bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective pressures of platinum compounds shape the evolution of therapy-related myeloid neoplasms
Authors: Bertrums Eline J. M. , de Kanter Jurrian K. , Derks Lucca L. M. , Verheul Mark , Trabut Laurianne , van Roosmalen Markus J. , Hasle Henrik , Antoniou Evangelia , Reinhardt Dirk , Dworzak Michael N. , Mühlegger Nora , van den Heuvel-Eibrink Marry M. , Zwaan C. Michel , Goemans Bianca F. , van Boxtel Ruben 
Published: July 2024

AbstractTherapy-related myeloid neoplasms (t-MN) arise as a complication of chemo- and/or radiotherapy. Although t-MN can occur both in adult and childhood cancer survivors, the mechanisms driving therapy-related leukemogenesis likely vary across different ages. Chemotherapy is thought to induce driver mutations in children, whereas in adults pre-existing mutant clones are selected by the exposure. However, selective pressures induced by chemotherapy early in life are less well studied. Here, we use single-cell whole genome sequencing and phylogenetic inference to show that the founding cell of t-MN in children starts expanding after cessation of platinum exposure. In patients with Li-Fraumeni syndrome, characterized by a germline TP53 mutation, we find that the t-MN already expands during treatment, suggesting that platinum-induced growth inhibition is TP53-dependent. Our results demonstrate that germline aberrations can interact with treatment exposures in inducing t-MN, which is important for the development of more targeted, patient-specific treatment regimens and follow-up.
Learning a reactive potential for silica-water through uncertainty attribution
Authors: Roy Swagata , Dürholt Johannes P. , Asche Thomas S. , Zipoli Federico , Gómez-Bombarelli Rafael 
Published: July 2024

AbstractThe reactivity of silicates in aqueous solution is relevant to various chemistries ranging from silicate minerals in geology, to the C-S-H phase in cement, nanoporous zeolite catalysts, or highly porous precipitated silica. While simulations of chemical reactions can provide insight at the molecular level, balancing accuracy and scale in reactive simulations in the condensed phase is a challenge. Here, we demonstrate how a machine-learning reactive interatomic potential trained on PaiNN architecture can accurately capture silicate-water reactivity. The model was trained on a dataset comprising 400,000 energies and forces of molecular clusters at the ωB97X-D3/def2-TZVP level. To ensure the robustness of the model, we introduce a general active learning strategy based on the attribution of the model uncertainty, that automatically isolates uncertain regions of bulk simulations to be calculated as small-sized clusters. The potential reproduces static and dynamic properties of liquid water and solid crystalline silicates, despite having been trained exclusively on cluster data. Furthermore, we utilize enhanced sampling simulations to recover the self-ionization reactivity of water accurately, and the acidity of silicate oligomers, and lastly study the silicate dimerization reaction in a water solution at neutral conditions and find that the reaction occurs through a flanking mechanism.
DHX9 SUMOylation is required for the suppression of R-loop-associated genome instability
Authors: Yang Bing-Ze , Liu Mei-Yin , Chiu Kuan-Lin , Chien Yuh-Ling , Cheng Ching-An , Chen Yu-Lin , Tsui Li-Yu , Lin Keng-Ru , Chu Hsueh-Ping Catherine , Wu Ching-Shyi Peter 
Published: July 2024

AbstractRNA helicase DHX9 is essential for genome stability by resolving aberrant R-loops. However, its regulatory mechanisms remain unclear. Here we show that SUMOylation at lysine 120 (K120) is crucial for DHX9 function. Preventing SUMOylation at K120 leads to R-loop dysregulation, increased DNA damage, and cell death. Cells expressing DHX9 K120R mutant which cannot be SUMOylated are more sensitive to genotoxic agents and this sensitivity is mitigated by RNase H overexpression. Unlike the mutant, wild-type DHX9 interacts with R-loop-associated proteins such as PARP1 and DDX21 via SUMO-interacting motifs. Fusion of SUMO2 to the DHX9 K120R mutant enhances its association with these proteins, reduces R-loop accumulation, and alleviates survival defects of DHX9 K120R. Our findings highlight the critical role of DHX9 SUMOylation in maintaining genome stability by regulating protein interactions necessary for R-loop balance.
Alloying and confinement effects on hierarchically nanoporous CuAu for efficient electrocatalytic semi-hydrogenation of terminal alkynes
Authors: Meng Linghu , Kao Cheng-Wei , Wang Zhen , Ma Jun , Huang Peifeng , Zhao Nan , Zheng Xin , Peng Ming , Lu Ying-Rui , Tan Yongwen 
Published: July 2024

AbstractElectrocatalytic alkynes semi-hydrogenation to produce alkenes with high yield and Faradaic efficiency remains technically challenging because of kinetically favorable hydrogen evolution reaction and over-hydrogenation. Here, we propose a hierarchically nanoporous Cu50Au50 alloy to improve electrocatalytic performance toward semi-hydrogenation of alkynes. Using Operando X-ray absorption spectroscopy and density functional theory calculations, we find that Au modulate the electronic structure of Cu, which could intrinsically inhibit the combination of H* to form H2 and weaken alkene adsorption, thus promoting alkyne semi-hydrogenation and hampering alkene over-hydrogenation. Finite element method simulations and experimental results unveil that hierarchically nanoporous catalysts induce a local microenvironment with abundant K+ cations by enhancing the electric field within the nanopore, accelerating water electrolysis to form more H*, thereby promoting the conversion of alkynes. As a result, the nanoporous Cu50Au50 electrocatalyst achieves highly efficient electrocatalytic semi-hydrogenation of alkynes with 94% conversion, 100% selectivity, and a 92% Faradaic efficiency over wide potential window. This work provides a general guidance of the rational design for high-performance electrocatalytic transfer semi-hydrogenation catalysts.
Clinical impact of drug-drug interactions on abemaciclib in the real-world experience of AB-ITALY study
Authors: Scagnoli Simone , Pisegna Simona , Toss Angela , Caputo Roberta , De Laurentiis Michelino , Palleschi Michela , de Giorgi Ugo , Cortesi Enrico , Fabbri Agnese , Fabi Alessandra , Paris Ida , Orlandi Armando , Curigliano Giuseppe , Criscitiello Carmen , Garrone Ornella , Tomasello Gianluca , D’Auria Giuliana , Vici Patrizia , Ricevuto Enrico , Domati Federica , Piombino Claudia , Parola Sara , Scafetta Roberta , Cirillo Alessio , Taurelli Salimbeni Beatrice , Di Lisa Francesca Sofia , Strigari Lidia , Preissner Robert , Simmaco Maurizio , Santini Daniele , Marchetti Paolo , Botticelli Andrea 
Published: July 2024

AbstractAbemaciclib demonstrated clinical benefit in women affected by HR+/HER2− advanced breast cancer (aBC). Drug-drug interactions (DDIs) can lead to reduced treatment efficacy or increased toxicity. This retro-prospective study aimed to evaluate outcomes, DDIs’ impact, and toxicities of abemaciclib combined with endocrine therapy in a real-world setting. Patients from 12 referral Italian hospitals with HR+/HER2− aBC who received abemaciclib were included. Clinical data about comorbidities, concurrent medications, outcomes, and adverse events (AE) were collected. Drug-PIN® (Personalized Interactions Network) is a tool recognizing the role of multiple interactions between active and/or pro-drug forms combined with biochemical and demographic patient data. The software was used to define the Drug-PIN score and Drug-PIN tier (green, yellow, dark yellow, and red) for each patient. Univariate and multivariate analyses were performed to identify predictors of patients’ PFS or toxicity. One hundred seventy-three patients were included. 13% of patients had >75years. The overall response rate (ORR) was 63%. The general population’s median PFS (mPFS) was 22 months (mo), while mOS were not reached. Patients treated with abemaciclib in combination with AI and fulvestrant had a mPFS of 36 and 19 mo, respectively. The most common toxicities were diarrhea, asthenia, and neutropenia detected in 63%,49%, and 49% of patients. The number of concomitant medications and comorbidities were not associated with survival outcomes (22 vs 17 mo, p = 0.068, p = 0.99). Drug-PIN tier from dark yellow to red and Drug-PIN score >12 were associated with shorter PFS compared to no/low-risk DDIs and score <12 (15 vs 23, p = 0.005, p = 0.0017). Drug interaction was confirmed as an independent biomarker in a multivariate model (p = 0.02). No difference in any grade AE, severe toxicities, and diarrhea were detected among different age subgroups. No association was found between Drug-PIN score or Drug-PIN tier and overall toxicity (p = 0.44), severe AEs (p = 0.11), or drug reduction (p = 0.27). The efficacy and safety of abemaciclib plus ET were confirmed in a real-world setting, even in the elderly population and patients with comorbidities. Evaluation of DDIs with Drug-PIN appears to be an independent predictor of PFS.
A holistic platform for accelerating sorbent-based carbon capture
Authors: Charalambous Charithea , Moubarak Elias , Schilling Johannes , Sanchez Fernandez Eva , Wang Jin-Yu , Herraiz Laura , Mcilwaine Fergus , Peh Shing Bo , Garvin Matthew , Jablonka Kevin Maik , Moosavi Seyed Mohamad , Van Herck Joren , Ozturk Aysu Yurdusen , Pourghaderi Alireza , Song Ah-Young , Mouchaham Georges , Serre Christian , Reimer Jeffrey A. , Bardow André , Smit Berend , Garcia Susana 
Published: July 2024

AbstractReducing carbon dioxide (CO2) emissions urgently requires the large-scale deployment of carbon-capture technologies. These technologies must separate CO2 from various sources and deliver it to different sinks1,2. The quest for optimal solutions for specific source–sink pairs is a complex, multi-objective challenge involving multiple stakeholders and depends on social, economic and regional contexts. Currently, research follows a sequential approach: chemists focus on materials design3 and engineers on optimizing processes4,5, which are then operated at a scale that impacts the economy and the environment. Assessing these impacts, such as the greenhouse gas emissions over the plant’s lifetime, is typically one of the final steps6. Here we introduce the PrISMa (Process-Informed design of tailor-made Sorbent Materials) platform, which integrates materials, process design, techno-economics and life-cycle assessment. We compare more than 60 case studies capturing CO2 from various sources in 5 global regions using different technologies. The platform simultaneously informs various stakeholders about the cost-effectiveness of technologies, process configurations and locations, reveals the molecular characteristics of the top-performing sorbents, and provides insights on environmental impacts, co-benefits and trade-offs. By uniting stakeholders at an early research stage, PrISMa accelerates carbon-capture technology development during this critical period as we aim for a net-zero world.
Sources of gene expression variation in a globally diverse human cohort
Authors: Taylor Dylan J. , Chhetri Surya B. , Tassia Michael G. , Biddanda Arjun , Yan Stephanie M. , Wojcik Genevieve L. , Battle Alexis , McCoy Rajiv C. 
Published: July 2024

AbstractGenetic variation that influences gene expression and splicing is a key source of phenotypic diversity1–5. Although invaluable, studies investigating these links in humans have been strongly biased towards participants of European ancestries, which constrains generalizability and hinders evolutionary research. Here to address these limitations, we developed MAGE, an open-access RNA sequencing dataset of lymphoblastoid cell lines from 731 individuals from the 1000 Genomes Project6, spread across 5 continental groups and 26 populations. Most variation in gene expression (92%) and splicing (95%) was distributed within versus between populations, which mirrored the variation in DNA sequence. We mapped associations between genetic variants and expression and splicing of nearby genes (cis-expression quantitative trait loci (eQTLs) and cis-splicing QTLs (sQTLs), respectively). We identified more than 15,000 putatively causal eQTLs and more than 16,000 putatively causal sQTLs that are enriched for relevant epigenomic signatures. These include 1,310 eQTLs and 1,657 sQTLs that are largely private to underrepresented populations. Our data further indicate that the magnitude and direction of causal eQTL effects are highly consistent across populations. Moreover, the apparent ‘population-specific’ effects observed in previous studies were largely driven by low resolution or additional independent eQTLs of the same genes that were not detected. Together, our study expands our understanding of human gene expression diversity and provides an inclusive resource for studying the evolution and function of human genomes.
Dataset of Post-Event Survey of the 2024 Noto Peninsula Earthquake Tsunami in Japan
Authors: Yuhi Masatoshi , Umeda Shinya , Arita Mamoru , Ninomiya Junichi , Gokon Hideomi , Arikawa Taro , Baba Toshitaka , Imamura Fumihiko , Kumagai Kenzou , Kure Shuichi , Miyashita Takuya , Suppasri Anawat , Kawai Akio , Nobuoka Hisamichi , Shibayama Tomoya , Koshimura Shunichi , Mori Nobuhito 
Published: July 2024

AbstractAn earthquake with a moment magnitude of 7.5 (Mw) struck the northern Noto Peninsula, Ishikawa Prefecture, Japan, at 16:10 local time on January 1, 2024. This earthquake triggered a tsunami that propagated along the coastline of Ishikawa, Toyama, and Niigata Prefectures facing the Sea of Japan and significantly damaged coastal communities and infrastructure. Approximately 70 researchers from 23 universities or other institutes throughout Japan formed a joint research group to conduct a post-tsunami survey along a 340 km stretch of the coast. Based on the watermarks and traces of the tsunami, the inundation and run-up heights were surveyed using total stations, automatic optical levels, laser range finders, and a real-time kinematic (RTK) Global Navigation Satellite System (GNSS). The tidal correction was adjusted using astronomical tidal tables. In total, 303 survey records have been compiled, generating the NP2024TS (Noto Peninsula 2024 Tsunami Survey) dataset. This dataset provides comprehensive information on the inundation and run-up heights of the tsunami, which is useful for understanding tsunami characteristics and validating numerical tsunami models.
Comparative transcriptomics analysis of tolerant and sensitive genotypes reveals genes involved in the response to cold stress in bitter gourd (Momordica charantia L.)
Authors: Ning Yu , Liu Zhiyang , Liu Jing , Qi Renjie , Xia Pengfei , Yuan Xihan , Xu Hai , Chen Longzheng 
Published: July 2024

AbstractBitter gourd is an economically important horticultural crop for its edible and medicinal value. However, the regulatory mechanisms of bitter gourd in response to cold stress are still poorly elucidated. In this study, phytohormone determination and comparative transcriptome analyses in XY (cold-tolerant) and QF (cold-sensitive) after low temperature treatment were conducted. Under cold stress, the endogenous contents of abscisic acid (ABA), jasmonic acid (JA) and salicylic acid (SA) in XY were significantly increased at 24 h after treatment (HAT), indicating that ABA, JA and SA might function in regulating cold resistance. RNA-seq results revealed that more differentially expressed genes were identified at 6 HAT in QF and 24 HAT in XY, respectively. KEGG analysis suggested that the plant hormone signal transduction pathway was significantly enriched in both genotypes at all the time points. In addition, transcription factors showing different expression patterns between XY and QF were identified, including CBF3, ERF2, NAC90, WRKY51 and WRKY70. Weighted gene co-expression network analysis suggested MARK1, ERF17, UGT74E2, GH3.1 and PPR as hub genes. These results will deepen the understanding of molecular mechanism of bitter gourd in response to cold stress and the identified genes may help to facilitate the genetic improvement of cold-resistant cultivars.
Exploring phylogeny and genomic vulnerability of Melastoma (Melastomataceae) endemic to a World Natural Heritage site, the Bonin Islands
Authors: Kobayashi Yukihiro , Komaki Yoshiteru , Isagi Yuji 
Published: July 2024

AbstractMelastoma (Melastomataceae) includes ca. 100 species across tropical to subtropical regions of Asia and Oceania. The Bonin Islands harbor three endemic taxa: M. tetramerum, M. tetramerum var. pentapetalum, and M. candidum var. alessandrense. Of these, M. tetramerum is critically endangered and faces near extinction in the wild. This study investigates the phylogenetic relationships among these endemic Melastoma species in the Bonin Islands based on the whole chloroplast genome and nuclear SNPs. The results revealed that M. candidum var. alessandrense was placed in the clade of the widespread East Asian M. candidum and has a distinct evolutionary origin from the other two taxa. The population genomics analyses (heterozygosity, rates of deleterious mutations, and numbers and lengths of runs of homozygosity) indicated lower genetic diversity and more vulnerable genomes of endemic Melastoma, especially M. tetramerum var. pentapetalum. M. tetramerum var. pentapetalum is not a target of any protection programs, however, conservation plans might be required for this variety because M. tetramerum var. pentapetalum would have a more vulnerable genome than M. tetramerum, which faces near extinction in the wild. This information can facilitate the development of effective conservation strategies in a precautionary way that anticipates imminent threats to the survival of the species.
The rate of W chromosome degeneration across multiple avian neo-sex chromosomes
Authors: Sigeman Hanna , Downing Philip A. , Zhang Hongkai , Hansson Bengt 
Published: July 2024

AbstractWhen sex chromosomes evolve recombination suppression, the sex-limited chromosome (Y/W) commonly degenerate by losing functional genes. The rate of Y/W degeneration is believed to slow down over time as the most essential genes are maintained by purifying selection, but supporting data are scarce especially for ZW systems. Here, we study W degeneration in Sylvioidea songbirds where multiple autosomal translocations to the sex chromosomes, and multiple recombination suppression events causing separate evolutionary strata, have occurred during the last ~ 28.1–4.5 million years (Myr). We show that the translocated regions have maintained 68.3–97.7% of their original gene content, compared to only 4.2% on the much older ancestral W chromosome. By mapping W gene losses onto a dated phylogeny, we estimate an average gene loss rate of 1.0% per Myr, with only moderate variation between four independent lineages. Consistent with previous studies, evolutionarily constrained and haploinsufficient genes were preferentially maintained on W. However, the gene loss rate did not show any consistent association with strata age or with the number of W genes at strata formation. Our study provides a unique account on the pace of W gene loss and reinforces the significance of purifying selection in maintaining essential genes on sex chromosomes.
Granulation compared to co-application of biochar plus mineral fertilizer and its impacts on crop growth and nutrient leaching
Authors: Grafmüller Jannis , Möllmer Jens , Muehe E. Marie , Kammann Claudia I. , Kray Daniel , Schmidt Hans-Peter , Hagemann Nikolas 
Published: July 2024

Abstract
Mechanized biochar field application remains challenging due to biochar’s poor flowability and bulk density. Granulation of biochar with fertilizer provides a product ready for application with well-established machinery. However, it’s unknown whether granulated biochar-based fertilizers (gBBF) are as effective as co-application of non-granulated biochar with fertilizer. Here, we compared a gBBF with a mineral compound fertilizer (control), and with a non-granulated biochar that was co-applied at a rate of 1.1 t ha−1 with the fertilizer in a white cabbage greenhouse pot trial. Half the pots received heavy rain simulation treatments to investigate nutrient leaching. Crop yields were not significantly increased by biochar without leaching compared to the control. With leaching, cabbage yield increased with gBBF and biochar-co-application by 14% (p > 0.05) and 34% (p < 0.05), respectively. Nitrogen leaching was reduced by 26–35% with both biochar amendments. Biochar significantly reduced potassium, magnesium, and sulfur leaching. Most nitrogen associated with gBBF was released during the trial and the granulated biochar regained its microporosity. Enriching fertilizers with biochar by granulation or co-application can improve crop yields and decrease nutrient leaching. While the gBBF yielded less biomass compared to biochar co-application, improved mechanized field application after granulation could facilitate the implementation of biochar application in agriculture.
Clinical outcomes of posterior scleral reinforcement in Chinese high myopia children
Authors: Ye Haiyun , Tang Ruizhi , Fang Wangyi , Di Yue , Qiao Tong 
Published: July 2024

AbstractWe aim to observe the posterior scleral reinforcement (PSR) clinical outcomes of children with high myopia and analyze the retinal vessel alteration before and after PSR by using angiography optical coherence tomography (angio-OCT). Fifty-six pediatric participants (112 eyes) clinically diagnosed high myopia were recruited and were treated by PSR in Shanghai Children’s Hospital from June 1, 2021 to May 1, 2023. The average age ranged from 5.42 to 14.83 years (mean 8.83 years) and mean follow up duration was 8.7 months (3–24 months). The axial length (AL) was significantly shortened after PSR (p < 0.05). The spherical equivalent (SE) and the best-corrected visual acuity (BCVA) were also improved without severe rejection in the follow-up. Compared with baseline, angio-OCT parafoveal vessel indices including vascular area density (VAD) and vascular skeleton density (VSD) on the superficial capillary plexus layer (SCPL), as well as VAD and vessel perimeter index (VPI) on the deep capillary plexus layer (DCPL), were significantly increased after PSR surgery (p < 0.05). VPI on the SCPL, vascular diameter index (VDI) and VSD on the DCPL were also improved without statistical difference after PSR. The VSD on SCPL, VAD on DCPL of the right eyes and the VPI on SCPL of the left eyes were significantly increased after PSR (p < 0.05). PSR surgery can shorten the AL and can stable BCVA and SE in high myopia children. The angio-OCT parameters indicated that the retinal microcirculation supply was significantly improved after PSR.
A paradigm shift in diagnosis and treatment innovation for mucinous cystic neoplasms of the liver
Authors: Shi Bin , Yu Peng , Meng Lingzhan , Li Hu , Wang Zizheng , Cao Li , Yan Jin , Shao Yanling , Zhang Ying , Zhu Zhenyu 
Published: July 2024

AbstractThis study comprehensively explores the clinical characteristics, diagnostic approaches, and treatment methods for liver mucinous cystic neoplasms (MCN). A retrospective analysis was conducted on seven individuals diagnosed with MCN, admitted to the Fifth Medical Center of the PLA General Hospital between October 2016 and May 2023. Preoperative AFP was negative, while CA19-9 was elevated in two cases. Surgical resection was performed for all patients. The patients showed favorable postoperative recovery. Follow-up revealed an excellent overall survival rate, except for one case of invasive carcinoma resulting in tumor recurrence and metastasis 6 months after surgery. MCN poses a diagnostic challenge due to the absence of distinct clinical and radiological features, leading to potential misdiagnosis and inappropriate treatment. Patients with suspected liver cystic diseases should consider the possibility of MCN. Surgical resection has proven to be a practical approach with satisfactory therapeutic outcomes.