bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controlling diurnal flower‐opening time by manipulating the jasmonate pathway accelerates development of indica–japonica hybrid rice breeding
Authors: Wang Mumei , Zhu Xiaopei , Huang Zhen , Chen Minghao , Xu Peng , Liao Shitang , Zhao Yongzhen , Gao Yannan , He Jiahui , Luo Yutong , Chen Huixuan , Wei Xiaoying , Nie Shuai , Dong Jingfang , Zhu Liya , Zhuang Chuxiong , Zhao Junliang , Liu Zhenlan , Zhou Hai 
Published: March 2024

SummaryInter‐subspecific indica–japonica hybrid rice (Oryza sativa) has the potential for increased yields over traditional indica intra‐subspecies hybrid rice, but limited yield of F1 hybrid seed production (FHSP) hinders the development of indica–japonica hybrid rice breeding. Diurnal flower‐opening time (DFOT) divergence between indica and japonica rice has been a major contributing factor to this issue, but few DFOT genes have been cloned. Here, we found that manipulating the expression of jasmonate (JA) pathway genes can effectively modulate DFOT to improve the yield of FHSP in rice. Treating japonica cultivar Zhonghua 11 (ZH11) with methyl jasmonate (MeJA) substantially advanced DFOT. Furthermore, overexpressing the JA biosynthesis gene OPDA REDUCTASE 7 (OsOPR7) and knocking out the JA inactivation gene CHILLING TOLERANCE 1 (OsHAN1) in ZH11 advanced DFOT by 1‐ and 2‐h respectively; and knockout of the JA signal suppressor genes JASMONATE ZIM‐DOMAIN PROTEIN 7 (OsJAZ7) and OsJAZ9 resulted in 50‐min and 1.5‐h earlier DFOT respectively. The yields of FHSP using japonica male‐sterile lines GAZS with manipulated JA pathway genes were significantly higher than that of GAZS wildtype. Transcriptome analysis, cytological observations, measurements of elastic modulus and determination of cell wall components indicated that the JA pathway could affect the loosening of the lodicule cell walls by regulating their composition through controlling sugar metabolism, which in turn influences DFOT. This research has vital implications for breeding japonica rice cultivars with early DFOT to facilitate indica–japonica hybrid rice breeding.
Comparative Analysis of Morphological Diversification in Large African Barbs of the Genus Barbus (Labeobarbus auctorum, Cyprinidae) and Altai Osmans of the Genus Oreoleuciscus (Leuciscidae)
Authors: Mina M. V. , Mironovsky A. N. , Dgebuadze Yu. Yu. 
Published: March 2024

AbstractThe study of diversity in characters of the skull in generalized and specialized morphotypes of the large African barbs Barbus (Labeobarbus auctorum) in Ethiopia is carried out using the multivariate analysis methods. It has been proven that in Lake Tana exhibiting great diversity in morphotypes, the eigenvector loadings on the first principal component of characters of bones, which form the jaws, compose a distinct self-standing cluster in specimens of a generalized form reaching over 15 cm in length. In barbs inhabiting other lakes, where only a generalized form is found, the lack of such cluster is observed, while the eigenvector loadings on the second principal component generate a cluster similar in composition. The same pattern is discovered in the Altai osmans (genus Oreoleuciscus) in Lake Orog within the Central Asian Closed Basin (Mongolia). In this case, however, the specimens of the generalized form tend to exhibit the characters of a bigmouth form after transition to feeding on fish whereas the progeny of bigmouth barbs in Lake Tana exhibit the parental characters even in the aquarium-based experiments. It is assumed that in the Altai osmans from Lake Orog we observe an early stage of morpho-ecological divergence between forms, when it is still reversible, while the divergence at a later stage, when it is irreversible, is detected in the barbs from Lake Tana, which may be regarded as an example of genetic assimilation.
Quantum gate sets for lattice QCD in the strong-coupling limit: $N_{f}=1$
Authors: Fromm Michael , Philipsen Owe , Unger Wolfgang , Winterowd Christopher 
Published: March 2024

AbstractWe derive the primitive quantum gate sets to simulate lattice quantum chromodynamics (LQCD) in the strong-coupling limit with one flavor of massless staggered quarks. This theory is of interest for studies at non-zero density as the sign problem can be overcome using Monte Carlo methods. In this work, we use it as a testing ground for quantum simulations. The key point is that no truncation of the bosonic Hilbert space is necessary as the theory is formulated in terms of color-singlet degrees of freedom (“baryons” and “mesons”). The baryons become static in the limit of continuous time and decouple, whereas the dynamics of the mesonic theory involves two qubits per lattice site. Lending dynamics also to the “baryons” simply requires to use the derived gate set in its controlled version.
Optical Coherence Tomography–Based Functional Stenosis Assessment: FUSION—A Prospective Multicenter Trial
Authors: Jeremias Allen , Maehara Akiko , Matsumura Mitsuaki , Shlofmitz Richard A. , Maksoud Aziz , Akasaka Takashi , Bezerra Hiram G. , Fearon William F. , Samady Habib , Samuels Bruce , Rapkin Joshua , Gopinath Ajay , Teraphongphom Nutte Tarn , Buccola Jana , Ali Ziad A. 
Published: March 2024

BACKGROUND:
Intravascular imaging and intracoronary physiology may both be used to guide and optimize percutaneous coronary intervention; however, they are rarely used together. The virtual flow reserve (VFR) is an optical coherence tomography (OCT)–based model of fractional flow reserve (FFR) facilitating the assessment of the physiological significance of coronary lesions. We aimed to validate the VFR assessment of intermediate coronary artery stenoses.

METHODS:
FUSION (Validation of OCT-Based Functional Diagnosis of Coronary Stenosis) was a multicenter, prospective, observational study comparing OCT-derived VFR to invasive FFR. VFR was mathematically derived from a lumped parameter flow model based on 3-dimensional lumen morphology. Patients undergoing coronary angiography with intermediate angiographic stenosis (40%–90%) requiring physiological assessment were enrolled. Investigational sites were blinded to the VFR analysis, and all OCT and FFR data were reviewed by an independent core laboratory. The coprimary end points were the sensitivity and specificity of VFR against FFR as the reference standard, each of which was tested against prespecified performance goals.

RESULTS:

After core laboratory review, 266 vessels in 224 patients from 25 US centers were included in the analysis. The mean angiographic diameter stenosis was 65.5%±14.9%, and the mean FFR was 0.83±0.11. Overall accuracy, sensitivity, and specificity of VFR versus FFR using a binary cutoff point of 0.80 were 82.0%, 80.4%, and 82.9%, respectively. The 97.5% lower confidence bound met the prespecified performance goal for sensitivity (71.6% versus 70%;
P
=0.01) and specificity (76.6% versus 75%;
P
=0.01). The area under the curve was 0.88 (95% CI, 0.84–0.92;
P
<0.0001).

CONCLUSIONS:
OCT-derived VFR demonstrates high sensitivity and specificity for predicting invasive FFR. Integrating high-resolution intravascular imaging with imaging-derived physiology may provide synergistic benefits as an adjunct to percutaneous coronary intervention.

REGISTRATION:

URL:
https://clinicaltrials.gov
; Unique identifier: NCT04356027.
The robot butler: How and why should we study predictive algorithms and artificial intelligence (AI) in healthcare?
Authors: Gjødsbøl Iben Mundbjerg , Ringgaard Anna Kirstine , Holm Peter Christoffer , Brunak Søren , Bundgaard Henning 
Published: March 2024

Artificial intelligence (AI) and algorithms are heralded as significant solutions to the widening gap between the rising healthcare needs of ageing and multi-morbid populations and the scarcity of resources to provide such care. Objective This article investigates how the PMHnet algorithm – an AI prognostication tool developed in Denmark to predict the one-year all-cause mortality risk for patients hospitalized with ischemic heart disease – was presented to cardiologists working in the hospital setting, and how they responded to this novel decision-support tool. Methods Empirically, we draw upon ethnographic fieldwork in the Danish-led international research project, PM Heart, which since 2019 has developed the PMHnet algorithm and implemented the software into the electronic health record system in hospitals in Eastern Denmark (the Capital Region and Region Zealand). Results Paying careful attention to the hopes and concerns of cardiologists who will have to embrace and adapt to algorithmic tools in their everyday work of diagnosing and treating patients, we identify three analytical themes meriting attention when AI is implemented in healthcare: 1) the re-negotiation of agency and autonomy in human-algorithm relations, 2) accountability in algorithmic prognostication and 3) the complex relationship between association and causation actualized by predictive algorithms. From these analytical themes, we elicit methodological questions to guide future ethnographic explorations of how AI and advanced algorithms are put to use in the healthcare system, with what implications, and for whom. Conclusion We conclude that local, qualitative investigations of how algorithms are used, embraced and contested in everyday clinical practice are needed in order to understand their implications – good and bad, intended and unintended – for clinicians, patients and healthcare provision.
Prevention, Diagnosis, and Management of Intraoperative Spinal Cord Injury in the Setting of Spine Surgery: A Proposed Care Pathway
Authors: Srikandarajah Nisaharan , Hejrati Nader , Alvi Mohammed Ali , Quddusi Ayesha , Tetreault Lindsay A. , Evaniew Nathan , Skelly Andrea C. , Douglas Sam , Rahimi-Movaghar Vafa , Arnold Paul M , Kirshblum Steven , Kwon Brian K. , Fehlings Michael G. 
Published: March 2024

Study Design This study is a mixed methods approach. Objectives Intraoperative spinal cord injury (ISCI) is a challenging complication in spine surgery. Intra-operative neuromonitoring (IONM) has been developed to detect changes in neural function. We report on the first multidisciplinary, international effort through AO Spine and the Praxis Spinal Cord Institute to develop a comprehensive guideline and care pathway for the prevention, diagnosis, and management of ISCI. Methods Three literature reviews were registered on PROSPERO (CRD 42022298841) and performed according to PRISMA guidelines: (1) Definitions, frequency, and risk factors for ISCI, (2) Meta-analysis of the accuracy of IONM for diagnosis of ISCI, (3) Reported management approaches for ISCI and related events. The results were presented in a consensus session to decide the definition of IONM and recommendation of its use in high-risk cases. Based on a literature review of management strategies for ISCI, an intra-operative checklist and overall care pathway was developed by the study team. Results An operational definition and high-risk patient categories for ISCI were established. The reported incidence of deficits was documented to be higher in intramedullary tumour spine surgery. Multimodality IONM has a high sensitivity and specificity. A guideline recommendation of IONM to be employed for high-risk spine cases was made. The different sections of the intraoperative checklist include surgery, anaesthetic and neurophysiology. The care pathway includes steps (1) initial clinical assessment, (2) pre-operative planning, (3) surgical/anaesthetic planning, (4) intra-operative management, and (5) post-operative management. Conclusions This is the first evidence based comprehensive guideline and care pathway for ISCI using the GRADE methodology. This will facilitate a reduction in the incidence of ISCI and improved outcomes from this complication. We welcome the wide implementation and validation of these guidelines and care pathways in prospective, multicentre studies.
Perspectives of Canadian Healthcare and Harm Reduction Workers on Mobile Overdose Response Services: A Qualitative Study
Authors: Sedaghat Navid , Seo Boogyung , Rider Nathan , Rioux William , Ghosh S. Monty 
Published: March 2024

Background: Supervised consumption sites (SCS) are an evidence-based intervention proven effective for preventing drug overdose deaths. Obstacles to accessing SCS include stigma, limited hours of operation, concerns about policing, and limited geographic availability. Mobile overdose response services (MORS) are novel technologies that provide virtual supervised consumption to help reduce the risk of fatal overdoses, especially for those who use alone. MORS can take various forms, such as phone-based hotlines and mobile apps. The aim of this article is to assess the perceptions of MORS among healthcare and harm reduction staff to determine if they would be comfortable educating clients about these services. Methods: Twenty-two healthcare and harm reduction staff were recruited from Canada using convenience, snowball, and purposive sampling techniques to complete semistructured interviews. Inductive thematic analysis informed by grounded theory was used to identify main themes and subthemes. Results: Four themes were identified: (1) increasing MORS awareness among healthcare providers was seen as useful; (2) MORS might lessen the burden of drug overdoses on the healthcare system but could also increase ambulance callouts; (3) MORS would benefit from certain improvements such as providing harm reduction resources and other supports; and (4) MORS are viewed as supplements for harm reduction, but SCS were preferred. Conclusions: This research provides valuable perspectives from healthcare and harm reduction workers to understand their perception of MORS and identifies key areas of potential improvement. Practical initiatives to improve MORS implementation outcomes exist.
Exploring Genetic Diversity within aus Rice Germplasm: Insights into the Variations in Agro-morphological Traits
Authors: Sar Puranjoy , Gupta Sonal , Behera Motilal , Chakraborty Koushik , Ngangkham Umakanta , Verma Bibhash Chandra , Banerjee Amrita , Hanjagi Prashantkumar S. , Bhaduri Debarati , Shil Sandip , Kumar Jitendra , Mandal Nimai Prasad , Kole Paresh Chandra , Purugganan Michael D. , Roy Somnath 
Published: March 2024

AbstractThe aus (Oryza sativa L.) varietal group comprises of aus, boro, ashina and rayada seasonal and/or field ecotypes, and exhibits unique stress tolerance traits, making it valuable for rice breeding. Despite its importance, the agro-morphological diversity and genetic control of yield traits in aus rice remain poorly understood. To address this knowledge gap, we investigated the genetic structure of 181 aus accessions using 399,115 SNP markers and evaluated them for 11 morpho-agronomic traits. Through genome-wide association studies (GWAS), we aimed to identify key loci controlling yield and plant architectural traits.Our population genetic analysis unveiled six subpopulations with strong geographical patterns. Subpopulation-specific differences were observed in most phenotypic traits. Principal component analysis (PCA) of agronomic traits showed that principal component 1 (PC1) was primarily associated with panicle traits, plant height, and heading date, while PC2 and PC3 were linked to primary grain yield traits. GWAS using PC1 identified OsSAC1 on Chromosome 7 as a significant gene influencing multiple agronomic traits. PC2-based GWAS highlighted the importance of OsGLT1 and OsPUP4/ Big Grain 3 in determining grain yield. Haplotype analysis of these genes in the 3,000 Rice Genome Panel revealed distinct genetic variations in aus rice.In summary, this study offers valuable insights into the genetic structure and phenotypic diversity of aus rice accessions. We have identified significant loci associated with essential agronomic traits, with GLT1, PUP4, and SAC1 genes emerging as key players in yield determination.
Full-length 16S rRNA gene sequencing by PacBio improves taxonomic resolution in human microbiome samples
Authors: Buetas Elena , Jordán-López Marta , López-Roldán Andrés , D’Auria Giuseppe , Martínez-Priego Llucia , De Marco Griselda , Carda-Diéguez Miguel , Mira Alex 
Published: March 2024

AbstractBackgroundSequencing variable regions of the 16S rRNA gene (≃300 bp) with Illumina technology is commonly used to study the composition of human microbiota. Unfortunately, short reads are unable to differentiate between highly similar species. Considering that species from the same genus can be associated with health or disease it is important to identify them at the lowest possible taxonomic rank. Third-generation sequencing platforms such as PacBio SMRT, increase read lengths allowing to sequence the whole gene with the maximum taxonomic resolution. Despite its potential, full length 16S rRNA gene sequencing is not widely used yet. The aim of the current study was to compare the sequencing output and taxonomic annotation performance of the two approaches (Illumina short read sequencing and PacBio long read sequencing of 16S rRNA gene) in different human microbiome samples. DNA from saliva, oral biofilms (subgingival plaque) and faeces of 9 volunteers was isolated. Regions V3-V4 and V1-V9 were amplified and sequenced by Illumina Miseq and by PacBio Sequel II sequencers, respectively.ResultsWith both platforms, a similar percentage of reads was assigned to the genus level (94.79% and 95.06% respectively) but with PacBio a higher proportion of reads were further assigned to the species level (55.23% vs 74.14%). Regarding overall bacterial composition, samples clustered by niche and not by sequencing platform. In addition, all genera with > 0.1% abundance were detected in both platforms for all types of samples. Although some genera such asStreptococcustended to be observed at higher frequency in PacBio than in Illumina (20.14% vs 14.12% in saliva, 10.63% vs 6.59% in subgingival plaque biofilm samples) none of the differences were statistically significant when correcting for multiple testing.ConclusionsThe results presented in the current manuscript suggest that samples sequenced using Illumina and PacBio are mostly comparable. Considering that PacBio reads were assigned at the species level with higher accuracy than Illumina, our data support the use of PacBio technology for future microbiome studies, although a higher cost is currently required to obtain an equivalent number of reads per sample.
Identification of potential cell death-related biomarkers for diagnosis and treatment of osteoporosis
Authors: Li Mingliang , Wang Xue , Guo Mingbo , Zhang Wenlong , Li Taotao , Zheng Jinyang 
Published: March 2024

Abstract
Background
This study aimed to identify potential biomarkers for the diagnosis and treatment of osteoporosis (OP).

Methods
Data sets were downloaded from the Gene Expression Omnibus database, and differentially programmed cell death-related genes were screened. Functional analyses were performed to predict the biological processes associated with these genes. Least absolute shrinkage and selection operator (LASSO), support vector machine (SVM), and random forest (RF) machine learning algorithms were used to screen for characteristic genes, and receiver operating characteristics were used to evaluate the diagnosis of disease characteristic gene values. Gene set enrichment analysis (GSEA) and single-sample GSEA were conducted to analyze the correlation between characteristic genes and immune infiltrates. Cytoscape and the Drug Gene Interaction Database (DGIdb) were used to construct the mitochondrial RNA-mRNA-transcription factor network and explore small-molecule drugs. Reverse transcription real-time quantitative PCR (RT-qPCR) analysis was performed to evaluate the expression of biomarker genes in clinical samples.

Results
In total, 25 differential cell death genes were identified. Among these, two genes were screened using the LASSO, SVM, and RF algorithms as characteristic genes, including BRSK2 and VPS35. In GSE56815, the area under the receiver operating characteristic curve of BRSK2 was 0.761 and that of VPS35 was 0.789. In addition, immune cell infiltration analysis showed that BRSK2 positively correlated with CD56dim natural killer cells and negatively correlated with central memory CD4 + T cells. Based on the data from DGIdb, hesperadin was associated with BRSK2, and melagatran was associated with VPS35. BRSK2 and VPS35 were expectably upregulated in OP group compared with controls (all p < 0.05).

Conclusions
BRSK2 and VPS35 may be important diagnostic biomarkers of OP.
RETRACTED ARTICLE: Potential use of
proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibition and prevention method
in viral infection
Authors: Muzammil Khursheed , Hooshiar Mohammad Hosseini , Varmazyar Shirin , Omar Thabit Moath , Karim Manal Morad , Aadi Sadeq , Kalavi Shaylan , Yasamineh Saman 
Published: March 2024

AbstractCellular lipid membranes serve as the primary barrier preventing viral
infection of the host cell and provide viruses with a critical initial point of
contact. Occasionally, viruses can utilize lipids as viral receptors. Viruses depend
significantly on lipid rafts for infection at virtually every stage of their life
cycle. The pivotal role that proprotein convertase subtilisin/kexin Type 9 (PCSK9)
plays in cholesterol homeostasis and atherosclerosis, primarily by
post-transcriptionally regulating hepatic low-density lipoprotein receptor (LDLR)
and promoting its lysosomal degradation, has garnered increasing interest.
Conversely, using therapeutic, fully humanized antibodies to block PCSK9 leads to a
significant reduction in high LDL cholesterol (LDL-C) levels. The Food and Drug
Administration (FDA) has approved PCSK9 inhibitors, including inclisiran
(Leqvio®), alirocumab (Praluent), and evolocumab (Repatha). At present,
active immunization strategies targeting PCSK9 present a compelling substitute for
passive immunization through the administration of antibodies. In addition to the
current inquiry into the potential therapeutic application of PCSK9 inhibition in
human immunodeficiency virus (HIV)-infected patients for hyperlipidemia associated
with HIV and antiretroviral therapy (ART), preclinical research suggests that PCSK9
may also play a role in inhibiting hepatitis C virus (HCV) replication. Furthermore,
PCSK9 inhibition has been suggested to protect against dengue virus (DENV)
potentially and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
viruses. Recent evidence regarding the impact of PCSK9 on a variety of viral
infections, including HCV, HIV, DENV, and SARS-CoV-2, is examined in this article.
As a result, PCSK9 inhibitors and vaccines may serve as viable host therapies for
viral infections, as our research indicates that PCSK9 is significantly involved in
the pathogenesis of viral infections.
Graphical abstract: the function of proprotein convertase subtilisin/kexin
type 9 (PCSK9) in reducing cholesterol uptake and low-density lipoprotein
receptor (LDLR) recycling in various viral infections, including hepatitis C
virus (HCV), human immunodeficiency viruses (HIV), dengue virus (DENV), rift
valley fever (RVF), and severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2) is summarized in this figure