictive validity of the Life Attachment Scale–Revised (LAS‐R).ResultsOur results support a seven‐factor structure of the scale, reflecting the aforementioned dimensions. Furthermore, convergent and predictive validity were established through correlations with related concepts of life satisfaction, flourishing, openness to the future, and perceived stress.ConclusionWe have devised and substantiated a scale adept at gauging dimensions of secure and insecure/disordered life attachment. Empirical evidence from statistical analyses supports the assumption that the LAS‐R is psychometrically sound, establishing its reliability and validity as a dependable instrument. Thus, the scale has promising implications for developing the empirical base for research in many areas of psychology, sociology, and the social sciences.
Why does international vertical specialisation affect within‐firm skill premium in China? Investigation and interpretation
Authors: Chen Bo 
Published: July 2024

AbstractWith highly disaggregated data during 2000–2006 in China, we construct the firm‐level international vertical specialisation index and find that China's ascension to WTO decreased the index in manufacturing firms. We investigate its relationship with measured skill premium in manufacturing firms and find that a one percentage point decrease in international vertical specialisation could lead to as much as a two‐tenth percentage point deduction in the skill premium. The effect is more pronounced when the specialisation is with OECD developed economies, while it is reversed with non‐OECD economies. Furthermore, the relationship is only significant in ordinary firms though processing firms also experienced changes in international vertical specialisation during the same period. Our results are robust to various empirical alternatives. We then propose a model that features a two‐stage production in Melitz's (2003, Econometrica, 71, 1695) heterogeneous firm model. The model can explain the puzzle why China's trade volume surged after entering WTO, while the degree of international vertical specialisation decreased. Furthermore, it also explains why vertical specialisation might affect within‐firm skill premium under trade liberalisation.
Donor knowledge and perceptions regarding donation‐induced iron depletion and iron supplementation as a blood service policy
Authors: Karregat Jan H. M. , Quee Franke A. , Twisk Jos W. R. , van den Hurk Katja 
Published: July 2024

AbstractBackground and ObjectivesRegular whole blood donations are associated with an increased risk of iron deficiency. Iron supplementation is an effective strategy to prevent donation‐induced iron deficiency. However, research on donor perceptions towards such a policy is limited. Therefore, we aim to evaluate donors' knowledge on donation‐induced iron depletion and their perceptions regarding iron supplementation as a blood service policy.Materials and MethodsThree thousand Dutch whole blood donors were invited to complete a survey assessing their knowledge of donation‐induced iron depletion and attitudes and perceptions towards iron supplementation as a policy. Linear regression modelling was used to evaluate associations between explanatory variables and perceptions.ResultsIn total, 1093 (77.1%) donors were included in the analysis. Donors had poor knowledge of current iron management policies, but a better understanding of iron metabolism and supplementation. Iron supplementation as a policy was perceived mainly positive by donors, and the majority were willing to use iron supplements if provided. Iron supplementation was not perceived as invasive or negatively affecting donors' motivation to continue donating. Additional iron monitoring, information and donor physician involvement were regarded as important conditions for implementation. Male sex, trust in the blood service, prior experience with iron supplements and openness towards dietary supplements were strongly positively associated with willingness to use iron supplementation.ConclusionDonors' knowledge regarding donation‐induced iron depletion is limited, but not associated with their perceptions regarding iron supplementation. Donors do not consider iron supplementation as invasive, deterring or demotivating, and a majority are willing to take supplements if offered.
Effect of different weed control techniques on the leaf yield and nutritional qualities of Ocimum sanctum
Authors: Osadebe Vivian Ogechi , Ukwu Uchenna Noble , Dauda Nathaniel , Nwamba Ifesinachi Martha , Ede Amos Ejike , Enyi Jacob Ikechukwu , Onah Anthony Ikechukwu 
Published: July 2024

AbstractOcimum sanctum is a leaf‐vegetable and spice crop with several nutritional, therapeutic, and curative properties. Economic losses due to weeds have posed a major challenge to farmers, who have adopted different techniques to manage weeds without regard to its effect on the crop's nutritional qualities. The objective of this study was to investigate the effect of weed control techniques on weed eradication, leaf yield, and nutritional qualities of O. sanctum. Nine weed control techniques comprising black, red, and transparent polyethylene mulches, rice husk and sawdust mulches, daily removal of weed (DROW), hoe‐weeded, application of Haloxyfop post‐emergence herbicide spray (PEHS), and un‐weeded were investigated in a randomized complete block design with three replications. Significant variations in leaf‐yield and nutritional qualities among the different weed control techniques were recorded. Leaf yield was higher in plots treated with rice husk and black polyethylene mulches. Haloxyfop PEHS and transparent polyethylene mulch were superior in enhancing the proximate and vitamin contents of O. sanctum while black polyethylene and DROW were more efficient in weed control compared with the other weed control techniques. The use of polyethylene mulch as an effective weed management option offers numerous benefits for agriculture and gardening. Its ability to conserve moisture, suppress weed growth, and improve the crop microclimate, makes it a sustainable and cost‐effective option for farmers globally. Additionally, the use of herbicide to exploit plant biosynthetic pathways could lead to the unearthing of chemical innovations that could in addition to eradicating weed, also improve the nutritional qualities of crop.
Co-infection dynamics of
B. afzelii
and TBEV in C3H mice: insights and implications for future research
Authors: Porcelli Stefania , Heckmann Aurélie , Deshuillers Pierre Lucien , Wu-Chuang Alejandra , Galon Cleménce , Mateos-Hernandez Lourdes , Rakotobe Sabine , Canini Laetitia , Rego Ryan O. M. , Simo Ladislav , Lagrée Anne-Claire , Cabezas-Cruz Alejandro , Moutailler Sara 
Published: July 2024

ABSTRACT

Ticks are important vectors of disease, particularly in the context of One Health, where tick-borne diseases (TBDs) are increasingly prevalent worldwide. TBDs often involve co-infections, where multiple pathogens co-exist in a single host. Patients with chronic Lyme disease often have co-infections with other bacteria or parasites. This study aimed to create a co-infection model with
Borrelia afzelii
and tick-borne encephalitis virus (TBEV) in C3H mice and to evaluate symptoms, mortality, and pathogen level compared to single infections. Successful co-infection of C3H mice with
B. afzelii
and TBEV was achieved. Outcomes varied, depending on the timing of infection. When TBEV infection followed
B. afzelii
infection by 9 days, TBEV symptoms worsened and virus levels increased. Conversely, mice infected 21 days apart with TBEV showed milder symptoms and lower mortality. Simultaneous infection resulted in mild symptoms and no deaths. However, our model did not effectively infect ticks with TBEV, possibly due to suboptimal dosing, highlighting the challenges of replicating natural conditions. Understanding the consequences of co-infection is crucial, given the increasing prevalence of TBD. Co-infected individuals may experience exacerbated symptoms, highlighting the need for a comprehensive understanding through refined animal models. This study advances knowledge of TBD and highlights the importance of exploring co-infection dynamics in host-pathogen interactions.
Complete genome sequences of
Arthrobacter globiformis
phages Uzumaki and Argan of cluster AU6
Authors: Mathew Brandon , Lee Andrew Sean , Chen Katie , Kaczmarski Michael , Oommen Nigel , Mehaboob Asweel , Patel Vrushali , Patel Yamini , Saji Hannah , Shamsi Muhammad Ayaan , Gibb Bryan 
Published: July 2024

ABSTRACT

Bacteriophages Uzumaki and Argan infect
Arthrobacter globiformis
B-2880 isolated from soil samples in Long Island, New York. These bacteriophages have lambda-like morphology with prolate capsid and share 97% gene content similarity. These traits place them in cluster AU6 with other related
Arthrobacter
phages.
Genomic analysis and identification of a novel superantigen, SargEY, in
Staphylococcus argenteus
isolated from atopic dermatitis lesions
Authors: Aziz Fatkhanuddin , Hisatsune Junzo , Ono Hisaya K. , Kajimura Junko , Yu Liansheng , Masuda Kanako , Kitagawa Hiroki , Sato'o Yusuke , Yahara Koji , Yamaoka Mika , Nakane Akio , Kawasaki Hiroshi , Obata Shoko , Fukushima-Nomura Ayano , Ito Yoshihiro , Aung Meiji Soe , Amagai Masayuki , Salasia Siti Isrina Oktavia , Ohge Hiroki , Kusunoki Yoichiro , Sugai Motoyuki 
Published: July 2024

ABSTRACT

During surveillance of
Staphylococcus aureus
in lesions from patients with atopic dermatitis (AD), we isolated
Staphylococcus argenteus
, a species registered in 2011 as a new member of the genus
Staphylococcus
and previously considered a lineage of
S. aureus
. Genome sequence comparisons between
S. argenteus
isolates and representative
S. aureus
clinical isolates from various origins revealed that the
S. argenteus
genome from AD patients closely resembles that of
S. aureus
causing skin infections. We previously reported that 17%–22% of
S. aureus
isolated from skin infections produce staphylococcal enterotoxin Y (SEY), which predominantly induces T-cell proliferation via the T-cell receptor (TCR) Vα pathway. Complete genome sequencing of
S. argenteus
isolates revealed a gene encoding a protein similar to superantigen SEY, designated as SargEY, on its chromosome. Population structure analysis of
S. argenteus
revealed that these isolates are ST2250 lineage, which was the only lineage positive for the SEY-like gene among
S. argenteus
. Recombinant SargEY demonstrated immunological cross-reactivity with anti-SEY serum. SargEY could induce proliferation of human CD4
+
and CD8
+
T cells, as well as production of TNF-α and IFN-γ. SargEY showed emetic activity in a marmoset monkey model. S
arg
EY and SET (a phylogenetically close but uncharacterized SE) revealed their dependency on TCR Vα in inducing human T-cell proliferation. Additionally, TCR sequencing revealed other previously undescribed Vα repertoires induced by SEH. S
arg
EY and SEY may play roles in exacerbating the respective toxin-producing strains in AD.

IMPORTANCE

Staphylococcus aureus
is frequently isolated from active lesions of atopic dermatitis (AD) patients. We reported that 17%–22% of
S. aureus
isolated from AD patients produced a novel superantigen staphylococcal enterotoxin Y (SEY). Unlike many
S
.
aureus
superantigens that activate T cells via T-cell receptor (TCR) Vß, SEY activates T cells via TCR Vα and stimulates cytokine secretion.
Staphylococcus argenteus
was isolated from AD patients during the surveillance for
S. aureus
. Phylogenetic comparison of the genome indicated that the isolate was very similar to
S. aureus
causing skin infections. The isolate encoded a SEY-like protein, designated SargEY, which, like SEY, activated T cells via the TCR Vα. ST2250 is the only lineage positive for SargEY gene. ST2250
S. argenteus
harboring a superantigen SargEY gene may be a novel staphylococcal clone that infects human skin and is involved in the exacerbation of AD.
Intraspecies interactions of
Streptococcus mutans
impact biofilm architecture and virulence determinants in childhood dental caries
Authors: Momeni Stephanie S. , Cao Xixi , Xie Baotong , Rainey Katherine , Childers Noel K. , Wu Hui 
Published: July 2024

ABSTRACT

Early childhood dental caries (ECC) is the most common chronic disease among children, especially among low socioeconomic populations.
Streptococcus mutans
is most frequently associated with initiation of ECC. Although many studies report children with multiple
S. mutans
strains (i.e., genotypes) have greater odds of developing ECC, studies investigating intraspecies interactions in dental caries are lacking. This study investigates the impact of intraspecies interactions on cariogenic and fitness traits of clinical
S. mutans
isolates using
in vitro
and
in vivo
approaches. Association analysis evaluated if presence of multiple
S. mutans
genotypes within the first year of colonization was associated with caries. Initially, clinical
S. mutans
isolates from 10 children were evaluated.
S. mutans
strains (G09 and G18, most prevalent) isolated from one child were used for subsequent analysis. Biofilm analysis was performed for single and mixed cultures to assess cariogenic traits, including biofilm biomass, intra-polysaccharide, pH, and glucan. Confocal laser scanning microscopy (CLSM) and time-lapse imaging were used to evaluate spatial and temporal biofilm dynamics, respectively. A
Drosophila
model was used to assess colonization
in vivo
. Results showed the mean biofilm pH was significantly lower in co-cultured biofilms versus monoculture. Doubling of
S. mutans
biofilms was observed by CLSM and
in vivo
colonization in
Drosophila
for co-cultured
S. mutans
. Individual strains occupied specific domains in co-culture and G09 contributed most to increased co-culture biofilm thickness and colonization in
Drosophila
. Biofilm formation and acid production displayed distinct signatures in time-lapsed experiments. This study illuminates that intraspecies interactions of
S. mutans
significantly impacts biofilm acidity, architecture, and colonization.

IMPORTANCE

This study sheds light on the complex dynamics of a key contributor to early childhood dental caries (ECC) by exploring intraspecies interactions of different
S. mutans
strains and their impact on cariogenic traits. Utilizing clinical isolates from children with ECC, the research highlights significant differences in biofilm architecture and acid production in mixed versus single genotype cultures. The findings reveal that co-cultured
S. mutans
strains exhibit increased cell density and acidity, with individual strains occupying distinct domains. These insights, enhanced by use of time-lapsed confocal laser scanning microscopy and a
Drosophila
model, offer a deeper understanding of ECC pathogenesis and potential avenues for targeted interventions.
Full-genome sequencing of dozens of new DNA viruses found in Spanish bat feces
Authors: Buigues Jaime , Viñals Adrià , Martínez-Recio Raquel , Monrós Juan S. , Sanjuán Rafael , Cuevas José M. 
Published: July 2024

ABSTRACT

Bats are natural hosts of multiple viruses, many of which have clear zoonotic potential. The search for emerging viruses has been aided by the implementation of metagenomic tools, which have also enabled the detection of unprecedented viral diversity. Currently, this search is mainly focused on RNA viruses, which are largely over-represented in databases. To compensate for this research bias, we analyzed fecal samples from 189 Spanish bats belonging to 22 different species using viral metagenomics. This allowed us to identify 52 complete or near-complete viral genomes belonging to the families
Adenoviridae
,
Circoviridae
,
Genomoviridae
,
Papillomaviridae
,
Parvoviridae, Polyomaviridae
and
Smacoviridae
. Of these, 30 could constitute new species, doubling the number of viruses currently described in Europe. These findings open the door to a more thorough analysis of bat DNA viruses and their zoonotic potential.

IMPORTANCE
Metagenomics has become a fundamental tool to characterize the global virosphere, allowing us not only to understand the existing viral diversity and its ecological implications but also to identify new and emerging viruses. RNA viruses have a higher zoonotic potential, but this risk is also present for some DNA virus families. In our study, we analyzed the DNA fraction of fecal samples from 22 Spanish bat species, identifying 52 complete or near-complete genomes of different viral families with zoonotic potential. This doubles the number of genomes currently described in Europe. Metagenomic data often produce partial genomes that can be difficult to analyze. Our work, however, has characterized a large number of complete genomes, thus facilitating their taxonomic classification and enabling different analyses to be carried out to evaluate their zoonotic potential. For example, recombination studies are relevant since this phenomenon could play a major role in cross-species transmission.
Marine redox and nutrient dynamics linked to the Cambrian radiation of animals
Authors: Liu Yang , Bowyer Fred T. , Zhu Maoyan , Xiong Yijun , He Tianchen , Han Meiling , Tang Xuan , Zhang Jinchuan , Poulton Simon W. 
Published: July 2024

Abstract
The early Cambrian witnessed an increase in metazoan ecosystem complexity, likely linked to enhanced oxygen and nutrient availability. However, while improved stratigraphic and geochemical records suggest that the Cambrian explosion occurred under highly dynamic redox conditions, mechanistic links to nutrient availability and early Cambrian evolutionary innovations are poorly constrained. Here, we report paleoredox and nutrient data for two drill cores documenting late Cambrian Stage 2 to Stage 3 (ca. 522–514 Ma) strata from the Yangtze block, South China. The development of water-column euxinia during Cambrian Stage 2 led to extensive recycling of P, fueling elevated primary production and hence an increase in atmospheric and shallow-marine oxygen concentrations. The resulting expansion of oxygenated shelf area promoted sedimentary P retention and, in combination with a diminished supply of P from upwelling, drove a transition to oligotrophic shallow-marine conditions during Cambrian Stage 3. Reduced primary production and limited water-column oxygen consumption allowed for the stabilization of oxygenated continental shelf habitats that supported a burgeoning biotic complexity.