bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recurrent photic zone euxinia limited ocean oxygenation and animal evolution during the Ediacaran
Authors: Zheng Wang , Zhou Anwen , Sahoo Swapan K. , Nolan Morrison R. , Ostrander Chadlin M. , Sun Ruoyu , Anbar Ariel D. , Xiao Shuhai , Chen Jiubin 
Published: July 2023

AbstractThe Ediacaran Period (~635–539 Ma) is marked by the emergence and diversification of complex metazoans linked to ocean redox changes, but the processes and mechanism of the redox evolution in the Ediacaran ocean are intensely debated. Here we use mercury isotope compositions from multiple black shale sections of the Doushantuo Formation in South China to reconstruct Ediacaran oceanic redox conditions. Mercury isotopes show compelling evidence for recurrent and spatially dynamic photic zone euxinia (PZE) on the continental margin of South China during time intervals coincident with previously identified ocean oxygenation events. We suggest that PZE was driven by increased availability of sulfate and nutrients from a transiently oxygenated ocean, but PZE may have also initiated negative feedbacks that inhibited oxygen production by promoting anoxygenic photosynthesis and limiting the habitable space for eukaryotes, hence abating the long-term rise of oxygen and restricting the Ediacaran expansion of macroscopic oxygen-demanding animals.
A medullary hub for controlling REM sleep and pontine waves
Authors: Schott Amanda L. , Baik Justin , Chung Shinjae , Weber Franz 
Published: July 2023

AbstractRapid-eye-movement (REM) sleep is a distinct behavioral state associated with vivid dreaming and memory processing. Phasic bursts of electrical activity, measurable as spike-like pontine (P)-waves, are a hallmark of REM sleep implicated in memory consolidation. However, the brainstem circuits regulating P-waves, and their interactions with circuits generating REM sleep, remain largely unknown. Here, we show that an excitatory population of dorsomedial medulla (dmM) neurons expressing corticotropin-releasing-hormone (CRH) regulates both REM sleep and P-waves in mice. Calcium imaging showed that dmM CRH neurons are selectively activated during REM sleep and recruited during P-waves, and opto- and chemogenetic experiments revealed that this population promotes REM sleep. Chemogenetic manipulation also induced prolonged changes in P-wave frequency, while brief optogenetic activation reliably triggered P-waves along with transiently accelerated theta oscillations in the electroencephalogram (EEG). Together, these findings anatomically and functionally delineate a common medullary hub for the regulation of both REM sleep and P-waves.
Cucurbit[8]uril-based water-dispersible assemblies with enhanced optoacoustic performance for multispectral optoacoustic imaging
Authors: Wu Yinglong , Sun Lihe , Chen Xiaokai , Liu Jiawei , Ouyang Juan , Zhang Xiaodong , Guo Yi , Chen Yun , Yuan Wei , Wang Dongdong , He Ting , Zeng Fang , Chen Hongzhong , Wu Shuizhu , Zhao Yanli 
Published: July 2023

AbstractOrganic small-molecule contrast agents have attracted considerable attention in the field of multispectral optoacoustic imaging, but their weak optoacoustic performance resulted from relatively low extinction coefficient and poor water solubility restrains their widespread applications. Herein, we address these limitations by constructing supramolecular assemblies based on cucurbit[8]uril (CB[8]). Two dixanthene-based chromophores (DXP and DXBTZ) are synthesized as the model guest compounds, and then included in CB[8] to prepare host-guest complexes. The obtained DXP-CB[8] and DXBTZ-CB[8] display red-shifted and increased absorption as well as decreased fluorescence, thereby leading to a substantial enhancement in optoacoustic performance. Biological application potential of DXBTZ-CB[8] is investigated after co-assembly with chondroitin sulfate A (CSA). Benefiting from the excellent optoacoustic property of DXBTZ-CB[8] and the CD44-targeting feature of CSA, the formulated DXBTZ-CB[8]/CSA can effectively detect and diagnose subcutaneous tumors, orthotopic bladder tumors, lymphatic metastasis of tumors and ischemia/reperfusion-induced acute kidney injury in mouse models with multispectral optoacoustic imaging.
The plant nuclear lamina disassembles to regulate genome folding in stress conditions
Authors: Wang Nan , Wang Zhidan , Tzourtzou Sofia , Wang Xu , Bi Xiuli , Leimeister Julia , Xu Linhao , Sakamoto Takuya , Matsunaga Sachihiro , Schaller Andreas , Jiang Hua , Liu Chang 
Published: July 2023

AbstractThe nuclear lamina is a complex network of nuclear lamins and lamin-associated nuclear membrane proteins, which scaffold the nucleus to maintain structural integrity. In Arabidopsis thaliana, nuclear matrix constituent proteins (NMCPs) are essential components of the nuclear lamina and are required to maintain the structural integrity of the nucleus and specific perinuclear chromatin anchoring. At the nuclear periphery, suppressed chromatin overlapping with repetitive sequences and inactive protein-coding genes are enriched. At a chromosomal level, plant chromatin organization in interphase nuclei is flexible and responds to various developmental cues and environmental stimuli. On the basis of these observations in Arabidopsis, and given the role of NMCP genes (CRWN1 and CRWN4) in organizing chromatin positioning at the nuclear periphery, one can expect considerable changes in chromatin–nuclear lamina interactions when the global chromatin organization patterns are being altered in plants. Here we report the highly flexible nature of the plant nuclear lamina, which disassembles substantially under various stress conditions. Focusing on heat stress, we reveal that chromatin domains, initially tethered to the nuclear envelope, remain largely associated with CRWN1 and become scattered in the inner nuclear space. By investigating the three-dimensional chromatin contact network, we further reveal that CRWN1 proteins play a structural role in shaping the changes in genome folding under heat stress. Also, CRWN1 acts as a negative transcriptional coregulator to modulate the shift of the plant transcriptome profile in response to heat stress.
A catalog of bacterial reference genomes from cultivated human oral bacteria
Authors: Li Wenxi , Liang Hewei , Lin Xiaoqian , Hu Tongyuan , Wu Zhinan , He Wenxin , Wang Mengmeng , Zhang Jiahao , Jie Zhuye , Jin Xin , Xu Xun , Wang Jian , Yang Huanming , Zhang Wenwei , Kristiansen Karsten , Xiao Liang , Zou Yuanqiang 
Published: July 2023

AbstractThe oral cavity harbors highly diverse communities of microorganisms. However, the number of isolated species and high-quality genomes is limited. Here we present a Cultivated Oral Bacteria Genome Reference (COGR), comprising 1089 high-quality genomes based on large-scale aerobic and anaerobic cultivation of human oral bacteria isolated from dental plaques, tongue, and saliva. COGR covers five phyla and contains 195 species-level clusters of which 95 include 315 genomes representing species with no taxonomic annotation. The oral microbiota differs markedly between individuals, with 111 clusters being person-specific. Genes encoding CAZymes are abundant in the genomes of COGR. Members of the Streptococcus genus make up the largest proportion of COGR and many of these harbor entire pathways for quorum sensing important for biofilm formation. Several clusters containing unknown bacteria are enriched in individuals with rheumatoid arthritis, emphasizing the importance of culture-based isolation for characterizing and exploiting oral bacteria.
Prospective controlled study on the effects of deep brain stimulation on driving in Parkinson’s disease
Authors: Fründt Odette , Mainka Tina , Vettorazzi Eik , Baspinar Ela , Schwarz Cindy , Südmeyer Martin , Gerloff Christian , Zangemeister Wolfgang H. , Poetter-Nerger Monika , Hidding Ute , Hamel Wolfgang , Moll Christian K. E. , Buhmann Carsten 
Published: July 2023

AbstractTo explore the influence of bilateral subthalamic deep brain stimulation (STN-DBS) on car driving ability in patients with Parkinson’s disease (PD), we prospectively examined two age-matched, actively driving PD patient groups: one group undergone DBS-surgery (PD-DBS, n = 23) and one group that was eligible for DBS but did not undergo surgery (PD-nDBS, n = 29). In PD-DBS patients, investigation at Baseline was done just prior and at Follow-up 6–12 month after DBS-surgery. In PD-nDBS patients, time interval between Baseline and Follow-up was aimed to be comparable. To assess the general PD driving level, driving was assessed once in 33 age-matched healthy controls at Baseline. As results, clinical and driving characteristics of PD-DBS, PD-nDBS and controls did not differ at Baseline. At Follow-up, PD-DBS patients drove unsafer than PD-nDBS patients. This effect was strongly driven by two single PD-DBS participants (9%) with poor Baseline and disastrous Follow-up driving performance. Retrospectively, we could not identify any of the assessed motor and non-motor clinical Baseline characteristics as predictive for this driving-deterioration at Follow-up. Excluding these two outliers, comparable driving performance between PD-DBS and PD-nDBS patients not only at Baseline but also at Follow-up was demonstrated. Age, disease duration and severity as well as Baseline driving insecurity were associated with poorer driving performance at Follow-up. This first prospective study on driving safety in PD after DBS surgery indicates that DBS usually does not alter driving safety but might increase the risk for driving deterioration, especially in single subjects with already unsafe driving prior to DBS surgery.
Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space
Authors: Hari Kishore , Duncan William , Ibrahim Mohammed Adil , Jolly Mohit Kumar , Cummins Breschine , Gedeon Tomas 
Published: July 2023

AbstractMathematical modeling of the emergent dynamics of gene regulatory networks (GRN) faces a double challenge of (a) dependence of model dynamics on parameters, and (b) lack of reliable experimentally determined parameters. In this paper we compare two complementary approaches for describing GRN dynamics across unknown parameters: (1) parameter sampling and resulting ensemble statistics used by RACIPE (RAndom CIrcuit PErturbation), and (2) use of rigorous analysis of combinatorial approximation of the ODE models by DSGRN (Dynamic Signatures Generated by Regulatory Networks). We find a very good agreement between RACIPE simulation and DSGRN predictions for four different 2- and 3-node networks typically observed in cellular decision making. This observation is remarkable since the DSGRN approach assumes that the Hill coefficients of the models are very high while RACIPE assumes the values in the range 1-6. Thus DSGRN parameter domains, explicitly defined by inequalities between systems parameters, are highly predictive of ODE model dynamics within a biologically reasonable range of parameters.
Synthesis of a glycan hairpin
Authors: Fittolani Giulio , Tyrikos-Ergas Theodore , Poveda Ana , Yu Yang , Yadav Nishu , Seeberger Peter H. , Jiménez-Barbero Jesús , Delbianco Martina 
Published: July 2023

AbstractThe primary sequence of a biopolymer encodes the essential information for folding, permitting to carry out sophisticated functions. Inspired by natural biopolymers, peptide and nucleic acid sequences have been designed to adopt particular three-dimensional (3D) shapes and programmed to exert specific functions. In contrast, synthetic glycans capable of autonomously folding into defined 3D conformations have so far not been explored owing to their structural complexity and lack of design rules. Here we generate a glycan that adopts a stable secondary structure not present in nature, a glycan hairpin, by combining natural glycan motifs, stabilized by a non-conventional hydrogen bond and hydrophobic interactions. Automated glycan assembly enabled rapid access to synthetic analogues, including site-specific 13C-labelled ones, for nuclear magnetic resonance conformational analysis. Long-range inter-residue nuclear Overhauser effects unequivocally confirmed the folded conformation of the synthetic glycan hairpin. The capacity to control the 3D shape across the pool of available monosaccharides has the potential to afford more foldamer scaffolds with programmable properties and functions.
Next-generation protein-based materials capture and preserve projectiles from supersonic impacts
Authors: Doolan Jack A. , Alesbrook Luke S. , Baker Karen , Brown Ian R. , Williams George T. , Hilton Kira L. F. , Tabata Makoto , Wozniakiewicz Penelope J. , Hiscock Jennifer R. , Goult Benjamin T. 
Published: July 2023

AbstractExtreme energy-dissipating materials are essential for a range of applications. The military and police force require ballistic armour to ensure the safety of their personnel, while the aerospace industry requires materials that enable the capture, preservation and study of hypervelocity projectiles. However, current industry standards display at least one inherent limitation, such as weight, breathability, stiffness, durability and failure to preserve captured projectiles. To resolve these limitations, we have turned to nature, using proteins that have evolved over millennia to enable effective energy dissipation. Specifically, a recombinant form of the mechanosensitive protein talin was incorporated into a monomeric unit and crosslinked, resulting in a talin shock-absorbing material (TSAM). When subjected to 1.5 km s−1 supersonic shots, TSAMs were shown to absorb the impact and capture and preserve the projectile.
Single multimode fibre for in vivo light-field-encoded endoscopic imaging
Authors: Wen Zhong , Dong Zhenyu , Deng Qilin , Pang Chenlei , Kaminski Clemens F. , Xu Xiaorong , Yan Huihui , Wang Liqiang , Liu Songguo , Tang Jianbin , Chen Wei , Liu Xu , Yang Qing 
Published: July 2023

AbstractSuper-resolution microscopy is typically not applicable to in situ imaging through a narrow channel due to the requirement for complex optics. Although multimode fibres (MMFs) have emerged as a potential platform for cost-effective and precise endoscopic imaging, they suffer from extreme sensitivity to bending and other external conditions. Here we demonstrate imaging through a single thin MMF for in vivo light-field encoded imaging with subcellular resolution. We refer to the technique as spatial-frequency tracking adaptive beacon light-field-encoded (STABLE) endoscopy. Spatial-frequency beacon tracking provides up to 1 kHz disorder tracking frequency, thus ensuring stable imaging through long-haul MMFs under fibre bending and various operating conditions. The full-vector modulation and fluorescence emission difference are combined to enhance the imaging signal-to-noise ratio and achieve a subdiffraction resolution of 250 nm. We integrate STABLE in a white-light endoscope and demonstrate cross-scale imaging in a bronchus model and in vivo imaging in mice models. The high-resolution and resilience to observation in a minimally invasive manner paves the way to the expansion of MMF in endoscopy to the study of disease mechanisms in biomedical sciences and clinical studies.
Discovery of VH domains that allosterically inhibit ENPP1
Authors: Solomon Paige E. , Bracken Colton J. , Carozza Jacqueline A. , Wang Haoqing , Young Elizabeth P. , Wellner Alon , Liu Chang C. , Sweet-Cordero E. Alejandro , Li Lingyin , Wells James A. 
Published: July 2023

AbstractEctodomain phosphatase/phosphodiesterase-1 (ENPP1) is overexpressed on cancer cells and functions as an innate immune checkpoint by hydrolyzing extracellular cyclic guanosine monophosphate adenosine monophosphate (cGAMP). Biologic inhibitors have not yet been reported and could have substantial therapeutic advantages over current small molecules because they can be recombinantly engineered into multifunctional formats and immunotherapies. Here we used phage and yeast display coupled with in cellulo evolution to generate variable heavy (VH) single-domain antibodies against ENPP1 and discovered a VH domain that allosterically inhibited the hydrolysis of cGAMP and adenosine triphosphate (ATP). We solved a 3.2 Å-resolution cryo-electron microscopy structure for the VH inhibitor complexed with ENPP1 that confirmed its new allosteric binding pose. Finally, we engineered the VH domain into multispecific formats and immunotherapies, including a bispecific fusion with an anti-PD-L1 checkpoint inhibitor that showed potent cellular activity.
Exploration of novel αβ-protein folds through de novo design
Authors: Minami Shintaro , Kobayashi Naohiro , Sugiki Toshihiko , Nagashima Toshio , Fujiwara Toshimichi , Tatsumi-Koga Rie , Chikenji George , Koga Nobuyasu 
Published: July 2023

AbstractA fundamental question in protein evolution is whether nature has exhaustively sampled nearly all possible protein folds throughout evolution, or whether a large fraction of the possible folds remains unexplored. To address this question, we defined a set of rules for β-sheet topology to predict novel αβ-folds and carried out a systematic de novo protein design exploration of the novel αβ-folds predicted by the rules. The designs for all eight of the predicted novel αβ-folds with a four-stranded β-sheet, including a knot-forming one, folded into structures close to the design models. Further, the rules predicted more than 10,000 novel αβ-folds with five- to eight-stranded β-sheets; this number far exceeds the number of αβ-folds observed in nature so far. This result suggests that a vast number of αβ-folds are possible, but have not emerged or have become extinct due to evolutionary bias.
Validation and enhancement of a vocal fold medial surface 3D reconstruction approach for in-vivo application
Authors: Schlegel Patrick , Döllinger Michael , Reddy Neha K. , Zhang Zhaoyan , Chhetri Dinesh K. 
Published: July 2023

AbstractIn laryngeal research, studying the vertical vocal fold oscillation component is often disregarded. However, vocal fold oscillation by its nature is a three-dimensional process. In the past, we have developed an in-vivo experimental protocol to reconstruct the full, three-dimensional vocal fold vibration. The goal of this study is to validate this 3D reconstruction method. We present an in-vivo canine hemilarynx setup using high-speed video recording and a right-angle prism for 3D reconstruction of vocal fold medial surface vibrations. The 3D surface is reconstructed from the split image provided by the prism. For validation, reconstruction error was calculated for objects located at a distance of up to 15 mm away from the prism. The influence of camera angle, changing calibrated volume, and calibration errors were determined. Overall average 3D reconstruction error is low and does not exceed 0.12 mm at 5 mm distance from the prism. Influence of a moderate (5°) and large (10°) deviation in camera angle led to a slight increase in error to 0.16 mm and 0.17 mm, respectively. This procedure is robust towards changes in calibration volume and small calibration errors. This makes this 3D reconstruction approach a useful tool for the reconstruction of accessible and moving tissue surfaces.
MHD micro polar fluid flow over a stretching surface with melting and slip effect
Authors: Sharma Surbhi , Dadheech Amit , Parmar Amit , Arora Jyoti , Al-Mdallal Qasem , Saranya S. 
Published: July 2023

AbstractObjective of the present analysis is to represent the phenomenon of Heat–mass transfer on MHD micro polar fluids caused by permeable and continuously stretching sheet along with slip impacts fostered in a porous medium. Consequently, the equation of energy includes the term of non-uniform heat source/sink. The equation regarding species concentration in cooperates the terms indicating order of chemical reaction to characterize the chemically reactive species. The application software MATLAB with governing syntax of bvp4c technique are employed to reduce equations of momentum, micro-rations, heat, and concentration into suitable required simplifications to derive necessary arithmetic manipulations of available non-linear equations. Various dimensionless parameters are portrayed in the available graphs with essential consequences. Analysis discovered that micro-polar fluid improves velocity and temperature profile while it suppresses micro-rations profile also magnetic parameter ($$M$$
M
) and porosity parameter ($$K_p$$

K
p

) reduces the momentum boundary layer thickness. The acquired deductions verify remarkable correspondence with already reported in an open literature.
An investigation of the flexural behaviour of large-span prestressed and steel-reinforced concrete slabs
Authors: Han Tiancheng , Liang Shuting , Zhu Xiaojun , Wang Wenkang , Yang Jian 
Published: July 2023

AbstractThe prestressed and steel-reinforced concrete slab (PSRCS) is an innovative composite structural member offering high load capacity and stiffness and exceptional anti-crack performance, making it a leading trend in composite structures. This paper presents the derived calculation formulas for bearing capacity, section stiffness, mid-span deflection of PSRCS. Additionally, a numerical analysis of PSRCS is conducted using ABAQUS software, with several models created to systematically investigate bearing capacity, section stiffness, anti-crack performance, and failure mode. Concurrently, PSRCS member parameters are analyzed for optimal design, and the results of finite element (FE) calculations are compared with theoretical formula calculations. The results demonstrate that PSRCS exhibits superior load capacity, section stiffness, and anti-crack performance comparing to conventional slabs. The parametric analysis offers optimal design for each parameter and presents the corresponding recommended span-to-depth ratios for various spans in PSRCS applications.
Disentangling potential genotypes for macro and micro nutrients and polymorphic markers in Chickpea
Authors: Mittal Neha , Bhardwaj Juhi , Verma Shruti , Singh Rajesh Kumar , Yadav Renu , Kaur D. , Talukdar Akshay , Yadav Neelam , Kumar Rajendra 
Published: July 2023

AbstractThe present investigation was conducted to assess the nutritional diverseness and identify novel genetic resources to be utilized in chickpea breeding for macro and micro nutrients. The plants were grown in randomized block design. Nutritional and phytochemical properties of nine chickpea genotypes were estimated. The EST sequences from NCBI database were downloaded in FASTA format, clustered into contigs using CAP3, mined for novel SSRs using TROLL analysis and primer pairs were designed using Primer 3 software. Jaccard’s similarity coefficients were used to compare the nutritional and molecular indexes followed by dendrograms construction employing UPGMA approach. The genotypes PUSA-1103, K-850, PUSA-1108, PUSA-1053 and the EST-SSR markers including the 5 newly designed namely ICCeM0012, ICCeM0049, ICCeM0067, ICCeM0070, ICCeM0078, SVP55, SVP95, SVP96, SVP146, and SVP217 were found as potential donor/marker resources for the macro–micro nutrients. The genotypes differed (p < 0.05) for nutritional properties. Amongst newly designed primers, 6 were found polymorphic with median PIC (0.46). The alleles per primer ranged 1 to 8. Cluster analysis based on nutritional and molecular diversities partially matched to each other in principle. The identified novel genetic resources may be used to widen the germplasm base, prepare maintainable catalogue and identify systematic blueprints for future chickpea breeding strategies targeting macro–micro nutrients.