bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective autophagy receptor‐encoding sequences in shallot transcriptome: In silico identification and expression patterns in response to asymptomatic shallot virus X infection
Authors: Vishnichenko Valeriy K. 
Published: March 2024

AbstractPlant host tolerance is a key plant defence response to parasites, including viruses. This complex genetic trait involves multiple molecular mechanisms and, in particular, selective autophagy. Experimental data on the role of various selective autophagy factors and, in particular, cargo receptors in plant tolerance to viral infection are extremely limited. In this communication, I present the results of in silico identification of sequences in the shallot transcriptome encoding homologues of several selective autophagy receptors (SARs) related to the immune response and their expression patterns in response to asymptomatic infection of shallot virus X, a member of the genus Allexivirus, subgenus Acarallexivirus, within the family Alphaflexiviridae. The results obtained, together with the relevant literature data, suggest that some SARs likely to be involved in the regulation of the unfolded protein response and programmed cell death may play an active role in the formation of the state of tolerance of the host plant to allexivirus infection.
A unified approach to parasitic gap and across‐the‐board constructions: Evidence based on Mandarin Chinese
Authors: Ting Jen 
Published: March 2024

AbstractDespite the lack of consensus on English facts, this study demonstrates that both parasitic gap (PG) and across‐the‐board (ATB) constructions in Mandarin Chinese exhibit parallel effects in variable binding reconstruction, while also displaying asymmetries in gap licensing categories. I argue that these patterns in Mandarin Chinese align with the sideward movement approach, supporting a version of the unified approach to deriving both constructions. Specifically, the gaps in question are filled by variables, consistent with both constructions being derived via sideward movement. The observed asymmetries lend support to the view that the licensing of ATB gaps is more permissive than that of PGs, as additional conditions (such as the Parallelsim Requirement) on coordinate structures can license sideward movement in ATB sentences.
Strengthening
Bordetella pertussis
genomic surveillance by direct sequencing of residual positive specimens
Authors: Peng Yanhui , Williams Margaret M. , Xiaoli Lingzi , Simon Ashley , Fueston Heather , Tondella Maria L. , Weigand Michael R. 
Published: March 2024

ABSTRACT

Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent methods to diagnose infectious diseases has resulted in few isolates available for WGS. Here, we report a novel culture-independent approach to genome characterization of
Bordetella pertussis
, the causative agent of pertussis and a paradigm for insufficient genomic surveillance due to limited culture of clinical isolates. Sequencing libraries constructed directly from residual pertussis-positive diagnostic nasopharyngeal specimens were hybridized with biotinylated RNA “baits” targeting
B. pertussis
fragments within complex mixtures that contained high concentrations of host and microbial background DNA. Recovery of
B. pertussis
genome sequence data was evaluated with mock and pooled negative clinical specimens spiked with reducing concentrations of either purified DNA or inactivated cells. Targeted enrichment increased the yield of
B. pertussis
sequencing reads up to 90% while simultaneously decreasing host reads to less than 10%. Filtered sequencing reads provided sufficient genome coverage to perform characterization via whole-genome single nucleotide polymorphisms and whole-genome multilocus sequencing typing. Moreover, these data were concordant with sequenced isolates recovered from the same specimens such that phylogenetic reconstructions from either consistently clustered the same putatively linked cases. The optimized protocol is suitable for nasopharyngeal specimens with diagnostic IS
481
Ct < 35 and >10 ng DNA. Routine implementation of these methods could strengthen surveillance and study of pertussis resurgence by capturing additional cases with genomic characterization.
Seasonal and geographical impact on the Irish raw milk microbiota correlates with chemical composition and climatic variables
Authors: Yap Min , O'Sullivan Orla , O'Toole Paul W. , Sheehan Jeremiah J. , Fenelon Mark A. , Cotter Paul D. 
Published: March 2024

ABSTRACT

Season and location have previously been shown to be associated with differences in the microbiota of raw milk, especially in milk from pasture-based systems. Here, we further advance research in this area by examining differences in the raw milk microbiota from several locations across Ireland over 12 months, and by investigating microbiota associations with climatic variables and chemical composition. Shotgun metagenomic sequencing was used to investigate the microbiota of raw milk collected from nine locations (
n
= 241). Concurrent chemical analysis of the protein, fat, lactose, total solids, nonprotein nitrogen contents, and titratable acidity (TA) of the same raw milk were performed. Although the raw milk microbiota was highly diverse, a core microbiota was found, with
Pseudomonas_E
,
Lactococcus, Acinetobacter
, and
Leuconostoc
present in all samples. Microbiota diversity significantly differed by season and location, with differences in seasonality and geography corresponding to 11.8% and 10.5% of the variation in the microbiota. Functional and antibiotic resistance profiles also varied across season and location. The analysis of other metadata revealed additional interactions, such as an association between mean daily air and grass temperatures with the abundance of spoilage taxa like
Pseudomonas
species. Correlations were identified between pathogenic, mastitis-related species, fat content, and the number of sun hours, suggesting a seasonal effect. Ultimately, this study expands our understanding of the interconnected nature of the microbiota, environment/climate variables, and chemical composition of raw milk and provides evidence of a season- and location-specific microbiota.

IMPORTANCE
The microbiota of raw milk is influenced by many factors that encourage or prevent the introduction and growth of both beneficial and undesirable microorganisms. The seasonal and geographical impacts on the microbial communities of raw milk have been previously seen, but the relationships with environmental factors and the chemical composition has yet to be investigated. In this year-long study, we found that while raw milk is highly diverse, a core microbiota was detected for Irish raw milk, with strong evidence of seasonal and geographical influence. We also found associations between groups of microorganisms, environmental factors, and milk composition, which expand current knowledge on the relationships between microbial and chemical composition and the climate. These results provide evidence for the development of a tool to allow for the prediction of raw milk quality and safety.
Phylogenomics reveals extensive misidentification of fungal strains from the genus
Aspergillus
Authors: Steenwyk Jacob L. , Balamurugan Charu , Raja Huzefa A. , Gonçalves Carla , Li Ningxiao , Martin Frank , Berman Judith , Oberlies Nicholas H. , Gibbons John G. , Goldman Gustavo H. , Geiser David M. , Houbraken Jos , Hibbett David S. , Rokas Antonis 
Published: March 2024

ABSTRACT

Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genus
Aspergillus
. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for
Aspergillus
and provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.

IMPORTANCE

Identification of fungal species relies on the use of molecular markers. Advances in genomic technologies have made it possible to sequence the genome of any fungal strain, making it possible to use genomic data for the accurate assignment of strains to fungal species (and for the discovery of new ones). We examined the usefulness and current limitations of genomic data using a large data set of 710 publicly available genomes from multiple strains and species of the biomedically, agriculturally, and industrially important genus
Aspergillus
. Our evolutionary genomic analyses revealed that nearly 8% of publicly available
Aspergillus
genomes are misidentified. Our work highlights the usefulness of genomic data for fungal systematic biology and suggests that systematic genome sequencing of multiple strains, including reference strains (e.g., type strains), of fungal species will be required to reduce misidentification errors in public databases.
Toxoplasma gondiiseropositivity and cognitive functioning in older adults: an analysis of cross-sectional data of the National Health and Nutrition Examination Survey 2011–2014
Authors: Song Ge , Zhao Qingxia , Chen Hongyu , Li Meng , Zhang Zeyu , Qu Zhe , Yang Chao , Lin Xuechun , Ma Weixia , Standlee Courtney Rose 
Published: March 2024

ObjectivesThis study sought to examine the relationship betweenToxoplasma gondiiseropositivity and cognitive function in older adults.DesignAn observational cross-sectional study.SettingThe National Health and Nutrition Examination Survey (NHANES) study took place at participants’ homes and mobile examination centres.ParticipantsA total of 2956 older adults aged 60 and above from the NHANES from 2011 to 2014 were included in the study. Exposure of interest: participants had serumToxoplasma gondiiantibody analysed in the laboratory. A value>33 IU/mL was categorised as seropositive forToxoplasma gondiiinfection; <27 IU/mL was categorised as seronegative forToxoplasma gondiiinfection.Primary and secondary outcome measuresCognitive tests included the Consortium to Establish a Registry for Alzheimer’s Disease Word Learning subtest (CERAD-WL) for immediate and delayed memory, the Animal Fluency Test (AFT), and the Digit Symbol Substitution Test (DSST).ResultsAbout half of the 2956 participants (mean age 70.0) were female (51.0%), non-Hispanic White (48.3%), and completed some college or above (48.3%). A total of 703 participants were positive forToxoplasma gondiiinfection (23.8%). Adjusted linear regression showed that compared with participants with negativeToxoplasma gondiiinfection, those with positiveToxoplasma gondiiinfection had lower CERAD-WL immediate memory (beta (β) −0.16, 95% CI −0.25 to –0.07), CERAD-WL delayed memory (β −0.15, 95% CI −0.24 to –0.06), AFT (β −0.15, 95% CI −0.24 to –0.06), DSST (β −0.34, 95% CI −0.43 to –0.26), and global cognition (β −0.24, 95% CI −0.32 to –0.16) z-scores after controlling for the covariates.ConclusionsToxoplasma gondiiseropositivity is associated with worse immediate and delayed verbal learning, language proficiency, executive functioning, processing speed, sustained attention, working memory, as well as global cognition in older adults. Public health measures aiming at preventingToxoplasma gondiiinfection may help preserve cognitive functioning in older adults.
Scoping review protocol of post-traumatic growth (PTG) in Korean cancer survivors
Authors: Park Yu-Jin , Lee Kyoung Suk 
Published: March 2024

IntroductionCancer, a life-threatening chronic disease, is the leading cause of death in Korea, accounting for 27% of all deaths in 2020. Due to advancements in medical technology and early detection of cancer in Korea, the 5-year relative survival rate reached 70.7% (2015–2019), highlighting remarkable progress over the past decades. Although cancer has been seen as a traumatic event, cancer survivors also go through a subjective process of self-maturation, which is called post-traumatic growth (PTG). Because research on PTG among Korean cancer survivors has not been systematically synthesised, a scoping review on this topic will provide a better understanding of the positive psychological changes that occur as a patient moves through the illness trajectory of cancer from a Korean cultural perspective. The purpose of this study was to describe the protocol of a scoping review regarding PTG in Korean cancer survivors.Methods and analysisThe scoping review framework suggested by Arksey and O’Malley and the manual refined by the Joanna Briggs Institute for scoping reviews will be used with the six framework guidelines developed by Levacet al. Searched databases will include Ovid-MEDLINE, PubMed, Embase, CINAHL, Cochrane Library and PsycInfo, as well as Korean databases, examining all articles published between 2012 and 2023 in Korean or English on PTG in Korean cancer survivors. Extracted data will be collated, charted and summarised.Ethics and disseminationBecause the scoping review methodology undertakes a secondary analysis of collected data from previous research studies, this study does not require ethical approval. The results of this scoping review will be disseminated through presentations at conferences and publication in a scientific journal.
Nuclear Physics Mid Term Plan at LNGS
Authors: Buompane R. , Cavanna F. , Curceanu C. , D’Onofrio A. , Di Leva A. , Formicola A. , Gialanella L. , Gustavino C. , Imbriani G. , Junker M. , Marcianò A. , Marzaioli F. , Nania R. , Napolitano F. , Piscicchia K. , Straniero O. , Abia C. , Aliotta M. , Bemmerer D. , Best A. , Boeltzig A. , Bruno C. , Caciolli A. , Chieffi A. , Ciani G. , D’Agata G. , deBoer R. J. , De Cesare M. , Dell’Aquila D. , Depalo R. , Dominguez I. , Ferraro F. , Garcia Duarte J. , Guglielmetti A. , Gyürky Gy. , Hayakawa S. , La Cognata M. , Lamia L. , Marcucci L. E. , Masha E. , Mazzocco M. , Morales-Gallegos E. L. , Palmerini S. , Passariello I. , Petraglia A. , Piatti D. , Pignatari M. , Pizzone R. G. , Porzio G. , Rapagnani D. , Rapisarda G. G. , Romano S. , Rubino M. , Santonastaso C. , Sergi M. L. , Skowronski J. , Spartà R. , Terrasi F. , Tumino A. , Turkat S. , Wiescher M. , Zavatarelli S. 
Published: March 2024

AbstractThe Istituto Nazionale di Fisica Nucleare—Laboratori Nazionali del Gran Sasso (LNGS) is one of the largest underground physics laboratory, a very peculiar environment suited for experiments in Astroparticle Physics, Nuclear Physics and Fundamental Symmetries. The newly established Bellotti Ion Beam facility represents a major advance in the possibilities of studying nuclear processes in an underground environment. A workshop was organized at LNGS in the framework of the Nuclear Physics Mid Term Plan in Italy, an initiative of the Nuclear Physics Division of the Instituto Nazionale di Fisica Nucleare to discuss the opportunities that will be possible to study in the near future by employing state-of-the-art detection systems. In this report, a detailed discussion of the outcome of the workshop is presented.
Dyslipidemia in American Indian Adolescents and Young Adults: Strong Heart Family Study
Authors: Reese Jessica A. , Roman Mary J. , Deen Jason F. , Ali Tauqeer , Cole Shelley A. , Devereux Richard B. , Fretts Amanda M. , Howard Wm. James , Lee Elisa T. , Malloy Kimberly , Umans Jason G. , Zhang Ying 
Published: March 2024

Background
Although many studies on the association between dyslipidemia and cardiovascular disease (CVD) exist in older adults, data on the association among adolescents and young adults living with disproportionate burden of cardiometabolic disorders are scarce.

Methods and Results
The SHFS (Strong Heart Family Study) is a multicenter, family‐based, prospective cohort study of CVD in an American Indian populations, including 12 communities in central Arizona, southwestern Oklahoma, and the Dakotas. We evaluated SHFS participants, who were 15 to 39 years old at the baseline examination in 2001 to 2003 (n=1440). Lipids were measured after a 12‐hour fast. We used carotid ultrasounds to detect plaque at baseline and follow‐up in 2006 to 2009 (median follow‐up=5.5 years). We identified incident CVD events through 2020 with a median follow‐up of 18.5 years. We used shared frailty proportional hazards models to assess the association between dyslipidemia and subclinical or clinical CVD, while controlling for covariates. Baseline dyslipidemia prevalence was 55.2%, 73.6%, and 78.0% for participants 15 to 19, 20 to 29, and 30 to 39 years old, respectively. Approximately 2.8% had low‐density lipoprotein cholesterol ≥160 mg/dL, which is higher than the recommended threshold for lifestyle or medical interventions in young adults of 20 to 39 years old. During follow‐up, 9.9% had incident plaque (109/1104 plaque‐free participants with baseline and follow‐up ultrasounds), 11.0% had plaque progression (128/1165 with both baseline and follow‐up ultrasounds), and 9% had incident CVD (127/1416 CVD‐free participants at baseline). Plaque incidence and progression were higher in participants with total cholesterol ≥200 mg/dL, low‐density lipoprotein cholesterol ≥160 mg/dL, or non–high‐density lipoprotein cholesterol ≥130 mg/dL, while controlling for covariates. CVD risk was independently associated with low‐density lipoprotein cholesterol ≥160 mg/dL.

Conclusions
Dyslipidemia is a modifiable risk factor that is associated with both subclinical and clinical CVD, even among the younger American Indian population who have unexpectedly high rates of significant CVD events. Therefore, this population is likely to benefit from a variety of evidence‐based interventions including screening, educational, lifestyle, and guideline‐directed medical therapy at an early age.
Incarnating Kannon: Eshinni, Shinran, and the Other-Power of Philosophy
Authors: Kalmanson Leah 
Published: March 2024

Abstract
Here the relationship between Shinran and Eshinni, founding family of the largest Buddhist sect in Japan, serves as a methodological model for philosophical engagement. Though the Pure Land notion of “easy practice” (Jp. igyō 易行) may be seen as Zen’s less rigorous counterpart, Shinran’s turn toward “other-power” (tariki 他力) is driven by the same philosophical debates over practice and liberation that occupied contemporaries such as Dōgen. The answers to such debates, which Shinran and Eshinni enacted concretely via their lifestyle choices, help us rethink both academic practices and the role of philosophers as engaged intellectuals today.
The Scarcity of Women’s Records in Antiquity: Where Did All the Women Go?
Authors: Rosenlee Li-Hsiang Lisa 
Published: March 2024

Abstract
The scarcity of women’s writings in antiquity presents an intractable problem for feminists intending to integrate women’s perspectives into the existing philosophical canon. One way to undo the erasure of women is for feminists to look to the east; in China, there is an abundance of well-preserved women’s writings, along with their biographical records, as early as the 6th century BCE. This essay will provide a survey of those women’s records, focusing on the 6th century BCE to the 4th century CE, as a way to reimagine the discipline of Philosophy and its canon.
The Railway Men
Authors: Jain Atharv , Jain Pankaj 
Published: March 2024

Abstract
The Bhopal Disaster, also known as the Bhopal Gas Tragedy, is recognized as the world’s worst industrial disaster. The Bhopal Disaster is the only industrial disaster affecting half a million people in the last few decades. Because of the sheer magnitude of this disaster, this topic remains relevant, especially to learn what preventive measures could have been taken to ensure such a tragedy never occurred. The disaster occurred from a mixture of chemicals that produced a toxic gas, a lack of employee reporting when issues arose in the plant and weak safety systems. In December 1984, a poison gas blanketed the city of Bhopal. Due to the mistakes mentioned above, over two thousand people and many more livestock died overnight and were discovered the next morning. The effects of the disaster still linger in the same location to this day.
Challenges of Operational Weather Forecast Verification and Evaluation
Authors: Pagano Thomas C. , Casati Barbara , Landman Stephanie , Loveday Nicholas , Taggart Robert , Ebert Elizabeth E. , Khanarmuei Mohammadreza , Jensen Tara L. , Mittermaier Marion , Roberts Helen , Willington Steve , Roberts Nigel , Sowko Mike , Strassberg Gordon , Kluepfel Charles , Bullock Timothy A. , Turner David D. , Pappenberger Florian , Osborne Neal , Noble Chris 
Published: March 2024

Abstract
Operational agencies face significant challenges related to the verification and evaluation of weather forecasts. These challenges were investigated in a series of online workshops and polls engaging operational personnel from six countries. Five key themes emerged: inadequate verification approaches for both existing and emerging products; incomplete and uncertain observations; difficulties in accurately capturing users’ real-world experiences using simplified metrics; poor communication and understanding of forecasts and complex verification information; and institutional factors such as limited resources, evolving meteorologist roles, and concerns over reputational damage. We identify nearly 50 operationally relevant scientific questions and suggest calls to action. Addressing these needs includes designing forecast systems with verification as a central consideration, enhancing the availability of observations, and developing and adopting community software systems. Additionally, we propose the establishment of an international community comprising environmental and social science researchers, statisticians, verification practitioners, and users to provide sustained support for this collective endeavor.