bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulation of functional additive and non-additive genetic effects using statistical estimates from quantitative genetic models
Authors: Chu Thinh Tuan , Kristensen Peter Skov , Jensen Just 
Published: May 2024

AbstractStochastic simulation software is commonly used to aid breeders designing cost-effective breeding programs and to validate statistical models used in genetic evaluation. An essential feature of the software is the ability to simulate populations with desired genetic and non-genetic parameters. However, this feature often fails when non-additive effects due to dominance or epistasis are modeled, as the desired properties of simulated populations are estimated from classical quantitative genetic statistical models formulated at the population level. The software simulates underlying functional effects for genotypic values at the individual level, which are not necessarily the same as effects from statistical models in which dominance and epistasis are included. This paper provides the theoretical basis and mathematical formulas for the transformation between functional and statistical effects in such simulations. The transformation is demonstrated with two statistical models analyzing individual phenotypes in a single population (common in animal breeding) and plot phenotypes of three-way hybrids involving two inbred populations (observed in some crop breeding programs). We also describe different methods for the simulation of functional effects for additive genetics, dominance, and epistasis to achieve the desired levels of variance components in classical statistical models used in quantitative genetics.
Regional uniqueness of tree species composition and response to forest loss and climate change
Authors: van Tiel Nina , Fopp Fabian , Brun Philipp , van den Hoogen Johan , Karger Dirk Nikolaus , Casadei Cecilia M. , Lyu Lisha , Tuia Devis , Zimmermann Niklaus E. , Crowther Thomas W. , Pellissier Loïc 
Published: May 2024

AbstractThe conservation and restoration of forest ecosystems require detailed knowledge of the native plant compositions. Here, we map global forest tree composition and assess the impacts of historical forest cover loss and climate change on trees. The global occupancy of 10,590 tree species reveals complex taxonomic and phylogenetic gradients determining a local signature of tree lineage assembly. Species occupancy analyses indicate that historical forest loss has significantly restricted the potential suitable range of tree species in all forest biomes. Nevertheless, tropical moist and boreal forest biomes display the lowest level of range restriction and harbor extremely large ranged tree species, albeit with a stark contrast in richness and composition. Climate change simulations indicate that forest biomes are projected to differ in their response to climate change, with the highest predicted species loss in tropical dry and Mediterranean ecoregions. Our findings highlight the need for preserving the remaining large forest biomes while regenerating degraded forests in a way that provides resilience against climate change.
Two noncompeting human neutralizing antibodies targeting MPXV B6 show protective effects against orthopoxvirus infections
Authors: Zhao Runchu , Wu Lili , Sun Junqing , Liu Dezhi , Han Pu , Gao Yue , Zhang Yi , Xu Yanli , Qu Xiao , Wang Han , Chai Yan , Chen Zhihai , Gao George F. , Wang Qihui 
Published: May 2024

AbstractThe recent outbreak of mpox epidemic, caused by monkeypox virus (MPXV), poses a new threat to global public health. Here, we initially assessed the preexisting antibody level to the MPXV B6 protein in vaccinia vaccinees born before the end of the immunization program and then identified two monoclonal antibodies (MAbs), hMB621 and hMB668, targeting distinct epitopes on B6, from one vaccinee. Binding assays demonstrate that both MAbs exhibit broad binding abilities to B6 and its orthologs in vaccinia (VACV), variola (VARV) and cowpox viruses (CPXV). Neutralizing assays reveal that the two MAbs showed potent neutralization against VACV. Animal experiments using a BALB/c female mouse model indicate that the two MAbs showed effective protection against VACV via intraperitoneal injection. Additionally, we determined the complex structure of B6 and hMB668, revealing the structural feature of B6 and the epitope of hMB668. Collectively, our study provides two promising antibody candidates for the treatment of orthopoxvirus infections, including mpox.
The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis
Authors: Weinand Kathryn , Sakaue Saori , Nathan Aparna , Jonsson Anna Helena , Zhang Fan , Watts Gerald F. M. , Al Suqri Majd , Zhu Zhu ,   Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network, Albrecht Jennifer , Apruzzese William , Banda Nirmal , Barnas Jennifer L. , Bathon Joan M. , Ben-Artzi Ami , Boyce Brendan F. , Boyle David L. , Bridges S. Louis , Bykerk Vivian P. , Campbell Debbie , Carr Hayley L. , Ceponis Arnold , Chicoine Adam , Cordle Andrew , Curtis Michelle , Deane Kevin D. , DiCarlo Edward , Dunn Patrick , Filer Andrew , Firestein Gary S. , Forbess Lindsy , Geraldino-Pardilla Laura , Goodman Susan M. , Gravallese Ellen M. , Gregersen Peter K. , Guthridge Joel M. , Gutierrez-Arcelus Maria , Gurajala Siddarth , Holers V. Michael , Horowitz Diane , Hughes Laura B. , Ishigaki Kazuyoshi , Ivashkiv Lionel B. , James Judith A. , Kang Joyce B. , Keras Gregory , Korsunsky Ilya , Lakhanpal Amit , Lederer James A. , Li Zhihan J. , Li Yuhong , Liao Katherine P. , Mandelin Arthur M. , Mantel Ian , Maybury Mark , McDavid Andrew , Mears Joseph , Meednu Nida , Millard Nghia , Moreland Larry W. , Nerviani Alessandra , Orange Dana E. , Perlman Harris , Pitzalis Costantino , Rangel-Moreno Javier , Raza Karim , Reshef Yakir , Ritchlin Christopher , Rivellese Felice , Robinson William H. , Rumker Laurie , Sahbudin Ilfita , Scheel-Toellner Dagmar , Seifert Jennifer A. , Slowikowski Kamil , Smith Melanie H. , Tabechian Darren , Utz Paul J. , Weisenfeld Dana , Weisman Michael H. , Xiao Qian , Rao Deepak A. , Anolik Jennifer H. , Brenner Michael B. , Donlin Laura T. , Wei Kevin , Raychaudhuri Soumya 
Published: May 2024

AbstractSynovial tissue inflammation is a hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T peripheral helper cells; however, the epigenetic regulation of these states has yet to be defined. Here, we examine genome-wide open chromatin at single-cell resolution in 30 synovial tissue samples, including 12 samples with transcriptional data in multimodal experiments. We identify 24 chromatin classes and predict their associated transcription factors, including a CD8 + GZMK+ class associated with EOMES and a lining fibroblast class associated with AP-1. By integrating with an RA tissue transcriptional atlas, we propose that these chromatin classes represent ‘superstates’ corresponding to multiple transcriptional cell states. Finally, we demonstrate the utility of this RA tissue chromatin atlas through the associations between disease phenotypes and chromatin class abundance, as well as the nomination of classes mediating the effects of putatively causal RA genetic variants.
Inward motion of diamond nanoparticles inside an iron crystal
Authors: Wang Yuecun , Wang Xudong , Ding Jun , Liang Beiming , Zuo Lingling , Zheng Shaochuan , Huang Longchao , Xu Wei , Fan Chuanwei , Duan Zhanqiang , Jia Chunde , Zheng Rui , Liu Zhang , Zhang Wei , Li Ju , Ma En , Shan Zhiwei 
Published: May 2024

AbstractIn the absence of externally applied mechanical loading, it would seem counterintuitive that a solid particle sitting on the surface of another solid could not only sink into the latter, but also continue its rigid-body motion towards the interior, reaching a depth as distant as thousands of times the particle diameter. Here, we demonstrate such a case using in situ microscopic as well as bulk experiments, in which diamond nanoparticles ~100 nm in size move into iron up to millimeter depth, at a temperature about half of the melting point of iron. Each diamond nanoparticle is nudged as a whole, in a displacive motion towards the iron interior, due to a local stress induced by the accumulation of iron atoms diffusing around the particle via a short and easy interfacial channel. Our discovery underscores an unusual mass transport mode in solids, in addition to the familiar diffusion of individual atoms.
Large out-of-plane spin–orbit torque in topological Weyl semimetal TaIrTe4
Authors: Bainsla Lakhan , Zhao Bing , Behera Nilamani , Hoque Anamul Md. , Sjöström Lars , Martinelli Anna , Abdel-Hafiez Mahmoud , Åkerman Johan , Dash Saroj P. 
Published: May 2024

AbstractThe unique electronic properties of topological quantum materials, such as protected surface states and exotic quasiparticles, can provide an out-of-plane spin-polarized current needed for external field-free magnetization switching of magnets with perpendicular magnetic anisotropy. Conventional spin–orbit torque (SOT) materials provide only an in-plane spin-polarized current, and recently explored materials with lower crystal symmetries provide very low out-of-plane spin-polarized current components, which are not suitable for energy-efficient SOT applications. Here, we demonstrate a large out-of-plane damping-like SOT at room temperature using the topological Weyl semimetal candidate TaIrTe4 with a lower crystal symmetry. We performed spin–torque ferromagnetic resonance (STFMR) and second harmonic Hall measurements on devices based on TaIrTe4/Ni80Fe20 heterostructures and observed a large out-of-plane damping-like SOT efficiency. The out-of-plane spin Hall conductivity is estimated to be (4.05 ± 0.23)×104 (ℏ ⁄ 2e) (Ωm)−1, which is an order of magnitude higher than the reported values in other materials.
AgRP neuron cis-regulatory analysis across hunger states reveals that IRF3 mediates leptin’s acute effects
Authors: Heyward Frankie D. , Liu Nan , Jacobs Christopher , Machado Natalia L. S. , Ivison Rachael , Uner Aykut , Srinivasan Harini , Patel Suraj J. , Gulko Anton , Sermersheim Tyler , Tsai Linus , Rosen Evan D. 
Published: May 2024

AbstractAgRP neurons in the arcuate nucleus of the hypothalamus (ARC) coordinate homeostatic changes in appetite associated with fluctuations in food availability and leptin signaling. Identifying the relevant transcriptional regulatory pathways in these neurons has been a priority, yet such attempts have been stymied due to their low abundance and the rich cellular diversity of the ARC. Here we generated AgRP neuron-specific transcriptomic and chromatin accessibility profiles from male mice during three distinct hunger states of satiety, fasting-induced hunger, and leptin-induced hunger suppression. Cis-regulatory analysis of these integrated datasets enabled the identification of 18 putative hunger-promoting and 29 putative hunger-suppressing transcriptional regulators in AgRP neurons, 16 of which were predicted to be transcriptional effectors of leptin. Within our dataset, Interferon regulatory factor 3 (IRF3) emerged as a leading candidate mediator of leptin-induced hunger-suppression. Measures of IRF3 activation in vitro and in vivo reveal an increase in IRF3 nuclear occupancy following leptin administration. Finally, gain- and loss-of-function experiments in vivo confirm the role of IRF3 in mediating the acute satiety-evoking effects of leptin in AgRP neurons. Thus, our findings identify IRF3 as a key mediator of the acute hunger-suppressing effects of leptin in AgRP neurons.
A parametrically programmable delay line for microwave photons
Authors: Makihara Takuma , Lee Nathan , Guo Yudan , Guan Wenyan , Safavi-Naeini Amir 
Published: May 2024

AbstractDelay lines that store quantum information are crucial for advancing quantum repeaters and hardware efficient quantum computers. Traditionally, they are realized as extended systems that support wave propagation but provide limited control over the propagating fields. Here, we introduce a parametrically addressed delay line for microwave photons that provides a high level of control over the stored pulses. By parametrically driving a three-wave mixing circuit element that is weakly hybridized with an ensemble of resonators, we engineer a spectral response that simulates that of a physical delay line, while providing fast control over the delay line’s properties. We demonstrate this novel degree of control by choosing which photon echo to emit, translating pulses in time, and even swapping two pulses, all with pulse energies on the order of a single photon. We also measure the noise added from our parametric interactions and find it is much less than one photon.
Photocatalytic toluene oxidation with nickel-mediated cascaded active units over Ni/Bi2WO6 monolayers
Authors: Shi Yingzhang , Li Peng , Chen Huiling , Wang Zhiwen , Song Yujie , Tang Yu , Lin Sen , Yu Zhiyang , Wu Ling , Yu Jimmy C. , Fu Xianzhi 
Published: May 2024

AbstractAdsorption and activation of C–H bonds by photocatalysts are crucial for the efficient conversion of C–H bonds to produce high-value chemicals. Nevertheless, the delivery of surface-active oxygen species for C–H bond oxygenation inevitably needs to overcome obstacles due to the separated active centers, which suppresses the catalytic efficiency. Herein, Ni dopants are introduced into a monolayer Bi2WO6 to create cascaded active units consisting of unsaturated W atoms and Bi/O frustrated Lewis pairs. Experimental characterizations and density functional theory calculations reveal that these special sites can establish an efficient and controllable C–H bond oxidation process. The activated oxygen species on unsaturated W are readily transferred to the Bi/O sites for C–H bond oxygenation. The catalyst with a Ni mass fraction of 1.8% exhibits excellent toluene conversion rates and high selectivity towards benzaldehyde. This study presents a fascinating strategy for toluene oxidation through the design of efficient cascaded active units.
Robotic versus laparoscopic distal gastrectomy for resectable gastric cancer: a randomized phase 2 trial
Authors: Lu Jun , Xu Bin-bin , Zheng Hua-Long , Li Ping , Xie Jian-wei , Wang Jia-bin , Lin Jian-xian , Chen Qi-yue , Cao Long-long , Lin Mi , Tu Ru-hong , Huang Ze-ning , Lin Ju-li , Yao Zi-hao , Zheng Chao-Hui , Huang Chang-Ming 
Published: May 2024

AbstractRobotic surgery may be an alternative to laparoscopic surgery for gastric cancer (GC). However, randomized controlled trials (RCTs) reporting the differences in survival between these two approaches are currently lacking. From September 2017 to January 2020, 300 patients with cT1-4a and N0/+ were enrolled and randomized to either the robotic (RDG) or laparoscopic distal gastrectomy (LDG) group (NCT03313700). The primary endpoint was 3-year disease-free survival (DFS); secondary endpoints reported here are the 3-year overall survival (OS) and recurrence patterns. The remaining secondary outcomes include intraoperative outcomes, postoperative recovery, quality of lymphadenectomy, and cost differences, which have previously been reported. There were 283 patients in the modified intention-to-treat analysis (RDG group: n = 141; LDG group: n = 142). The trial has met pre-specified endpoints. The 3-year DFS rates were 85.8% and 73.2% in the RDG and LDG groups, respectively (p = 0.011). Multivariable Cox regression model including age, tumor size, sex, ECOG PS, lymphovascular invasion, histology, pT stage, and pN stage showed that RDG was associated with better 3-year DFS (HR: 0.541; 95% CI: 0.314-0.932). The RDG also improved the 3-year cumulative recurrence rate (RDG vs. LDG: 12.1% vs. 21.1%; HR: 0.546, 95% CI: 0.302-0.990). Compared to LDG, RDG demonstrated non-inferiority in 3-year DFS rate.
Circular single-stranded DNA as a programmable vector for gene regulation in cell-free protein expression systems
Authors: Tian Zhijin , Shao Dandan , Tang Linlin , Li Zhen , Chen Qian , Song Yongxiu , Li Tao , Simmel Friedrich C. , Song Jie 
Published: May 2024

AbstractCell-free protein expression (CFE) systems have emerged as a critical platform for synthetic biology research. The vectors for protein expression in CFE systems mainly rely on double-stranded DNA and single-stranded RNA for transcription and translation processing. Here, we introduce a programmable vector - circular single-stranded DNA (CssDNA), which is shown to be processed by DNA and RNA polymerases for gene expression in a yeast-based CFE system. CssDNA is already widely employed in DNA nanotechnology due to its addressability and programmability. To apply above methods in the context of synthetic biology, CssDNA can not only be engineered for gene regulation via the different pathways of sense CssDNA and antisense CssDNA, but also be constructed into several gene regulatory logic gates in CFE systems. Our findings advance the understanding of how CssDNA can be utilized in gene expression and gene regulation, and thus enrich the synthetic biology toolbox.
Conformations of Bcs1L undergoing ATP hydrolysis suggest a concerted translocation mechanism for folded iron-sulfur protein substrate
Authors: Zhan Jingyu , Zeher Allison , Huang Rick , Tang Wai Kwan , Jenkins Lisa M. , Xia Di 
Published: May 2024

AbstractThe human AAA-ATPase Bcs1L translocates the fully assembled Rieske iron-sulfur protein (ISP) precursor across the mitochondrial inner membrane, enabling respiratory Complex III assembly. Exactly how the folded substrate is bound to and released from Bcs1L has been unclear, and there has been ongoing debate as to whether subunits of Bcs1L act in sequence or in unison hydrolyzing ATP when moving the protein cargo. Here, we captured Bcs1L conformations by cryo-EM during active ATP hydrolysis in the presence or absence of ISP substrate. In contrast to the threading mechanism widely employed by AAA proteins in substrate translocation, subunits of Bcs1L alternate uniformly between ATP and ADP conformations without detectable intermediates that have different, co-existing nucleotide states, indicating that the subunits act in concert. We further show that the ISP can be trapped by Bcs1 when its subunits are all in the ADP-bound state, which we propose to be released in the apo form.
Multiple photofluorochromic luminogens via catalyst-free alkene oxidative cleavage photoreaction for dynamic 4D codes encryption
Authors: Lu Lin , Wu Bo , He Xinyuan , Zhao Fen , Feng Xing , Wang Dong , Qiu Zijie , Han Ting , Zhao Zheng , Tang Ben Zhong 
Published: May 2024

AbstractControllable photofluorochromic systems with high contrast and multicolor in both solutions and solid states are ideal candidates for the development of dynamic artificial intelligence. However, it is still challenging to realize multiple photochromism within one single molecule, not to mention good controllability. Herein, we report an aggregation-induced emission luminogen TPE-2MO2NT that undergoes oxidation cleavage upon light irradiation and is accompanied by tunable multicolor emission from orange to blue with time-dependence. The photocleavage mechanism revealed that the self-generation of reactive oxidants driving the catalyst-free oxidative cleavage process. A comprehensive analysis of TPE-2MO2NT and other comparative molecules demonstrates that the TPE-2MO2NT molecular scaffold can be easily modified and extended. Further, the multicolor microenvironmental controllability of TPE-2MO2NT photoreaction within polymer matrices enables the fabrication of dynamic fluorescence images and 4D information codes, providing strategies for advanced controllable information encryption.
A multidimensional selective landscape drives adaptive divergence between and within closely related Phlox species
Authors: Goulet-Scott Benjamin E. , Farnitano Matthew C. , Brown Andrea L. M. , Hale Charles O. , Blumstein Meghan , Hopkins Robin 
Published: May 2024

AbstractSelection causes local adaptation across populations within species and simultaneously divergence between species. However, it is unclear if either the force of or the response to selection is similar across these scales. We show that natural selection drives divergence between closely related species in a pattern that is distinct from local adaptation within species. We use reciprocal transplant experiments across three species of Phlox wildflowers to characterize widespread adaptive divergence. Using provenance trials, we also find strong local adaptation between populations within a species. Comparing divergence and selection between these two scales of diversity we discover that one suite of traits predicts fitness differences between species and that an independent suite of traits predicts fitness variation within species. Selection drives divergence between species, contributing to speciation, while simultaneously favoring extensive diversity that is maintained across populations within a species. Our work demonstrates how the selection landscape is complex and multidimensional.
Global biogeography of microbes driving ocean ecological status under climate change
Authors: Zhang Zhenyan , Zhang Qi , Chen Bingfeng , Yu Yitian , Wang Tingzhang , Xu Nuohan , Fan Xiaoji , Penuelas Josep , Fu Zhengwei , Deng Ye , Zhu Yong-Guan , Qian Haifeng 
Published: May 2024

AbstractMicrobial communities play a crucial role in ocean ecology and global biogeochemical processes. However, understanding the intricate interactions among diversity, taxonomical composition, functional traits, and how these factors respond to climate change remains a significant challenge. Here, we propose seven distinct ecological statuses by systematically considering the diversity, structure, and biogeochemical potential of the ocean microbiome to delineate their biogeography. Anthropogenic climate change is expected to alter the ecological status of the surface ocean by influencing environmental conditions, particularly nutrient and oxygen contents. Our predictive model, which utilizes machine learning, indicates that the ecological status of approximately 32.44% of the surface ocean may undergo changes from the present to the end of this century, assuming no policy interventions. These changes mainly include poleward shifts in the main taxa, increases in photosynthetic carbon fixation and decreases in nutrient metabolism. However, this proportion can decrease significantly with effective control of greenhouse gas emissions. Our study underscores the urgent necessity for implementing policies to mitigate climate change, particularly from an ecological perspective.
High-performance near-infrared OLEDs maximized at 925 nm and 1022 nm through interfacial energy transfer
Authors: Hung Chieh-Ming , Wang Sheng-Fu , Chao Wei-Chih , Li Jian-Liang , Chen Bo-Han , Lu Chih-Hsuan , Tu Kai-Yen , Yang Shang-Da , Hung Wen-Yi , Chi Yun , Chou Pi-Tai 
Published: May 2024

AbstractUsing a transfer printing technique, we imprint a layer of a designated near-infrared fluorescent dye BTP-eC9 onto a thin layer of Pt(II) complex, both of which are capable of self-assembly. Before integration, the Pt(II) complex layer gives intense deep-red phosphorescence maximized at ~740 nm, while the BTP-eC9 layer shows fluorescence at > 900 nm. Organic light emitting diodes fabricated under the imprinted bilayer architecture harvest most of Pt(II) complex phosphorescence, which undergoes triplet-to-singlet energy transfer to the BTP-eC9 dye, resulting in high-intensity hyperfluorescence at > 900 nm. As a result, devices achieve 925 nm emission with external quantum efficiencies of 2.24% (1.94 ± 0.18%) and maximum radiance of 39.97 W sr−1 m−2. Comprehensive morphology, spectroscopy and device analyses support the mechanism of interfacial energy transfer, which also is proved successful for BTPV-eC9 dye (1022 nm), making bright and far-reaching the prospective of hyperfluorescent OLEDs in the near-infrared region.