bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ice shelf basal channel shape determines channelized ice-ocean interactions
Authors: Cheng Chen , Jenkins Adrian , Holland Paul R. , Wang Zhaomin , Dong Jihai , Liu Chengyan 
Published: April 2024

AbstractGrowing evidence has confirmed the critical role played by basal channels beneath Antarctic ice shelves in both ice shelf stability and freshwater input to the surrounding ocean. Here we show, using a 3D ice shelf-ocean boundary current model, that deeper basal channels can lead to a significant amplification in channelized basal melting, meltwater channeling, and warming and salinization of the channel flow. All of these channelized quantities are also modulated by channel width, with the level of modulation determined by channel height. The explicit quantification of channelized basal melting and the meltwater transport in terms of channel cross-sectional shape is potentially beneficial for the evaluation of ice shelf mass balance and meltwater contribution to the nearshore oceanography. Complicated topographically controlled circulations are revealed to be responsible for the unique thermohaline structure inside deep channels. Our study emphasizes the need for improvement in observations of evolving basal channels and the hydrography inside them, as well as adjacent to the ice front where channelized meltwater emerges.
Cryo-EM structures of prokaryotic ligand-gated ion channel GLIC provide insights into gating in a lipid environment
Authors: Bharambe Nikhil , Li Zhuowen , Seiferth David , Balakrishna Asha Manikkoth , Biggin Philip C. , Basak Sandip 
Published: April 2024

AbstractGLIC, a proton-activated prokaryotic ligand-gated ion channel, served as a model system for understanding the eukaryotic counterparts due to their structural and functional similarities. Despite extensive studies conducted on GLIC, the molecular mechanism of channel gating in the lipid environment requires further investigation. Here, we present the cryo-EM structures of nanodisc-reconstituted GLIC at neutral and acidic pH in the resolution range of 2.6 – 3.4 Å. In our apo state at pH 7.5, the extracellular domain (ECD) displays conformational variations compared to the existing apo structures. At pH 4.0, three distinct conformational states (C1, C2 and O states) are identified. The protonated structures exhibit a compacted and counter-clockwise rotated ECD compared with our apo state. A gradual widening of the pore in the TMD is observed upon reducing the pH, with the widest pore in O state, accompanied by several layers of water pentagons. The pore radius and molecular dynamics (MD) simulations suggest that the O state represents an open conductive state. We also observe state-dependent interactions between several lipids and proteins that may be involved in the regulation of channel gating. Our results provide comprehensive insights into the importance of lipids impact on gating.
Long lifetimes white afterglow in slightly crosslinked polymer systems
Authors: Chen Qingao , Qu Lunjun , Hou Hui , Huang Jiayue , Li Chen , Zhu Ying , Wang Yongkang , Chen Xiaohong , Zhou Qian , Yang Yan , Yang Chaolong 
Published: April 2024

AbstractIntrinsic polymer room-temperature phosphorescence (IPRTP) materials have attracted considerable attention for application in flexible electronics, information encryption, lighting displays, and other fields due to their excellent processabilities and luminescence properties. However, achieving multicolor long-lived luminescence, particularly white afterglow, in undoped polymers is challenging. Herein, we propose a strategy of covalently coupling different conjugated chromophores with poly(acrylic acid (AA)-AA-N-succinimide ester) (PAA-NHS) by a simple and rapid one-pot reaction to obtain pure polymers with long-lived RTPs of various colors. Among these polymers, the highest phosphorescence quantum yield of PAPHE reaches 14.7%. Furthermore, the afterglow colors of polymers can be modulated from blue to red by introducing three chromophores into them. Importantly, the acquired polymer TPAP-514 exhibits a white afterglow at room temperature with the chromaticity coordinates (0.33, 0.33) when the ratio of chromophores reaches a suitable value owing to the three-primary-color mechanism. Systematic studies prove that the emission comes from the superposition of different triplet excited states of the three components. Moreover, the potential applications of the obtained polymers in light-emitting diodes and dynamic anti-counterfeiting are explored. The proposed strategy provides a new idea for constructing intrinsic polymers with diverse white-light emission RTPs.
Improving prime editing with an endogenous small RNA-binding protein
Authors: Yan Jun , Oyler-Castrillo Paul , Ravisankar Purnima , Ward Carl C. , Levesque Sébastien , Jing Yangwode , Simpson Danny , Zhao Anqi , Li Hui , Yan Weihao , Goudy Laine , Schmidt Ralf , Solley Sabrina C. , Gilbert Luke A. , Chan Michelle M. , Bauer Daniel E. , Marson Alexander , Parsons Lance R. , Adamson Britt 
Published: April 2024

Abstract
Prime editing enables the precise modification of genomes through reverse transcription of template sequences appended to the 3′ ends of CRISPR–Cas guide RNAs1. To identify cellular determinants of prime editing, we developed scalable prime editing reporters and performed genome-scale CRISPR-interference screens. From these screens, a single factor emerged as the strongest mediator of prime editing: the small RNA-binding exonuclease protection factor La. Further investigation revealed that La promotes prime editing across approaches (PE2, PE3, PE4 and PE5), edit types (substitutions, insertions and deletions), endogenous loci and cell types but has no consistent effect on genome-editing approaches that rely on standard, unextended guide RNAs. Previous work has shown that La binds polyuridine tracts at the 3′ ends of RNA polymerase III transcripts2. We found that La functionally interacts with the 3′ ends of polyuridylated prime editing guide RNAs (pegRNAs). Guided by these results, we developed a prime editor protein (PE7) fused to the RNA-binding, N-terminal domain of La. This editor improved prime editing with expressed pegRNAs and engineered pegRNAs (epegRNAs), as well as with synthetic pegRNAs optimized for La binding. Together, our results provide key insights into how prime editing components interact with the cellular environment and suggest general strategies for stabilizing exogenous small RNAs therein.
The variation and evolution of complete human centromeres
Authors: Logsdon Glennis A. , Rozanski Allison N. , Ryabov Fedor , Potapova Tamara , Shepelev Valery A. , Catacchio Claudia R. , Porubsky David , Mao Yafei , Yoo DongAhn , Rautiainen Mikko , Koren Sergey , Nurk Sergey , Lucas Julian K. , Hoekzema Kendra , Munson Katherine M. , Gerton Jennifer L. , Phillippy Adam M. , Ventura Mario , Alexandrov Ivan A. , Eichler Evan E. 
Published: April 2024

AbstractHuman centromeres have been traditionally very difficult to sequence and assemble owing to their repetitive nature and large size1. As a result, patterns of human centromeric variation and models for their evolution and function remain incomplete, despite centromeres being among the most rapidly mutating regions2,3. Here, using long-read sequencing, we completely sequenced and assembled all centromeres from a second human genome and compared it to the finished reference genome4,5. We find that the two sets of centromeres show at least a 4.1-fold increase in single-nucleotide variation when compared with their unique flanks and vary up to 3-fold in size. Moreover, we find that 45.8% of centromeric sequence cannot be reliably aligned using standard methods owing to the emergence of new α-satellite higher-order repeats (HORs). DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by >500 kb. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan and macaque genomes. Comparative analyses reveal a nearly complete turnover of α-satellite HORs, with characteristic idiosyncratic changes in α-satellite HORs for each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the short (p) and long (q) arms across centromeres and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.
A brain-specific angiogenic mechanism enabled by tip cell specialization
Authors: Schevenels Giel , Cabochette Pauline , America Michelle , Vandenborne Arnaud , De Grande Line , Guenther Stefan , He Liqun , Dieu Marc , Christou Basile , Vermeersch Marjorie , Germano Raoul F. V. , Perez-Morga David , Renard Patricia , Martin Maud , Vanlandewijck Michael , Betsholtz Christer , Vanhollebeke Benoit 
Published: April 2024

AbstractVertebrate organs require locally adapted blood vessels1,2. The gain of such organotypic vessel specializations is often deemed to be molecularly unrelated to the process of organ vascularization. Here, opposing this model, we reveal a molecular mechanism for brain-specific angiogenesis that operates under the control of Wnt7a/b ligands—well-known blood–brain barrier maturation signals3–5. The control mechanism relies on Wnt7a/b-dependent expression of Mmp25, which we find is enriched in brain endothelial cells. CRISPR–Cas9 mutagenesis in zebrafish reveals that this poorly characterized glycosylphosphatidylinositol-anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface. Mechanistically, Mmp25 confers brain invasive competence by cleaving meningeal fibroblast-derived collagen IV α5/6 chains within a short non-collagenous region of the central helical part of the heterotrimer. After genetic interference with the pial basement membrane composition, the Wnt–β-catenin-dependent organotypic control of brain angiogenesis is lost, resulting in properly patterned, yet blood–brain-barrier-defective cerebrovasculatures. We reveal an organ-specific angiogenesis mechanism, shed light on tip cell mechanistic angiodiversity and thereby illustrate how organs, by imposing local constraints on angiogenic tip cells, can select vessels matching their distinctive physiological requirements.
Optimizing PCF-SPR sensor design through Taguchi approach, machine learning, and genetic algorithms
Authors: Kaziz Sameh , Echouchene Fraj , Gazzah Mohamed Hichem 
Published: April 2024

AbstractDesigning Photonic Crystal Fibers incorporating the Surface Plasmon Resonance Phenomenon (PCF-SPR) has led to numerous interesting applications. This investigation presents an exceptionally responsive surface plasmon resonance sensor, seamlessly integrated into a dual-core photonic crystal fiber, specifically designed for low refractive index (RI) detection. The integration of a plasmonic material, namely silver (Ag), externally deposited on the fiber structure, facilitates real-time monitoring of variations in the refractive index of the surrounding medium. To ensure long-term functionality and prevent oxidation, a thin layer of titanium dioxide (TiO2) covers the silver coating. To optimize the sensor, five key design parameters, including pitch, air hole diameter, and silver thickness, are fine-tuned using the Taguchi L8(25) orthogonal array. The optimal results obtained present spectral and amplitude sensitivities that reach remarkable values of 10,000 nm/RIU and 235,882 RIU-1, respectively. In addition, Artificial Neural Network (ANN) optimization techniques, specifically Multi-Layer Perceptron (MLP) and Particle Swarm Optimization (PSO), are used to predict a critical optical property of the sensor confinement loss (αloss). These predictions are derived from the same input structure parameters that are present in the full L32(25) design experiment. A genetic algorithm (GA) is then applied for optimization with the goal of maximizing the confinement loss. Our results highlight the effectiveness of training PSO artificial neural networks and demonstrate their ability to quickly and accurately predict results for unknown geometric dimensions, demonstrating their significant potential in this innovative context. The proposed sensor design can be used for various applications including pharmaceutical inspection and detection of low refractive index analytes.
Gene expression plasticity facilitates acclimatization of a long-lived Caribbean coral across divergent reef environments
Authors: Castillo Karl D. , Bove Colleen B. , Hughes Annabel M. , Powell Maya E. , Ries Justin B. , Davies Sarah W. 
Published: April 2024

AbstractLocal adaptation can increase fitness under stable environmental conditions. However, in rapidly changing environments, compensatory mechanisms enabled through plasticity may better promote fitness. Climate change is causing devastating impacts on coral reefs globally and understanding the potential for adaptive and plastic responses is critical for reef management. We conducted a four-year, three-way reciprocal transplant of the Caribbean coral Siderastrea siderea across forereef, backreef, and nearshore populations in Belize to investigate the potential for environmental specialization versus plasticity in this species. Corals maintained high survival within forereef and backreef environments, but transplantation to nearshore environments resulted in high mortality, suggesting that nearshore environments present strong environmental selection. Only forereef-sourced corals demonstrated evidence of environmental specialization, exhibiting the highest growth in the forereef. Gene expression profiling 3.5 years post-transplantation revealed that transplanted coral hosts exhibited profiles more similar to other corals in the same reef environment, regardless of their source location, suggesting that transcriptome plasticity facilitates acclimatization to environmental change in S. siderea. In contrast, algal symbiont (Cladocopium goreaui) gene expression showcased functional variation between source locations that was maintained post-transplantation. Our findings suggest limited acclimatory capacity of some S. siderea populations under strong environmental selection and highlight the potential limits of coral physiological plasticity in reef restoration.
Exogenously applied gibberellic acid and benzylamine modulate growth and chemical constituents of dwarf schefflera: a stepwise regression analysis
Authors: Sardoei Ali Salehi , Tahmasebi Mojtaba , Bovand Fatemeh , Ghorbanpour Mansour 
Published: April 2024

AbstractOrnamental foliage plants that have a dense appearance are highly valued. One way to achieve this is by using plant growth regulators as a tool for plant growth management. In a greenhouse with a mist irrigation system, a study was conducted on dwarf schefflera, an ornamental foliage plant, which was exposed to foliar application of gibberellic acid and benzyladenine hormones. The hormones were sprayed on dwarf schefflera leaves at 0, 100, and 200 mg/l concentrations, at 15-day intervals in three stages. The experiment was conducted as a factorial based on a completely randomized design, with four replicates. The combination of gibberellic acid and benzyladenine at 200 mg/l concentration had a significant effect on leaf number, leaf area, and plant height. The treatment also resulted in the highest content of photosynthetic pigments. Furthermore, the highest soluble carbohydrate to reducing sugars ratio was observed in treatments of 100 and 200 mg/l benzyladenine, and 200 mg/l gibberellic acid + benzyladenine. Stepwise regression analysis showed that root volume was the first variable to enter the model, explaining 44% of variations. The next variable was root fresh weight, and the two-variable model explained 63% of variations in leaf number. The greatest positive effect on leaf number was related to root fresh weight (0.43), which had a positive correlation with leaf number (0.47). The results showed that 200 mg/l concentration of gibberellic acid and benzyladenine significantly improved morphological growth, chlorophyll and carotenoid synthesis, and reducing sugar and soluble carbohydrate contents in dwarf schefflera.
Differentiation and functioning of the lateral line organ in zebrafish require Smpx activity
Authors: Diana Alberto , Ghilardi Anna , Del Giacco Luca 
Published: April 2024

AbstractThe small muscle protein, X-linked (SMPX) gene encodes a cytoskeleton-associated protein, highly expressed in the inner ear hair cells (HCs), possibly regulating auditory function. In the last decade, several mutations in SMPX have been associated with X-chromosomal progressive non syndromic hearing loss in humans and, in line with this, Smpx-deficient animal models, namely zebrafish and mouse, showed significant impairment of inner ear HCs development, maintenance, and functioning. In this work, we uncovered smpx expression in the neuromast mechanosensory HCs of both Anterior and Posterior Lateral Line (ALL and PLL, respectively) of zebrafish larvae and focused our attention on the PLL. Smpx was subcellularly localized throughout the cytoplasm of the HCs, as well as in their primary cilium. Loss-of-function experiments, via both morpholino-mediated gene knockdown and CRISPR/Cas9 F0 gene knockout, revealed that the lack of Smpx led to fewer properly differentiated and functional neuromasts, as well as to a smaller PLL primordium (PLLp), the latter also Smpx-positive. In addition, the kinocilia of Smpx-deficient neuromast HCs appeared structurally and numerically altered. Such phenotypes were associated with a significant reduction in the mechanotransduction activity of the neuromast HCs, in line with their positivity for Smpx. In summary, this work highlights the importance of Smpx in lateral line development and, specifically, in proper HCs differentiation and/or maintenance, and in the mechanotransduction process carried out by the neuromast HCs. Because lateral line HCs are both functionally and structurally analogous to the cochlear HCs, the neuromasts might represent an invaluable—and easily accessible—tool to dissect the role of Smpx in HCs development/functioning and shed light on the underlying mechanisms involved in hearing loss.
Increases in pre-stimulus theta and alpha oscillations precede successful encoding of crossmodal associations
Authors: Ostrowski Jan , Rose Michael 
Published: April 2024

AbstractA central aspect of episodic memory is the formation of associations between stimuli from different modalities. Current theoretical approaches assume a functional role of ongoing oscillatory power and phase in the theta band (3–7 Hz) for the encoding of crossmodal associations. Furthermore, ongoing activity in the theta range as well as alpha (8–12 Hz) and low beta activity (13–20 Hz) before the presentation of a stimulus is thought to modulate subsequent cognitive processing, including processes that are related to memory. In this study, we tested the hypothesis that pre-stimulus characteristics of low frequency activity are relevant for the successful formation of crossmodal memory. The experimental design that was used specifically allowed for the investigation of associative memory independent from individual item memory. Participants (n = 51) were required to memorize associations between audiovisual stimulus pairs and distinguish them from newly arranged ones consisting of the same single stimuli in the subsequent recognition task. Our results show significant differences in the state of pre-stimulus theta and alpha power between remembered and not remembered crossmodal associations, clearly relating increased power to successful recognition. These differences were positively correlated with memory performance, suggesting functional relevance for behavioral measures of associative memory. Further analysis revealed similar effects in the low beta frequency ranges, indicating the involvement of different pre-stimulus-related cognitive processes. Phase-based connectivity measures in the theta band did not differ between remembered and not remembered stimulus pairs. The findings support the assumed functional relevance of theta band oscillations for the formation of associative memory and demonstrate that an increase of theta as well as alpha band oscillations in the pre-stimulus period is beneficial for the establishment of crossmodal memory.
Fairness and bias correction in machine learning for depression prediction across four study populations
Authors: Dang Vien Ngoc , Cascarano Anna , Mulder Rosa H. , Cecil Charlotte , Zuluaga Maria A. , Hernández-González Jerónimo , Lekadir Karim 
Published: April 2024

AbstractA significant level of stigma and inequality exists in mental healthcare, especially in under-served populations. Inequalities are reflected in the data collected for scientific purposes. When not properly accounted for, machine learning (ML) models learned from data can reinforce these structural inequalities or biases. Here, we present a systematic study of bias in ML models designed to predict depression in four different case studies covering different countries and populations. We find that standard ML approaches regularly present biased behaviors. We also show that mitigation techniques, both standard and our own post-hoc method, can be effective in reducing the level of unfair bias. There is no one best ML model for depression prediction that provides equality of outcomes. This emphasizes the importance of analyzing fairness during model selection and transparent reporting about the impact of debiasing interventions. Finally, we also identify positive habits and open challenges that practitioners could follow to enhance fairness in their models.
National prevalence of smoking among adolescents at tobacco tax increase and COVID-19 pandemic in South Korea, 2005–2022
Authors: Hong Seohyun , Woo Selin , Kim Seokjun , Park Jaeyu , Lee Myeongcheol , Kim Sunyoung , Koyanagi Ai , Smith Lee , Kim Min Seo , López Sánchez Guillermo F. , Dragioti Elena , Rahmati Masoud , Fond Guillaume , Boyer Laurent , Oh Jiyeon , Lee Hojae , Yon Dong Keon 
Published: April 2024

AbstractPrior research has predominantly focused on the overall effects of the tobacco tax increase and the COVID-19 pandemic on adolescent smoking behavior. However, there is a need to examine both the immediate and sustained associations of these two factors on subgroups of adolescents, employing an interrupted time-series model. We aimed to investigate the immediate and sustained association of tobacco tax increase and the COVID-19 pandemic on adolescent smoking prevalence. This study utilized data from the Korea Youth Risk Behavior Web-Based Survey to analyze the prevalence of current smoking among all participants (CSP) and the prevalence of daily smoking among current smokers (DSP) of Korean adolescents (n = 1,159,995; mean, age 14.99; male 51.5%) over 18 years from 2005 to 2022. The study examined 18-year trends in CSP and DSP among Korean adolescents, emphasizing the influences of the 2015 tobacco tax increase and the COVID-19 pandemic, using β coefficients and their differences (βdiff) from an interrupted time-series ARIMA model. While CSP exhibited a decreasing trend, DSP exhibited an increasing trend. Tobacco tax increase was associated with both the short and long terms in smoking prevalence, however, the short-term association on prevalence (CSP, − 3.076 [95% CI, − 3.707 to − 2.445]; DSP, − 4.112 [95% CI, − 6.488 to − 1.735]) was stronger. The pandemic was associated with an immediate increase in DSP (9.345 [95% CI, 5.285–13.406]). These effects were strongest among adolescents from low economic status and those exposed to familial secondhand smoking. Supportive programs for adolescents in low-income families will help overcome the effects associated with the pandemic. As a tobacco tax increase was associated with a reduction in smoking prevalence, this could be one method to overcome the effects of the pandemic.