bluuebunny/crossref_metadata_2025_split huggingface dataset:
Upper limits of HO2 in the atmosphere of Mars from the ExoMars Trace Gas Orbiter
Authors: Alday Juan , Trokhimovskiy Alexander , Belyaev Denis A , Fedorova Anna A , Holmes James A , Patel Manish R , Mason Jonathon P , Lefèvre Franck , Olsen Kevin S , Montmessin Franck , Korablev Oleg , Baggio Lucio , Patrakeev Andrey 
Published: July 2024

ABSTRACT
Odd-hydrogen (HO$_\mathrm{x}$) species have a crucial role in regulating the chemistry of the atmosphere of Mars and are important to understand some of the most fundamental aspects regarding its atmospheric composition such as the long-term stability of CO$_2$. Despite the key role of these species for our understanding of the Martian photochemistry, there is little observational evidence constraining their abundances. In this study, we use infrared solar occultation observations from the Atmospheric Chemistry Suite aboard the ExoMars Trace Gas Orbiter to search for spectral signatures of HO$_2$ in the atmosphere of Mars. In our analysis of the data, we retrieve vertical profiles of pressure, temperature, and water vapour mixing ratio, but are unable to confidently detect the presence of HO$_2$ features in the spectra. We report upper limits of 15 ppbv (5$\sigma$), which represents an order of magnitude improvement with respect to previous investigations. Comparing the derived upper limits with the expectations from 3-dimensional Global Climate Models, we find that approximately an order of magnitude improvement in the instrument sensitivity would be required to detect this molecule and/or constrain the models.
The translesion polymerase Pol Y1 is a constitutive component of the B. subtilis replication machinery
Authors: Marrin McKayla E , Foster Michael R , Santana Chloe M , Choi Yoonhee , Jassal Avtar S , Rancic Sarah J , Greenwald Carolyn R , Drucker Madeline N , Feldman Denholm T , Thrall Elizabeth S 
Published: July 2024

Abstract
Unrepaired DNA damage encountered by the cellular replication machinery can stall DNA replication, ultimately leading to cell death. In the DNA damage tolerance pathway translesion synthesis (TLS), replication stalling is alleviated by the recruitment of specialized polymerases to synthesize short stretches of DNA near a lesion. Although TLS promotes cell survival, most TLS polymerases are low-fidelity and must be tightly regulated to avoid harmful mutagenesis. The gram-negative bacterium Escherichia coli has served as the model organism for studies of the molecular mechanisms of bacterial TLS. However, it is poorly understood whether these same mechanisms apply to other bacteria. Here, we use in vivo single-molecule fluorescence microscopy to investigate the TLS polymerase Pol Y1 in the model gram-positive bacterium Bacillus subtilis. We find significant differences in the localization and dynamics of Pol Y1 in comparison to its E. coli homolog, Pol IV. Notably, Pol Y1 is constitutively enriched at or near sites of replication in the absence of DNA damage through interactions with the DnaN clamp; in contrast, Pol IV has been shown to be selectively enriched only upon replication stalling. These results suggest key differences in the roles and mechanisms of regulation of TLS polymerases across different bacterial species.
Site-specific N-alkylation of DNA oligonucleotide nucleobases by DNAzyme-catalyzed reductive amination
Authors: Boyd Robert D , Kennebeck Morgan M , Miranda Aurora A , Liu Zehui , Silverman Scott K 
Published: July 2024

Abstract
DNA and RNA nucleobase modifications are biologically relevant and valuable in fundamental biochemical and biophysical investigations of nucleic acids. However, directly introducing site-specific nucleobase modifications into long unprotected oligonucleotides is a substantial challenge. In this study, we used in vitro selection to identify DNAzymes that site-specifically N-alkylate the exocyclic nucleobase amines of particular cytidine, guanosine, and adenosine (C, G and A) nucleotides in DNA substrates, by reductive amination using a 5′-benzaldehyde oligonucleotide as the reaction partner. The new DNAzymes each require one or more of Mg2+, Mn2+, and Zn2+ as metal ion cofactors and have kobs from 0.04 to 0.3 h–1, with rate enhancement as high as ∼104 above the splinted background reaction. Several of the new DNAzymes are catalytically active when an RNA substrate is provided in place of DNA. Similarly, several new DNAzymes function when a small-molecule benzaldehyde compound replaces the 5′-benzaldehyde oligonucleotide. These findings expand the scope of DNAzyme catalysis to include nucleobase N-alkylation by reductive amination. Further development of this new class of DNAzymes is anticipated to facilitate practical covalent modification and labeling of DNA and RNA substrates.
RNA encoded peptide barcodes enable efficient in vivo screening of RNA delivery systems
Authors: Odunze Uchechukwu , Rustogi Nitin , Devine Paul , Miller Lorraine , Pereira Sara , Vashist Surender , Snijder Harm Jan , Corkill Dominic , Sabirsh Alan , Douthwaite Julie , Bond Nick , Desai Arpan 
Published: July 2024

Abstract
Lipid nanoparticles (LNPs) have been demonstrated to hold great promise for the clinical advancement of RNA therapeutics. Continued exploration of LNPs for application in new disease areas requires identification and optimization of leads in a high throughput way. Currently available high throughput in vivo screening platforms are well suited to screen for cellular uptake but less so for functional cargo delivery. We report on a platform which measures functional delivery of LNPs using unique peptide ‘barcodes’. We describe the design and selection of the peptide barcodes and the evaluation of these for the screening of LNPs. We show that proteomic analysis of peptide barcodes correlates with quantification and efficacy of barcoded reporter proteins both in vitro and in vivo and, that the ranking of selected LNPs using peptide barcodes in a pool correlates with ranking using alternative methods in groups of animals treated with individual LNPs. We show that this system is sensitive, selective, and capable of reducing the size of an in vivo study by screening up to 10 unique formulations in a single pool, thus accelerating the discovery of new technologies for mRNA delivery.
Cerebrospinal fluid liquid biopsy by low-pass whole genome sequencing for clinical disease monitoring in pediatric embryonal tumors
Authors: Crotty Erin E , Paulson Vera A , Ronsley Rebecca , Vitanza Nicholas A , Lee Amy , Hauptman Jason , Goldstein Hannah E , Lockwood Christina M , Leary Sarah E S , Cole Bonnie L 
Published: July 2024

Abstract

Background
Liquid biopsy assays that detect cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) are a promising tool for disease monitoring in pediatric patients with primary central nervous system (CNS) tumors. As a compliment to tissue-derived molecular analyses, CSF liquid biopsy has the potential to transform risk stratification, prognostication, and precision medicine approaches.

Methods
In this pilot study, we evaluated a clinical pipeline to determine feasibility and sensitivity of low-pass whole genome sequencing (LP-WGS) of CSF-derived cfDNA from patients with CNS embryonal tumors. Thirty-two longitudinal CSF samples collected from 17 patients with molecularly characterized medulloblastoma (12), embryonal tumor with multilayered rosettes (2), CNS embryonal tumor, not elsewhere classified (NEC) (2), and atypical teratoid/rhabdoid tumor (1) were analyzed.

Results
Adequate CSF-derived cfDNA for LP-WGS analysis was obtained in 94% of samples (30/32). Copy number variants compatible with neoplasia were detected in 90% (27/30) and included key alterations, such as isodicentric ch17, monosomy 6, and MYCN amplification, among others. Compared to tissue specimens, LP-WGS detected additional aberrations in CSF not previously identified in corresponding primary tumor specimens, suggesting a more comprehensive profile of tumor heterogeneity or evolution of cfDNA profiles over time. Among the 12 CSF samples obtained at initial staging, only 2 (17%) were cytologically positive, compared to 11 (92%) that were copy number positive by LP-WGS.

Conclusions
LP-WGS of CSF-derived cfDNA is feasible using a clinical platform, with greater sensitivity for tumor detection compared to conventional CSF cytologic analysis at initial staging. Large prospective studies are needed to further evaluate LP-WGS as a predictive biomarker.
18F-FDG PET/CT for early prediction of pathological complete response in breast cancer neoadjuvant therapy: a retrospective analysis
Authors: Wu Yilin , Li Yanling , Chen Bin , Zhang Ying , Xing Wanying , Guo Baoliang , Wang Wan 
Published: July 2024

Abstract

Background
Neoadjuvant treatment has been developed as a systematic approach for patients with early breast cancer and has resulted in improved breast-conserving rate and survival. However, identifying treatment-sensitive patients at the early phase of therapy remains a problem, hampering disease management and raising the possibility of disease progression during treatment.

Methods
In this retrospective analysis, we collected 2-deoxy-2-[F-18] fluoro-d-glucose (18F-FDG) positron emission tomography (PET)/computed tomography (CT) images of primary tumor sites and axillary areas and reciprocal clinical pathological data from 121 patients who underwent neoadjuvant treatment and surgery in our center. The univariate and multivariate logistic regression analyses were performed to investigate features associated with pathological complete response (pCR). An 18F-FDG PET/CT-based prediction model was trained, and the performance was evaluated by receiver operating characteristic curves (ROC).

Results
The maximum standard uptake values (SUVmax) of 18F-FDG PET/CT were a powerful indicator of tumor status. The SUVmax values of axillary areas were closely related to metastatic lymph node counts (R = 0.62). Moreover, the early SUVmax reduction rates (between baseline and second cycle of neoadjuvant treatment) were statistically different between pCR and non-pCR patients. The early SUVmax reduction rates-based model showed great ability to predict pCR (AUC = 0.89), with all molecular subtypes (HR+HER2−, HR+HER2+, HR−HER2+, and HR−HER2−) considered.

Conclusion
Our research proved that the SUVmax reduction rate of 18F-FDG PET/CT contributed to the early prediction of pCR, providing rationales for utilizing PET/CT in NAT in the future.
Isotopic variation of non-carbonaceous meteorites caused by dust leakage across the Jovian gap in the solar nebula
Authors: Homma Kazuaki A , Okuzumi Satoshi , Arakawa Sota , Fukai Ryota 
Published: July 2024

Abstract
High-precision isotopic measurements of meteorites revealed that they are classified into non-carbonaceous (NC) and carbonaceous (CC) meteorites. One plausible scenario for achieving this grouping is the early formation of Jupiter, because massive planets can create gaps that suppress the mixing of dust across the gap in protoplanetary disks. However, the efficiency of this suppression by the gaps depends on dust size and the strength of turbulent diffusion, allowing some fraction of the dust particles to leak across the Jovian gap. In this study, we investigate how isotopic ratios of NC and CC meteorites are varied by the dust leaking across the Jovian gap in the solar nebula. To do this, we constructed a model to simulate the evolution of the dust size distribution and the $^{54}$Cr-isotopic anomaly $\varepsilon ^{54}$Cr in isotopically heterogeneous disks with Jupiter. Assuming that the parent bodies of NC and CC meteorites are formed in two dust-concentrated locations inside and outside Jupiter’s orbit, referred to as the NC reservoir and the CC reservoir, we derive the temporal variation of $\varepsilon ^{54}$Cr at the NC and CC reservoirs. Our results indicate that substantial contamination from CC materials occurs at the NC reservoir in the fiducial run. Nevertheless, the values of $\varepsilon ^{54}$Cr at the NC reservoir and the CC reservoir in the run are still consistent with those of NC and CC meteorites formed around $2\:$Myr after the formation of calcium–aluminum-rich inclusions (Sugiura & Fujiya 2014, Meteorit. Planet. Sci., 49, 772). Moreover, this dust leakage causes a positive correlation between the $\varepsilon ^{54}$Cr value of NC meteorites and the accretion ages of their parent bodies.
Conceptualizing ‘Liberated Africans’ and Slave Trade Abolition: Government Schemes to Indenture Enslaved People Captured from Slavery, 1800–1920
Authors: Lovejoy Henry B 
Published: July 2024

Abstract
A new survey of ‘Liberated Africans’ exposes how global calculations of involuntary African indentured labour after 1800 have been significantly underestimated. This analysis of the suppression of the slave trade draws upon a publicly accessible database and digital archive at LiberatedAfricans.org. A quantitative, spatial and chronological visualization of abolition in action, the website memorializes lived experiences of the victims of abolition on micro and macro levels. Results show that there were more than 700,000 individuals captured from the slave trade, ‘liberated’, and forced into periods of indenture according to anti-slave-trade law. This article consolidates the historiography to challenge dominant narratives that British-led efforts were the most voluminous, instead revealing a more complex and multifaceted global phenomenon involving the mass registration of upwards of 200,000 people by name. Digital humanities methodologies facilitate tracking migratory patterns of ‘Liberated Africans’ in diaspora, that is from African regions of departure through documented capture locations in slave trade blockades, judicial processes resulting in ‘liberation’, and settlements of indenture often involving secondary migrations. With the participation of at least eighteen different nations, key findings determine that Portugal and France contributed to upwards of 370,000 ‘Liberated Africans’, surpassing Britain which supplied about a third of global estimates.
ASYNAPSIS3 has diverse dosage-dependent effects on meiotic crossover formation in Brassica napus
Authors: Chu Lei , Zhuang Jixin , Geng Miaowei , Zhang Yashi , Zhu Jing , Zhang Chunyu , Schnittger Arp , Yi Bin , Yang Chao 
Published: July 2024

Abstract
Crossovers create genetic diversity and are required for equal chromosome segregation during meiosis. Crossover number and distribution are highly regulated by different mechanisms that are not yet fully understood, including crossover interference. The chromosome axis is crucial for crossover formation. Here, we explore the function of the axis protein ASYNAPSIS3. To this end, we use the allotetraploid species Brassica napus; due to its polyploid nature, this system allows a fine-grained dissection of the dosage of meiotic regulators. The simultaneous mutation of all 4 ASY3 alleles results in defective synapsis and drastic reduction of crossovers, which is largely rescued by the presence of only one functional ASY3 allele. Crucially, while the number of class I crossovers in mutants with 2 functional ASY3 alleles is comparable to that in wild type, this number is significantly increased in mutants with only one functional ASY3 allele, indicating that reducing ASY3 dosage increases crossover formation. Moreover, the class I crossovers on each bivalent in mutants with 1 functional ASY3 allele follow a random distribution, indicating compromised crossover interference. These results reveal the distinct dosage-dependent effects of ASY3 on crossover formation and provide insights into the role of the chromosome axis in patterning recombination.
Strigolactone-induced degradation of SMXL7 and SMXL8 contributes to gibberellin- and auxin-mediated fiber cell elongation in cotton
Authors: Sun Yaru , Tian Zailong , Zuo Dongyun , Cheng Hailiang , Wang Qiaolian , Zhang Youping , Lv Limin , Song Guoli 
Published: July 2024

Abstract
Cotton (Gossypium) fiber length, a key trait determining fiber yield and quality, is highly regulated by a class of recently identified phytohormones, strigolactones (SLs). However, the underlying molecular mechanisms of SL signaling involved in fiber cell development are largely unknown. Here, we show that the SL signaling repressors MORE AXILLARY GROWTH2-LIKE7 (GhSMXL7) and GhSMXL8 negatively regulate cotton fiber elongation. Specifically, GhSMXL7 and GhSMXL8 inhibit the polyubiquitination and degradation of the gibberellin (GA)-triggered DELLA protein (GhSLR1). Biochemical analysis revealed that GhSMXL7 and GhSMXL8 physically interact with GhSLR1, which interferes with the association of GhSLR1 with the E3 ligase GA INSENSITIVE2 (GhGID2), leading to the repression of GA signal transduction. GhSMXL7 also interacts with the transcription factor GhHOX3, preventing its binding to the promoters of essential fiber elongation regulatory genes. Moreover, both GhSMXL7 and GhSMXL8 directly bind to the promoter regions of the AUXIN RESPONSE FACTOR (ARF) genes GhARF18-10A, GhARF18-10D, and GhARF19-7D to suppress their expression. Cotton plants in which GhARF18-10A, GhARF18-10D, and GhARF19-7D transcript levels had been reduced by virus-induced gene silencing (VIGS) displayed reduced fiber length compared with control plants. Collectively, our findings reveal a mechanism illustrating how SL integrates GA and auxin signaling to coordinately regulate plant cell elongation at the single-cell level.
Jasmonate signaling modulates root growth by suppressing iron accumulation during ammonium stress
Authors: Pandey Anshika , Devi Loitongbam Lorinda , Gupta Shreya , Prasad Priti , Agrwal Kanupriya , Asif Mehar Hasan , Pandey Ajay Kumar , Bandyopadhyay Kaustav , Singh Amar Pal 
Published: July 2024

Abstract
Plants adapt to changing environmental conditions by adjusting their growth physiology. Nitrate (NO3−) and ammonium (NH4+) are the major inorganic nitrogen forms for plant uptake. However, high NH4+ inhibits plant growth, and roots undergo striking changes, such as inhibition of cell expansion and division, leading to reduced root elongation. In this work, we show that high NH4+ modulates nitrogen metabolism and root developmental physiology by inhibiting iron (Fe)-dependent Jasmonate (JA) signaling and response in Arabidopsis (Arabidopsis thaliana). Transcriptomic data suggested that NH4+ availability regulates Fe and JA-responsive genes. High NH4+ levels led to enhanced root Fe accumulation, which impaired nitrogen balance and growth by suppressing JA biosynthesis and signaling response. Integrating pharmacological, physiological, and genetic experiments revealed the involvement of NH4+ and Fe-derived responses in regulating root growth and nitrogen metabolism through modulation of the JA pathway during NH4+ stress. The JA signaling transcription factor MYC2 directly bound the promoter of the NITRATE TRANSPORTER 1.1 (NRT1.1) and repressed it to optimize the NH4+/Fe-JA balance for plant adaptation during NH4+ stress. Our findings illustrate the intricate balance between nutrient and hormone-derived signaling pathways that appear essential for optimizing plant growth by adjusting physiological and metabolic responses during NH4+/Fe stress.
An anthocyanin activation gene underlies the purple central flower pigmentation in wild carrot
Authors: Duan Ao-Qi , Deng Yuan-Jie , Liu Hui , Xu Zhi-Sheng , Xiong Ai-Sheng 
Published: July 2024

Abstract
Many organisms have complex pigmentation patterns. However, how these patterns are formed remains largely unknown. In wild carrot (Daucus carota subsp. carota), which is also known as Queen Anne's lace, one or several purple central flowers occur in white umbels. Here, we investigated the unique central flower pigmentation pattern in wild carrot umbels. Using wild and cultivated carrot (D. carota subsp. sativus L.) accessions, transcriptome analysis, protein interaction, stable transformation, and CRISPR/Cas9-mediated knockout, an anthocyanin-activating R2R3-myeloblastosis (MYB) gene, Purple Central Flower (DcPCF), was identified as the causal gene that triggers only central flowers to possess the purple phenotype. The expression of DcPCF was only detected in tiny central flowers. We propose that the transition from purple to nonpurple flowers in the center of the umbel occurred after 3 separate adverse events: insertion of transposons in the promoter region, premature termination of the coding sequence (caused by a C–T substitution in the open reading frame), and the emergence of unknown anthocyanin suppressors. These 3 events could have occurred either consecutively or independently. The intriguing purple central flower pattern and its underlying mechanism may provide evidence that it is a remnant of ancient conditions of the species, reflecting the original appearance of Umbelliferae (also called Apiaceae) when a single flower was present.
Regional variation in the role of humidity on city-level heat-related mortality
Authors: Guo Qiang , Mistry Malcolm N , Zhou Xudong , Zhao Gang , Kino Kanon , Wen Bo , Yoshimura Kei , Satoh Yusuke , Cvijanovic Ivana , Kim Yoonhee , Ng Chris Fook Sheng , Vicedo-Cabrera Ana M , Armstrong Ben , Urban Aleš , Katsouyanni Klea , Masselot Pierre , Tong Shilu , Sera Francesco , Huber Veronika , Bell Michelle L , Kyselý Jan , Gasparrini Antonio , Hashizume Masahiro , Oki Taikan ,   Multi-Country Multi-City (MCC) Collaborative Research Network, Abrutzky Rosana , Guo Yuming , de Sousa Zanotti Stagliorio Coelho Micheline , Nascimento Saldiva Paulo Hilario , Lavigne Eric , Ortega Nicolás Valdés , Correa Patricia Matus , Kan Haidong , Osorio Samuel , Roye Dominic , Indermitte Ene , Orru Hans , Jaakkola Jouni J K , Ryti Niilo , Pascal Mathilde , Schneider Alexandra , Analitis Antonis , Entezari Alireza , Mayvaneh Fatemeh , Zeka Ariana , Goodman Patrick , de'Donato Francesca , Michelozzi Paola , Alahmad Barrak , De la Cruz Valencia César , Hurtado Diaz Magali , Overcenco Ala , Ameling Caroline , Houthuijs Danny , Rao Shilpa , Carrasco Gabriel , Seposo Xerxes , Madureira Joana , das Neves Pereira da Silva Susana , Holobaca Iulian-Horia , Acquaotta Fiorella , Scovronick Noah , Kim Ho , Lee Whanhee , Tobias Aurelio , Íñiguez Carmen , Forsberg Bertil , Ragettli Martina S , Pan Shih-Chun , Guo Yue Leon , Li Shanshan , Schneider Rochelle , Colistro Valentina , Zanobetti Antonella , Schwartz Joel , Van Dung Do , Ngoc Dang Tran , Honda Yasushi 
Published: July 2024

Abstract
The rising humid heat is regarded as a severe threat to human survivability, but the proper integration of humid heat into heat-health alerts is still being explored. Using state-of-the-art epidemiological and climatological datasets, we examined the association between multiple heat stress indicators (HSIs) and daily human mortality in 739 cities worldwide. Notable differences were observed in the long-term trends and timing of heat events detected by HSIs. Air temperature (Tair) predicts heat-related mortality well in cities with a robust negative Tair-relative humidity correlation (CT-RH). However, in cities with near-zero or weak positive CT-RH, HSIs considering humidity provide enhanced predictive power compared to Tair. Furthermore, the magnitude and timing of heat-related mortality measured by HSIs could differ largely from those associated with Tair in many cities. Our findings provide important insights into specific regions where humans are vulnerable to humid heat and can facilitate the further enhancement of heat-health alert systems.