bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enantiomer-specific analysis of amphetamine in urine, oral fluid and blood
Authors: Bakke Eirin , Nilsen Terland Mariann , Strand Dag Helge , Øiestad Elisabeth Leere , Høiseth Gudrun 
Published: May 2024

Abstract
Illegal amphetamine is usually composed of a racemic mixture of the two enantiomers (S)- and (R)-amphetamine. However, when amphetamine is used in medical treatment, the more potent (S)-amphetamine enantiomer is used. Enantiomer-specific analysis of (S)- and (R)-amphetamine is therefore used to separate legal medical use from illegal recreational use. The aim of the present study was to describe our experience with enantiomer-specific analysis of amphetamine in urine and oral fluid, as well as blood, and examine whether the distribution of the two enantiomers seems to be the same in different matrices. We investigated 1,722 urine samples and 1,977 oral fluid samples from prison inmates, and 652 blood samples from suspected drugged drivers, where prescription of amphetamine was reported. Analyses were performed using ultra high performance liquid chromatography–tandem mass spectrometry (UHPLC–MS-MS). The enantiomer separation was achieved by using a chiral column, and results from the method validation are reported. Samples containing &lt;60% (S)-amphetamine were interpreted as representing illegal use of amphetamine. The distribution of the two enantiomers was compared between different matrices. In urine and oral fluid, the mean amount of (S)-amphetamine was 45.2 and 43.7%, respectively, while in blood, the mean amount of (S)-amphetamine was 45.8%. There was no statistically significant difference in the amount of (S)-amphetamine between urine and oral fluid samples and between urine and blood samples, but the difference was significant in blood compared to oral fluid samples (P &lt; 0.001). Comparison of urine and oral fluid between similar populations indicated that enantiomers of amphetamine can be interpreted in the same way, although marginally higher amounts of (R)-amphetamine may occur in oral fluid. Oral fluid, having several advantages, especially during collection, could be a preferred matrix in testing for illegal amphetamine intake in users of medical amphetamine.
SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 13 (SPL13) together with SPL9 redundantly regulates wax biosynthesis under drought stress
Authors: Huang Haodong , Zheng Minglü , Jenks Matthew A , Yang Pingfang , Zhao Huayan , Lü Shiyou 
Published: May 2024

Abstract
Wax biosynthesis is closely controlled by many regulators under different environmental conditions. We have previously shown that the module miR156–SQUAMOSA PROMOTER BINDING PROTEIN-LIKE9 (SPL9)–DEWAX is involved in the diurnal regulation of wax production; however, it was not determined whether other SPLs are also involved in wax synthesis. Here, we report that SPL13 also regulates drought-induced wax production, by directly and indirectly affecting the expression of the two wax biosynthesis genes ECERIFERUM1 (CER1) and CER4, respectively. In addition, we show that SPL13 together with SPL9 redundantly regulates wax accumulation under both normal and drought stress conditions, and that simultaneous mutation of both genes additively increases cuticle permeability and decreases drought tolerance. However, in contrast to SPL9, SPL13 does not seem to participate in the DEWAX-mediated diurnal regulation of wax production.
Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum
Authors: Gutiérrez-Valencia Juanita , Zervakis Panagiotis-Ioannis , Postel Zoé , Fracassetti Marco , Losvik Aleksandra , Mehrabi Sara , Bunikis Ignas , Soler Lucile , Hughes P William , Désamoré Aurélie , Laenen Benjamin , Abdelaziz Mohamed , Pettersson Olga Vinnere , Arroyo Juan , Slotte Tanja 
Published: May 2024

Abstract
Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility. Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly in Linum trigynum, which is closely related to distylous Linum tenue. Building on a high-quality genome assembly, we show that L. trigynum harbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles in L. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylous Primula and Fagopyrum, L. trigynum harbors no fixed loss-of-function mutations in coding sequences of S-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating the S-linked LtWDR-44 candidate gene for male self-incompatibility and/or anther height could underlie homostyly and self-compatibility in L. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate that L. trigynum is highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative to L. tenue. Our analyses shed light on the loss of distyly in L. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.
PRMT5-mediated arginine methylation of FXR1 is essential for RNA binding in cancer cells
Authors: Vijayakumar Anitha , Majumder Mrinmoyee , Yin Shasha , Brobbey Charles , Karam Joseph , Howley Breege , Howe Philip H , Berto Stefano , Madan Lalima K , Gan Wenjian , Palanisamy Viswanathan 
Published: May 2024

Abstract
Emerging evidence indicates that arginine methylation promotes the stability of arginine-glycine-rich (RGG) motif-containing RNA-binding proteins (RBPs) and regulates gene expression. Here, we report that post-translational modification of FXR1 enhances the binding with mRNAs and is involved in cancer cell growth and proliferation. Independent point mutations in arginine residues of FXR1’s nuclear export signal (R386 and R388) and RGG (R453, R455 and R459) domains prevent it from binding to RNAs that form G-quadruplex (G4) RNA structures. Disruption of G4-RNA structures by lithium chloride failed to bind with FXR1, indicating its preference for G4-RNA structure containing mRNAs. Furthermore, loss-of-function of PRMT5 inhibited FXR1 methylation both in vivo and in vitro, affecting FXR1 protein stability, inhibiting RNA-binding activity and cancer cell growth and proliferation. Finally, the enhanced crosslinking and immunoprecipitation (eCLIP) analyses reveal that FXR1 binds with the G4-enriched mRNA targets such as AHNAK, MAP1B, AHNAK2, HUWE1, DYNC1H1 and UBR4 and controls its mRNA expression in cancer cells. Our findings suggest that PRMT5-mediated FXR1 methylation is required for RNA/G4-RNA binding, which promotes gene expression in cancer cells. Thus, FXR1’s structural characteristics and affinity for RNAs preferentially G4 regions provide new insights into the molecular mechanism of FXR1 in oral cancer cells.
LipidSig 2.0: integrating lipid characteristic insights into advanced lipidomics data analysis
Authors: Liu Chia-Hsin , Shen Pei-Chun , Lin Wen-Jen , Liu Hsiu-Cheng , Tsai Meng-Hsin , Huang Tzu-Ya , Chen I-Chieh , Lai Yo-Liang , Wang Yu-De , Hung Mien-Chie , Cheng Wei-Chung 
Published: May 2024

Abstract
In the field of lipidomics, where the complexity of lipid structures and functions presents significant analytical challenges, LipidSig stands out as the first web-based platform providing integrated, comprehensive analysis for efficient data mining of lipidomic datasets. The upgraded LipidSig 2.0 (https://lipidsig.bioinfomics.org/) simplifies the process and empowers researchers to decipher the complex nature of lipids and link lipidomic data to specific characteristics and biological contexts. This tool markedly enhances the efficiency and depth of lipidomic research by autonomously identifying lipid species and assigning 29 comprehensive characteristics upon data entry. LipidSig 2.0 accommodates 24 data processing methods, streamlining diverse lipidomic datasets. The tool's expertise in automating intricate analytical processes, including data preprocessing, lipid ID annotation, differential expression, enrichment analysis, and network analysis, allows researchers to profoundly investigate lipid properties and their biological implications. Additional innovative features, such as the ‘Network’ function, offer a system biology perspective on lipid interactions, and the ‘Multiple Group’ analysis aids in examining complex experimental designs. With its comprehensive suite of features for analyzing and visualizing lipid properties, LipidSig 2.0 positions itself as an indispensable tool for advanced lipidomics research, paving the way for new insights into the role of lipids in cellular processes and disease development.
SCTC: inference of developmental potential from single-cell transcriptional complexity
Authors: Lin Hai , Hu Huan , Feng Zhen , Xu Fei , Lyu Jie , Li Xiang , Liu Liyu , Yang Gen , Shuai Jianwei 
Published: May 2024

AbstractInferring the developmental potential of single cells from scRNA-Seq data and reconstructing the pseudo-temporal path of cell development are fundamental but challenging tasks in single-cell analysis. Although single-cell transcriptional diversity (SCTD) measured by the number of expressed genes per cell has been widely used as a hallmark of developmental potential, it may lead to incorrect estimation of differentiation states in some cases where gene expression does not decrease monotonously during the development process. In this study, we propose a novel metric called single-cell transcriptional complexity (SCTC), which draws on insights from the economic complexity theory and takes into account the sophisticated structure information of scRNA-Seq count matrix. We show that SCTC characterizes developmental potential more accurately than SCTD, especially in the early stages of development where cells typically have lower diversity but higher complexity than those in the later stages. Based on the SCTC, we provide an unsupervised method for accurate, robust, and transferable inference of single-cell pseudotime. Our findings suggest that the complexity emerging from the interplay between cells and genes determines the developmental potential, providing new insights into the understanding of biological development from the perspective of complexity theory.
IsoVis – a webserver for visualization and annotation of alternative RNA isoforms
Authors: Wan Ching Yin , Davis Jack , Chauhan Manveer , Gleeson Josie , Prawer Yair D J , De Paoli-Iseppi Ricardo , Wells Christine A , Choi Jarny , Clark Michael B 
Published: May 2024

Abstract
Genes commonly express multiple RNA products (RNA isoforms), which differ in exonic content and can have different functions. Making sense of the plethora of known and novel RNA isoforms being identified by transcriptomic approaches requires a user-friendly way to visualize gene isoforms and how they differ in exonic content, expression levels and potential functions. Here we introduce IsoVis, a freely available webserver that accepts user-supplied transcriptomic data and visualizes the expressed isoforms in a clear, intuitive manner. IsoVis contains numerous features, including the ability to visualize all RNA isoforms of a gene and their expression levels; the annotation of known isoforms from external databases; mapping of protein domains and features to exons, allowing changes to protein sequence and function between isoforms to be established; and extensive species compatibility. Datasets visualised on IsoVis remain private to the user, allowing analysis of sensitive data. IsoVis visualisations can be downloaded to create publication-ready figures. The IsoVis webserver enables researchers to perform isoform analyses without requiring programming skills, is free to use, and available at https://isomix.org/isovis/.
A bisulfite-assisted and ligation-based qPCR amplification technology for locus-specific pseudouridine detection at base resolution
Authors: Fang Xin , Zhao Ruiqi , Wang Yafen , Sun Mei , Xu Jin , Long Shengrong , Mo Jing , Liu Hudan , Li Xiang , Wang Fang , Zhou Xiang , Weng Xiaocheng 
Published: May 2024

Abstract
Over 150 types of chemical modifications have been identified in RNA to date, with pseudouridine (Ψ) being one of the most prevalent modifications in RNA. Ψ plays vital roles in various biological processes, and precise, base-resolution detection methods are fundamental for deep analysis of its distribution and function. In this study, we introduced a novel base-resolution Ψ detection method named pseU-TRACE. pseU-TRACE relied on the fact that RNA containing Ψ underwent a base deletion after treatment of bisulfite (BS) during reverse transcription, which enabled efficient ligation of two probes complementary to the cDNA sequence on either side of the Ψ site and successful amplification in subsequent real-time quantitative PCR (qPCR), thereby achieving selective and accurate Ψ detection. Our method accurately and sensitively detected several known Ψ sites in 28S, 18S, 5.8S, and even mRNA. Moreover, pseU-TRACE could be employed to measure the Ψ fraction in RNA and explore the Ψ metabolism of different pseudouridine synthases (PUSs), providing valuable insights into the function of Ψ. Overall, pseU-TRACE represents a reliable, time-efficient and sensitive Ψ detection method.
Identifying Ultrahigh-Temperature Metamorphism in Basic Granulites
Authors: Wang Bin , Wei Chunjing 
Published: May 2024

Abstract
Identifying ultrahigh-temperature (UHT) metamorphism in basic granulites is challenged by the uncertainty of peak temperatures. Consequently, available temperature indicators are desiderated all along. In this study, we investigated low-pressure basic granulites from the Daqingshan, North China Craton and determined a UHT peak condition around 1000–1050 °C and 0.8–0.9 GPa. This peak condition was constrained by combining the AlT of 0.10–0.12 in clinopyroxene (Cpx) cores, maximum Ti of 0.36–0.38 in amphibole (Amp) cores and anorthite proportion (XAn) of 0.67–0.70 and 0.61–0.63 in plagioclase (Pl) cores/mantles analyzed in two selected samples. The P–T records obtained from several thermobarometers related to amphibole, plagioclase and/or clinopyroxene were also verified to be in agreement with the phase equilibria modeling results. Notably, AlT-in-Cpx is assessed to be a reliable temperature indicator in basic granulites with the Opx–Cpx–Pl–Amp assemblage, albeit could be influenced by bulk-rock compositions in some extent and has a temperature standard error of ~70 °C. Besides, the post-peak evolution was dominated by near-isobaric cooling at 1.94–1.93 Ga, to a fluid-absent solidus as high as ~940 °C. During the cooling process, plagioclase and amphibole grew together at the expense of Al-rich clinopyroxene and unsegregated melts, accompanied by the (rimward) decrease of AlT-in-Cpx, Ti-in-Amp and XAn-in-Pl. A pre-peak process is inferred to be decompressional heating. The UHT metamorphism in Daqingshan is interpreted to result from asthenosphere upwelling and thermal advection from regional mantle-derived magmatism during post-orogenic extension, in a newly developed back-arc-related environment.
Chloroplast biogenesis involves spatial coordination of nuclear and organellar gene expression in Chlamydomonas
Authors: Sun Yi , Bakhtiari Shiva , Valente-Paterno Melissa , Wu Yanxia , Nishimura Yoshiki , Shen Weike , Law Christopher , Dhaliwal James , Dai Daniel , Bui Khanh Huy , Zerges William 
Published: May 2024

Abstract
The localization of translation can direct the polypeptide product to the proper intracellular compartment. Our results reveal translation by cytosolic ribosomes on a domain of the chloroplast envelope in the unicellular green alga Chlamydomonas (Chlamydomonas reinhardtii). We show that this envelope domain of isolated chloroplasts retains translationally active ribosomes and mRNAs encoding chloroplast proteins. This domain is aligned with localized translation by chloroplast ribosomes in the translation zone, a chloroplast compartment where photosystem subunits encoded by the plastid genome are synthesized and assembled. Roles of localized translation in directing newly synthesized subunits of photosynthesis complexes to discrete regions within the chloroplast for their assembly are suggested by differences in localization on the chloroplast of mRNAs encoding either subunit of the light-harvesting complex II or the small subunit of Rubisco. Transcription of the chloroplast genome is spatially coordinated with translation, as revealed by our demonstration of a subpopulation of transcriptionally active chloroplast nucleoids at the translation zone. We propose that the expression of chloroplast proteins by the nuclear-cytosolic and organellar genetic systems is organized in spatially aligned subcompartments of the cytoplasm and chloroplast to facilitate the biogenesis of the photosynthetic complexes.
Nanobody-based CAR NK cells for possible immunotherapy of MICA+ tumors
Authors: Verhaar Elisha R , van Keizerswaard Willemijn J C , Knoflook Anouk , Balligand Thomas , Ploegh Hidde L 
Published: May 2024

Abstract
The glycoproteins MICA and MICB are upregulated on the surface of cells undergoing stress, for instance due to (viral) infection or malignant transformation. MICA/B are the ligands for the activating receptor NKG2D, found on cytotoxic immune cells like NK cells, CD8+ T cells, and γδ T cells. Upon engagement of NKG2D, these cells are activated to eradicate the MICA/B-positive targets, assisted by the secretion of cytokines. Nanobodies, or VHHs, are derived from the variable regions of camelid heavy-chain only immunoglobulins. Nanobodies are characterized by their small size, ease of production, stability, and specificity of recognition. We generated nanobodies that recognize membrane-bound MICA with high affinity. Here, we use these nanobodies as building blocks for a chimeric antigen receptor (CAR) to establish VHH-based CAR NK cells. These anti-MICA nanobody-based CAR NK cells recognize and selectively kill MICA-positive tumor cells in vitro and in vivo. We track localization of the VHH-based CAR NK cells to MICA-positive lung metastases by immuno-positron emission tomography imaging.
Assessment of the effect of cannabis use before partnered sex on women with and without orgasm difficulty
Authors: Mulvehill Suzanne , Tishler Jordan 
Published: May 2024

AbstractBackgroundUp to 41% of women face challenges achieving orgasm, a statistic unchanged for 50 years.AimTo evaluate the effect of cannabis use before partnered sex on women with and without difficulty achieving orgasm.MethodsThis observational study evaluated responses from female study participants relating to their demographics, sexual activities, mental well-being, cannabis usage, and orgasm-related questions from the Female Sexual Function Index (FSFI).OutcomesOutcomes included orgasm frequency, difficulty, and satisfaction related to cannabis use or lack of use before partnered sex, largely based on the FSFI orgasm subscale.ResultsOf the 1037 survey responses, 410 were valid and complete. Twenty-three surveys (5.6% returned) were excluded due to failure to meet the study’s criteria. Of the valid surveys, most women (52%, n = 202) reported difficulty achieving orgasm during sexual activity with a partner. These women were primarily between 25 and 34 years of age (45%, n = 91); 75% identified their race as White (n = 152/202); 52% (n = 105) identified as LGBTQI+ (lesbian, gay, bisexual, transgender, queer/questioning, intersex, or other); and 82% (n = 165) were married or in a relationship. Among participants who experienced challenges in achieving orgasm, 72.8% (n = 147, P &lt; .001) reported that cannabis use before partnered sex increased orgasm frequency, 67% stated that it improved orgasm satisfaction (n = 136, P &lt; .001), and 71% indicated that cannabis use made orgasm easier (n = 143, P &lt; .001). The frequency of cannabis use before partnered sex correlated with increased orgasm frequency for women who experienced difficulties achieving orgasm (n = 202, P &lt; .001). The reasons for cannabis use before partnered sex resulted in a more positive orgasm response (n = 202, P = .22).Clinical ImplicationsCannabis may be a treatment for women with difficulty achieving orgasm during partnered sex.Strengths and LimitationsThe researchers examined the challenge of achieving orgasm and considered the covariates reported in the literature, including the FSFI orgasm subscale. The findings may not be generalizable to women who rarely or never use cannabis before sex, women who have never experienced an orgasm, or women who do not have female genitalia. Additionally, the specific type of cannabis used, its chemical composition, the quantity used, and whether or not the partner used cannabis were not assessed in this study.ConclusionCannabis-related treatment appears to provide benefit to women who have female orgasm difficulties or dysfunction.
Resisting and Reclaiming: Squatting as Contentious Urban Politics in the U.S.
Authors: Herbert Claire W , Ricketts Amanda V 
Published: May 2024

Abstract
Squatting as contentious politics has been well studied globally, expanding knowledge of how everyday people resist injustices, strive to remake cities, and respond to local/regional conditions. These histories and contemporary struggles have largely been overlooked in the U.S. This article uses qualitative data to compare three recent cases of organized housing occupations in Detroit (2011), Oakland (2019), and Philadelphia (2020) by mothers of color with their children, to better understand how this form of global urban politics manifests in the U.S. Using this comparison, we identify important dimensions that have shaped these three cases of contentious politics and their outcomes, including differences in goals, tactics, and socio-spatial context. We also uncover the diagnostic and prognostic frames reflected in each case: despite common legal violations, each case purposefully diagnoses locally-rooted housing problems and suggests different property-relations as solutions. We find that each case varies in terms of what kind of property squatters target, how these spaces reflect broader structural problems in the U.S. housing market, and what kind of property-relations they envision with these occupations. In turn, our findings also advance understanding of this global urban politics by showing how squatting efforts may dovetail with place-based legacies, such as racial segregation and settler colonialism in the U.S. Researchers have long attended to organized housing struggles in their varied manifestations, but by foregrounding resistance to and reclaiming of property by squatters, we draw out understudied problems and possibilities related to land and housing occupations that are subverted within broader housing studies.