bluuebunny/crossref_metadata_2025_split huggingface dataset:
A universal molecular control for DNA, mRNA and protein expression
Authors: Gunter Helen M. , Youlten Scott E. , Reis Andre L. M. , McCubbin Tim , Madala Bindu Swapna , Wong Ted , Stevanovski Igor , Cipponi Arcadi , Deveson Ira W. , Santini Nadia S. , Kummerfeld Sarah , Croucher Peter I. , Marcellin Esteban , Mercer Tim R. 
Published: March 2024

AbstractThe expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides a universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.
Light-driven polymer recycling to monomers and small molecules
Authors: Wimberger Laura , Ng Gervase , Boyer Cyrille 
Published: March 2024

AbstractOnly a small proportion of global plastic waste is recycled, of which most is mechanically recycled into lower quality materials. The alternative, chemical recycling, enables renewed production of pristine materials, but generally comes at a high energy cost, particularly for processes like pyrolysis. This review focuses on light-driven approaches for chemically recycling and upcycling plastic waste, with emphasis on reduced energy consumption and selective transformations not achievable with heat-driven methods. We focus on challenging to recycle backbone structures composed of mainly C‒C bonds, which lack functional groups i.e., esters or amides, that facilitate chemical recycling e.g., by solvolysis. We discuss the use of light, either in conjunction with heat to drive depolymerization to monomers or via photocatalysis to transform polymers into valuable small molecules. The structural prerequisites for these approaches are outlined, highlighting their advantages as well as limitations. We conclude with an outlook, addressing key challenges, opportunities, and provide guidelines for future photocatalyst (PC) development.
Structure of antiviral drug bulevirtide bound to hepatitis B and D virus receptor protein NTCP
Authors: Liu Hongtao , Zakrzewicz Dariusz , Nosol Kamil , Irobalieva Rossitza N. , Mukherjee Somnath , Bang-Sørensen Rose , Goldmann Nora , Kunz Sebastian , Rossi Lorenzo , Kossiakoff Anthony A. , Urban Stephan , Glebe Dieter , Geyer Joachim , Locher Kaspar P. 
Published: March 2024

AbstractCellular entry of the hepatitis B and D viruses (HBV/HDV) requires binding of the viral surface polypeptide preS1 to the hepatobiliary transporter Na+-taurocholate co-transporting polypeptide (NTCP). This interaction can be blocked by bulevirtide (BLV, formerly Myrcludex B), a preS1 derivative and approved drug for treating HDV infection. Here, to elucidate the basis of this inhibitory function, we determined a cryo-EM structure of BLV-bound human NTCP. BLV forms two domains, a plug lodged in the bile salt transport tunnel of NTCP and a string that covers the receptor’s extracellular surface. The N-terminally attached myristoyl group of BLV interacts with the lipid-exposed surface of NTCP. Our structure reveals how BLV inhibits bile salt transport, rationalizes NTCP mutations that decrease the risk of HBV/HDV infection, and provides a basis for understanding the host specificity of HBV/HDV. Our results provide opportunities for structure-guided development of inhibitors that target HBV/HDV docking to NTCP.
Allele-specific transcriptional effects of subclonal copy number alterations enable genotype-phenotype mapping in cancer cells
Authors: Shi Hongyu , Williams Marc J. , Satas Gryte , Weiner Adam C. , McPherson Andrew , Shah Sohrab P. 
Published: March 2024

AbstractSubclonal copy number alterations are a prevalent feature in tumors with high chromosomal instability and result in heterogeneous cancer cell populations with distinct phenotypes. However, the extent to which subclonal copy number alterations contribute to clone-specific phenotypes remains poorly understood. We develop TreeAlign, which computationally integrates independently sampled single-cell DNA and RNA sequencing data from the same cell population. TreeAlign accurately encodes dosage effects from subclonal copy number alterations, the impact of allelic imbalance on allele-specific transcription, and obviates the need to define genotypic clones from a phylogeny a priori, leading to highly granular definitions of clones with distinct expression programs. These improvements enable clone-clone gene expression comparisons with higher resolution and identification of expression programs that are genomically independent. Our approach sets the stage for dissecting the relative contribution of fixed genomic alterations and dynamic epigenetic processes on gene expression programs in cancer.
Sub-8 nm networked cage nanofilm with tunable nanofluidic channels for adaptive sieving
Authors: Liu Si-Hua , Zhou Jun-Hao , Wu Chunrui , Zhang Peng , Cao Xingzhong , Sun Jian-Ke 
Published: March 2024

AbstractBiological cell membrane featuring smart mass-transport channels and sub-10 nm thickness was viewed as the benchmark inspiring the design of separation membranes; however, constructing highly connective and adaptive pore channels over large-area membranes less than 10 nm in thickness is still a huge challenge. Here, we report the design and fabrication of sub-8 nm networked cage nanofilms that comprise of tunable, responsive organic cage-based water channels via a free-interface-confined self-assembly and crosslinking strategy. These cage-bearing composite membranes display outstanding water permeability at the 10−5 cm2 s−1 scale, which is 1–2 orders of magnitude higher than that of traditional polymeric membranes. Furthermore, the channel microenvironments including hydrophilicity and steric hindrance can be manipulated by a simple anion exchange strategy. In particular, through ionically associating light-responsive anions to cage windows, such ‘smart’ membrane can even perform graded molecular sieving. The emergence of these networked cage-nanofilms provides an avenue for developing bio-inspired ultrathin membranes toward smart separation.
Structural basis of ligand recognition and design of antihistamines targeting histamine H4 receptor
Authors: Xia Ruixue , Shi Shuang , Xu Zhenmei , Vischer Henry F. , Windhorst Albert D. , Qian Yu , Duan Yaning , Liang Jiale , Chen Kai , Zhang Anqi , Guo Changyou , Leurs Rob , He Yuanzheng 
Published: March 2024

AbstractThe histamine H4 receptor (H4R) plays key role in immune cell function and is a highly valued target for treating allergic and inflammatory diseases. However, structural information of H4R remains elusive. Here, we report four cryo-EM structures of H4R/Gi complexes, with either histamine or synthetic agonists clobenpropit, VUF6884 and clozapine bound. Combined with mutagenesis, ligand binding and functional assays, the structural data reveal a distinct ligand binding mode where D943.32 and a π-π network determine the orientation of the positively charged group of ligands, while E1825.46, located at the opposite end of the ligand binding pocket, plays a key role in regulating receptor activity. The structural insight into H4R ligand binding allows us to identify mutants at E1825.46 for which the agonist clobenpropit acts as an inverse agonist and to correctly predict inverse agonism of a closely related analog with nanomolar potency. Together with the findings regarding receptor activation and Gi engagement, we establish a framework for understanding H4R signaling and provide a rational basis for designing novel antihistamines targeting H4R.
Lactobacillus rhamnosus GG ameliorates hyperuricemia in a novel model
Authors: Fu Yang , Chen Yong-Song , Xia Dai-Yang , Luo Xiao-Dan , Luo Hao-Tong , Pan Jie , Ma Wei-Qing , Li Jin-Ze , Mo Qian-Yuan , Tu Qiang , Li Meng-Meng , Zhao Yue , Li Yu , Huang Yi-Teng , Chen Zhi-Xian , Li Zhen-Jun , Bernard Lukuyu , Dione Michel , Zhang You-Ming , Miao Kai , Chen Jian-Ying , Zhu Shan-Shan , Ren Jie , Zhou Ling-Juan , Jiang Xian-Zhi , Chen Juan , Lin Zhen-Ping , Chen Jun-Peng , Ye Hui , Cao Qing-Yun , Zhu Yong-Wen , Yang Lin , Wang Xue , Wang Wen-Ce 
Published: March 2024

AbstractHyperuricemia (HUA) is a metabolic syndrome caused by abnormal purine metabolism. Although recent studies have noted a relationship between the gut microbiota and gout, whether the microbiota could ameliorate HUA-associated systemic purine metabolism remains unclear. In this study, we constructed a novel model of HUA in geese and investigated the mechanism by which Lactobacillus rhamnosus GG (LGG) could have beneficial effects on HUA. The administration of antibiotics and fecal microbiota transplantation (FMT) experiments were used in this HUA goose model. The effects of LGG and its metabolites on HUA were evaluated in vivo and in vitro. Heterogeneous expression and gene knockout of LGG revealed the mechanism of LGG. Multi-omics analysis revealed that the Lactobacillus genus is associated with changes in purine metabolism in HUA. This study showed that LGG and its metabolites could alleviate HUA through the gut-liver-kidney axis. Whole-genome analysis, heterogeneous expression, and gene knockout of LGG enzymes ABC-type multidrug transport system (ABCT), inosine-uridine nucleoside N-ribohydrolase (iunH), and xanthine permease (pbuX) demonstrated the function of nucleoside degradation in LGG. Multi-omics and a correlation analysis in HUA patients and this goose model revealed that a serum proline deficiency, as well as changes in Collinsella and Lactobacillus, may be associated with the occurrence of HUA. Our findings demonstrated the potential of a goose model of diet-induced HUA, and LGG and proline could be promising therapies for HUA.
Levels of evidence for human system risk evaluation
Authors: Ward Jessica , Reynolds Robert J. , Connell Erin , Anton Wilma , Kabeel Avalon , Charvat Jacqueline M. , Nartey Nicholas , Marotta Kristina , Abukmail Ahmed , Buckland Dan M. , Van Baalen Mary , Antonsen Erik 
Published: March 2024

AbstractNASA uses a continuous risk management process to seek out new knowledge of spaceflight-induced risk to human health and performance. The evidence base that informs the risk assessments in this domain is constantly changing as more information is gleaned from a continuous human presence in space and from ongoing research. However, the limitations of this evidence are difficult to characterize because fewer than 700 humans have ever flown in space, and information comes from a variety of sources that span disciplines, including engineering, medicine, food and nutrition, and many other life sciences. The Human System Risk Board (HSRB) at NASA is responsible for assessing risk to astronauts and communicating this risk to agency decision-makers. A critical part of that communication is conveying the uncertainty regarding the understanding of the changes that spaceflight induces in human processes and the complex interactions between humans and the spacecraft. Although the strength of evidence grades is common in the academic literature, these scores are often not useful for the problems of human spaceflight. The HSRB continues to update the processes used to report the levels of evidence. This paper describes recent updates to the methods used to assign the level of evidence scores to the official risk postures and to the causal diagrams used by the HSRB.
Open-top multisample dual-view light-sheet microscope for live imaging of large multicellular systems
Authors: Moos Franziska , Suppinger Simon , de Medeiros Gustavo , Oost Koen Cornelius , Boni Andrea , Rémy Camille , Weevers Sera Lotte , Tsiairis Charisios , Strnad Petr , Liberali Prisca 
Published: March 2024

AbstractMulticellular systems grow over the course of weeks from single cells to tissues or even full organisms, making live imaging challenging. To bridge spatiotemporal scales, we present an open-top dual-view and dual-illumination light-sheet microscope dedicated to live imaging of large specimens at single-cell resolution. The configuration of objectives together with a customizable multiwell mounting system combines dual view with high-throughput multiposition imaging. We use this microscope to image a wide variety of samples and highlight its capabilities to gain quantitative single-cell information in large specimens such as mature intestinal organoids and gastruloids.
Global spatial dataset of mangrove genus distribution in seaward and riverine margins
Authors: Twomey Alice , Lovelock Catherine 
Published: March 2024

AbstractMangroves are nature-based solutions for coastal protection however their ability to attenuate waves and stabilise and accrete sediment varies with their species-specific architecture and frontal area. Hydrodynamic models are typically used to predict and assess the protection afforded by mangroves, but without species or genus distribution information, the results can be significantly different from reality. Data on the frontal genus of mangroves exposed to waves and tides can provide information that can be used in hydrodynamic models to more accurately forecast the protection benefit provided by mangroves. Globally, frontal species were identified from existing mangrove zonation diagrams to create a global mangrove genus distribution map. This dataset aims to improve the accuracy of hydrodynamic models. Data may be of interest to researchers in coastal engineering, marine science, wetland ecology and blue carbon.
The Arctic Plant Aboveground Biomass Synthesis Dataset
Authors: Berner Logan T. , Orndahl Kathleen M. , Rose Melissa , Tamstorf Mikkel , Arndal Marie F. , Alexander Heather D. , Humphreys Elyn R. , Loranty Michael M. , Ludwig Sarah M. , Nyman Johanna , Juutinen Sari , Aurela Mika , Happonen Konsta , Mikola Juha , Mack Michelle C. , Vankoughnett Mathew R. , Iversen Colleen M. , Salmon Verity G. , Yang Dedi , Kumar Jitendra , Grogan Paul , Danby Ryan K. , Scott Neal A. , Olofsson Johan , Siewert Matthias B. , Deschamps Lucas , Lévesque Esther , Maire Vincent , Morneault Amélie , Gauthier Gilles , Gignac Charles , Boudreau Stéphane , Gaspard Anna , Kholodov Alexander , Bret-Harte M. Syndonia , Greaves Heather E. , Walker Donald , Gregory Fiona M. , Michelsen Anders , Kumpula Timo , Villoslada Miguel , Ylänne Henni , Luoto Miska , Virtanen Tarmo , Forbes Bruce C. , Hölzel Norbert , Epstein Howard , Heim Ramona J. , Bunn Andrew , Holmes Robert M. , Hung Jacqueline K. Y. , Natali Susan M. , Virkkala Anna-Maria , Goetz Scott J. 
Published: March 2024

AbstractPlant biomass is a fundamental ecosystem attribute that is sensitive to rapid climatic changes occurring in the Arctic. Nevertheless, measuring plant biomass in the Arctic is logistically challenging and resource intensive. Lack of accessible field data hinders efforts to understand the amount, composition, distribution, and changes in plant biomass in these northern ecosystems. Here, we present The Arctic plant aboveground biomass synthesis dataset, which includes field measurements of lichen, bryophyte, herb, shrub, and/or tree aboveground biomass (g m−2) on 2,327 sample plots from 636 field sites in seven countries. We created the synthesis dataset by assembling and harmonizing 32 individual datasets. Aboveground biomass was primarily quantified by harvesting sample plots during mid- to late-summer, though tree and often tall shrub biomass were quantified using surveys and allometric models. Each biomass measurement is associated with metadata including sample date, location, method, data source, and other information. This unique dataset can be leveraged to monitor, map, and model plant biomass across the rapidly warming Arctic.
A longitudinal study on the effect of labor values on benign/malicious envy: the mindfulness reperceiving model
Authors: Zhang Qingji , Chao Xiaomei , Tu Yeman , Yao Shunyu , Quan Peng 
Published: March 2024

AbstractThis study investigates the relationship between labor values and two forms of envy—benign and malicious—as well as the potential mediating role of mindfulness using a mindfulness reperceiving model. Two thousand three hundred sixty three Chinese teenagers participated in a longitudinal study over an eight-month period, completing questionnaires measuring labor values, benign envy, malicious envy, and mindfulness. The cross-sectional data showed that labor values had an immediate negative effect on malicious envy, with mindfulness partially mediating this relationship. Additionally, labor values had an immediate positive effect on benign envy, but mindfulness did not mediate this relationship. Longitudinal data analysis revealed that the delayed effect of labor values on later benign/malicious envy was similar to its immediate effect. However, mindfulness only played a mediating role in the relationship between labor values and later malicious envy. Cross-gender stability was found in both the immediate effect model and the delayed effect model. Overall, this study sheds light on the influence of labor values on the development of social emotions and the potential mediating role of mindfulness in the Chinese cultural context.
Changes in landscape and climate in Mexico and Texas reveal small effects on migratory habitat of monarch butterflies (Danaus plexippus)
Authors: Diffendorfer Jay E. , Botello Francisco , Drummond Mark A. , Ancona Zach H. , Corro Lucila M. , Thogmartin Wayne E. , Ibsen Peter C. , Moreno-Sanchez Rafael , Lukens Laura , Sánchez-Cordero Victor 
Published: March 2024

AbstractThe decline of the iconic monarch butterfly (Danaus plexippus) in North America has motivated research on the impacts of land use and land cover (LULC) change and climate variability on monarch habitat and population dynamics. We investigated spring and fall trends in LULC, milkweed and nectar resources over a 20-year period, and ~ 30 years of climate variables in Mexico and Texas, U.S. This region supports spring breeding, and spring and fall migration during the annual life cycle of the monarch. We estimated a − 2.9% decline in milkweed in Texas, but little to no change in Mexico. Fall and spring nectar resources declined < 1% in both study extents. Vegetation greenness increased in the fall and spring in Mexico while the other climate variables did not change in both Mexico and Texas. Monarch habitat in Mexico and Texas appears relatively more intact than in the midwestern, agricultural landscapes of the U.S. Given the relatively modest observed changes in nectar and milkweed, the relatively stable climate conditions, and increased vegetation greenness in Mexico, it seems unlikely that habitat loss (quantity or quality) in Mexico and Texas has caused large declines in population size or survival during migration.
The tale of an endemic shrimp’s exceptional osmoregulation and the ancient Athalassic mangrove oasis
Authors: Giraldes Bruno W. , Boughattas Sonia , Benslimane Fatiha M. , Althani Asmaa A. , Schubart Christoph D. , Huber Carla S. R. , Utz Laura R. P. , Al-Khayat Jassim A. A. , Sadooni Fadhil N. , Amado Enelise M. 
Published: March 2024

AbstractThe hyperarid mangrove in the Middle East is characterised by the absence of rivers or freshwater inputs and is one of the most extreme settings of this ecosystem on Earth. Endemic to Qatar’s hyperarid mangroves, a Palaemon shrimp is uniquely confined to a sole mangrove site in the Arabian Gulf. Within these mangrove channels, we unveiled brine groundwater sources exceeding 70 ppt salinity, contrasting the local marine standard of 42 ppt. Concurrently, a mysid species typically linked to salt pans and groundwater coexists. Stable isotopic analysis implied the existence of a predator–prey dynamic between this mysid species and the studied shrimp. Then, investigating the endemic shrimp’s adaptation to extreme salinity, we conducted osmolarity experiments and phylogenetic studies. Our findings demonstrate that this shrimp transitions from hypo- to hyper-osmoregulation, tolerating salinities from 18 to 68 ppt—an unprecedented osmoregulatory capacity among caridean shrimps. This speciation pattern likely arises from the species osmolarity adaptation, as suggested for other Palaemon congeners. Phylogenetic analysis of the studied Palaemon, along with the mangrove’s geological history, suggests a profound evolutionary interplay between the ecosystem and the shrimp since the Eocene. This study proposes the hyperarid mangrove enclave as an Athalassic mangrove oasis—a distinctive, isolated ecosystem within the desert landscape.
GeSe ovonic threshold switch: the impact of functional layer thickness and device size
Authors: Zhao Jiayi , Zhao Zihao , Song Zhitang , Zhu Min 
Published: March 2024

AbstractThree-dimensional phase change memory (3D PCM), possessing fast-speed, high-density and nonvolatility, has been successfully commercialized as storage class memory. A complete PCM device is composed of a memory cell and an associated ovonic threshold switch (OTS) device, which effectively resolves the leakage current issue in the crossbar array. The OTS materials are chalcogenide glasses consisting of chalcogens such as Te, Se and S as central elements, represented by GeTe6, GeSe and GeS. Among them, GeSe-based OTS materials are widely utilized in commercial 3D PCM, their scalability, however, has not been thoroughly investigated. Here, we explore the miniaturization of GeSe OTS selector, including functional layer thickness scalability and device size scalability. The threshold switching voltage of the GeSe OTS device almost lineally decreases with the thinning of the thickness, whereas it hardly changes with the device size. This indicates that the threshold switching behavior is triggered by the electric field, and the threshold switching field of the GeSe OTS selector is approximately 105 V/μm, regardless of the change in film thickness or device size. Systematically analyzing the threshold switching field of Ge–S and Ge–Te OTSs, we find that the threshold switching field of the OTS device is larger than 75 V/μm, significantly higher than PCM devices (8.1–56 V/μm), such as traditional Ge2Sb2Te5, Ag–In–Sb–Te, etc. Moreover, the required electric field is highly correlated with the optical bandgap. Our findings not only serve to optimize GeSe-based OTS device, but also may pave the approach for exploring OTS materials in chalcogenide alloys.