bluuebunny/crossref_metadata_2025_split huggingface dataset:
The importance of patient characteristics, operators, and image quality for the accuracy of heart failure diagnosis by general practitioners using handheld ultrasound devices
Authors: Magelssen Malgorzata Izabela , Hjorth-Hansen Anna Katarina , Andersen Garrett Newton , Graven Torbjørn , Kleinau Jens Olaf , Skjetne Kyrre , Lovstakken Lasse , Dalen Havard , Mjølstad Ole Christian 
Published: December 2023

Abstract

Aims
To evaluate whether the characteristics of patients, operators, and image quality could explain the accuracy of heart failure (HF) diagnostics by general practitioners (GPs) using handheld ultrasound devices (HUDs) with automatic decision-support software and telemedical support.

Methods and results
Patients referred to an outpatient cardiac clinic due to symptoms indicating HF were examined by one of five GPs after dedicated training. In total, 166 patients were included [median (inter-quartile range) age 73 (63–78) years; mean ± standard deviation ejection fraction 53 ± 10%]. The GPs considered whether the patients had HF in four diagnostic steps: (i) clinical examination, (ii) adding focused cardiac HUD examination, (iii) adding automatic decision-support software measuring mitral annular plane systolic excursion (autoMAPSE) and ejection fraction (autoEF), and (iv) adding telemedical support. Overall, the characteristics of patients, operators, and image quality explained little of the diagnostic accuracy. Except for atrial fibrillation [lower accuracy for HUD alone and after adding autoEF (P &lt; 0.05)], no patient characteristics influenced the accuracy. Some differences between operators were found after adding autoMAPSE (P &lt; 0.05). Acquisition errors of the four-chamber view and a poor visualization of the mitral plane were associated with reduced accuracy after telemedical support (P &lt; 0.05).

Conclusion
The characteristics of patients, operators, and image quality explained just minor parts of the modest accuracy of GPs’ HF diagnostics using HUDs with and without decision-support software. Atrial fibrillation and not well-standardized recordings challenged the diagnostic accuracy. However, the accuracy was only modest in well-recorded images, indicating a need for refinement of the technology.
Associations Between Blood Concentrations of Sex Hormones and Physical Function in Community-Dwelling Older Women: A Prospective Cohort Study
Authors: Wang Yuanyuan , Islam Rakibul M , Hussain Sultana Monira , McNeil John J , Davis Susan R 
Published: December 2023

Abstract

Background
Blood concentrations of testosterone and estrone tend to increase in women aged ≥70 years, whereas concentrations of their precursor hormone dehydroepiandrosterone decline. It is unknown whether these changes influence physical function. We investigated whether concentrations of these hormones were associated with grip strength and self-reported physical function in community-dwelling older women.

Methods
A total of 9 179 Australian women, aged ≥70 years, were recruited to the ASPirin in Reducing Events in the Elderly (ASPREE) trial. Sex hormones were measured in Sex Hormones in Older Women, an ASPREE substudy, by liquid chromatography–tandem mass spectrometry in 6 358 women. The associations between hormone concentrations and physical function (handgrip strength and self-reported physical function assessed by SF-12v2 physical component summary [PCS]) were examined using multiple linear regression.

Results
The median age of the 5,447 participants was 74.0 (interquartile range 71.7–77.6) years. Testosterone concentrations above the lowest quartile were associated with less decline in grip strength (mean –1.39 [95% CI –1.54 to –1.24] vs –1.75 [–2.00 to –1.50] kg, p = .02), and dehydroepiandrosterone concentrations above the lowest quartile were associated with less decline in grip strength (–1.39 [–1.54 to –1.25] vs –1.82 [–2.11 to –1.55] kg, p = .007) and PCS scores (–1.49 [–1.80 to –1.17] vs –2.33 [–2.93 to –1.72], p = .02) over 4 years, compared with those in the respective lowest quartile.

Conclusions
Low endogenous concentrations of testosterone and dehydroepiandrosterone were associated the greatest likelihood of physical function decline in community-based women aged ≥70 years. Further studies are warranted to determine whether testosterone and dehydroepiandrosterone therapy prevent functional decline in this at-risk group using sensitive measures of muscle strength and performance.
COVID-19 and Cognitive and Mental Health During Post-Infection Phase: A Study Among Middle-Aged and Older Indigenous Adults From Brazilian Amazons
Authors: Bezerra Camila Carlos , Toledo Noeli das Neves , Brucki Sonia Maria Dozzi , Souza-Talarico Juliana Nery 
Published: December 2023

Abstract

Objectives
To examine the rate of self-reported coronavirus disease-2019 (COVID-19) and its association with mental and cognitive health during the post-infection phase among middle-aged and older indigenous adults.

Methods
A cross-sectional study was conducted, including 141 individuals ≥50 and over from an urban indigenous community in Amazonas, Brazil. COVID-19 was deduced from self-reported infections. Cognitive function was evaluated using the Mini-Mental State Exam, Brief Cognitive Screening Battery (BCSB), and language fluency tests. Meanwhile, mental health was assessed through validated scales examining happiness, stress, and depression symptoms. The association between the rate of COVID-19 and cognitive and mental well-being was analyzed using logistic and linear regressions, adjusted for covariates.

Results
From March 2020 to February 2022, 65.2% of the urban indigenous group tested positive for COVID-19. Lower functional capacity decreased the odds of contracting COVID-19 (p = .03). Adjusted linear regression models showed that COVID-19 was associated with higher BCSB learning (p = .017) and delayed recall (p = .028). Women, higher age, lower functional capacity, and hospitalization were associated with worse cognitive performance (p &lt; .05). No impact of mental health indicators on past COVID-19 infection was noted.

Discussion
COVID-19 was prevalent among urban Indigenous Brazilians. Unexpectedly, it was linked to enhanced learning and memory, not mental health issues. Cognitive performance was lower for men, older individuals, those with less functional ability, and hospitalized patients, indicating that participant characteristics and disease severity affect the COVID-19 and cognition relationship. Longitudinal studies across diverse Indigenous communities are necessary to understand COVID-19’s impact on their cognitive and mental health.
Co-methylation analyses identify CpGs associated with lipid traits in Chinese discordant monozygotic twins
Authors: Li Zhaoying , Wang Weijing , Li Weilong , Duan Haiping , Xu Chunsheng , Tian Xiaocao , Ning Feng , Zhang Dongfeng 
Published: December 2023

Abstract
To control genetic background and early life milieu in genome-wide DNA methylation analysis for blood lipids, we recruited Chinese discordant monozygotic twins to explore the relationships between DNA methylations and total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). 132 monozygotic (MZ) twins were included with discordant lipid levels and completed data. A linear mixed model was conducted in Epigenome-wide association study (EWAS). Generalized estimating equation model was for gene expression analysis. We conducted Weighted correlation network analysis (WGCNA) to build co-methylated interconnected network. Additional Qingdao citizens were recruited for validation. Inference about Causation through Examination of Familial Confounding (ICE FALCON) was used to infer the possible direction of these relationships. A total of 476 top CpGs reached suggestively significant level (P &lt; 10−4), of which, 192 CpGs were significantly associated with TG (FDR &lt; 0.05). They were used to build interconnected network and highlight crucial genes from WGCNA. Finally, four CpGs in GATA4 were validated as risk factors for TC; six CpGs at ITFG2-AS1 were negatively associated with TG; two CpGs in PLXND1 played protective roles in HDL-C. ICE FALCON indicated abnormal TC was regarded as the consequence of DNA methylation in CpGs at GATA4, rather than vice versa. Four CpGs in ITFG2-AS1 were both causes and consequences of modified TG levels. Our results indicated that DNA methylation levels of 12 CpGs in GATA4, ITFG2-AS1, and PLXND1 were relevant to TC, TG, and HDL-C, respectively, which might provide new epigenetic insights into potential clinical treatment of dyslipidemia.
Construction of a prognostic model for lung adenocarcinoma based on m6A/m5C/m1A genes
Authors: Ding Hao , Teng Yuanyuan , Gao Ping , Zhang Qi , Wang Mengdi , Yu Yi , Fan Yueping , Zhu Li 
Published: December 2023

Abstract

Background
Developing a prognostic model for lung adenocarcinoma (LUAD) that utilizes m6A/m5C/m1A genes holds immense importance in providing precise prognosis predictions for individuals.

Methods
This study mined m6A/m5C/m1A-related differential genes in LUAD based on public databases, identified LUAD tumor subtypes based on these genes, and further built a risk prognostic model grounded in differential genes between subtypes. The immune status between high- and low-risk groups was investigated, and the distribution of feature genes in tumor immune cells was analyzed using single-cell analysis. Based on the expression levels of feature genes, a projection of chemotherapeutic and targeted drugs was made for individuals identified as high-risk. Ultimately, cell experiments were further verified.

Results
The 6-gene risk prognosis model based on differential genes between tumor subtypes had good predictive performance. Individuals classified as low-risk exhibited a higher (P &lt; 0.05) abundance of infiltrating immune cells. Feature genes were mainly distributed in tumor immune cells like CD4+T cells, CD8+T cells, and regulatory T cells. Four drugs with relatively low IC50 values were found in the high-risk group: Elesclomol, Pyrimethamine, Saracatinib, and Temsirolimus. In addition, four drugs with significant positive correlation (P &lt; 0.001) between IC50 values and feature gene expression were found, including Alectinib, Estramustine, Brigatinib, and Elesclomol. The low expression of key gene NTSR1 reduced the IC50 value of irinotecan.

Conclusion
Based on the m6A/m5C/m1A-related genes in LUAD, LUAD patients were divided into 2 subtypes, and a m6A/m5C/m1A-related LUAD prognostic model was constructed to provide a reference for the prognosis prediction of LUAD.
Exploring N6-methyladenosine (m6A) modification in tree species: opportunities and challenges
Authors: Ramakrishnan Muthusamy , Rajan K Shanmugha , Mullasseri Sileesh , Ahmad Zishan , Zhou Mingbing , Sharma Anket , Ramasamy Subbiah , Wei Qiang 
Published: December 2023

Abstract
N 6-methyladenosine (m6A) in eukaryotes is the most common and widespread internal modification in mRNA. The modification regulates mRNA stability, translation efficiency, and splicing, thereby fine-tuning gene regulation. In plants, m6A is dynamic and critical for various growth stages, embryonic development, morphogenesis, flowering, stress response, crop yield, and biomass. Although recent high-throughput sequencing approaches have enabled the rapid identification of m6A modification sites, the site-specific mechanism of this modification remains unclear in trees. In this review, we discuss the functional significance of m6A in trees under different stress conditions and discuss recent advancements in the quantification of m6A. Quantitative and functional insights into the dynamic aspect of m6A modification could assist researchers in engineering tree crops for better productivity and resistance to various stress conditions.
AlliumDB: a central portal for comparative and functional genomics in Allium
Authors: Yang Pengtao , Yuan Yu , Yan Chao , Jia Yue , You Qi , Da Lingling , Lou Ao , Lv Bingsheng , Zhang Zhonghua , Liu Yue 
Published: December 2023

Abstract
The genus Allium belongs to the botanical family Amaryllidaceae and includes economically important crops such as onion, garlic, bunching onion, and leek, used as vegetables, spices, and traditional medicines. The large sizes of Allium genomes hamper the genetic dissection of agronomically important traits and molecular breeding. With the growing accumulation of genomic, resequencing, transcriptome, and phenotypic data, the demand for an integrative Allium database is increasing. Here we present a user-friendly database, AlliumDB (https://allium.qau.edu.cn), as a functional genomics hub integrating public and in-house data. The database contains all currently available nuclear and organelle genomes for Allium species, with genes comprehensively annotated based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, orthology, gene families, protein families (Pfam), and non-coding RNA families (Rfam). Transcriptome and variation profiles are integrated into dynamic visualization tools. We took phenotypic photographs and generated trait records for hundreds of Allium germplasms collected worldwide, which are included in the database. We incorporated JBrowse for the visualization of gene structures, RNA sequencing data, and variation data. Analysis tools such as the basic local alignment search tool (BLAST), sequence fetch, enrichment, and motif analyses are available to explore potential gene functions. This database incorporates comprehensive Allium genotypic and phenotypic datasets. As the community assembles new genomes and generates resequencing data for Allium germplasms, the database will be improved and continuously updated with these multi-omics data and comparative genomic studies. We expect the AlliumDB database to become a key resource for the study of Allium crops.
Unique Metabolomic and Lipidomic Profile in Serum From Patients With Crohn’s Disease and Ulcerative Colitis Compared With Healthy Control Individuals
Authors: Tews Hauke Christian , Schmelter Franziska , Kandulski Arne , Büchler Christa , Schmid Stephan , Schlosser Sophie , Elger Tanja , Loibl Johanna , Sommersberger Stefanie , Fererberger Tanja , Gunawan Stefan , Kunst Claudia , Gülow Karsten , Bettenworth Dominik , Föh Bandik , Maaß Carlos , Solbach Philipp , Günther Ulrich L , Derer Stefanie , Marquardt Jens U , Sina Christian , Müller Martina 
Published: December 2023

Abstract

Background
Accurate biomarkers for disease activity and progression in patients with inflammatory bowel disease (IBD) are a prerequisite for individual disease characterization and personalized therapy. We show that metabolic profiling of serum from IBD patients is a promising approach to establish biomarkers. The aim of this work was to characterize metabolomic and lipidomic serum profiles of IBD patients in order to identify metabolic fingerprints unique to the disease.

Methods
Serum samples were obtained from 55 patients with Crohn’s disease (CD), 34 patients with ulcerative colitis (UC), and 40 healthy control (HC) individuals and analyzed using proton nuclear magnetic resonance spectroscopy. Classification of patients and HC individuals was achieved by orthogonal partial least squares discriminant analysis and univariate analysis approaches. Disease activity was assessed using the Gastrointestinal Symptom Rating Scale.

Results
Serum metabolome significantly differed between CD patients, UC patients, and HC individuals. The metabolomic differences of UC and CD patients compared with HC individuals were more pronounced than the differences between UC and CD patients. Differences in serum levels of pyruvic acid, histidine, and the branched-chain amino acids leucine and valine were detected. The size of low-density lipoprotein particles shifted from large to small dense particles in patients with CD. Of note, apolipoprotein A1 and A2 serum levels were decreased in CD and UC patients with higher fecal calprotectin levels. The Gastrointestinal Symptom Rating Scale is negatively associated with the concentration of apolipoprotein A2.

Conclusions
Metabolomic assessment of serum samples facilitated the differentiation of IBD patients and HC individuals. These differences were constituted by changes in amino acid and lipoprotein levels. Furthermore, disease activity in IBD patients was associated with decreased levels of the atheroprotective apolipoproteins A1 and A2.
A Multiseason Randomized Controlled Trial of Advax-Adjuvanted Seasonal Influenza Vaccine in Participants With Chronic Disease or Older Age
Authors: Sajkov Dimitar , Woodman Richard , Honda-Okubo Yoshikazu , Barbara Jeffrey , Chew Derek , Toson Barbara , Petrovsky Nikolai 
Published: December 2023

Abstract

Background
The aim of the current study was to determine the safety and immunogenicity of trivalent inactivated influenza vaccine (TIV) alone or formulated with Advax delta inulin adjuvant in those who were older (aged &gt;60 years) or had chronic disease.

Methods
Over 4 consecutive years from 2008 through 2011, adult participants with chronic disease or &gt;60 years of age were recruited into a randomized controlled study to assess the safety, tolerability and immunogenicity of Advax-adjuvanted TIV (TIV + Adj) versus standard TIV. The per-protocol population with ≥1 postbaseline measurement of influenza antibodies comprised 1297 participants, 447 in the TIV and 850 in the TIV + Adj) group.

Results
No safety issues were identified. Variables negatively affecting vaccine responses included obesity and diabetes mellitus. Advax adjuvant had a positive impact on anti-influenza immunoglobulin M responses and on H3N2 and B strain seropositivity as assessed by hemagglutination inhibition.

Conclusions
TIV + Adj was safe and well tolerated in individuals with chronic disease. There is an ongoing need for research into improved influenza vaccines for high-risk populations.

Clinical Trials Registration
Australia New Zealand Clinical Trial Registry: ACTRN 12608000364370.
A Qualitative Method to Detect Paraproteins from Serum Using Ultra Performance Liquid Chromatography Electrospray Triple Quadrupole Mass Spectrometry
Authors: Putchen Deepalakshmi D , Nambiar Athira , Gondkar Akshata R , Bhujangashayi Venkatesh D , Prasad Sujay R 
Published: December 2023

Abstract

Background
Mass spectrometry-based techniques are increasingly reported in the literature for identifying paraproteins due to their improved specificity and sensitivity. The present study demonstrates the capability of ultra performance liquid chromatography (UPLC) electrospray ionization triple quadrupole mass spectrometry for the qualitative analysis of paraproteins.

Methods
Paraproteins from patient serum (n = 40) were immunopurified using agarose beads coated with camelid antibodies that are specific for various subtypes of immunoglobulins (Igs; G, A, M, and light chains κ, λ). The extracted Igs are reduced to separate light chains from heavy chains in solution. The reduced sample was subjected to UPLC and mass measured using electrospray ionization-mass spectrometry. The mass spectral peaks at specific retention times were deconvoluted after clean-up to obtain the mass of light chains. The interpretation of liquid chromatography peaks and LC-MS data was validated by comparing them with immunofixation electrophoresis (IFE) results.

Results
The interpretation from the chromatographic pattern had a 92.5% (37/40) agreement when compared with mass information. The correlation of mass spectrometry data to IFE was 90% (36/40). The high mass of light chains (&gt;25 kDa) was suggestive of glycosylation. Patient sera positive for IgGκ on IFE (n = 15) were analyzed for the interference of tAbs. The mass of Daratumumab observed in a sample was confirmed by the treating physician. A biclonal of same isotype (IgGκ) was identified.

Conclusions
The feasibility of using liquid chromatography triple quadrupole mass spectrometry for the identification of the subtype of paraproteins has been demonstrated. The method’s applicability to screen for interference from tAbs and identification of biclonals of the same isotype has been highlighted.
Residual activity of insecticides against adult Systena frontalis (Coleoptera: Chrysomelidae) under semi-field conditions
Authors: Arshad Rehan , Joseph Shimat V 
Published: December 2023

Abstract
Systena frontalis (Fabricius) (Coleoptera: Chrysomelidae) is a serious insect pest in nursery production. Insecticides are an important control tactic for S. frontalis adults to reduce economic losses associated with its injury. Because densities and activity of S. frontalis adults are influenced by many biotic (e.g., adult emergence timing) and abiotic (e.g., fluctuating temperatures) factors in the nurseries, it is challenging to reliably determine the efficacy and residual activity of insecticides under field conditions. Thus, the objective was to determine the residual activity of common and alternative insecticides on adult S. frontalis under semi-field conditions. Field-collected S. frontalis adults were exposed to 0-, 7-, 14-, and 21-d-old, field-aged residue of 13 insecticides applied on panicled hydrangea (Hydrangea paniculata Siebold) shoots and maintained in the field. The fresh residues of tetraniliprole, cyclaniliprole, and sulfoxaflor + spinetoram were the most effective against S. frontalis adults, whereas only tetraniliprole and cyclaniliprole elicited evidence of efficacy when their residues were aged for a week. Fourteen- and 21-d-old residues of tetraniliprole were still effective on S. frontalis adults and reduced the injury. Based on the results, tetraniliprole, cyclaniliprole, and sulfoxaflor + spinetoram were effective for immediate management, cyclaniliprole can provide short-term efficacy, and tetraniliprole provides longer-term efficacy.
Evaluation of reflective mulch and insect exclusion coverings for allium leafminer (Diptera: Agromyzidae) management in allium crops
Authors: Lai Pin-Chu , Grundberg Ethan A , Rusinek Teresa , Nault Brian A 
Published: December 2023

Abstract
Allium leafminer (Phytomyza gymnostoma Loew) is a recent invasive pest in the United States causing serious economic loss in organic allium crops. Organic management of P. gymnostoma is currently limited to foliar applications of spinosad, but this strategy is not always sufficient under high infestations. Nonchemical management tools used either alone or in combination with spinosad are needed to improve P. gymnostoma management. Reflective mulch alone or combined with spinosad as well as insect exclusion coverings were evaluated for managing P. gymnostoma in allium crops in New York from 2018 to 2021. Reflective mulch alone reduced the numbers of oviposition marks by 16% and densities of larvae plus pupae by 40% compared with those in standard plastic mulch. Reflective mulch combined with 1 spinosad application reduced P. gymnostoma densities to levels lower than those in reflective mulch alone, but 2 spinosad applications were required to provide an acceptable control level. Combining with reflective mulch, row covers, and insect netting reduced P. gymnostoma densities by 76% compared with those without physical barriers, and the level of control was comparable to that provided by 2 spinosad applications. Phytomyza gymnostoma densities in allium crops grown under row covers deployed throughout the entire period when flies were active tended to be lower than those protected during shorter periods (80% reduction). Future management of P. gymnostoma in allium crops should consider either combining reflective mulch with 2 foliar spinosad applications or deploying insect exclusion coverings. The advantages and challenges of using these management strategies are discussed.