bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of chia seed (Salvia hispanica L.) supplementation on cardiometabolic health in overweight subjects: a systematic review and meta-analysis of RCTs
Authors: Karimi Mehdi , Pirzad Samira , Shirsalimi Niyousha , Ahmadizad Sajad , Hashemi Seyyed Mohammad , Karami Shaghayegh , Kazemi Kimia , Shahir-Roudi Erfan , Aminzadeh Anita 
Published: September 2024

Abstract
Background
Obesity is a significant public health issue associated with various chronic diseases. Research has indicated that chia seeds have the potential to improve cardiometabolic health. However, due to the diversity of research and inconsistencies in study design, further investigation is needed to fully understand their clinical effects on overweight individuals. This review aims to comprehensively analyze the available evidence on the effects of chia seeds on cardiometabolic indices in overweight populations through a meta-analysis.

Methods
A comprehensive literature search was performed across PubMed, Web of Science, Scopus, and Embase databases from their inception until 01-03-2024 to identify randomized controlled trials (RCTs) evaluating the effect of chia on cardiometabolic indices in overweight subjects. The search strategy incorporated both Medical Subject Headings (MeSH). Following the screening, ten RCTs were finally included. The data, including subject characteristics, study design, and changes in serum biomarkers, were extracted and analyzed using Stata software version 18.

Results
The meta-analysis results reveal that chia supplementation no significant changes in lipid profile, including triglycerides (TG) (MD: − 5.80 mg/dL, p = 0.47), total cholesterol (TC) (MD: − 0.29 mg/dL, p = 0.95), high-density lipoprotein (HDL) (MD: 1.53 mg/dL, p = 0.33), and low-density lipoprotein (LDL) (MD: 0.63 mg/dL, p = 0.88). Similarity fasting blood glucose (FBG) (MD: − 0.03 mg/dL, p = 0.98), hemoglobin A1c (HbA1c) (MD: − 0.13%, p = 0.13), and insulin levels (MD: 0.45 µIU/mL, p = 0.78). However, chia seed supplementation was associated with a significant reduction in C-reactive protein (CRP) (MD: − 1.18 mg/L, p < 0.0001), but no significant changes were observed in interleukin-6 (IL-6) (MD: − 0.15, p = 0.70) or tumor necrosis factor-alpha (TNF-α) (MD: 0.03, p = 0.91). There was no significant effect on body mass index (BMI) (MD: 0.1 kg/m2, p = 0.91), but a significant reduction in waist circumference (WC) (MD: − 2.82 cm, p < 0.001) was noted. Additionally, chia seed supplementation resulted in a significant reduction in systolic blood pressure (BP) (MD: − 3.27 mmHg, p = 0.03), though diastolic BP changes were non-significant (MD: − 2.69 mmHg, p = 0.09). The studies showed low to moderate heterogeneity in outcome measures, with I2 < 50%.

Conclusion
Chia seed supplementation does not significantly impact most lipid profile parameters and glycemic markers. However, it shows potential benefits in reducing WC, BP, and CRP. While chia seeds can be a valuable addition to cardiometabolic health management, they should be part of a broader health strategy that includes a balanced diet, exercise, and lifestyle modifications for optimal results.
Optimization of ribosome profiling in plants including structural analysis of rRNA fragments
Authors: Ting Michael K. Y. , Gao Yang , Barahimipour Rouhollah , Ghandour Rabea , Liu Jinghan , Martinez-Seidel Federico , Smirnova Julia , Gotsmann Vincent Leon , Fischer Axel , Haydon Michael J. , Willmund Felix , Zoschke Reimo 
Published: September 2024

Abstract
Background
Ribosome profiling (or Ribo-seq) is a technique that provides genome-wide information on the translational landscape (translatome). Across different plant studies, variable methodological setups have been described which raises questions about the general comparability of data that were generated from diverging methodologies. Furthermore, a common problem when performing Ribo-seq are abundant rRNA fragments that are wastefully incorporated into the libraries and dramatically reduce sequencing depth. To remove these rRNA contaminants, it is common to perform preliminary trials to identify these fragments because they are thought to vary depending on nuclease treatment, tissue source, and plant species.

Results
Here, we compile valuable insights gathered over years of generating Ribo-seq datasets from different species and experimental setups. We highlight which technical steps are important for maintaining cross experiment comparability and describe a highly efficient approach for rRNA removal. Furthermore, we provide evidence that many rRNA fragments are structurally preserved over diverse nuclease regimes, as well as across plant species. Using a recently published cryo-electron microscopy (cryo-EM) structure of the tobacco 80S ribosome, we show that the most abundant rRNA fragments are spatially derived from the solvent-exposed surface of the ribosome.

Conclusion
The guidelines presented here shall aid newcomers in establishing ribosome profiling in new plant species and provide insights that will help in customizing the methodology for individual research goals.
Process evaluation of two large randomized controlled trials to understand factors influencing family physicians’ use of antibiotic audit and feedback reports
Authors: Shuldiner Jennifer , Lacroix Meagan , Saragosa Marianne , Reis Catherine , Schwartz Kevin L. , Gushue Sharon , Leung Valerie , Grimshaw Jeremy , Silverman Michael , Thavorn Kednapa , Leis Jerome A. , Kidd Michael , Daneman Nick , Tradous Mina , Langford Bradley , Morris Andrew M. , Lam Jonathan , Garber Gary , Brehaut Jamie , Taljaard Monica , Greiver Michelle , Ivers Noah Michael 
Published: September 2024

Abstract
Background
Unnecessary antibiotic prescriptions in primary care are common and contribute to antimicrobial resistance in the population. Audit and feedback (A&F) on antibiotic prescribing to primary care can improve the appropriateness of antibiotic prescribing, but the optimal approach is uncertain. We performed two pragmatic randomized controlled trials of different approaches to audit and feedback. The trial results showed that A&F was associated with significantly reducing antibiotic prescribing. Still, the effect size was small, and the modifications to the A&F interventions tested in the trials were not associated with any change. Herein, we report a theory-informed qualitative process evaluation to explore potential mechanisms underlying the observed effects.

Methods
Ontario family physicians in the intervention arms of both trials who were sent A&F letters were invited for one-on-one interviews. Purposive sampling was used to seek variation across interested participants in personal and practice characteristics. Qualitative analysis utilized inductive and deductive techniques informed by the Clinical Performance Feedback Intervention Theory.

Results
Modifications to the intervention design tested in the trial did not alter prescribing patterns beyond the changes made in response to the A&F overall for various reasons. Change in antibiotic prescribing in response to A&F depended on whether it led to the formation of specific intentions and whether those intentions translated to particular behaviours. Those without intentions to change tended to feel that their unique clinical context was not represented in the A&F. Those with intentions but without specific actions taken tended to express a lack of self-efficacy for avoiding a prescription in contexts with time constraints and/or without an ongoing patient relationship. Many participants noted that compared to overall prescribing, A&F on antibiotic prescription duration was perceived as new information and easily actionable.

Conclusion
Our findings indicate that contextual factors, including the types of patients and the setting where they are seen, affect how clinicians react to audit and feedback. These results suggest a need to test tailored feedback reports that reflect the context of how, where, and why physicians prescribe antibiotics so that they might be perceived as more personal and more actionable.

Trial registration
Clinical Trial registration IDs: NCT04594200, NCT05044052.
The improvement of modified Si-Miao granule on hepatic insulin resistance and glycogen synthesis in type 2 diabetes mellitus involves the inhibition of TNF-α/JNK1/IRS-2 pathway: network pharmacology, molecular docking, and experimental validation
Authors: Cao Zebiao , Wang Xianzhe , Zeng Zhili , Yang Zhaojun , Lin Yuping , Sun Lu , Lu Qiyun , Fan Guanjie 
Published: September 2024

Abstract
Background
Modified Si-Miao granule (mSMG), a traditional Chinese medicine, is beneficial for T2DM and insulin resistance (IR), but the underlying mechanism remains unknown.

Methods
Using network pharmacology, we screened the compounds of mSMG and identified its targets and pathway on hepatic IR in T2DM. Using molecular docking, we identified the affinity between the compounds and hub target TNF-α. Then these were verified in KK-Ay mice and HepG2 cells.

Results
50 compounds and 170 targets of mSMG against IR in T2DM were screened, and 9 hub targets such as TNF and MAPK8 were identified. 170 targets were mainly enriched in insulin resistance and TNF pathway, so we speculated that mSMG might act on TNF-α, JNK1 and then regulate insulin signaling to mitigate IR. Experimental validation proved that mSMG ameliorated hyperglycemia, IR, and TNF-α, enhanced glucose consumption and glycogen synthesis, relieved the phosphorylation of JNK1 and IRS-2 (Ser388), and elevated the phosphorylation of Akt (Ser473) and GSK-3β (Ser9) and GLUT2 expression in KK-Ay mice. Molecular docking further showed berberine from mSMG had excellent binding capacity with TNF-α. Then, in vitro validation experiments, we found that 20% mSMG-MS or 50 μM berberine had little effect in IR-HepG2 cell viability, but significantly increased glucose consumption and glycogen synthesis and regulated TNF-α/JNK1/IRS-2 pathway.

Conclusion
Network pharmacology and molecular docking help us predict potential mechanism of mSMG and further guide experimental validation. mSMG and its representative compound berberine improve hepatic IR and glycogen synthesis, and its mechanism may be related to the inhibition of TNF-α/JNK1/IRS-2 pathway.
Exploring ambulance clinicians’ clinical reasoning when training mass casualty incidents using virtual reality: a qualitative study
Authors: Heldring S. , Lindström V. , Jirwe M. , Wihlborg J. 
Published: September 2024

Abstract
Background
How ambulance clinicians (ACs) handle a mass casualty incident (MCI) is essential for the suffered, but the training and learning for the ACs are sparse and they don’t have the possibility to learn without realistic simulation training. In addition, it is unclear what type of dilemmas ACs process in their clinical reasoning during an MCI. With virtual reality (VR) simulation, the ACs clinical reasoning can be explored in a systematic way. Therefore, the objective was to explore ambulance clinicians’ clinical reasoning when simulating a mass casualty incident using virtual reality.

Methods
This study was conducted as an explorative interview study design using chart- stimulated recall technique for data collection. A qualitative content analysis was done, using the clinical reasoning cycle as a deductive matrix. A high-fidelity VR simulation with MCI scenarios was used and participants eligible for inclusion were 11 senior ACs.

Results/conclusion
All phases of the clinical reasoning cycle were found to be reflected upon by the participants during the interviews, however with a varying richness of analytic reflectivity. Non-analytic reasoning predominated when work tasks followed specific clinical guidelines, but analytical reasoning appeared when the guidelines were unclear or non-existent. Using VR simulation led to training and reflection on action in a safe and systematic way and increased self-awareness amongst the ACs regarding their preparedness for MCIs. This study increases knowledge both regarding ACs clinical reasoning in MCIs, and insights regarding the use of VR for simulation training.
Group A Streptococcus infections in children and adolescents in the post-COVID-19 era: a regional Italian survey
Authors: Cinicola Bianca Laura , Sani Ilaria , Pulvirenti Federica , Capponi Martina , Leone Fabrizio , Spalice Alberto , Montalbano Agata , Macari Alessandra , Fonte Maria Teresa , Giampietro Paolo Gianni , Buonsenso Danilo , Zicari Anna Maria , Rongai Teresa ,   On behalf of the Italian Pediatrician Federation (FIMP), Lazio Region, Baldini Ferroli B , Brugnoli R , Carpita FM , Caruso G , Castellano C , Cives C , Costabile L , D’agostino R , De Vittori V , Fostira A , Grassi C , La Bella I , Le Pera AM , Masetti A , Morano D , Pontesilli C , Ragno A , Reali L , Rotili PL , Serafinelli J , Triarico S , Zirletta E 
Published: September 2024

Abstract
Background
Despite the worldwide increasing incidence of Group A Streptococcus (GAS) infections reported since December 2022, data on noninvasive GAS (nGAS) infections in the post COVID-19 era are limited. By a self-reported survey performed in an outpatient setting, we investigated the number and clinical features of GAS infections, the diagnostic work-up and the type of treatment utilized. In addition, the rate of influenza vaccination was evaluated.

Methods
In June 2023 family pediatricians involved in the study sent the survey to parents of patients aged 0–16 years. The survey included questions on GAS infections that occurred from January 1 to May 31, 2023.

Results
Among 3580 children, 20.3% had a GAS infection (0,8% < 1 year, 16,4% 1–3 years, 42,3% 3–6 years, 26,5% 6–9 years, 11,4%, 9–12 years, and 2,6% 12–16 years). Symptoms reported were sore throat (76.9%), fever (75.2%), tonsillar exudate (25.2%), lymphadenopathy (21.8%), and scarlet fever (14.7%). A single patient was hospitalized due to GAS meningitis.
Twenty four percent of children had more than one GAS infection. In this group, frequencies of symptoms reported in the first and in the following infection were similar, except for fever and scarlet fever which were less frequent during relapses. GAS was identified by rapid antigen detection test in 81.0% of children. Eighty-nine per cent of children were treated with antibiotics, mostly amoxicillin/clavulanate (40.4%) and amoxicillin (39.4%). Thirty four percent of children received influenza vaccine. No difference was observed among immunized and not immunized regarding the number and characteristics of GAS infection.

Conclusions
We reported a certain prevalence of nGAS infections in children, mainly those aged 3–6 years age, who were mostly characterized by a low score of symptoms, and in most of the cases diagnosed and treated using a microbiological test as confirmatory tool.
In this new clinical setting, a national study would be useful to reach more significant data for the definition of a correct diagnosis and clinical management of nGAS infections in children. Moreover, it is important to improve flu vaccination campaign and coverage to protect children from coinfections that could worsen the disease and misdiagnose the etiology of pharyngitis.
Clinical characteristics and risk factors of severe COVID-19 in hospitalized neonates with omicron variant infection: a retrospective study
Authors: Wei Huijing , Wei Fu , Peng Xiaokang , Liu Pan , Tang Li , Liu Yishan , Liao Shan , Bo Yajing , Zhao Yuzhen , Li Ruina , Liu Xiaoguai , Ji Fanpu 
Published: September 2024

Abstract
Background
Reports on coronavirus disease 2019 (COVID-19) in neonates are limited, especially in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) Omicron variant. This study aims to analyze the clinical characteristics and identify risk factors associated with severe COVID-19 in neonates infected with Omicron variant.

Methods
The study population was represented by neonates with COVID-19, who were admitted to The Affiliated Children’s Hospital of Xi’an Jiaotong University in northwest China, from December 10, 2022 to January 20, 2023. Chinese Center for Disease Control and Prevention (CDC) announced that all local COVID-19 cases were infected with Omicron variant during the study period. Clinical and laboratory data were collected retrospectively. We used logistic regression analysis to investigate the risk factors for severe COVID-19, and derived odds ratios (ORs) and the corresponding 95% confidence intervals (CIs).

Results
A total of 108 neonates, with median age of 18.1 days (interquartile range 9.4–23.0), were affected by COVID-19, of whom 84 had a mild disease, while 24 a severe one (22.2%). Of them, 6.5% were premature. No deaths were observed in the study population. The most common clinical manifestations were fever (88.9%) and cough (55.6%), with 5 cases (4.6%) complicated by pneumonia. 4 cases (3.7%) received respiratory support, including 2 cases of high-flow oxygen and 2 cases of continuous positive airway pressure. Gestational age at birth (OR: 0.615; 95% CI: 0.393–0.961), neutrophil count (NEU) (OR:0.576; 95% CI : 0.344–0.962) and lymphocyte count (LYM) (OR: 0.159; 95% CI: 0.063–0.401) were independent risk factors for severe COVID-19. The combination of NEU and LYM had the largest receiver operating characteristic area under the curve [0.912 (95% CI:0.830–0.993)] for identifying severe COVID-19, with a sensitivity of 0.833 and a specificity of 0.917.

Conclusions
The general presentations and outcomes of neonatal COVID-19 caused by Omicron variant were not severe, and very few patients required respiratory support. The simultaneous decrease in NEU and LYM can be used to identify severe infection.
Atlas of telomeric repeat diversity in Arabidopsis thaliana
Authors: Tao Yueqi , Xian Wenfei , Bao Zhigui , Rabanal Fernando A. , Movilli Andrea , Lanz Christa , Shirsekar Gautam , Weigel Detlef 
Published: September 2024

Abstract
Background
Telomeric repeat arrays at the ends of chromosomes are highly dynamic in composition, but their repetitive nature and technological limitations have made it difficult to assess their true variation in genome diversity surveys.

Results
We have comprehensively characterized the sequence variation immediately adjacent to the canonical telomeric repeat arrays at the very ends of chromosomes in 74 genetically diverse Arabidopsis thaliana accessions. We first describe several types of distinct telomeric repeat units and then identify evolutionary processes such as local homogenization and higher-order repeat formation that shape diversity of chromosome ends. By comparing largely isogenic samples, we also determine repeat number variation of the degenerate and variant telomeric repeat array at both the germline and somatic levels. Finally, our analysis of haplotype structure uncovers chromosome end-specific patterns in the distribution of variant telomeric repeats, and their linkage to the more proximal non-coding region.

Conclusions
Our findings illustrate the spectrum of telomeric repeat variation at multiple levels in A. thaliana—in germline and soma, across all chromosome ends, and across genetic groups—thereby expanding our knowledge of the evolution of chromosome ends.
Deep-learning generated B-line score mirrors clinical progression of disease for patients with heart failure
Authors: Baloescu Cristiana , Chen Alvin , Varasteh Alexander , Hall Jane , Toporek Grzegorz , Patil Shubham , McNamara Robert L. , Raju Balasundar , Moore Christopher L. 
Published: September 2024

Abstract
Background
Ultrasound can detect fluid in the alveolar and interstitial spaces of the lung using the presence of artifacts known as B-lines. The aim of this study was to determine whether a deep learning algorithm generated B-line severity score correlated with pulmonary congestion and disease severity based on clinical assessment (as identified by composite congestion score and Rothman index) and to evaluate changes in the score with treatment. Patients suspected of congestive heart failure underwent daily ultrasonography. Eight lung zones (right and left anterior/lateral and superior/inferior) were scanned using a tablet ultrasound system with a phased-array probe. Mixed effects modeling explored the association between average B-line score and the composite congestion score, and average B-line score and Rothman index, respectively. Covariates tested included patient and exam level data (sex, age, presence of selected comorbidities, baseline sodium and hemoglobin, creatinine, vital signs, oxygen delivery amount and delivery method, diuretic dose).

Results
Analysis included 110 unique subjects (3379 clips). B-line severity score was significantly associated with the composite congestion score, with a coefficient of 0.7 (95% CI 0.1–1.2 p = 0.02), but was not significantly associated with the Rothman index.

Conclusions
Use of this technology may allow clinicians with limited ultrasound experience to determine an objective measure of B-line burden.
Genetic composition, virulence factors, and antimicrobial resistance profiles of Bacillus cereus and Bacillus subtilis isolates from food vendors in Ondo State, Nigeria: implications for food safety
Authors: Fayanju Aderonke Mary , Akinyele Bamidele Juliet , Oladejo Babayemi Olawale , Osunla Ayodeji Charles 
Published: September 2024

Abstract
Background
This study investigated Bacillus cereus and Bacillus subtilis from food vendors in Ondo State, Nigeria.

Methods
A comprehensive whole-genome sequencing (WGS) analysis of Bacillus genomes, including genome assembly, plasmid prediction, species identification, antimicrobial resistance (AMR) gene identification, virulence gene identification, and multilocus sequencing typing, was conducted.

Results
The genome assembly revealed a B. cereus genome with 87 contigs, a length of 5,798,917 base pairs, and a GC content of 34.79%, whereas B. subtilis had a genome length of 4,238,143 bp and was composed of 253 contigs with a contig L50 of 24, a contig N50 of 55,053, and a GC content of 43.14904%. Plasmid prediction revealed the absence of prominent plasmids in the assembled B. cereus genome, whereas the repUS12 plasmid was recognized with an identity of less than 95.63% for the B. subtilis genome. Species identification via the average nucleotide identity (ANI) calculation confirmed that Bacillus cereus had a 98.97% ANI value, whereas a 98.39% ANI value was confirmed for B. subtilis WAUSV36. AMR genes were identified, with virulence genes such as the alo, cytK, and hbl genes also detected in B. cereus, whereas clpX, codY, purA, and purB genes were detected in B. subtilis. Multiple-locus sequence typing (MLST) revealed that B. cereus belongs to sequence type 73 with 100% identity, identifying housekeeping gene alleles, including glp_13, gmk_8, and ilv_9, whereas B. subtilis belongs to sequence type 130, with the ilvD gene showing a perfect match and the highest allele length of 471 for the housekeeping genes identified.

Conclusions
This detailed WGS analysis provides valuable insights into the genetic composition, potential virulence factors, and resistance profiles of B. cereus and B. subtilis, enhancing the understanding of their pathogenicity and epidemiology. The genomic analysis of B. cereus and B. subtilis revealed potential genomic applications in the context of food safety.