bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of extrachromosomal circular DNA in rice
Authors: Zhuang Jundong , Zhang Yaoxin , Zhou Congcong , Fan Danlin , Huang Tao , Feng Qi , Lu Yiqi , Zhao Yan , Zhao Qiang , Han Bin , Lu Tingting 
Published: March 2024

AbstractThe genome’s dynamic nature, exemplified by elements like extrachromosomal circular DNA (eccDNA), is crucial for biodiversity and adaptation. Yet, the role of eccDNA in plants, particularly rice, remains underexplored. Here, we identify 25,598 eccDNAs, unveiling the widespread presence of eccDNA across six rice tissues and revealing its formation as a universal and random process. Interestingly, we discover that direct repeats play a pivotal role in eccDNA formation, pointing to a unique origin mechanism. Despite eccDNA’s prevalence in coding sequences, its impact on gene expression is minimal, implying its roles beyond gene regulation. We also observe the association between eccDNA’s formation and minor chromosomal deletions, providing insights of its possible function in regulating genome stability. Further, we discover eccDNA specifically accumulated in rice leaves, which may be associated with DNA damage caused by environmental stressors like intense light. In summary, our research advances understanding of eccDNA’s role in the genomic architecture and offers valuable insights for rice cultivation and breeding.
Co-targeting the kappa opioid receptor and dopamine transporter reduces motivation to self-administer cocaine and partially reverses dopamine system dysregulation
Authors: Estave Paige M. , Albertson Steven E. , Karkhanis Anushree N. , Jones Sara R. 
Published: March 2024

AbstractCocaine disrupts dopamine (DA) and kappa opioid receptor (KOR) system activity, with long-term exposure reducing inhibiton of DA uptake by cocaine and increasing KOR system function. Single treatment therapies have not been successful for cocaine use disorder; therefore, this study focuses on a combination therapy targeting the dopamine transporter (DAT) and KOR. Sprague Dawley rats self-administered 5 days of cocaine (1.5 mg/kg/inf, max 40 inf/day, FR1), followed by 14 days on a progressive ratio (PR) schedule (0.19 mg/kg/infusion). Behavioral effects of individual and combined administration of phenmetrazine and nBNI were then examined using PR. Additionally, ex vivo fast scan cyclic voltammetry was then used to assess alterations in DA and KOR system activity in the nucleus accumbens before and after treatments. Chronic administration of phenmetrazine as well as the combination of phenmetrazine and nBNI—but not nBNI alone—significantly reduced PR breakpoints. In addition, the combination of phenmetrazine and nBNI partially reversed cocaine-induced neurodysregulations of the KOR and DA systems, indicating therapeutic benefits of targeting the DA and KOR systems in tandem. These data highlight the potential benefits of the DAT and KOR as dual-cellular targets to reduce motivation to administer cocaine and reverse cocaine-induced alterations of the DA system.
Ultra-compact and efficient photonic waveguide bends with different configurations designed by topology optimization
Authors: Irfan Sabaina , Kim Jae-Yong , Kurt Hamza 
Published: March 2024

AbstractTransporting light signals over the corners and sharp bends imposes high optical loss and distortion on the mode profiles. Usually, bends with larger radii are used in circuits to minimize the loss over transmission, resulting in a severe limitation in integration density. In this paper, we propose novel topology-optimized optimized L-bend and U-bend structures designed for a 220 nm silicon-on-insulator (SOI) platform. Optimized L-bends with footprints of 2.5 µm × 2.5 µm, 1.5 µm × 1.5 µm, and 1 µm × 1 µm show maximum insertion losses of only 0.07 dB, 0.26 dB, and 0.78 dB, respectively. For optimized U-bends with footprints of 3 µm × 3.6 µm, 2.5 µm × 2.5 µm, and 1.5 µm × 1.5 µm, the maximum insertion losses are 0.07 dB, 0.21 dB, and 3.16 dB. These optimized bends reduce the maximum insertion loss by over 50% compared to un-optimized arc-type bends across a broad wavelength range of 1450–1650 nm. Experimental verification of a meander line with 16 optimized U-bends (3 µm × 3.6 µm) demonstrates an averaged insertion loss of 1.23 dB in the wavelength range of 1520–1580 nm, agreeing with simulated results and indicating a high potential of loss reduction with optimized bends.
Estimate the burden of malnutrition among children with cerebral palsy in Sub-Saharan Africa: a systematic review with meta-analysis
Authors: Chanie Ermias Sisay , Moges Natnael , Baye Fikadie Dagnew , Mekonnen Gebrehiwot Berie , Fekadie Mengistu Melak , Bazezew Lakachew Yismaw , Anley Denekew Tenaw , Zemene Melkamu Aderajew , Gebeyehu Natnael Atnafu , Adella Getachew Asmare , Kassie Gizachew Ambaw , Mengstie Misganaw Asmamaw , Seid Mohammed Abdu , Abebe Endeshaw Chekol , Gesese Molalegn Mesele , Tegegne Kirubel Dagnaw , Kebede Yenealem Solomon , Bantie Berihun , Feleke Sefineh Fenta , Dejenie Tadesse Asmamaw , Bayih Wubet Alebachew , Kassaw Amare , Dessie Anteneh Mengist , Azanaw Melkalem Mamuye , Chanie Sewunt Sisay 
Published: March 2024

AbstractMalnutrition is more prevalent among children with cerebral palsy and a major factor for child morbidity and mortality in children with different co-morbidity, especially in Sub-Saharan Africa: The main aim of this systematic review and meta-analysis was to estimate the burden of malnutrition among children with cerebral palsy in Sub-Saharan Africa. We searched PubMed, Web of Science, Google Scholar, Research Gate, and institutional repositories for papers that reported the proportion of malnutrition among children with cerebral palsy that were published between December 2010 and September 2023. Data were retrieved using the standardized JBI data extraction checklist through Microsoft Excel, and then exported to STATA 17 for further analysis. DerSimonian and Laird’s estimator was used to calculate the pooled effect size in the random-effects model. Statistics such as the Cochran Q test and I2 test were employed to measure heterogeneity. Egger's test and the funnel plot were used to look for publication bias. This systematic review and meta-analysis used 16 studies from Sub-Saharan Africa to estimate the proportion of malnutrition among 2,120 children with cerebral palsy. The pooled proportion of malnutrition among children with cerebral palsy in Sub-Saharan Africa by using random-effects model analysis was found to be 59.7% (95% CI; 49.8–69.6). The proportion of malnutrition was also estimated by sample sizes categorized as ≤ 120 and > 120, and the proportion of malnutrition was found to be 54.0 (95% CI: 44.7–63.3) and 64.5 (95% CI: 50.5–78.5). Moreover, the proportion of malnutrition was estimated by accounting for the difference in the year of publication. In this regard, the study classified before ≤ 2017 and > 2017, and the proportion of malnutrition was found to be 53.7 (95% CI: 38.0–69.3) and 62.5 (95% CI: 49.7–75.3) in Sub-Saharan Africa respectively. Malnutrition among children with cerebral in Sub-Saharan Africa was found to be very high. Hence, enhancing and developing strategic guidelines for malnutrition screening, prevention, and nutritional support are crucial among children with cerebral palsy. Furthermore, systematic review, randomized control trials, and qualitative studies are recommended to understand the burden more among children with cerebral palsy in the continent.
The level of active DNA demethylation compounds in leukocytes and urine samples as potential epigenetic biomarkers in breast cancer patients
Authors: Linowiecka Kinga , Guz Jolanta , Dziaman Tomasz , Urbanowska–Domańska Olga , Zarakowska Ewelina , Szpila Anna , Szpotan Justyna , Skalska-Bugała Aleksandra , Mijewski Paweł , Siomek-Górecka Agnieszka , Różalski Rafał , Gackowski Daniel , Oliński Ryszard , Foksiński Marek 
Published: March 2024

AbstractThe active DNA demethylation process, which involves TET proteins, can affect DNA methylation pattern. TET dependent demethylation results in DNA hypomethylation by oxidation 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) and its derivatives. Moreover, TETs’ activity may be upregulated by ascorbate. Given that aberrant DNA methylation of genes implicated in breast carcinogenesis may be involved in tumor progression, we wanted to determine whether breast cancer patients exert changes in the active DNA demethylation process. The study included blood samples from breast cancer patients (n = 74) and healthy subjects (n = 71). We analyzed the expression of genes involved in the active demethylation process (qRT-PCR), and 5–mC and its derivatives level (2D-UPLC MS/MS). The ascorbate level was determined using UPLC-MS. Breast cancer patients had significantly higher TET3 expression level, lower 5-mC and 5-hmC DNA levels. TET3 was significantly increased in luminal B breast cancer patients with expression of hormone receptors. Moreover, the ascorbate level in the plasma of breast cancer patients was decreased with the accompanying increase of sodium-dependent vitamin C transporters (SLC23A1 and SLC23A2). The presented study indicates the role of TET3 in DNA demethylation in breast carcinogenesis.
Successful skipping of abnormal pseudoexon by antisense oligonucleotides in vitro for a patient with beta-propeller protein-associated neurodegeneration
Authors: Yamada Mamiko , Maeta Kazuhiro , Suzuki Hisato , Kurosawa Ryo , Takenouchi Toshiki , Awaya Tomonari , Ajiro Masahiko , Takeuchi Atsuko , Nishio Hisahide , Hagiwara Masatoshi , Miya Fuyuki , Matsuo Masafumi , Kosaki Kenjiro 
Published: March 2024

AbstractPathogenic variants in WDR45 on chromosome Xp11 cause neurodegenerative disorder beta-propeller protein-associated neurodegeneration (BPAN). Currently, there is no effective therapy for BPAN. Here we report a 17-year-old female patient with BPAN and show that antisense oligonucleotide (ASO) was effective in vitro. The patient had developmental delay and later showed extrapyramidal signs since the age of 15 years. MRI findings showed iron deposition in the globus pallidus and substantia nigra on T2 MRI. Whole genome sequencing and RNA sequencing revealed generation of pseudoexon due to inclusion of intronic sequences triggered by an intronic variant that is remote from the exon–intron junction: WDR45 (OMIM #300526) chrX(GRCh37):g.48935143G > C, (NM_007075.4:c.235 + 159C > G). We recapitulated the exonization of intron sequences by a mini-gene assay and further sought antisense oligonucleotide that induce pseudoexon skipping using our recently developed, a dual fluorescent splicing reporter system that encodes two fluorescent proteins, mCherry, a transfection marker designed to facilitate evaluation of exon skipping and split eGFP, a splicing reaction marker. The results showed that the 24-base ASO was the strongest inducer of pseudoexon skipping. Our data presented here have provided supportive evidence for in vivo preclinical studies.
Prediction model and assessment of malnutrition in patients with stable chronic obstructive pulmonary disease
Authors: Shen Xurui , Qian Ruiqi , Wei Yuan , Tang Zhichao , Zhong Huafei , Huang Jianan , Zhang Xiuqin 
Published: March 2024

AbstractChronic obstructive pulmonary disease (COPD) combined with malnutrition results in decreased exercise capacity and a worse quality of life. We aimed to develop an observational case–control study to explore the effective and convenient method to identify potential individuals is lacking. This study included data from 251 patients with COPD and 85 participants in the control group. Parameters and body composition were compared between groups, and among patients with varied severity. The LASSO approach was employed to select the features for fitting a logistic model to predict the risk of malnutrition in patients with stable COPD. Patients with COPD exhibited significantly lower 6-min walk distance (6MWD), handgrip strength, fat-free mass index (FFMI), skeletal muscle mass (SMM) and protein. The significant predictors identified following LASSO selection included 6MWD, waist-to-hip ratio (WHR), GOLD grades, the COPD Assessment Test (CAT) score, and the prevalence of acute exacerbations. The risk score model yielded good accuracy (C-index, 0.866 [95% CI 0.824–0.909]) and calibration (Brier score = 0.150). After internal validation, the adjusted C-index and Brier score were 0.849, and 0.165, respectively. This model may provide primary physicians with a simple scoring system to identify malnourished patients with COPD and develop appropriate rehabilitation interventions.
Effects of releasing ankle joint during electrically evoked cycling in persons with motor complete spinal cord injury
Authors: Hamdan Puteri Nur Farhana , Hamzaid Nur Azah , Hasnan Nazirah , Abd Razak Nasrul Anuar , Razman Rizal , Usman Juliana 
Published: March 2024

AbstractLiterature has shown that simulated power production during conventional functional electrical stimulation (FES) cycling was improved by 14% by releasing the ankle joint from a fixed ankle setup and with the stimulation of the tibialis anterior and triceps surae. This study aims to investigate the effect of releasing the ankle joint on the pedal power production during FES cycling in persons with spinal cord injury (SCI). Seven persons with motor complete SCI participated in this study. All participants performed 1 min of fixed-ankle and 1 min of free-ankle FES cycling with two stimulation modes. In mode 1 participants performed FES-evoked cycling with the stimulation of quadriceps and hamstring muscles only (QH stimulation), while Mode 2 had stimulation of quadriceps, hamstring, tibialis anterior, and triceps surae muscles (QHT stimulation). The order of each trial was randomized in each participant. Free-ankle FES cycling offered greater ankle plantar- and dorsiflexion movement at specific slices of 20° crank angle intervals compared to fixed-ankle. There were significant differences in the mean and peak normalized pedal power outputs (POs) [F(1,500) = 14.03, p < 0.01 and F(1,500) = 7.111, p = 0.008, respectively] between fixed- and free-ankle QH stimulation, and fixed- and free-ankle QHT stimulation. Fixed-ankle QHT stimulation elevated the peak normalized pedal PO by 14.5% more than free-ankle QH stimulation. Releasing the ankle joint while providing no stimulation to the triceps surae and tibialis anterior reduces power output. The findings of this study suggest that QHT stimulation is necessary during free-ankle FES cycling to maintain power production as fixed-ankle.
A comparison of two gene regions for assessing community composition of eukaryotic marine microalgae from coastal ecosystems
Authors: Stuart Jacqui , Ryan Ken G. , Pearman John K. , Thomson-Laing Jacob , Hampton Hannah G. , Smith Kirsty F. 
Published: March 2024

AbstractTwo gene regions commonly used to characterise the diversity of eukaryotic communities using metabarcoding are the 18S ribosomal DNA V4 and V9 gene regions. We assessed the effectiveness of these two regions for characterising diverisity of coastal eukaryotic microalgae communities (EMCs) from tropical and temperate sites. We binned amplicon sequence variants (ASVs) into the high level taxonomic groups: dinoflagellates, pennate diatoms, radial centric diatoms, polar centric diatoms, chlorophytes, haptophytes and ‘other microalgae’. When V4 and V9 generated ASV abundances were compared, the V9 region generated a higher number of raw reads, captured more diversity from all high level taxonomic groups and was more closely aligned with the community composition determined using light microscopy. The V4 region did resolve more ASVs to a deeper taxonomic resolution within the dinoflagellates, but did not effectively resolve other major taxonomic divisions. When characterising these communities via metabarcoding, the use of multiple gene regions is recommended, but the V9 gene region can be used in isolation to provide high-level community biodiversity to reflect relative abundances within groups. This approach reduces the cost of sequencing multiple gene regions whilst still providing important baseline ecosystem function information.
Clustering analysis for the evolutionary relationships of SARS-CoV-2 strains
Authors: Chen Xiangzhong , Wang Mingzhao , Liu Xinglin , Zhang Wenjie , Yan Huan , Lan Xiang , Xu Yandi , Tang Sanyi , Xie Juanying 
Published: March 2024

AbstractTo explore the differences and relationships between the available SARS-CoV-2 strains and predict the potential evolutionary direction of these strains, we employ the hierarchical clustering analysis to investigate the evolutionary relationships between the SARS-CoV-2 strains utilizing the genomic sequences collected in China till January 7, 2023. We encode the sequences of the existing SARS-CoV-2 strains into numerical data through k-mer algorithm, then propose four methods to select the representative sample from each type of strains to comprise the dataset for clustering analysis. Three hierarchical clustering algorithms named Ward-Euclidean, Ward-Jaccard, and Average-Euclidean are introduced through combing the Euclidean and Jaccard distance with the Ward and Average linkage clustering algorithms embedded in the OriginPro software. Experimental results reveal that BF.28, BE.1.1.1, BA.5.3, and BA.5.6.4 strains exhibit distinct characteristics which are not observed in other types of SARS-CoV-2 strains, suggesting their being the majority potential sources which the future SARS-CoV-2 strains’ evolution from. Moreover, BA.2.75, CH.1.1, BA.2, BA.5.1.3, BF.7, and B.1.1.214 strains demonstrate enhanced abilities in terms of immune evasion, transmissibility, and pathogenicity. Hence, closely monitoring the evolutionary trends of these strains is crucial to mitigate their impact on public health and society as far as possible.
Non-fluorescent transient states of tyrosine as a basis for label-free protein conformation and interaction studies
Authors: Bagheri Niusha , Chen Hongjian , Rabasovic Mihailo , Widengren Jerker 
Published: March 2024

AbstractThe amino acids tryptophan, tyrosine, and phenylalanine have been extensively used for different label-free protein studies, based on the intensity, lifetime, wavelength and/or polarization of their emitted fluorescence. Similar to most fluorescent organic molecules, these amino acids can undergo transitions into dark meta-stable states, such as triplet and photo-radical states. On the one hand, these transitions limit the fluorescence signal, but they are also highly environment-sensitive and can offer an additional set of parameters, reflecting interactions, folding states, and immediate environments around the proteins. In this work, by analyzing the average intensity of tyrosine emission under different excitation modulations with the transient state monitoring (TRAST) technique, we explored the photo physics of tyrosine as a basis for such environment-sensitive readouts. From how the dark state transitions of tyrosine varied with excitation intensity and solvent conditions we first established a photophysical model for tyrosine. Next, we studied Calmodulin (containing two tyrosines), and how its conformation is changed upon calcium binding. From these TRAST experiments, performed with 280 nm time-modulated excitation, we show that tyrosine dark state transitions clearly change with the calmodulin conformation, and may thus represent a useful source of information for (label-free) analyses of protein conformations and interactions.
Study on the material source and enrichment mechanism of REE-rich phosphorite in Zhijin, Guizhou
Authors: Wang Jingya , Qiao Zhongkun 
Published: March 2024

AbstractRare earth element (REE)-rich phosphorite in the Guizhou region mainly exists in the Doushantuo Formation and Gezhongwu Formation in early Cambrian strata, which are some of the important strata containing phosphorite resources in China. The early Cambrian Zhijin phosphorite in Guizhou Province, China, has high rare earth element and yttrium (REY) contents of up to 2500 ppm, with heavy REY (HREY) contents accounting for ~ 30% of the total REY contents. However, the specific controlling source and environment of phosphorite (especially the REEs in Zhijin phosphorite) are still unsolved. Through field geological investigations; mineralogical, geochemical, Sr–Nd isotope analyses; and tectonic characteristics, the material source, sedimentary environment and seawater dynamics of REEs in phosphorite are studied. It is considered that the REEs enriched in the Zhijin phosphorite are mainly affected by precipitation from hydrothermal fluid. Moreover, from the late Ediacaran to the early Cambrian, the depositional environment from the bottom to the top of the water tended to be hypoxic, and the activity of hot water fluid tended to be strong. The change in redox conditions is closely related to the rise and fall of sea level. Combined with the tectonic background, these results show that the weakly oxidized environment may be an important factor controlling the enrichment of REEs. The enrichment of REEs may be closely related to volcanic hydrothermal activity, later diagenesis and seawater dynamics.
Association between circadian physical activity trajectories and incident type 2 diabetes in the UK Biobank
Authors: Bai Pufei , Shao Xian , Chen Lianqin , Zhou Saijun , Lin Yao , Liu Hongyan , Yu Pei 
Published: March 2024

AbstractPhysical activity (PA) is linked to a decreased risk of type 2 diabetes mellitus (T2DM). However, the influence of circadian PA trajectories remains uncertain. This study aims to explore the optimal circadian PA trajectory pattern for reducing the risk of T2DM. Methods: A total of 502,400 participants were recruited from the UK Biobank between 2006 and 2010, and 102,323 participants provided valid accelerometer-captured acceleration data. After excluding individuals with prior T2DM, 99,532 participants were included in the final analysis. We initially investigated the association between PA intensity at 24 hourly time points and T2DM. Subsequently, PA trajectories were identified using K-means cluster analysis. Cox proportional hazard models were employed to estimate hazard ratios (HR). Four distinct PA trajectories were identified: consistently low, single peak, double peak, and intense trajectories. Compared to consistently low, single peak, double peak and intense PA trajectory reduced the risk of T2DM progressively. Sensitivity analyses, further excluding individuals with glycated hemoglobin (HbA1c) ≥ 6.5% or random glucose ≥ 11.1 mmol/L and adjusted for daily average acceleration, yielded consistent results. This confirms that the ideal circadian PA trajectory serves as a protective factor, independently of PA intensity. Subgroup analyses indicated that these effects were more pronounced in men and individuals with eGFR < 60 mL/(min*1.73 m2). In conclusion, ideal circadian PA trajectory patterns (especially intense and then double peak) reduced risk of T2DM.