bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amphiregulin, ST2, and REG3α biomarker risk algorithms as predictors of nonrelapse mortality in patients with acute GVHD
Authors: Etra Aaron , El Jurdi Najla , Katsivelos Nikolaos , Kwon Deukwoo , Gergoudis Stephanie , Morales George , Spyrou Nikolaos , Kowalyk Steven , Aguayo-Hiraldo Paibel , Akahoshi Yu , Ayuk Francis , Baez Janna , Betts Brian C. , Chanswangphuwana Chantiya , Chen Yi-Bin , Choe Hannah , DeFilipp Zachariah , Gleich Sigrun , Hexner Elizabeth , Hogan William J. , Holler Ernst , Kitko Carrie L. , Kraus Sabrina , Al Malki Monzr , MacMillan Margaret , Pawarode Attaphol , Quagliarella Francesco , Qayed Muna , Reshef Ran , Schechter Tal , Vasova Ingrid , Weisdorf Daniel , Wölfl Matthias , Young Rachel , Nakamura Ryotaro , Ferrara James L. M. , Levine John E. , Holtan Shernan 
Published: June 2024

Abstract
Graft-versus-host disease (GVHD) is a major cause of nonrelapse mortality (NRM) after allogeneic hematopoietic cell transplantation. Algorithms containing either the gastrointestinal (GI) GVHD biomarker amphiregulin (AREG) or a combination of 2 GI GVHD biomarkers (suppressor of tumorigenicity-2 [ST2] + regenerating family member 3 alpha [REG3α]) when measured at GVHD diagnosis are validated predictors of NRM risk but have never been assessed in the same patients using identical statistical methods. We measured the serum concentrations of ST2, REG3α, and AREG by enzyme-linked immunosorbent assay at the time of GVHD diagnosis in 715 patients divided by the date of transplantation into training (2004-2015) and validation (2015-2017) cohorts. The training cohort (n = 341) was used to develop algorithms for predicting the probability of 12-month NRM that contained all possible combinations of 1 to 3 biomarkers and a threshold corresponding to the concordance probability was used to stratify patients for the risk of NRM. Algorithms were compared with each other based on several metrics, including the area under the receiver operating characteristics curve, proportion of patients correctly classified, sensitivity, and specificity using only the validation cohort (n = 374). All algorithms were strong discriminators of 12-month NRM, whether or not patients were systemically treated (n = 321). An algorithm containing only ST2 + REG3α had the highest area under the receiver operating characteristics curve (0.757), correctly classified the most patients (75%), and more accurately risk-stratified those who developed Minnesota standard-risk GVHD and for patients who received posttransplant cyclophosphamide-based prophylaxis. An algorithm containing only AREG more accurately risk-stratified patients with Minnesota high-risk GVHD. Combining ST2, REG3α, and AREG into a single algorithm did not improve performance.
CircR-loop: a novel RNA:DNA interaction on genome instability
Authors: Su Xinming , Feng Yaojie , Chen Ruixiu , Duan Shiwei 
Published: June 2024

AbstractCircR-loop, a recently unearthed regulatory mechanism situated at the crossroads of circular RNA and DNA interactions, constitute a subset of R-loop. This circR-loop have emerged as a crucial player in pivotal regulatory functions within both animal and plant systems. The journey into the realm of circR-loop commenced with their discovery within the human mitochondrial genome, where they serve as critical directors of mitochondrial DNA replication. In the plant kingdom, circR-loop wield influence over processes such as alternative splicing and centromere organization, impacting the intricacies of floral development and genome stability, respectively. Their significance extends to the animal domain, where circR-loop has captured attention for their roles in cancer-related phenomena, exerting control over transcription, chromatin architecture, and orchestrating responses to DNA damage. Moreover, their involvement in nuclear export anomalies further underscores their prominence in cellular regulation. This article summarizes the important regulatory mechanisms and physiological roles of circR-loop in plants and animals, and offers a comprehensive exploration of the methodologies employed for the identification, characterization, and functional analysis of circR-loop, underscoring the pressing need for innovative approaches that can effectively distinguish them from their linear RNA counterparts while elucidating their precise functions. Lastly, the article sheds light on the challenges and opportunities that lie ahead in the field of circR-loop research, emphasizing the vital importance of continued investigations to uncover their regulatory roles and potential applications in the realm of biology. In summary, circR-loop represents a captivating and novel regulatory mechanism with broad-reaching implications spanning the realms of genetics, epigenetics, and disease biology. Their exploration opens new avenues for comprehending gene regulation and holds significant promise for future therapeutic interventions.
Genetic Effects of Grain Quality Enhancement in Indica Hybrid Rice: Insights for Molecular Design Breeding
Authors: Gao Ju , Gao Lijun , Chen Weiwei , Huang Juan , Qing Dongjin , Pan Yinghua , Ma Chonglie , Wu Hao , Zhou Weiyong , Li Jingcheng , Yang Xinghai , Dai Gaoxing , Deng Guofu 
Published: June 2024

AbstractImproving rice quality remains a crucial breeding objective, second only to enhancing yield, yet progress in quality improvement lags behind yield. The high temperature and ripening conditions in Southern China often result in poor rice quality, impacting hybrid rice production and utilization. Therefore, to address this challenge, analyzing the molecular basis of high-quality traits is essential for molecular design breeding of high-quality hybrid rice varieties. In this study, we investigated the molecular basis of grain shape, amylose content, gel consistency, gelatinization temperature, and aroma, which influence rice quality. We discovered that quality related alleles gs3, GW7TFA, gw8, chalk5, Wxb, ALKTT, and fgr can enhance rice quality when applied in breeding programs. Polymerization of gs3, GW7TFA, gw8, and chalk5 genes improves rice appearance quality. The gs3 and GW7TFA allele polymerization increasing the grain’s length-width ratio, adding the aggregation of gw8 allele can further reducing grain width. The chalk5 gene regulates low chalkiness, but low correlation to chalkiness was exhibited with grain widths below 2.0 mm, with minimal differences between Chalk5 and chalk5 alleles. Enhancing rice cooking and eating quality is achieved through Wxb and ALKTT gene polymerization, while introducing the fgr(E7) gene significantly improved rice aroma. Using molecular marker-assisted technology, we aggregated these genes to develop a batch of indica hybrid rice parents with improved rice quality are obtained. Cross-combining these enhanced parents can generate new, high-quality hybrid rice varieties suitable for cultivation in Southern China. Therefore, our findings contribute to a molecular breeding model for grain quality improvement in high-quality indica hybrid rice. This study, along with others, highlights the potential of molecular design breeding for enhancing complex traits, particularly rice grain quality.
Transcriptome analysis reveals the key role of overdominant expression of photosynthetic and respiration-related genes in the formation of tobacco(Nicotiana tabacum L.) biomass heterosis
Authors: Lu Anbin , Zeng Shuaibo , Pi Kai , Long Benshan , Mo Zejun , Liu Renxiang 
Published: June 2024

Abstract
Background
Leaves are the nutritional and economic organs of tobacco, and their biomass directly affects tobacco yield and the economic benefits of farmers. In the early stage, our research found that tobacco hybrids have more leaves and larger leaf areas, but the performance and formation reasons of biomass heterosis are not yet clear.

Results
This study selected 5 parents with significant differences in tobacco biomass and paired them with hybrid varieties. It was found that tobacco hybrid varieties have a common biomass heterosis, and 45 days after transplantation is the key period for the formation of tobacco biomass heterosis; By analyzing the biomass heterosis of hybrids, Va116×GDH94 and its parents were selected for transcriptome analysis. 76.69% of the differentially expressed genes between Va116×GDH94 and its parents showed overdominant expression pattern, and these overdominant expression genes were significantly enriched in the biological processes of photosynthesis and TCA cycle; During the process of photosynthesis, the overdominant up-regulation of genes such as Lhc, Psa, and rbcl promotes the progress of photosynthesis, thereby increasing the accumulation of tobacco biomass; During the respiratory process, genes such as MDH, ACO, and OGDH are overedominantly down-regulated, inhibiting the TCA cycle and reducing substrate consumption in hybrid offspring; The photosynthetic characteristics of the hybrid and its parents were measured, and the net photosynthetic capacity of the hybrid was significantly higher than that of the parents.

Conclusion
These results indicate that the overdominant expression effect of differentially expressed genes in Va116×GDH94 and its parents plays a crucial role in the formation of tobacco biomass heterosis. The overdominant expression of genes related to photosynthesis and respiration enhances the photosynthetic ability of Va116×GDH94, reduces respiratory consumption, promotes the increase of biomass, and exhibits obvious heterosis.
Offsetting pb induced oxidative stress in Vicia faba plants by foliar spray of chitosan through adjustment of morpho-biochemical and molecular indices
Authors: Abdelhameed Reda E. , Abdalla Hanan , Abdel-Haleem Mohamed 
Published: June 2024

AbstractIn the course of their life, plants face a multitude of environmental anomaly that affects their growth and production. In recent decades, lead (Pb) gained an increasing attention as it is among the most significant contaminants in the environment. Therefore, in this study the effects of Pb concentrations (0, 50 and 100 ppm) on Vicia faba plants and attempts to alleviate this stress using chitosan (Chs; 0 and 0.1%) were performed. The results validated that with increasing Pb concentrations, a decline in growth, pigments and protein contents was observed. In the same time, a significant upsurge in the stress markers, both malondialdehyde (MDA) and H2O2, was observed under Pb stress. Nonetheless, foliar spraying with Chs improves the faba bean growth, pigment fractions, protein, carbohydrates, reduces MDA and H2O2 contents and decreases Pb concentrations under Pb stress. Pb mitigation effects by Chs are probably related with the activity of antioxidant enzymes, phenylalanine ammonia lyase (PAL) and proline. The application of Chs enhanced the activities of peroxidase, catalase and PAL by 25.77, 17.71 and 20.07%, respectively at 100 ppm Pb compared to their control. Plant genomic material exhibits significant molecular polymorphism, with an average polymorphism of 91.66% across all primers. To assess the genetic distance created among treatments, the dendrogram was constructed and the results of the similarity index ranged from 0.75 to 0.95, indicating genetic divergence. Our research offers a thorough comprehension of the role of Chs in lessening the oxidative stress, which will encourage the use of Chs in agricultural plant protection.
PFOA accumulation in the leaves of basil (Ocimum basilicum L.) and its effects on plant growth, oxidative status, and photosynthetic performance
Authors: Pietrini Fabrizio , Wyrwicka-Drewniak Anna , Passatore Laura , Nogués Isabel , Zacchini Massimo , Donati Enrica 
Published: June 2024

Abstract
Background
Perfluoroalkyl substances (PFASs) are emerging contaminants of increasing concern due to their presence in the environment, with potential impacts on ecosystems and human health. These substances are considered “forever chemicals” due to their recalcitrance to degradation, and their accumulation in living organisms can lead to varying levels of toxicity based on the compound and species analysed. Furthermore, concerns have been raised about the possible transfer of PFASs to humans through the consumption of edible parts of food plants. In this regard, to evaluate the potential toxic effects and the accumulation of perfluorooctanoic acid (PFOA) in edible plants, a pot experiment in greenhouse using three-week-old basil (Ocimum basilicum L.) plants was performed adding PFOA to growth substrate to reach 0.1, 1, and 10 mg Kg− 1 dw.

Results
After three weeks of cultivation, plants grown in PFOA-added substrate accumulated PFOA at different levels, but did not display significant differences from the control group in terms of biomass production, lipid peroxidation levels (TBARS), content of α-tocopherol and activity of ascorbate peroxidase (APX), catalase (CAT) and guaiacol peroxidase (POX) in the leaves. A reduction of total phenolic content (TPC) was instead observed in relation to the increase of PFOA content in the substrate. Furthermore, chlorophyll content and photochemical reflectance index (PRI) did not change in plants exposed to PFAS in comparison to control ones. Chlorophyll fluorescence analysis revealed an initial, rapid photoprotective mechanism triggered by PFOA exposure, with no impact on other parameters (Fv/Fm, ΦPSII and qP). Higher activity of glutathione S-transferase (GST) in plants treated with 1 and 10 mg Kg− 1 PFOA dw (30 and 50% to control, respectively) paralleled the accumulation of PFOA in the leaves of plants exposed to different PFOA concentration in the substrate (51.8 and 413.9 ng g− 1 dw, respectively).

Conclusion
Despite of the absorption and accumulation of discrete amount of PFOA in the basil plants, the analysed parameters at biometric, physiological and biochemical level in the leaves did not reveal any damage effect, possibly due to the activation of a detoxification pathway likely involving GST.
Role of silicon in alleviating boron toxicity and enhancing growth and physiological traits in hydroponically cultivated Zea mays var. Merit
Authors: Behtash Farhad , Mogheri Farima , Aghaee Ahmad , Seyed Hajizadeh Hanifeh , Kaya Ozkan 
Published: June 2024

Abstract
Background
Boron (B) is a micronutrient, but excessive levels can cause phytotoxicity, impaired growth, and reduced photosynthesis. B toxicity arises from over-fertilization, high soil B levels, or irrigation with B-rich water. Conversely, silicon (Si) is recognized as an element that mitigates stress and alleviates the toxic effects of certain nutrients. In this study, to evaluate the effect of different concentrations of Si on maize under boron stress conditions, a factorial experiment based on a randomized complete block design was conducted with three replications in a hydroponic system. The experiment utilized a nutrient solution for maize var. Merit that contained three different boron (B) concentrations (0.5, 2, and 4 mg L−1) and three Si concentrations (0, 28, and 56 mg L−1).

Results
Our findings unveiled that exogenous application of B resulted in a substantial escalation of B concentration in maize leaves. Furthermore, B exposure elicited a significant diminution in fresh and dry plant biomass, chlorophyll index, chlorophyll a (Chl a), chlorophyll b (Chl b), carotenoids, and membrane stability index (MSI). As the B concentration augmented, malondialdehyde (MDA) content and catalase (CAT) enzyme activity exhibited a concomitant increment. Conversely, the supplementation of Si facilitated an amelioration in plant fresh and dry weight, total carbohydrate, and total soluble protein. Moreover, the elevated activity of antioxidant enzymes culminated in a decrement in hydrogen peroxide (H2O2) and MDA content. In addition, the combined influence of Si and B had a statistically significant impact on the leaf chlorophyll index, total chlorophyll (a + b) content, Si and B accumulation levels, as well as the enzymatic activities of guaiacol peroxidase (GPX), ascorbate peroxidase (APX), and H2O2 levels. These unique findings indicated the detrimental impact of B toxicity on various physiological and biochemical attributes of maize, while highlighting the potential of Si supplementation in mitigating the deleterious effects through modulation of antioxidant machinery and biomolecule synthesis.

Conclusions
This study highlights the potential of Si supplementation in alleviating the deleterious effects of B toxicity in maize. Increased Si consumption mitigated chlorophyll degradation under B toxicity, but it also caused a significant reduction in the concentrations of essential micronutrients iron (Fe), copper (Cu), and zinc (Zn). While Si supplementation shows promise in counteracting B toxicity, the observed decrease in Fe, Cu, and Zn concentrations warrants further investigation to optimize this approach and maintain overall plant nutritional status.
Data-driven collaborative QUality improvement in Cardiac Rehabilitation (QUICR) to increase program completion: protocol for a cluster randomized controlled trial
Authors: Candelaria Dion , Redfern Julie , O’Neil Adrienne , Brieger David , Clark Robyn A , Briffa Tom , Bauman Adrian , Hyun Karice , Cunich Michelle , Figtree Gemma A , Cartledge Susie , Gallagher Robyn 
Published: June 2024

Abstract
Background
Coronary heart disease (CHD) is the leading cause of deaths and disability worldwide. Cardiac rehabilitation (CR) effectively reduces the risk of future cardiac events and is strongly recommended in international clinical guidelines. However, CR program quality is highly variable with divergent data systems, which, when combined, potentially contribute to persistently low completion rates. The QUality Improvement in Cardiac Rehabilitation (QUICR) trial aims to determine whether a data-driven collaborative quality improvement intervention delivered at the program level over 12 months: (1) increases CR program completion in eligible patients with CHD (primary outcome), (2) reduces hospital admissions, emergency department presentations and deaths, and costs, (3) improves the proportion of patients receiving guideline-indicated CR according to national and international benchmarks, and (4) is feasible and sustainable for CR staff to implement routinely.

Methods
QUICR is a multi-centre, type-2, hybrid effectiveness-implementation cluster-randomized controlled trial (cRCT) with 12-month follow-up. Eligible CR programs (n = 40) and the individual patient data within them (n ~ 2,000) recruited from two Australian states (New South Wales and Victoria) are randomized 1:1 to the intervention (collaborative quality improvement intervention that uses data to identify and manage gaps in care) or control (usual care with data collection only). This sample size is required to achieve 80% power to detect a difference in completion rate of 22%. Outcomes will be assessed using intention-to-treat principles. Mixed-effects linear and logistic regression models accounting for clusters within allocated groupings will be applied to analyse primary and secondary outcomes.

Discussion
Addressing poor participation in CR by patients with CHD has been a longstanding challenge that needs innovative strategies to change the status-quo. This trial will harness the collaborative power of CR programs working simultaneously on common problem areas and using local data to drive performance. The use of data linkage for collection of outcomes offers an efficient way to evaluate this intervention and support the improvement of health service delivery.

Ethics
Primary ethical approval was obtained from the Northern Sydney Local Health District Human Research Ethics Committee (2023/ETH01093), along with site-specific governance approvals.

Trial registration
Australian New Zealand Clinical Trials Registry (ANZCTR) ACTRN12623001239651 (30/11/2023) (https://anzctr.org.au/Trial/Registration/TrialReview.aspx?id=386540&isReview=true).
A bayesian network meta-analysis to explore modifying factors in randomized controlled trials: what works for whom to reduce depression in nursing home residents?
Authors: Declercq Ine J. N. , Leontjevas Ruslan , Verboon Peter , De Vriendt Patricia , Gerritsen Debby L. , van Hooren Susan 
Published: June 2024

Abstract
Background
Reviews of depression interventions in nursing home residents resulted in positive findings. However, because of the heterogeneity of the studies, it remains unclear what works for whom. Considering moderator effects may contribute to a comprehensive understanding of depression treatment in residents. Therefore, this study aims to review depression interventions, examining moderator effects of (1) residents’ factors, and (2) components specific of interventions.

Methods
A Bayesian network meta-analysis of randomized controlled trials primarily aimed at reducing depressive symptoms among residents was conducted. First, intervention types, e.g., exercise interventions, were compared to care as usual. Second, meta-regression analyses were conducted for moderator effects of residents’ factors (i.e., severity of depressive symptoms, physical dependency, and cognitive impairment) and components identified as specific to an intervention (e.g., music, creativity, positivity).

Results
Our search across six databases resulted in 118 eligible studies: 16 on neurobiological interventions, 102 on non-pharmacological interventions. Compared to care as usual, cognitive interventions, such as cognitive behavioral therapy and goal-oriented therapy, showed the strongest effects (MD = -1.00, 95% CrI [-1.40 to -0.66]). Furthermore, the severity of depressive symptoms moderated the effect of interventions (ƅ = -0.63, CrI 95% [-1.04 to -0.22]), while none of fifteen identified intervention-specific components did. In residents with a depression diagnosis, there were larger effect sizes for interventions including daily structure, psychoeducation, healthy food, creativity, positivity, and an activating/encouraging environment, whereas interventions focusing on distraction and relaxation had larger effect sizes in those residents without.

Conclusions
By examining the moderator effects, we provided an integrative perspective on the observed variations in effects across different target groups, and components of depression interventions. This approach underscores the complex nature of interventions, emphasizing the need for continued transdisciplinary research, and the exploration of potential moderators. Future investigations should carefully assess residents’ factors and choose interventions and their components accordingly.