bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defect-driven nanostructuring of low-nuclearity Pt-Mo ensembles for continuous gas-phase formic acid dehydrogenation
Authors: Guo Luyao , Zhuge Kaixuan , Yan Siyang , Wang Shiyi , Zhao Jia , Wang Saisai , Qiao Panzhe , Liu Jiaxu , Mou Xiaoling , Zhu Hejun , Zhao Ziang , Yan Li , Lin Ronghe , Ding Yunjie 
Published: November 2023

AbstractSupported metal clusters comprising of well-tailored low-nuclearity heteroatoms have great potentials in catalysis owing to the maximized exposure of active sites and metal synergy. However, atomically precise design of these architectures is still challenging for the lack of practical approaches. Here, we report a defect-driven nanostructuring strategy through combining defect engineering of nitrogen-doped carbons and sequential metal depositions to prepare a series of Pt and Mo ensembles ranging from single atoms to sub-nanoclusters. When applied in continuous gas-phase decomposition of formic acid, the low-nuclearity ensembles with unique Pt3Mo1N3 configuration deliver high-purity hydrogen at full conversion with unexpected high activity of 0.62 molHCOOH molPt−1 s−1 and remarkable stability, significantly outperforming the previously reported catalysts. The remarkable performance is rationalized by a joint operando dual-beam Fourier transformed infrared spectroscopy and density functional theory modeling study, pointing to the Pt-Mo synergy in creating a new reaction path for consecutive HCOOH dissociations.
Activation and substrate specificity of the human P4-ATPase ATP8B1
Authors: Dieudonné Thibaud , Kümmerer Felix , Laursen Michelle Juknaviciute , Stock Charlott , Flygaard Rasmus Kock , Khalid Syma , Lenoir Guillaume , Lyons Joseph A. , Lindorff-Larsen Kresten , Nissen Poul 
Published: November 2023

AbstractAsymmetric distribution of phospholipids in eukaryotic membranes is essential for cell integrity, signaling pathways, and vesicular trafficking. P4-ATPases, also known as flippases, participate in creating and maintaining this asymmetry through active transport of phospholipids from the exoplasmic to the cytosolic leaflet. Here, we present a total of nine cryo-electron microscopy structures of the human flippase ATP8B1-CDC50A complex at 2.4 to 3.1 Å overall resolution, along with functional and computational studies, addressing the autophosphorylation steps from ATP, substrate recognition and occlusion, as well as a phosphoinositide binding site. We find that the P4-ATPase transport site is occupied by water upon phosphorylation from ATP. Additionally, we identify two different autoinhibited states, a closed and an outward-open conformation. Furthermore, we identify and characterize the PI(3,4,5)P3 binding site of ATP8B1 in an electropositive pocket between transmembrane segments 5, 7, 8, and 10. Our study also highlights the structural basis of a broad lipid specificity of ATP8B1 and adds phosphatidylinositol as a transport substrate for ATP8B1. We report a critical role of the sn-2 ester bond of glycerophospholipids in substrate recognition by ATP8B1 through conserved S403. These findings provide fundamental insights into ATP8B1 catalytic cycle and regulation, and substrate recognition in P4-ATPases.
A toxin-antidote system contributes to interspecific reproductive isolation in rice
Authors: You Shimin , Zhao Zhigang , Yu Xiaowen , Zhu Shanshan , Wang Jian , Lei Dekun , Zhou Jiawu , Li Jing , Chen Haiyuan , Xiao Yanjia , Chen Weiwei , Wang Qiming , Lu Jiayu , Chen Keyi , Zhou Chunlei , Zhang Xin , Cheng Zhijun , Guo Xiuping , Ren Yulong , Zheng Xiaoming , Liu Shijia , Liu Xi , Tian Yunlu , Jiang Ling , Tao Dayun , Wu Chuanyin , Wan Jianmin 
Published: November 2023

AbstractBreakdown of reproductive isolation facilitates flow of useful trait genes into crop plants from their wild relatives. Hybrid sterility, a major form of reproductive isolation exists between cultivated rice (Oryza sativa) and wild rice (O. meridionalis, Mer). Here, we report the cloning of qHMS1, a quantitative trait locus controlling hybrid male sterility between these two species. Like qHMS7, another locus we cloned previously, qHMS1 encodes a toxin-antidote system, but differs in the encoded proteins, their evolutionary origin, and action time point during pollen development. In plants heterozygous at qHMS1, ~ 50% of pollens carrying qHMS1-D (an allele from cultivated rice) are selectively killed. In plants heterozygous at both qHMS1 and qHMS7, ~ 75% pollens without co-presence of qHMS1-Mer and qHMS7-D are selectively killed, indicating that the antidotes function in a toxin-dependent manner. Our results indicate that different toxin-antidote systems provide stacked reproductive isolation for maintaining species identity and shed light on breakdown of hybrid male sterility.
LncRNA INHEG promotes glioma stem cell maintenance and tumorigenicity through regulating rRNA 2’-O-methylation
Authors: Liu Lihui , Liu Ziyang , Liu Qinghua , Wu Wei , Lin Peng , Liu Xing , Zhang Yuechuan , Wang Dongpeng , Prager Briana C. , Gimple Ryan C. , Yu Jichuan , Zhao Weixi , Wu Qiulian , Zhang Wei , Wu Erzhong , Chen Xiaomin , Luo Jianjun , Rich Jeremy N. , Xie Qi , Jiang Tao , Chen Runsheng 
Published: November 2023

AbstractGlioblastoma (GBM) ranks among the most lethal of human cancers, containing glioma stem cells (GSCs) that display therapeutic resistance. Here, we report that the lncRNA INHEG is highly expressed in GSCs compared to differentiated glioma cells (DGCs) and promotes GSC self-renewal and tumorigenicity through control of rRNA 2’-O-methylation. INHEG induces the interaction between SUMO2 E3 ligase TAF15 and NOP58, a core component of snoRNP that guides rRNA methylation, to regulate NOP58 sumoylation and accelerate the C/D box snoRNP assembly. INHEG activation enhances rRNA 2’-O-methylation, thereby increasing the expression of oncogenic proteins including EGFR, IGF1R, CDK6 and PDGFRB in glioma cells. Taken together, this study identifies a lncRNA that connects snoRNP-guided rRNA 2’-O-methylation to upregulated protein translation in GSCs, supporting an axis for potential therapeutic targeting of gliomas.
scReadSim: a single-cell RNA-seq and ATAC-seq read simulator
Authors: Yan Guanao , Song Dongyuan , Li Jingyi Jessica 
Published: November 2023

AbstractBenchmarking single-cell RNA-seq (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) computational tools demands simulators to generate realistic sequencing reads. However, none of the few read simulators aim to mimic real data. To fill this gap, we introduce scReadSim, a single-cell RNA-seq and ATAC-seq read simulator that allows user-specified ground truths and generates synthetic sequencing reads (in a FASTQ or BAM file) by mimicking real data. At both read-sequence and read-count levels, scReadSim mimics real scRNA-seq and scATAC-seq data. Moreover, scReadSim provides ground truths, including unique molecular identifier (UMI) counts for scRNA-seq and open chromatin regions for scATAC-seq. In particular, scReadSim allows users to design cell-type-specific ground-truth open chromatin regions for scATAC-seq data generation. In benchmark applications of scReadSim, we show that UMI-tools achieves the top accuracy in scRNA-seq UMI deduplication, and HMMRATAC and MACS3 achieve the top performance in scATAC-seq peak calling.
Key role of eg* band broadening in nickel-based oxyhydroxides on coupled oxygen evolution mechanism
Authors: Zhong Haoyin , Zhang Qi , Yu Junchen , Zhang Xin , Wu Chao , An Hang , Ma Yifan , Wang Hao , Zhang Jun , Zhang Yong-Wei , Diao Caozheng , Yu Zhi Gen , Xi Shibo , Wang Xiaopeng , Xue Junmin 
Published: November 2023

AbstractA coupled oxygen evolution mechanism (COM) during oxygen evolution reaction (OER) has been reported in nickel oxyhydroxides (NiOOH)-based materials by realizing eg* band (3d electron states with eg symmetry) broadening and light irradiation. However, the link between the eg* band broadening extent and COM-based OER activities remains unclear. Here, Ni1-xFexOOH (x = 0, 0.05, 0,2) are prepared to investigate the underlying mechanism governing COM-based activities. It is revealed that in low potential region, realizing stronger eg* band broadening could facilitate the *OH deprotonation. Meanwhile, in high potential region where the photon utilization is the rate-determining step, a stronger eg* band broadening would widen the non-overlapping region between dz2 and a1g* orbitals, thereby enhancing photon utilization efficiency. Consequently, a stronger eg* band broadening could effectuate more efficient OER activities. Moreover, we demonstrate the universality of this concept by extending it to reconstruction-derived X-NiOOH (X = NiS2, NiSe2, Ni4P5) with varying extent of eg* band broadening. Such an understanding of the COM would provide valuable guidance for the future development of highly efficient OER electrocatalysts.
Regulation of species metabolism in synthetic community systems by environmental pH oscillations
Authors: Li Shubin , Zhao Yingming , Wu Shuqi , Zhang Xiangxiang , Yang Boyu , Tian Liangfei , Han Xiaojun 
Published: November 2023

AbstractConstructing a synthetic community system helps scientist understand the complex interactions among species in a community and its environment. Herein, a two-species community is constructed with species A (artificial cells encapsulating pH-responsive molecules and sucrose) and species B (Saccharomyces cerevisiae), which causes the environment to exhibit pH oscillation behaviour due to the generation and dissipation of CO2. In addition, a three-species community is constructed with species A′ (artificial cells containing sucrose and G6P), species B, and species C (artificial cells containing NAD+ and G6PDH). The solution pH oscillation regulates the periodical release of G6P from species A′; G6P then enters species C to promote the metabolic reaction that converts NAD+ to NADH. The location of species A′ and B determines the metabolism behaviour in species C in the spatially coded three-species communities with CA′B, CBA′, and A′CB patterns. The proposed synthetic community system provides a foundation to construct a more complicated microecosystem.
c-di-GMP inhibits the DNA binding activity of H-NS in Salmonella
Authors: Li Shuyu , Liu Qinmeng , Duan Chongyi , Li Jialin , Sun Hengxi , Xu Lei , Yang Qiao , Wang Yao , Shen Xihui , Zhang Lei 
Published: November 2023

AbstractCyclic di-GMP (c-di-GMP) is a second messenger that transduces extracellular stimuli into cellular responses and regulates various biological processes in bacteria. H-NS is a global regulatory protein that represses expression of many genes, but how H-NS activity is modulated by environmental signals remains largely unclear. Here, we show that high intracellular c-di-GMP levels, induced by environmental cues, relieve H-NS-mediated transcriptional silencing inSalmonella entericaserovar Typhimurium. We find that c-di-GMP binds to the H-NS protein to inhibit its binding to DNA, thus derepressing genes silenced by H-NS. However, c-di-GMP is unable to displace H-NS from DNA. In addition, a K107A mutation in H-NS abolishes response to c-di-GMP but leaves its DNA binding activity unaffected in vivo. Our results thus suggest a mechanism by which H-NS acts as an environment-sensing regulator in Gram-negative bacteria.
Metaproteogenomic analysis of saliva samples from Parkinson’s disease patients with cognitive impairment
Authors: Arıkan Muzaffer , Demir Tuğçe Kahraman , Yıldız Zeynep , Nalbantoğlu Özkan Ufuk , Korkmaz Nur Damla , Yılmaz Nesrin H. , Şen Aysu , Özcan Mutlu , Muth Thilo , Hanoğlu Lütfü , Yıldırım Süleyman 
Published: November 2023

AbstractCognitive impairment (CI) is very common in patients with Parkinson’s Disease (PD) and progressively develops on a spectrum from mild cognitive impairment (PD-MCI) to full dementia (PDD). Identification of PD patients at risk of developing cognitive decline, therefore, is unmet need in the clinic to manage the disease. Previous studies reported that oral microbiota of PD patients was altered even at early stages and poor oral hygiene is associated with dementia. However, data from single modalities are often unable to explain complex chronic diseases in the brain and cannot reliably predict the risk of disease progression. Here, we performed integrative metaproteogenomic characterization of salivary microbiota and tested the hypothesis that biological molecules of saliva and saliva microbiota dynamically shift in association with the progression of cognitive decline and harbor discriminatory key signatures across the spectrum of CI in PD. We recruited a cohort of 115 participants in a multi-center study and employed multi-omics factor analysis (MOFA) to integrate amplicon sequencing and metaproteomic analysis to identify signature taxa and proteins in saliva. Our baseline analyses revealed contrasting interplay between the genus Neisseria and Lactobacillus and Ligilactobacillus genera across the spectrum of CI. The group specific signature profiles enabled us to identify bacterial genera and protein groups associated with CI stages in PD. Our study describes compositional dynamics of saliva across the spectrum of CI in PD and paves the way for developing non-invasive biomarker strategies to predict the risk of CI progression in PD.
No graph state is preparable in quantum networks with bipartite sources and no classical communication
Authors: Makuta Owidiusz , Ligthart Laurens T. , Augusiak Remigiusz 
Published: November 2023

AbstractIn research concerning quantum networks, it is often assumed that the parties can classically communicate with each other. However, classical communication might introduce a substantial delay to the network, especially if it is large. As the latency of a network is one of its most important characteristics, it is interesting to consider quantum networks in which parties cannot communicate classically and ask what limitations this assumption imposes on the possibility of preparing multipartite states in such networks. We show that graph states of an arbitrary prime local dimension known for their numerous applications in quantum information cannot be generated in a quantum network in which parties are connected via sources of bipartite quantum states and the classical communication is replaced by some pre-shared classical correlations. We then generalise our result to arbitrary quantum states that are sufficiently close to graph states.
An integrated model for pre- and post-harvest aflatoxin contamination in maize
Authors: Stutt Richard O.J.H. , Castle Matthew D. , Markwell Peter , Baker Robert , Gilligan Christopher A. 
Published: November 2023

AbstractAflatoxin contamination caused by colonization of maize by Aspergillus flavus continues to pose a major human and livestock health hazard in the food chain. Increasing attention has been focused on the development of models to predict risk and to identify effective intervention strategies. Most risk prediction models have focused on elucidating weather and site variables on the pre-harvest dynamics of A. flavus growth and aflatoxin production. However fungal growth and toxin accumulation continue to occur after harvest, especially in countries where storage conditions are limited by logistical and cost constraints. In this paper, building on previous work, we introduce and test an integrated meteorology-driven epidemiological model that covers the entire supply chain from planting to delivery. We parameterise the model using approximate Bayesian computation with monthly time-series data over six years for contamination levels of aflatoxin in daily shipments received from up to three sourcing regions at a high-volume maize processing plant in South Central India. The time series for aflatoxin levels from the parameterised model successfully replicated the overall profile, scale and variance of the historical aflatoxin datasets used for fitting and validation. We use the model to illustrate the dynamics of A. flavus growth and aflatoxin production during the pre- and post-harvest phases in different sourcing regions, in short-term predictions to inform decision making about sourcing supplies and to compare intervention strategies to reduce the risks of aflatoxin contamination.
Photos and rendered images of LEGO bricks
Authors: Boiński Tomasz Maria 
Published: November 2023

AbstractThe paper describes a collection of datasets containing both LEGO brick renders and real photos. The datasets contain around 155,000 photos and nearly 1,500,000 renders. The renders aim to simulate real-life photos of LEGO bricks allowing faster creation of extensive datasets. The datasets are publicly available via the Gdansk University of Technology “Most Wiedzy” institutional repository. The source files of all tools used during the creation of the dataset were made publicly available via GitHub repositories. The images, both photos and the renders were annotated with the unique brick ID and category from the official LEGO catalog. The proposed datasets are stored in easy-to-read formats and are labeled via directory structure allowing easy manipulation and conversion of metadata to other formats.
In silico investigation on interaction of small Ag6 nano-particle cluster with tyramine neurotransmitter
Authors: Chakroborty Subhendu , Shakerzadeh E. , Yadav T. , Mishra Nilima Priyadarsini , Barik Arundhati , Upadhyay Versha , Abhilasha  , Soren Siba , Malviya Jitendra , Panda Amiya Ranjan , Uniyal Kartik , Kumar Narendra , Wagadre Shradha , Pandey F. P. 
Published: November 2023

AbstractThe interaction of tyramine neurotransmitter with silver nano-particle (Ag6) cluster is explored in terms of the molecular structure, electronic properties and NBO analysis of tyramine-AgNPs bio-molecular conjugate. The adsorption mechanism of tyramine onto the Ag6 cluster has been investigated through computing of the electronic and geometrical properties in addition to the adsorption energies in various possible configurations. The magnitude of adsorption energy corresponding to the most favorable tyramine-Ag6 bio-molecular conjugate has been computed to be − 14.36 kcal/mol in the gas phase, which infers a good adsorption of tyramine with AgNPs cluster suggesting the practical applications of tyramine-AgNPs bio-molecular conjugates in bio-sensing, drug delivery, bio-imaging and other applications. Different electronic properties such as the energy gap of HOMO–LUMO, Fermi level and work function have been investigated in detail. Moreover, the effect of aqueous media on adsorption energy and electronic properties of the most favorable tyramine-AgNPs bio-molecular conjugate is investigated in order to understand the impact of the real biological situation.
Modelling droplet size distribution in inline electrostatic coalescers for improved crude oil processing
Authors: Kooti Ghazal , Dabir Bahram , Taherdangkoo Reza , Butscher Christoph 
Published: November 2023

AbstractWater-in-oil emulsions pose significant challenges in the petroleum and chemical industrial processes, necessitating the coalescence enhancement of dispersed water droplets in emulsified oils. This study develops a mathematical model to predict the evolution of water droplet size distribution in inline electrostatic coalescers (IEC) as a promising means to improve the water separation efficiency of current oil processing systems. The proposed model utilizes the population balance modelling approach to effectively simulate the dynamic and complex processes of coalescence and breakage of droplets in crude oil which directly influence the separation efficiency of the process. The method of classes as an effective mathematical technique is selected to solve the population balance equation (PBE). The accuracy of the model and considered assumptions agree well with experimental data collected from the literature. The results demonstrate the model's ability to accurately simulate droplet coalescence and breakage in emulsified oil while predicting droplet size distribution and water removal efficiency. The electric field strength, residence time, and fluid flow rate significantly influence the coalescence of droplets. At 4 kV and 5 m3/h after 4 s the mean diameter of droplets (D50) and separation efficiency reach the maximum of 94.3% and 432 µm, respectively. The model enables the optimization of operational conditions, resulting in increased performance and reliability of oil-processing systems while reducing the energy consumption and use of chemical demulsifiers. Additionally, utilization of the device in optimized conditions significantly reduces the size and weight of downstream separation equipment, which is particularly advantageous for heavy oils and offshore fields.
Construction of an anoikis-associated lncRNA-miRNA-mRNA network reveals the prognostic role of β-elemene in non-small cell lung cancer
Authors: Tan Kai , Zhang Changhui , He Zuomei , Zeng Puhua 
Published: November 2023

Abstractβ-Elemene is the main active ingredient in Curcumae Rhizoma that exerts antitumour effects. Anoikis affects tumour development through various biological pathways in non-small cell lung cancer (NSCLC), but the regulation between β-elemene and anoikis remains to be explored. First, we explored the molecular expression patterns of anoikis-associated genes (AAGs) using consensus clustering and characterized the impact of AAGs on patient prognosis, clinical characteristics, and genomic instability. In addition, we revealed that AAG regulatory genes have rich interactions with β-elemene targets, and established a lncRNA-miRNA-mRNA network to explain the effect of β-elemene on anoikis. Finally, to reveal the prognostic effect of their correlation, the prognostic scoring model and clinical nomogram of β-elemene and anoikis were successfully established by least absolute shrinkage and selection operator (LASSO) and random forest algorithms. This prognostic scoring model containing noncoding RNA (ncRNA) can indicate the immunotherapy and mutational landscape, providing a novel theoretical basis and direction for the study of the antitumour mechanism of β-elemene in NSCLC patients.
Novel role of folate (vitamin B9) released by fermenting bacteria under Human Intestine like environment
Authors: Nara Sharda , Parasher Gulshan , Malhotra Bansi Dhar , Rawat Manmeet 
Published: November 2023

AbstractThe anaerobic region of the gastrointestinal (GI) tract has been replicated in the anaerobic chamber of a microbial fuel cell (MFC). Electroactive biomolecules released by the facultative anaerobes (Providencia rettgeri) under anoxic conditions have been studied for their potential role for redox balance. MALDI study reveals the presence of vitamin B9 (folate), 6-methylpterin, para-aminobenzoic acid (PABA) and pteroic acid called pterin pool. ATR-FTIR studies further confirm the presence of the aromatic ring and side chains of folate, 6-methylpterin and PABA groups. The photoluminescence spectra of the pool exhibit the maximum emission at 420, 425, 440, and 445 nm when excited by 310, 325, 350, and 365 nm wavelengths (day 20 sample) highlighting the presence of tunable bands. The cyclic voltammetric studies indicate the active participation of pterin pool molecules in the transfer of electrons with redox potentials at − 0.2 V and − 0.4 V for p-aminobenzoate and pterin groups, respectively. In addition, it is observed that under prolonged conditions of continuous oxidative stress (> 20 days), quinonoid tetrahydrofolate is formed, leading to temporary storage of charge. The results of the present study may potentially be useful in designing effective therapeutic strategies for the management of various GI diseases by promoting or blocking folate receptors.