bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages
Authors: Zhang Taikui , Huang Weichen , Zhang Lin , Li De-Zhu , Qi Ji , Ma Hong 
Published: April 2024

AbstractPoaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.
Interface-induced dual-pinning mechanism enhances low-frequency electromagnetic wave loss
Authors: Cai Bo , Zhou Lu , Zhao Pei-Yan , Peng Hua-Long , Hou Zhi-Ling , Hu Pengfei , Liu Li-Min , Wang Guang-Sheng 
Published: April 2024

AbstractImproving the absorption of electromagnetic waves at low-frequency bands (2-8 GHz) is crucial for the increasing electromagnetic (EM) pollution brought about by the innovation of the fifth generation (5G) communication technology. However, the poor impedance matching and intrinsic attenuation of material in low-frequency bands hinders the development of low-frequency electromagnetic wave absorbing (EMWA) materials. Here we propose an interface-induced dual-pinning mechanism and establish a magnetoelectric bias interface by constructing bilayer core-shell structures of NiFe2O4 (NFO)@BiFeO3 (BFO)@polypyrrole (PPy). Such heterogeneous interface could induce distinct magnetic pinning of the magnetic moment in the ferromagnetic NFO and dielectric pinning of the dipole rotation in PPy. The establishment of the dual-pinning effect resulted in optimized impedance and enhanced attenuation at low-frequency bands, leading to better EMWA performance. The minimum reflection loss (RLmin) at thickness of 4.43 mm reaches -65.30 dB (the optimal absorption efficiency of 99.99997%), and the effective absorption bandwidth (EAB) can almost cover C-band (4.72 ~ 7.04 GHz) with low filling of 15.0 wt.%. This work proposes a mechanism to optimize low-frequency impedance matching with electromagnetic wave (EMW) loss and pave an avenue for the research of high-performance low-frequency absorbers.
Ultrafast photoluminescence and multiscale light amplification in nanoplasmonic cavity glass
Authors: Piotrowski Piotr , Buza Marta , Nowaczyński Rafał , Kongsuwan Nuttawut , Surma Hańcza B. , Osewski Paweł , Gajc Marcin , Strzep Adam , Ryba-Romanowski Witold , Hess Ortwin , Pawlak Dorota A. 
Published: April 2024

AbstractInteractions between plasmons and exciton nanoemitters in plexcitonic systems lead to fast and intense luminescence, desirable in optoelectonic devices, ultrafast optical switches and quantum information science. While luminescence enhancement through exciton-plasmon coupling has thus far been mostly demonstrated in micro- and nanoscale structures, analogous demonstrations in bulk materials have been largely neglected. Here we present a bulk nanocomposite glass doped with cadmium telluride quantum dots (CdTe QDs) and silver nanoparticles, nAg, which act as exciton and plasmon sources, respectively. This glass exhibits ultranarrow, FWHM = 13 nm, and ultrafast, 90 ps, amplified photoluminescence (PL), λem≅503 nm, at room temperature under continuous-wave excitation, λexc = 405 nm. Numerical simulations confirm that the observed improvement in emission is a result of a multiscale light enhancement owing to the ensemble of QD-populated plasmonic nanocavities in the material. Power-dependent measurements indicate that >100 mW coherent light amplification occurs. These types of bulk plasmon-exciton composites could be designed comprising a plethora of components/functionalities, including emitters (QDs, rare earth and transition metal ions) and nanoplasmonic elements (Ag/Au/TCO, spherical/anisotropic/miscellaneous), to achieve targeted applications.
Re-order parameter of interacting thermodynamic magnets
Authors: Park Byung Cheol , Lee Howon , Oh Sang Hyup , Shin Hyun Jun , Choi Young Jai , Ha Taewoo 
Published: April 2024

AbstractPhase diagrams of materials are typically based on a static order parameter, but it faces challenges when distinguishing subtle phase changes, such as re-ordering. Here, we report a dynamic nonequilibrium order parameter termed re-order parameter to determine subtle phases and their transitions in interacting magnets. The dynamical precession of magnetization, so-called magnon, premises as a reliable re-order parameter of strong spin-orbit coupled magnets. We employ orthoferrites YFeO3 and its Mn-doped variations, where diverse magnetic phases, including canted antiferromagnetic (Γ4) and collinear antiferromagnetic (Γ1) states, have been well-established. Low-energy magnon uncovers the spin-orbit coupling-induced subtle magnetic structures, resulting in distinct terahertz emissions. The temporal and spectral parameters of magnon emission exhibit characteristics akin to BCS-type order parameters, constructing the magnetic phase diagram of Mn-doped YFeO3. This approach further reveals a concealed ferrimagnetic phase within the Γ1 state, underscoring its potential to search for hidden phases of materials, completing their phase diagrams.
Rapid room-temperature phosphorescence chiral recognition of natural amino acids
Authors: Chen Xiaoyu , Zhu Renlong , Zhang Baicheng , Zhang Xiaolong , Cheng Aoyuan , Liu Hongping , Gao Ruiying , Zhang Xuepeng , Chen Biao , Ye Shuji , Jiang Jun , Zhang Guoqing 
Published: April 2024

AbstractChiral recognition of amino acids is very important in both chemical and life sciences. Although chiral recognition with luminescence has many advantages such as being inexpensive, it is usually slow and lacks generality as the recognition module relies on structural complementarity. Here, we show that one single molecular-solid sensor, L-phenylalanine derived benzamide, can manifest the structural difference between the natural, left-handed amino acid and its right-handed counterpart via the difference of room-temperature phosphorescence (RTP) irrespective of the specific chemical structure. To realize rapid and reliable sensing, the doped samples are obtained as nanocrystals from evaporation of the tetrahydrofuran solutions, which allows for efficient triplet-triplet energy transfer to the chiral analytes generated in situ from chiral amino acids. The results show that L-analytes induce strong RTP, whereas the unnatural D-analytes produce barely any afterglow. The method expands the scope of luminescence chiral sensing by lessening the requirement for specific molecular structures.
Selenium catalysis enables negative feedback organic oscillators
Authors: Li Xiuxiu , Fomitskaya Polina , Smaliak Viktoryia A. , Smith Barbara S. , Skorb Ekaterina V. , Semenov Sergey N. 
Published: April 2024

AbstractThe construction of materials regulated by chemical reaction networks requires regulatory motifs that can be stacked together into systems with desired properties. Multiple autocatalytic reactions producing thiols are known. However, negative feedback loop motifs are unavailable for thiol chemistry. Here, we develop a negative feedback loop based on the selenocarbonates. In this system, thiols induce the release of aromatic selenols that catalyze the oxidation of thiols by organic peroxides. This negative feedback loop has two important features. First, catalytic oxidation of thiols follows Michaelis-Menten-like kinetics, thus increasing nonlinearity for the negative feedback. Second, the strength of the negative feedback can be tuned by varying substituents in selenocarbonates. When combined with the autocatalytic production of thiols in a flow reactor, this negative feedback loop induces sustained oscillations. The availability of this negative feedback motif enables the future construction of oscillatory, homeostatic, adaptive, and other regulatory circuits in life-inspired systems and materials.
Defect scattering can lead to enhanced phonon transport at nanoscale
Authors: Hu Yue , Xu Jiaxuan , Ruan Xiulin , Bao Hua 
Published: April 2024

AbstractDefect scattering is well known to suppress thermal transport. In this study, however, we perform both molecular dynamics and Boltzmann transport equation calculations, to demonstrate that introducing defect scattering in nanoscale heating zone could surprisingly enhance thermal conductance of the system by up to 75%. We further reveal that the heating zone without defects yields directional nonequilibrium with overpopulated oblique-propagating phonons which suppress thermal transport, while introducing defects redirect phonons randomly to restore directional equilibrium, thereby enhancing thermal conductance. We demonstrate that defect scattering can enable such thermal transport enhancement in a wide range of temperatures, materials, and sizes, and offer an unconventional strategy for enhancing thermal transport via the manipulation of phonon directional nonequilibrium.
Tight Lieb–Robinson Bound for approximation ratio in quantum annealing
Authors: Braida Arthur , Martiel Simon , Todinca Ioan 
Published: April 2024

AbstractQuantum annealing (QA) holds promise for optimization problems in quantum computing, especially for combinatorial optimization. This analog framework attracts attention for its potential to address complex problems. Its gate-based homologous, QAOA with proven performance, has attracted a lot of attention to the NISQ era. Several numerical benchmarks try to compare these two metaheuristics, however, classical computational power highly limits the performance insights. In this work, we introduce a parametrized version of QA enabling a precise 1-local analysis of the algorithm. We develop a tight Lieb–Robinson bound for regular graphs, achieving the best-known numerical value to analyze QA locally. Studying MaxCut over cubic graph as a benchmark optimization problem, we show that a linear-schedule QA with a 1-local analysis achieves an approximation ratio over 0.7020, outperforming any known 1-local algorithms.
SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity
Authors: Corell-Sierra Julia , Marquez-Molins Joan , Marqués María-Carmen , Hernandez-Azurdia Andrea Gabriela , Montagud-Martínez Roser , Cebriá-Mendoza María , Cuevas José M. , Albert Eliseo , Navarro David , Rodrigo Guillermo , Gómez Gustavo 
Published: April 2024

AbstractThe COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has significantly impacted global health, stressing the necessity of basic understanding of the host response to this viral infection. In this study, we investigated how SARS-CoV-2 remodels the landscape of small non-coding RNAs (sncRNA) from a large collection of nasopharyngeal swab samples taken at various time points from patients with distinct symptom severity. High-throughput RNA sequencing analysis revealed a global alteration of the sncRNA landscape, with abundance peaks related to species of 21-23 and 32-33 nucleotides. Host-derived sncRNAs, including microRNAs (miRNAs), transfer RNA-derived small RNAs (tsRNAs), and small nucleolar RNA-derived small RNAs (sdRNAs) exhibited significant differential expression in infected patients compared to controls. Importantly, miRNA expression was predominantly down-regulated in response to SARS-CoV-2 infection, especially in patients with severe symptoms. Furthermore, we identified specific tsRNAs derived from Glu- and Gly-tRNAs as major altered elements upon infection, with 5’ tRNA halves being the most abundant species and suggesting their potential as biomarkers for viral presence and disease severity prediction. Additionally, down-regulation of C/D-box sdRNAs and altered expression of tinyRNAs (tyRNAs) were observed in infected patients. These findings provide valuable insights into the host sncRNA response to SARS-CoV-2 infection and may contribute to the development of further diagnostic and therapeutic strategies in the clinic.
T-cell commitment inheritance—an agent-based multi-scale model
Authors: Andersson Emil , Rothenberg Ellen V. , Peterson Carsten , Olariu Victor 
Published: April 2024

AbstractT-cell development provides an excellent model system for studying lineage commitment from a multipotent progenitor. The intrathymic development process has been thoroughly studied. The molecular circuitry controlling it has been dissected and the necessary steps like programmed shut off of progenitor genes and T-cell genes upregulation have been revealed. However, the exact timing between decision-making and commitment stage remains unexplored. To this end, we implemented an agent-based multi-scale model to investigate inheritance in early T-cell development. Treating each cell as an agent provides a powerful tool as it tracks each individual cell of a simulated T-cell colony, enabling the construction of lineage trees. Based on the lineage trees, we introduce the concept of the last common ancestors (LCA) of committed cells and analyse their relations, both at single-cell level and population level. In addition to simulating wild-type development, we also conduct knockdown analysis. Our simulations predicted that the commitment is a three-step process that occurs on average over several cell generations once a cell is first prepared by a transcriptional switch. This is followed by the loss of the Bcl11b-opposing function approximately two to three generations later. This is when our LCA analysis indicates that the decision to commit is taken even though in general another one to two generations elapse before the cell actually becomes committed by transitioning to the DN2b state. Our results showed that there is decision inheritance in the commitment mechanism.
tRNA modification reprogramming contributes to artemisinin resistance in Plasmodium falciparum
Authors: Small-Saunders Jennifer L. , Sinha Ameya , Bloxham Talia S. , Hagenah Laura M. , Sun Guangxin , Preiser Peter R. , Dedon Peter C. , Fidock David A. 
Published: April 2024

AbstractPlasmodium falciparum artemisinin (ART) resistance is driven by mutations in kelch-like protein 13 (PfK13). Quiescence, a key aspect of resistance, may also be regulated by a yet unidentified epigenetic pathway. Transfer RNA modification reprogramming and codon bias translation is a conserved epitranscriptomic translational control mechanism that allows cells to rapidly respond to stress. We report a role for this mechanism in ART-resistant parasites by combining tRNA modification, proteomic and codon usage analyses in ring-stage ART-sensitive and ART-resistant parasites in response to drug. Post-drug, ART-resistant parasites differentially hypomodify mcm5s2U on tRNA and possess a subset of proteins, including PfK13, that are regulated by Lys codon-biased translation. Conditional knockdown of the terminal s2U thiouridylase, PfMnmA, in an ART-sensitive parasite background led to increased ART survival, suggesting that hypomodification can alter the parasite ART response. This study describes an epitranscriptomic pathway via tRNA s2U reprogramming that ART-resistant parasites may employ to survive ART-induced stress.
Vimentin filaments integrate low-complexity domains in a complex helical structure
Authors: Eibauer Matthias , Weber Miriam S. , Kronenberg-Tenga Rafael , Beales Charlie T. , Boujemaa-Paterski Rajaa , Turgay Yagmur , Sivagurunathan Suganya , Kraxner Julia , Köster Sarah , Goldman Robert D. , Medalia Ohad 
Published: April 2024

AbstractIntermediate filaments (IFs) are integral components of the cytoskeleton. They provide cells with tissue-specific mechanical properties and are involved in numerous cellular processes. Due to their intricate architecture, a 3D structure of IFs has remained elusive. Here we use cryo-focused ion-beam milling, cryo-electron microscopy and tomography to obtain a 3D structure of vimentin IFs (VIFs). VIFs assemble into a modular, intertwined and flexible helical structure of 40 α-helices in cross-section, organized into five protofibrils. Surprisingly, the intrinsically disordered head domains form a fiber in the lumen of VIFs, while the intrinsically disordered tails form lateral connections between the protofibrils. Our findings demonstrate how protein domains of low sequence complexity can complement well-folded protein domains to construct a biopolymer with striking mechanical strength and stretchability.
Towards Gender Harmony Dataset: Gender Beliefs and Gender Stereotypes in 62 Countries
Authors: Kosakowska-Berezecka Natasza , Besta Tomasz , Jurek Paweł , Olech Michał , Sobiecki Jurand , Bosson Jennifer , Vandello Joseph A. , Best Deborah , Zawisza Magdalena , Safdar Saba , Włodarczyk Anna , Żadkowska Magdalena 
Published: April 2024

AbstractThe Towards Gender Harmony (TGH) project began in September 2018 with over 160 scholars who formed an international consortium to collect data from 62 countries across six continents. Our overarching goal was to analyze contemporary perceptions of masculinity and femininity using quantitative and qualitative methods, marking a groundbreaking effort in social science research. The data collection took place between January 2018 and February 2020, and involved undergraduate students who completed a series of randomized scales and the data was collected through the SurveyMonkey or Qualtrics platforms, with paper surveys being used in rare cases. All the measures used in the project were translated into 22 languages. The dataset contains 33,313 observations and 286 variables, including contemporary measures of gendered self-views, attitudes, and stereotypes, as well as relevant demographic data. The TGH dataset, linked with accessible country-level data, provides valuable insights into the dynamics of gender relations worldwide, allowing for multilevel analyses and examination of how gendered self-views and attitudes are linked to behavioral intentions and demographic variables.
Total irrigation by crop in the Continental United States from 2008 to 2020
Authors: Ruess P. J. , Konar Megan , Wanders Niko , Bierkens Marc F. P. 
Published: April 2024

AbstractWe provide a dataset of irrigation water withdrawals by crop, county, year, and water source within the United States. We employ a framework we previously developed to establish a companion dataset to our original estimates. The main difference is that we now use the U.S. Geological Survey (USGS) variable ‘irrigation — total’ to partition PCR-GLOBWB 2 hydrology model estimates, instead of ‘irrigation — crop’ as used in previous estimates. Our findings for Surface Water Withdrawals (SWW), total Groundwater Withdrawals (GWW), and nonrenewable Groundwater Depletion (GWD) are similar to those of prior estimates but now have better spatial coverage, since several states are missing from the USGS ‘irrigation — crop’ variable that was originally used. Irrigation water use increases in this study, since more states are included and ‘irrigation — total’ includes more categories of irrigation than ‘irrigation — crop’. Notably, irrigation in the Mississippi Embayment Aquifer is now captured for rice and soy. We provide nearly 2.5 million data points with this paper (3,142 counties; 13 years; 3 water sources; and 20 crops).
Deciphering Aphanomyces euteiches-pea-biocontrol bacterium interactions through untargeted metabolomics
Authors: Hossain Zakir , Zhao Shuang , Luo Xian , Liu Kui , Li Liang , Hubbard Michelle 
Published: April 2024

AbstractAphanomyces euteiches causes root rot in pea, leading to significant yield losses. However, the metabolites involved in this pathosystem have not been thoroughly studied. This study aimed to fill this gap and explore mechanisms of bacterial suppression of A. euteiches via untargeted metabolomics using pea grown in a controlled environment. Chemical isotope labeling (CIL), followed by liquid chromatography-mass spectrometry (LC–MS), was used for metabolite separation and detection. Univariate and multivariate analyses showed clear separation of metabolites from pathogen-treated pea roots and roots from other treatments. A three-tier approach positively or putatively identified 5249 peak pairs or metabolites. Of these, 403 were positively identified in tier 1; 940 were putatively identified with high confidence in tier 2. There were substantial changes in amino acid pool, and fatty acid and phenylpropanoid pathway products. More metabolites, including salicylic and jasmonic acids, were upregulated than downregulated in A. euteiches-infected roots. 1-aminocyclopropane-1-carboxylic acid and 12-oxophytodienoic acid were upregulated in A. euteiches + bacterium-treated roots compared to A. euteiches-infected roots. A great number of metabolites were up- or down-regulated in response to A. euteiches infection compared with the control and A. euteiches + bacterium-treated plants. The results of this study could facilitate improved disease management.
Using optical coherence tomography to optimize Mohs micrographic surgery
Authors: Akella Sruti S. , Lee Jenna , May Julia Roma , Puyana Carolina , Kravets Sasha , Dimitropolous Vassilios , Tsoukas Maria , Manwar Rayyan , Avanaki Kamran 
Published: April 2024

AbstractMohs micrographic surgery (MMS) is considered the gold standard for treating high-risk cutaneous basal cell carcinoma (BCC), but is expensive, time-consuming, and can be unpredictable as to how many stages will be required or how large the final lesion and corresponding surgical defect will be. This study is meant to investigate whether optical coherence tomography (OCT), a highly researched modality in dermatology, can be used preoperatively to map out the borders of BCC, resulting in fewer stages of MMS or a smaller final defect. In this prospective study, 22 patients with BCC undergoing surgical excision were enrolled at a single institution. All patients had previously received a diagnostic biopsy providing confirmation of BCC and had been referred to our center for excision with MMS. Immediately prior to performing MMS, OCT was used to map the borders of the lesion. MMS then proceeded according to standard protocol. OCT images were compared to histopathology for agreement. Histopathologic analysis of 7 of 22 MMS specimens (32%) revealed a total absence of BCC, indicating resolution of BCC after previous diagnostic biopsy. This outcome was correctly predicted by OCT imaging in 6 of 7 cases (86%). Nine tumors (9/22, 41%) had true BCC and required a single MMS stage, which was successfully predicted by pre-operative OCT analysis in 7 of 9 cases (78%). The final six tumors (27%) had true BCC and required two MMS stages for complete excision; preoperative OCT successfully predicted the need for a second stage in five cases (5/6, 83.3%). Overall, OCT diagnosed BCC with 95.5% accuracy (Cohen’s kappa, κ = 0.89 (p-value =  < 0.01) in the center of the lesion. Following a diagnostic biopsy, OCT can be used to verify the existence or absence of residual basal cell carcinoma. When residual tumor is present that requires excision with MMS, OCT can be used to predict tumor borders, optimize surgery and minimize the need for additional surgical stages.