bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oxynitrides enabled photoelectrochemical water splitting with over 3,000 hrs stable operation in practical two-electrode configuration
Authors: Xiao Yixin , Kong Xianghua , Vanka Srinivas , Dong Wan Jae , Zeng Guosong , Ye Zhengwei , Sun Kai , Navid Ishtiaque Ahmed , Zhou Baowen , Toma Francesca M. , Guo Hong , Mi Zetian 
Published: April 2023

AbstractSolar photoelectrochemical reactions have been considered one of the most promising paths for sustainable energy production. To date, however, there has been no demonstration of semiconductor photoelectrodes with long-term stable operation in a two-electrode configuration, which is required for any practical application. Herein, we demonstrate the stable operation of a photocathode comprising Si and GaN, the two most produced semiconductors in the world, for 3,000 hrs without any performance degradation in two-electrode configurations. Measurements in both three- and two-electrode configurations suggest that surfaces of the GaN nanowires on Si photocathode transform in situ into Ga-O-N that drastically enhances hydrogen evolution and remains stable for 3,000 hrs. First principles calculations further revealed that the in-situ Ga-O-N species exhibit atomic-scale surface metallization. This study overcomes the conventional dilemma between efficiency and stability imposed by extrinsic cocatalysts, offering a path for practical application of photoelectrochemical devices and systems for clean energy.
Increasing deep-water overflow from the Pacific into the South China Sea revealed by mooring observations
Authors: Zhou Chun , Xiao Xin , Zhao Wei , Yang Jiayan , Huang Xiaodong , Guan Shoude , Zhang Zhiwei , Tian Jiwei 
Published: April 2023

AbstractCold and dense water from the North Pacific Ocean that spills through the Luzon Strait, the only deep conduit between the South China Sea (SCS) and the Pacific Ocean, renews deep-water mass, modulates hydrographic and biogeochemical cycles, and drives abyssal and overturning circulations in the SCS. The variability of this key oceanic process, however, has been poorly studied, mainly due to a lack of sustained observations. A comprehensive observational program that started in 2009 has provided 12 years of continuous time series of velocity and volume transport within the Luzon Strait. Here we show the observation-based assessment of decadal trends of deep-water transport through this vital passage. With the estimated 12-year mean volume transport of the deep-water overflow into the SCS of 0.84 ± 0.39 Sv (1 Sv = 106 m3 s−1), a significant linear upward trend of 9% is revealed during this period. This is consistent with long-term changes in satellite-observed ocean bottom pressure. The results of this study may have broad implications for the overturning circulations and biogeochemical processes, including carbon cycles in this region.
Integrative modeling of tumor genomes and epigenomes for enhanced cancer diagnosis by cell-free DNA
Authors: Bae Mingyun , Kim Gyuhee , Lee Tae-Rim , Ahn Jin Mo , Park Hyunwook , Park Sook Ryun , Song Ki Byung , Jun Eunsung , Oh Dongryul , Lee Jeong-Won , Park Young Sik , Song Ki-Won , Byeon Jeong-Sik , Kim Bo Hyun , Sohn Joo Hyuk , Kim Min Hwan , Kim Gun Min , Chie Eui Kyu , Kang Hyun-Cheol , Kong Sun-Young , Woo Sang Myung , Lee Jeong Eon , Ryu Jai Min , Lee Junnam , Kim Dasom , Ki Chang-Seok , Cho Eun-Hae , Choi Jung Kyoon 
Published: April 2023

AbstractMulti-cancer early detection remains a key challenge in cell-free DNA (cfDNA)-based liquid biopsy. Here, we perform cfDNA whole-genome sequencing to generate two test datasets covering 2125 patient samples of 9 cancer types and 1241 normal control samples, and also a reference dataset for background variant filtering based on 20,529 low-depth healthy samples. An external cfDNA dataset consisting of 208 cancer and 214 normal control samples is used for additional evaluation. Accuracy for cancer detection and tissue-of-origin localization is achieved using our algorithm, which incorporates cancer type-specific profiles of mutation distribution and chromatin organization in tumor tissues as model references. Our integrative model detects early-stage cancers, including those of pancreatic origin, with high sensitivity that is comparable to that of late-stage detection. Model interpretation reveals the contribution of cancer type-specific genomic and epigenomic features. Our methodologies may lay the groundwork for accurate cfDNA-based cancer diagnosis, especially at early stages.
Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining
Authors: Bryer Alexander J. , Rey Juan S. , Perilla Juan R. 
Published: April 2023

AbstractDimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive capability. Here, we present substantial advances to the shape based coarse graining (SBCG) method, which we refer to as SBCG2. SBCG2 utilizes a revitalized formulation of the topology representing network which makes high-granularity modeling possible, preserving atomistic details that maintain assembly characteristics. Further, we present a method of granularity selection based on charge density Fourier Shell Correlation and have additionally developed a refinement method to optimize, adjust and validate high-granularity models. We demonstrate our approach with the conical HIV-1 capsid and heteromultimeric cofilin-2 bound actin filaments. Our approach is available in the Visual Molecular Dynamics (VMD) software suite, and employs a CHARMM-compatible Hamiltonian that enables high-performance simulation in the GPU-resident NAMD3 molecular dynamics engine.
Coupling acid catalysis and selective oxidation over MoO3-Fe2O3 for chemical looping oxidative dehydrogenation of propane
Authors: Wang Xianhui , Pei Chunlei , Zhao Zhi-Jian , Chen Sai , Li Xinyu , Sun Jiachen , Song Hongbo , Sun Guodong , Wang, Wei , Chang Xin , Zhang Xianhua , Gong Jinlong 
Published: April 2023

AbstractRedox catalysts play a vital role in chemical looping oxidative dehydrogenation processes, which have recently been considered to be a promising prospect for propylene production. This work describes the coupling of surface acid catalysis and selective oxidation from lattice oxygen over MoO3-Fe2O3 redox catalysts for promoted propylene production. Atomically dispersed Mo species over γ-Fe2O3 introduce effective acid sites for the promotion of propane conversion. In addition, Mo could also regulate the lattice oxygen activity, which makes the oxygen species from the reduction of γ-Fe2O3 to Fe3O4 contribute to selectively oxidative dehydrogenation instead of over-oxidation in pristine γ-Fe2O3. The enhanced surface acidity, coupled with proper lattice oxygen activity, leads to a higher surface reaction rate and moderate oxygen diffusion rate. Consequently, this coupling strategy achieves a robust performance with 49% of propane conversion and 90% of propylene selectivity for at least 300 redox cycles and ultimately demonstrates a potential design strategy for more advanced redox catalysts.
Engineered CRISPR-OsCas12f1 and RhCas12f1 with robust activities and expanded target range for genome editing
Authors: Kong Xiangfeng , Zhang Hainan , Li Guoling , Wang Zikang , Kong Xuqiang , Wang Lecong , Xue Mingxing , Zhang Weihong , Wang Yao , Lin Jiajia , Zhou Jingxing , Shen Xiaowen , Wei Yinghui , Zhong Na , Bai Weiya , Yuan Yuan , Shi Linyu , Zhou Yingsi , Yang Hui 
Published: April 2023

AbstractThe type V-F CRISPR-Cas12f system is a strong candidate for therapeutic applications due to the compact size of the Cas12f proteins. In this work, we identify six uncharacterized Cas12f1 proteins with nuclease activity in mammalian cells from assembled bacterial genomes. Among them, OsCas12f1 (433 aa) from Oscillibacter sp. and RhCas12f1 (415 aa) from Ruminiclostridium herbifermentans, which respectively target 5’ T-rich Protospacer Adjacent Motifs (PAMs) and 5’ C-rich PAMs, show the highest editing activity. Through protein and sgRNA engineering, we generate enhanced OsCas12f1 (enOsCas12f1) and enRhCas12f1 variants, with 5’-TTN and 5’-CCD (D = not C) PAMs respectively, exhibiting much higher editing efficiency and broader PAMs, compared with the engineered variant Un1Cas12f1 (Un1Cas12f1_ge4.1). Furthermore, by fusing the destabilized domain with enOsCas12f1, we generate inducible-enOsCas12f1 and demonstate its activity in vivo by single adeno-associated virus delivery. Finally, dead enOsCas12f1-based epigenetic editing and gene activation can also be achieved in mammalian cells. This study thus provides compact gene editing tools for basic research with remarkable promise for therapeutic applications.
Temporal and spatial variability of dynamic microstate brain network in early Parkinson’s disease
Authors: Chu Chunguang , Zhang Zhen , Wang Jiang , Li Zhen , Shen Xiao , Han Xiaoxuan , Bai Lipeng , Liu Chen , Zhu Xiaodong 
Published: April 2023

AbstractChanges of brain network dynamics reveal variations in macroscopic neural activity patterns in behavioral and cognitive aspects. Quantification and application of changed dynamics in brain functional connectivity networks may contribute to a better understanding of brain diseases, and ultimately provide better prognostic indicators or auxiliary diagnostic tools. At present, most studies are focused on the properties of brain functional connectivity network constructed by sliding window method. However, few studies have explored evidence-based brain network construction algorithms that reflect disease specificity. In this work, we first proposed a novel approach to characterize the spatiotemporal variability of dynamic functional connectivity networks based on electroencephalography (EEG) microstate, and then developed a classification framework for integrating spatiotemporal variability of brain networks to improve early Parkinson’s disease (PD) diagnostic performance. The experimental results indicated that compared with the brain network construction method based on conventional sliding window, the proposed method significantly improved the performance of early PD recognition, demonstrating that the dynamic spatiotemporal variability of microstate-based brain networks can reflect the pathological changes in the early PD brain. Furthermore, we observed that the spatiotemporal variability of early PD brain network has a specific distribution pattern in brain regions, which can be quantified as the degree of motor and cognitive impairment, respectively. Our work offers innovative methodological support for future research on brain network, and provides deeper insights into the spatiotemporal interaction patterns of brain activity and their variabilities in early PD.
Optimization of Cas9 activity through the addition of cytosine extensions to single-guide RNAs
Authors: Kawamata Masaki , Suzuki Hiroshi I. , Kimura Ryota , Suzuki Atsushi 
Published: April 2023

AbstractThe precise regulation of the activity of Cas9 is crucial for safe and efficient editing. Here we show that the genome-editing activity of Cas9 can be constrained by the addition of cytosine stretches to the 5′-end of conventional single-guide RNAs (sgRNAs). Such a ‘safeguard sgRNA’ strategy, which is compatible with Cas12a and with systems for gene activation and interference via CRISPR (clustered regularly interspaced short palindromic repeats), leads to the length-dependent inhibition of the formation of functional Cas9 complexes. Short cytosine extensions reduced p53 activation and cytotoxicity in human pluripotent stem cells, and enhanced homology-directed repair while maintaining bi-allelic editing. Longer extensions further decreased on-target activity yet improved the specificity and precision of mono-allelic editing. By monitoring indels through a fluorescence-based allele-specific system and computational simulations, we identified optimal windows of Cas9 activity for a number of genome-editing applications, including bi-allelic and mono-allelic editing, and the generation and correction of disease-associated single-nucleotide substitutions via homology-directed repair. The safeguard-sgRNA strategy may improve the safety and applicability of genome editing.
Expanding known viral diversity in the healthy infant gut
Authors: Shah Shiraz A. , Deng Ling , Thorsen Jonathan , Pedersen Anders G. , Dion Moïra B. , Castro-Mejía Josué L. , Silins Ronalds , Romme Fie O. , Sausset Romain , Jessen Leon E. , Ndela Eric Olo , Hjelmsø Mathis , Rasmussen Morten A. , Redgwell Tamsin A. , Leal Rodríguez Cristina , Vestergaard Gisle , Zhang Yichang , Chawes Bo , Bønnelykke Klaus , Sørensen Søren J. , Bisgaard Hans , Enault Francois , Stokholm Jakob , Moineau Sylvain , Petit Marie-Agnès , Nielsen Dennis S. 
Published: April 2023

AbstractThe gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis and lysogeny, with the latter being especially prominent in the infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes and standardized detection methods. Here we systematically resolved the viral diversity in faecal viromes from 647 1-year-olds belonging to Copenhagen Prospective Studies on Asthma in Childhood 2010, an unselected Danish cohort of healthy mother–child pairs. By assembly and curation we uncovered 10,000 viral species from 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, belonging to theCaudoviricetesviral class. Hosts were determined for 79% of phage using clustered regularly interspaced short palindromic repeat spacers within bacterial metagenomes from the same children. TypicalBacteroides-infecting crAssphages were outnumbered by undescribed phage families infectingClostridialesandBifidobacterium. Phage lifestyles were conserved at the viral family level, with 33 virulent and 118 temperate phage families. Virulent phages were more abundant, while temperate ones were more prevalent and diverse. Together, the viral families found in this study expand existing phage taxonomy and provide a resource aiding future infant gut virome research.
Observation of strong backscattering in valley-Hall photonic topological interface modes
Authors: Rosiek Christian Anker , Arregui Guillermo , Vladimirova Anastasiia , Albrechtsen Marcus , Vosoughi Lahijani Babak , Christiansen Rasmus Ellebæk , Stobbe Søren 
Published: April 2023

AbstractThe unique properties of light underpin the visions of photonic quantum technologies, optical interconnects and a wide range of novel sensors, but a key limiting factor today is losses due to either absorption or backscattering on defects. Recent developments in topological photonics have fostered the vision of backscattering-protected waveguides made from topological interface modes, but, surprisingly, measurements of their propagation losses were so far missing. Here we report on measurements of losses in the slow-light regime of valley-Hall topological waveguides and find no indications of topological protection against backscattering on ubiquitous structural defects. We image the light scattered out from the topological waveguides and find that the propagation losses are due to Anderson localization. The only photonic topological waveguides proposed for materials without intrinsic absorption in the optical domain are quantum spin-Hall and valley-Hall interface states, but the former exhibit strong out-of-plane losses, and our work, therefore, raises fundamental questions about the real-world value of topological protection in reciprocal photonics.
DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins
Authors: Xing Yu-Hang , Dong Rui , Lee Lukuo , Rengarajan Shruthi , Riggi Nicolò , Boulay Gaylor , Rivera Miguel N. 
Published: April 2023

AbstractIntrinsically disordered regions (IDRs) in DNA-associated proteins are known to influence gene regulation, but their distribution and cooperative functions in genome-wide regulatory programs remain poorly understood. Here we describe DisP-seq (disordered protein precipitation followed by DNA sequencing), an antibody-independent chemical precipitation assay that can simultaneously map endogenous DNA-associated disordered proteins genome-wide through a combination of biotinylated isoxazole precipitation and next-generation sequencing. DisP-seq profiles are composed of thousands of peaks that are associated with diverse chromatin states, are enriched for disordered transcription factors (TFs) and are often arranged in large lineage-specific clusters with high local concentrations of disordered proteins and different combinations of histone modifications linked to regulatory potential. We use DisP-seq to analyze cancer cells and reveal how disordered protein-associated islands enable IDR-dependent mechanisms that control the binding and function of disordered TFs, including oncogene-dependent sequestration of TFs through long-range interactions and the reactivation of differentiation pathways upon loss of oncogenic stimuli in Ewing sarcoma.
Comparative analysis of bacterial diversity in two hot springs in Hefei, China
Authors: Zhang Feng-Qin , Liu Jun , Chen Xiao-Ju 
Published: April 2023

AbstractHot springs are extreme ecological environments of microbes. The study is the first comparative analysis of bacterial diversity of Tangchi and Bantang hot spring water samples collected in Hefei, China, which is conducive to the further development and utilization of microbial resources in hot springs. Illumina MiSeq system was utilized to sequence and analyze the bacterial 16S rRNA gene from hot spring water samples by bioinformatics, to probe into the bacterial abundance and diversity of two hot springs in Hefei. Results revealed that prevalent bacterial phyla in Tangchi hot spring were Bacillota and Aquificota, and the prevalent bacterial genus was Hydrogenobacter; prevalent phyla in Bantang hot spring were Pseudomonadota followed by Actinobacteriota, and prevalent genera were CL500-29_marine_group and Polynucleobacter. More species and higher evenness in Bantang hot spring than those in Tangchi hot spring. In MetaCyc pathway analysis, the major pathways of metabolism existed in the bacteria from the two hot springs were ‘pyruvate fermentation to isobutanol (engineered)’, ‘acetylene degradation’, ‘carbon fixation pathways in prokaryotes’, ‘nitrate reduction I (denitrification)’, ‘methanogenesis from acetate’, ‘superpathway of glucose and xylose degradation’, etc.
Contact time and disinfectant formulation significantly impact the efficacies of disinfectant towelettes against Candida auris on hard, non-porous surfaces
Authors: Voorn Maxwell G. , Kelley Alyssa M. , Chaggar Gurpreet K. , Li Xiaobao , Teska Peter J. , Oliver Haley F. 
Published: April 2023

AbstractThere has been an increase in Candida auris healthcare-associated infections, which result from cross-contamination from surfaces and equipment. In this study, we tested the efficacies of EPA-registered disinfectant towelettes products that are increasingly used for infection control against C. auris at a range of contact times following modifications to standard EPA protocol MB-33-00. Hydrogen peroxide (HP)-based disinfectant towelettes were more efficacious against C. auris than the quaternary ammonium chloride (QAC)-alcohol-based disinfectant towelettes irrespective of tested contact times. Thirty s contact time was significantly less effective in reducing C. auris compared to 1-, 2-, 3-, and 10-min contact times. However, there were no statistically significant differences in the level of disinfection among 1-min and longer contact times regardless of product chemistry. None of the products achieved a standard six-log10 reduction at any tested contact times. Overall, the HP-based disinfectant towelette was significantly more fungicidal than the QAC-alcohol-based disinfectant towelette. For all product types, 30 s contact time did not achieve the same level of disinfection as 1-min or longer contact times. Overall, disinfectant towelette efficacy is dependent upon product formulation and contact time.
Effects of adipose derived stem cells pretreated with resveratrol on sciatic nerve regeneration in rats
Authors: Zhang Ziqiang , Zhang Mengyu , Sun Yingying , Li Monan , Chang Chenhao , Liu Weiqi , Zhu Xuemin , Wei Lan , Wen Fengyun , Liu Yumei 
Published: April 2023

AbstractAdipose derived stem cells (ADSCs) are popular in regenerative medicine due to their easy availability, low immunogenicity and lack of controversy regarding their ethical debate use. Although ADSCs can repair nerve damage, the oxidative microenvironment of damaged tissue can induce apoptosis of transplanted stem cells, which weakens the therapeutic efficacy of ADSCs. Resveratrol (Res) is a type of natural polyphenol compound that regulates the proliferation, senescence and differentiation of stem cells. Therefore, we investigated whether incubation of ADSCs with Res improves their to promote peripheral nerve regeneration. ADSCs were cultured in vitro and treated with H2O2 to establish an apoptosis model. The control, H2O2 and Res groups were set up. The cell survival rate was detected by the CCK-8 method. The TUNEL assay was used to detect the apoptosis of the cells. qRT‒PCR was used to analyze the expression of apoptosis-related mRNA, and the effect of Res on the proliferation of ADSCs was investigated. In vivo, 40 SD rats were randomly divided into the control, model, ADSCs and ADSC + Res groups, with 13 rats in each group. The sciatic nerve injury rat model was established by the clamp method. Gait was observed on Days 7, 14, 21, and 28. Sciatic nerve regeneration was detected on Day 28. Res had no effect on the proliferation of ADSCs, and the TUNEL assay confirmed that Res pretreatment could significantly improve H2O2-induced apoptosis in ADSCs. Compared with the control group, caspase-3, Bax and Bcl-2 expression levels were significantly increased in the H2O2 group. Compared with the H2O2 group caspase-3 and Bax expression levels were significantly decreased, and Bcl-2 expression levels were significantly increased in ADSCs + Res group. At 4 weeks after surgery, the functional index of the sciatic nerve in the ADSCs + Res group was significantly higher than that in the model group. On Day 28, the average density of the sciatic nerve myelin sheath in the ADSCs + Res group was significantly increased compared with that in the model group, and Nissl staining showed that the number of motor neurons in the spinal cord was significant compared with that in the model group. Compared with the control group, the wet weight ratio of gastrocnemius muscle and muscle fiber area in ADSCs + Res group were significantly increased. Res enhanced the ability of ADSCs to promote sciatic nerve regeneration in rats.