bluuebunny/crossref_metadata_2025_split huggingface dataset:
Episodic magmatism of the Gongga batholith (eastern Tibet) revealed by detrital zircon U-Pb geochronology: Insights into phased Xianshuihe fault activity and plateau growth
Authors: Zhao Yanglin , Shen Xiaoming , He Zhiyuan , Yuan Xiaoping , Ge Yukui , Wang Shiguang , Wu Lin , Jia Yingying , Tang Xiudang 
Published: April 2024

Abstract
Understanding the onset and episodes of magmatism is essential for comprehending tectonic history, crustal extension, and geodynamic processes. However, due to physical constraints, many places have remained unexplored, which makes it difficult to understand their geological evolution. Following thorough sedimentary provenance analysis, the chronology and periods of magmatism within a drainage area can be revealed through the detrital zircon U-Pb dating method. Here, we present detrital zircon U-Pb ages (n = 1429) obtained from sediments in modern rivers of the Gongga batholith in the eastern Tibetan Plateau. Our results reveal five major magmatic episodes since the early Mesozoic. Three episodes of magmatism occurred in the early to middle Mesozoic (ca. 230–200 Ma, ca. 200–180 Ma, and ca. 180–160 Ma), followed by a protracted period of magmatic quiescence. During the Cenozoic, there were two main periods of magmatism at ca. 50–25 Ma and ca. 25–5 Ma. This is consistent with bedrock geochronological data acquired previously. We propose that the Mesozoic magmatism was most likely caused by postcollisional extension after the closure of the Paleo-Tethys Ocean. The two Cenozoic magmatic episodes are coeval with the progressive intensification of Xianshuihe fault activity. Consequently, these episodes highlight two significant phases of plateau growth in the eastern Tibetan Plateau: the northward push of the Indian plate and “lateral extrusion,” which is consistent with the ongoing subduction of the Indian plate beneath the Eurasian plate.
No tillage and leguminous cover crop improve soil quality in a typical rainfed Mediterranean system
Authors: Farina Roberta , Piccini Chiara , Di Bene Claudia , Fornasier Flavio , Francaviglia Rosa , Pennelli Bruno , Vanino Silvia , Russo Mario , Cerasuolo Marianna , Troccoli Antonio 
Published: April 2024

Soil and crop management influence soil organic carbon (SOC), chemical composition, and overall soil quality. In a Mediterranean region, a study initiated in 1994 examined the long-term effects of conventional tillage (CT) versus no-tillage (NT) practices. Initially focusing on continuous durum wheat cultivation until 2009, the experiment later introduced a 2-year rotation of durum wheat and Vicia faba L. cover crops in half of the CT and NT fields. SOC was monitored from 2008 to 2018, while microbial biomass (as dsDNA), soluble nitrogen (N), and enzyme activities (EAs) were monitored from 2011 to 2014 to evaluate the rotation’s impact. Between 2009 and 2018, CT yields were on average 15% higher than NT, especially during high rainfall years. NT significantly increased SOC content in the 0–30 cm soil layer, along with higher levels of soluble N, dsDNA, and EAs at 0–10 cm depth. NT led to a 23% and 10% increase in SOC stock and SOC stock per equivalent soil mass compared to CT. EAs increased by over 50% under NT, indicating enhanced biological activity. The SOC increase due to NT was limited to the top 10 cm, with a decrease at deeper depths (up to 50 cm). Introducing cover crops over 4 years did not yield significant impacts, suggesting the need for a longer period to observe noticeable effects. Overall, adopting NT practices resulted in higher SOC concentration, enhanced soil biological activity, and improved biogeochemical cycles, emphasizing the positive impact of NT on soil health and sustainability.
Proteogenomic Characterization Reveals Estrogen Signaling as a Target for Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations
Authors: Park Seung-Jin , Ju Shinyeong , Goh Sung-Ho , Yoon Byoung-Ha , Park Jong-Lyul , Kim Jeong-Hwan , Lee Seonjeong , Lee Sang-Jin , Kwon Yumi , Lee Wonyeop , Park Kyung Chan , Lee Geon Kook , Park Seog Yun , Kim Sunshin , Kim Seon-Young , Han Ji-Youn , Lee Cheolju 
Published: April 2024

Abstract

Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations, particularly in women. EGFR mutations and anaplastic lymphoma kinase (ALK) fusions are major genetic alterations observed in NSLA, and NSLA with these alterations have been well studied and can be treated with targeted therapies. To provide insights into the molecular profile of NSLA without EGFR and ALK alterations (NENA), we selected 141 NSLA tissues and performed proteogenomic characterization, including whole genome sequencing (WGS), transcriptomic, methylation EPIC array, total proteomic, and phosphoproteomic analyses. Forty patients with NSLA harboring EGFR and ALK alterations and seven patients with NENA with microsatellite instability were excluded. Genome analysis revealed that TP53 (25%), KRAS (22%), and SETD2 (11%) mutations and ROS1 fusions (14%) were the most frequent genetic alterations in NENA patients. Proteogenomic impact analysis revealed that STK11 and ERBB2 somatic mutations had broad effects on cancer-associated genes in NENA. DNA copy number alteration analysis identified 22 prognostic proteins that influenced transcriptomic and proteomic changes. Gene set enrichment analysis revealed estrogen signaling as the key pathway activated in NENA. Increased estrogen signaling was associated with proteogenomic alterations, such as copy number deletions in chromosomes 14 and 21, STK11 mutation, and DNA hypomethylation of LLGL2 and ST14. Finally, saracatinib, an Src inhibitor, was identified as a potential drug for targeting activated estrogen signaling in NENA and was experimentally validated in vitro. Collectively, this study enhanced our understanding of NENA NSLA by elucidating the proteogenomic landscape and proposed saracatinib as a potential treatment for this patient population that lacks effective targeted therapies.

Significance:
The proteogenomic landscape in never-smoker lung cancer without known driver mutations reveals prognostic proteins and enhanced estrogen signaling that can be targeted as a potential therapeutic strategy to improve patient outcomes.
Cardiovascular Risk in Patients With Treated Isolated Diastolic Hypertension and Isolated Low Diastolic Blood Pressure
Authors: Chang Wei‐Lun , Chen Ying‐Fan , Lee Yu‐Hsuan , Shiu Ming‐Neng , Chang Po‐Yin , Guo Chao‐Yu , Huang Chi‐Jung , Chiang Chern‐En , Chen Chen‐Huan , Chuang Shao‐Yuan , Cheng Hao‐Min 
Published: April 2024

Background
The prognosis of high or markedly low diastolic blood pressure (DBP) with normalized on‐treatment systolic blood pressure on major adverse cardiovascular events (MACEs) is uncertain. This study examined whether treated isolated diastolic hypertension (IDH) and treated isolated low DBP (ILDBP) were associated with MACEs in patients with hypertension.

Methods and Results

A total of 7582 patients with on‐treatment systolic blood pressure <130 mm Hg from SPRINT (Systolic Blood Pressure Intervention Trial) were categorized on the basis of average DBP: <60 mm Hg (n=1031; treated ILDBP), 60 to 79 mm Hg (n=5432), ≥80 mm Hg (n=1119; treated IDH). MACE risk was estimated using Cox proportional‐hazards models. Among the SPRINT participants, median age was 67.0 years and 64.9% were men. Over a median follow‐up of 3.4 years, 512 patients developed a MACE. The incidence of MACEs was 3.9 cases per 100 person‐years for treated ILDBP, 1.9 cases for DBP 60 to 79 mm Hg, and 1.8 cases for treated IDH. Comparing with DBP 60 to 79 mm Hg, treated ILDBP was associated with an 1.32‐fold MACE risk (hazard ratio [HR], 1.32, 95% CI, 1.05–1.66), whereas treated IDH was not (HR, 1.18 [95% CI, 0.87–1.59]). There was no effect modification by age, sex, atherosclerotic cardiovascular disease risk, or cardiovascular disease history (all
P
values for interaction >0.05).

Conclusions
In this secondary analysis of SPRINT, among treated patients with normalized systolic blood pressure, excessively low DBP was associated with an increased MACE risk, while treated IDH was not. Further research is required for treated ILDBP management.
A Comparison of 5 Measures of Accelerated Biological Aging and Their Association With Incident Cardiovascular Disease: The CARDIA Study
Authors: Forrester Sarah N. , Baek Jonggyu , Hou Lifang , Roger Veronique , Kiefe Catarina I. 
Published: April 2024

Background
Accelerated biological aging is an increasingly popular way to track the acceleration of biology over time that may not be captured by calendar time. Biological aging has been linked to external and internal chronic stressors and has the potential to be used clinically to understand a person's personalized functioning and predict future disease. We compared the association of different measures of biological aging and incident cardiovascular disease (CVD) overall and by race.

Methods and Results
We used multiple informants models to compare the strength of clinical marker–derived age acceleration, 5 measures of epigenetic age acceleration (intrinsic and extrinsic epigenetic age acceleration, GrimAge acceleration, and PhenoAge acceleration), and 1 established clinical predictor of future CVD, Framingham 10‐year risk score, with incident CVD over an 11‐year period (2007–2018). Participants were 913 self‐identified Black or White (41% and 59%, respectively) female or male (51% and 49%, respectively) individuals enrolled in the US‐based CARDIA (Coronary Artery Risk Development in Young Adults) cohort study. The analytic baseline for this study was the 20‐year follow‐up examination (2005–2006; median age 45 years). We also included race‐specific analysis. We found that all measures were modestly correlated with one another. However, clinical marker–derived age acceleration and Framingham 10‐year risk score were more strongly associated with incident CVD than all the epigenetic measures. Clinical marker–derived age acceleration and Framingham 10‐year risk score were not significantly different than one another in their association with incident CVD.

Conclusions
The type of accelerated aging measure should be taken into consideration when comparing their association with clinical outcomes. A multisystem clinical composite shows associations with incident CVD equally to a well‐known clinical predictor.
Hypothermic Oxygenated Perfusion Improves Vascular and Contractile Function by Preserving Endothelial Nitric Oxide Production in Cardiac Grafts Obtained With Donation After Circulatory Death
Authors: Egle Manuel , Mendez‐Carmona Natalia , Segiser Adrian , Graf Selianne , Siepe Matthias , Longnus Sarah 
Published: April 2024

Background
Cardiac donation after circulatory death is a promising option to increase graft availability. Graft preservation with 30 minutes of hypothermic oxygenated perfusion (HOPE) before normothermic machine perfusion may improve cardiac recovery as compared with cold static storage, the current clinical standard. We investigated the role of preserved nitric oxide synthase activity during HOPE on its beneficial effects.

Methods and Results

Using a rat model of donation after circulatory death, hearts underwent in situ ischemia (21 minutes), were explanted for a cold storage period (30 minutes), and then reperfused under normothermic conditions (60 minutes) with left ventricular loading. Three cold storage conditions were compared: cold static storage, HOPE, and HOPE with Nω‐nitro‐L‐arginine methyl ester (nitric oxide synthase inhibitor). To evaluate potential confounding effects of high coronary flow during early reperfusion in HOPE hearts, bradykinin was administered to normalize coronary flow to HOPE levels in 2 additional groups (cold static storage and HOPE with Nω‐nitro‐L‐arginine methyl ester). Cardiac recovery was significantly improved in HOPE versus cold static storage hearts, as determined by cardiac output, left ventricular work, contraction and relaxation rates, and coronary flow (
P
<0.05). Furthermore, HOPE attenuated postreperfusion calcium overload. Strikingly, the addition of Nω‐nitro‐L‐arginine methyl ester during HOPE largely abolished its beneficial effects, even when early reperfusion coronary flow was normalized to HOPE levels.

Conclusions
HOPE provides superior preservation of ventricular and vascular function compared with the current clinical standard. Importantly, HOPE's beneficial effects require preservation of nitric oxide synthase activity during the cold storage. Therefore, the application of HOPE before normothermic machine perfusion is a promising approach to optimize graft recovery in donation after circulatory death cardiac grafts.
Factors Associated With Premature Termination of Hyperacute Stroke Trials: A Review
Authors: Aziz Yasmin N. , Sucharew Heidi , Reeves Mathew J. , Broderick Joseph P. 
Published: April 2024

Background
We performed a review of acute stroke trials to determine features associated with premature termination of trial enrollment, defined by the authors as not meeting preplanned sample size.

Methods and Results
MEDLINE was searched for randomized clinical stroke trials published in 9 major clinical journals between 2013 and 2022. We included randomized clinical trials that were phase 2 or 3 with a preplanned sample size ≥100 and a time‐to‐treatment within 24 hours of onset for transient ischemic attack, ischemic stroke, or intracerebral hemorrhage. Data were abstracted on trial features including trial design, inclusion criteria, imaging, location and number of sites, masking, treatment complexity, control group (standard therapy, placebo), industry involvement, and preplanned stopping rules (futility and efficacy). Least absolute shrinkage and selection operator regression was used to select the most important factors associated with premature termination; then, a multivariable logistic regression was fit including only the least absolute shrinkage and selection operator selected variables. Of 1475 studies assessed, 98 trials met eligibility criteria. Forty‐five (46%) trials were prematurely terminated, of which 27% were stopped for benefit/efficacy, 20% for lack of money/slow enrollment, 18% for futility, 16% for newly available evidence, 17% for other reasons, and 4% due to harm. Complex trials (adjusted odds ratio [aOR], 2.76 [95% CI, 1.13–7.49]), presence of a futility rule (aOR, 4.43 [95% CI, 1.62–17.91]), and exclusion of prestroke dependency (none/slight disability only; aOR, 2.19 [95% CI, 0.84–6.72] versus dependency allowed) were identified as the strongest predictors.

Conclusions
Nearly half of acute stroke trials were terminated prematurely. Broadening inclusion criteria and simplifying trial design may decrease the likelihood of unplanned termination, whereas planned futility analyses may appropriately terminate trials early, saving money and resources.
Explicitly Representing Syntax Improves Sentence-to-Layout Prediction of Unexpected Situations
Authors: Nuyts Wolf , Cartuyvels Ruben , Moens Marie-Francine 
Published: April 2024

Abstract
Recognizing visual entities in a natural language sentence and arranging them in a 2D spatial layout require a compositional understanding of language and space. This task of layout prediction is valuable in text-to-image synthesis as it allows localized and controlled in-painting of the image. In this comparative study it is shown that we can predict layouts from language representations that implicitly or explicitly encode sentence syntax, if the sentences mention similar entity-relationships to the ones seen during training. To test compositional understanding, we collect a test set of grammatically correct sentences and layouts describing compositions of entities and relations that unlikely have been seen during training. Performance on this test set substantially drops, showing that current models rely on correlations in the training data and have difficulties in understanding the structure of the input sentences. We propose a novel structural loss function that better enforces the syntactic structure of the input sentence and show large performance gains in the task of 2D spatial layout prediction conditioned on text. The loss has the potential to be used in other generation tasks where a tree-like structure underlies the conditioning modality. Code, trained models, and the USCOCO evaluation set are available via Github.1
To Diverge or Not to Diverge: A Morphosyntactic Perspective on Machine Translation vs Human Translation
Authors: Luo Jiaming , Cherry Colin , Foster George 
Published: April 2024

Abstract
We conduct a large-scale fine-grained comparative analysis of machine translations (MTs) against human translations (HTs) through the lens of morphosyntactic divergence. Across three language pairs and two types of divergence defined as the structural difference between the source and the target, MT is consistently more conservative than HT, with less morphosyntactic diversity, more convergent patterns, and more one-to-one alignments. Through analysis on different decoding algorithms, we attribute this discrepancy to the use of beam search that biases MT towards more convergent patterns. This bias is most amplified when the convergent pattern appears around 50% of the time in training data. Lastly, we show that for a majority of morphosyntactic divergences, their presence in HT is correlated with decreased MT performance, presenting a greater challenge for MT systems.
The Impact of Word Splitting on the Semantic Content of Contextualized Word Representations
Authors: Soler Aina Garí , Labeau Matthieu , Clavel Chloé 
Published: April 2024

Abstract
When deriving contextualized word representations from language models, a decision needs to be made on how to obtain one for out-of-vocabulary (OOV) words that are segmented into subwords. What is the best way to represent these words with a single vector, and are these representations of worse quality than those of in-vocabulary words? We carry out an intrinsic evaluation of embeddings from different models on semantic similarity tasks involving OOV words. Our analysis reveals, among other interesting findings, that the quality of representations of words that are split is often, but not always, worse than that of the embeddings of known words. Their similarity values, however, must be interpreted with caution.
How to reduce waste using black soldier fly larvae and produce a high-quality product
Authors: Ben-Mordechay T. , Gutman R. , Shaltiel-Harpaz L. , Opatovsky I. 
Published: April 2024

Abstract
With the growing human population the demand for protein is rising and waste production is increasing. Insects can provide a sustainable solution for both problems and produce food (protein and fat) from waste. Our study tested the ability of the black soldier fly (BSF) to reduce agricultural waste and produce a high-value product rich in unsaturated fatty acids. Initially, we tested the diet limitations of the larvae. We tested the composition of the agricultural wastes (brewery and avocado wastes) and the ability of the larvae to grow on them. A mixed diet based on brewery and avocado wastes was composed to increase larval weight and improve their fatty acid composition. The larvae were limited by the protein and water content of the diet (7% and 70%, respectively). The mixed diet that met the requirements of a minimal ratio of protein (7%) and optimal water content (70%), did not improve larval weight but increased the unsaturated fatty acid content. Therefore, using BSF larvae to reduce waste and produce protein is feasible; however, the end product should be considered when composing their diet from a waste mixture.
Unraveling wheat’s response to salt stress during early growth stages through transcriptomic analysis and co-expression network profiling
Authors: Wang Wei , Huang Sufang , Wang Zhi , Cao Pingping , Luo Meng , Wang Fengzhi 
Published: April 2024

Abstract
Background
Soil salinization is one of the vital factors threatening the world’s food security. To reveal the biological mechanism of response to salt stress in wheat, this study was conducted to resolve the transcription level difference to salt stress between CM6005 (salt-tolerant) and KN9204 (salt-sensitive) at the germination and seedling stage.

Results
To investigate the molecular mechanism underlying salt tolerance in wheat, we conducted comprehensive transcriptome analyses at the seedling and germination stages. Two wheat cultivars, CM6005 (salt-tolerant) and KN9204 (salt-sensitive) were subjected to salt treatment, resulting in a total of 24 transcriptomes. Through expression-network analysis, we identified 17 modules, 16 and 13 of which highly correlate with salt tolerance-related phenotypes in the germination and seedling stages, respectively. Moreover, we identified candidate Hub genes associated with specific modules and explored their regulatory relationships using co-expression data. Enrichment analysis revealed specific enrichment of gibberellin-related terms and pathways in CM6005, highlighting the potential importance of gibberellin regulation in enhancing salt tolerance. In contrast, KN9204 exhibited specific enrichment in glutathione-related terms and activities, suggesting the involvement of glutathione-mediated antioxidant mechanisms in conferring resistance to salt stress. Additionally, glucose transport was found to be a fundamental mechanism for salt tolerance during wheat seedling and germination stages, indicating its potential universality in wheat. Wheat plants improve their resilience and productivity by utilizing adaptive mechanisms like adjusting osmotic balance, bolstering antioxidant defenses, accumulating compatible solutes, altering root morphology, and regulating hormones, enabling them to better withstand extended periods of salt stress.

Conclusion
Through utilizing transcriptome-level analysis employing WGCNA, we have revealed a potential regulatory mechanism that governs the response to salt stress and recovery in wheat cultivars. Furthermore, we have identified key candidate central genes that play a crucial role in this mechanism. These central genes are likely to be vital components within the gene expression network associated with salt tolerance. The findings of this study strongly support the molecular breeding of salt-tolerant wheat, particularly by utilizing the genetic advancements based on CM6005 and KN9204.