bluuebunny/crossref_metadata_2025_split huggingface dataset:
A substitutional quantum defect in WS2 discovered by high-throughput computational screening and fabricated by site-selective STM manipulation
Authors: Thomas John C. , Chen Wei , Xiong Yihuang , Barker Bradford A. , Zhou Junze , Chen Weiru , Rossi Antonio , Kelly Nolan , Yu Zhuohang , Zhou Da , Kumari Shalini , Barnard Edward S. , Robinson Joshua A. , Terrones Mauricio , Schwartzberg Adam , Ogletree D. Frank , Rotenberg Eli , Noack Marcus M. , Griffin Sinéad , Raja Archana , Strubbe David A. , Rignanese Gian-Marco , Weber-Bargioni Alexander , Hautier Geoffroy 
Published: April 2024

AbstractPoint defects in two-dimensional materials are of key interest for quantum information science. However, the parameter space of possible defects is immense, making the identification of high-performance quantum defects very challenging. Here, we perform high-throughput (HT) first-principles computational screening to search for promising quantum defects within WS2, which present localized levels in the band gap that can lead to bright optical transitions in the visible or telecom regime. Our computed database spans more than 700 charged defects formed through substitution on the tungsten or sulfur site. We found that sulfur substitutions enable the most promising quantum defects. We computationally identify the neutral cobalt substitution to sulfur ($${\rm{Co}}_{{{{{{{{\rm{S}}}}}}}}}^{0}$$

Co

S

0

) and fabricate it with scanning tunneling microscopy (STM). The $${\rm{Co}}_{{{{{{{{\rm{S}}}}}}}}}^{0}$$

Co

S

0

electronic structure measured by STM agrees with first principles and showcases an attractive quantum defect. Our work shows how HT computational screening and nanoscale synthesis routes can be combined to design promising quantum defects.
Probing the surface charge of condensates using microelectrophoresis
Authors: van Haren Merlijn H. I. , Visser Brent S. , Spruijt Evan 
Published: April 2024

AbstractBiomolecular condensates play an important role in cellular organization. Coacervates are commonly used models that mimic the physicochemical properties of biomolecular condensates. The surface of condensates plays a key role in governing molecular exchange between condensates, accumulation of species at the interface, and the stability of condensates against coalescence. However, most important surface properties, including the surface charge and zeta potential, remain poorly characterized and understood. The zeta potential of coacervates is often measured using laser doppler electrophoresis, which assumes a size-independent electrophoretic mobility. Here, we show that this assumption is incorrect for liquid-like condensates and present an alternative method to study the electrophoretic mobility of coacervates and in vitro condensate models by microelectrophoresis and single-particle tracking. Coacervates have a size-dependent electrophoretic mobility, originating from their fluid nature, from which a well-defined zeta potential is calculated. Interestingly, microelectrophoresis measurements reveal that polylysine chains are enriched at the surface of polylysine/polyaspartic acid complex coacervates, which causes the negatively charged protein ɑ-synuclein to adsorb and accumulate at the interface. Addition of ATP inverts the surface charge, displaces ɑ-synuclein from the surface and may help to suppress its interface-catalyzed aggregation. Together, these findings show how condensate surface charge can be measured and altered, making this microelectrophoresis platform combined with automated single-particle tracking a promising characterization technique for both biomolecular condensates and coacervate protocells.
HBO1 catalyzes lysine lactylation and mediates histone H3K9la to regulate gene transcription
Authors: Niu Ziping , Chen Chen , Wang Siyu , Lu Congcong , Wu Zhiyue , Wang Aiyuan , Mo Jing , Zhang Jianji , Han Yanpu , Yuan Ye , Zhang Yingao , Zang Yong , He Chaoran , Bai Xue , Tian Shanshan , Zhai Guijin , Wu Xudong , Zhang Kai 
Published: April 2024

AbstractLysine lactylation (Kla) links metabolism and gene regulation and plays a key role in multiple biological processes. However, the regulatory mechanism and functional consequence of Kla remain to be explored. Here, we report that HBO1 functions as a lysine lactyltransferase to regulate transcription. We show that HBO1 catalyzes the addition of Kla in vitro and intracellularly, and E508 is a key site for the lactyltransferase activity of HBO1. Quantitative proteomic analysis further reveals 95 endogenous Kla sites targeted by HBO1, with the majority located on histones. Using site-specific antibodies, we find that HBO1 may preferentially catalyze histone H3K9la and scaffold proteins including JADE1 and BRPF2 can promote the enzymatic activity for histone Kla. Notably, CUT&Tag assays demonstrate that HBO1 is required for histone H3K9la on transcription start sites (TSSs). Besides, the regulated Kla can promote key signaling pathways and tumorigenesis, which is further supported by evaluating the malignant behaviors of HBO1- knockout (KO) tumor cells, as well as the level of histone H3K9la in clinical tissues. Our study reveals HBO1 serves as a lactyltransferase to mediate a histone Kla-dependent gene transcription.
Single-cell analyses reveal transient retinal progenitor cells in the ciliary margin of developing human retina
Authors: Dorgau Birthe , Collin Joseph , Rozanska Agata , Zerti Darin , Unsworth Adrienne , Crosier Moira , Hussain Rafiqul , Coxhead Jonathan , Dhanaseelan Tamil , Patel Aara , Sowden Jane C. , FitzPatrick David R. , Queen Rachel , Lako Majlinda 
Published: April 2024

AbstractThe emergence of retinal progenitor cells and differentiation to various retinal cell types represent fundamental processes during retinal development. Herein, we provide a comprehensive single cell characterisation of transcriptional and chromatin accessibility changes that underline retinal progenitor cell specification and differentiation over the course of human retinal development up to midgestation. Our lineage trajectory data demonstrate the presence of early retinal progenitors, which transit to late, and further to transient neurogenic progenitors, that give rise to all the retinal neurons. Combining single cell RNA-Seq with spatial transcriptomics of early eye samples, we demonstrate the transient presence of early retinal progenitors in the ciliary margin zone with decreasing occurrence from 8 post-conception week of human development. In retinal progenitor cells, we identified a significant enrichment for transcriptional enhanced associate domain transcription factor binding motifs, which when inhibited led to loss of cycling progenitors and retinal identity in pluripotent stem cell derived organoids.
Programming viscoelastic properties in a complexation gel composite by utilizing entropy-driven topologically frustrated dynamical state
Authors: Wang Gui Kang , Yang Yi Ming , Jia Di 
Published: April 2024

AbstractHydrogel composites in an aqueous media with viscoelastic properties and elastic modulus that can be precisely tailored are desirable to mimic many biological tissues ranging from mucus, vitreous humor, and nucleus pulposus as well as build up biosensors. Without altering the chemistry, tuning the physical interactions and structures to govern the viscoelastic properties of the hydrogels is indispensable for their applications but quite limited. Here we design a complexation gel composite and utilize the physical principle of topologically frustrated dynamical state to tune the correlated structures between the guest polycation chains and negatively charged host gels. We precisely quantify the mesh size of the host gel and guest chain size. By designing various topologically correlated structures, a viscoelastic moduli map can be built up, ranging from tough to ultrasoft, and from elastic-like with low damping properties to viscous-like with high damping properties. We also tune the swelling ratio by using entropy effect and discover an Entropy-driven Topologically Isovolumetric Point. Our findings provide essential physics to understand the relationship between entropy-driven correlated structures and their viscoelastic properties of the complexation hydrogel composites and will have diverse applications in tissue engineering and soft biomaterials.
No evidence for an association of voxel-based morphometry with short-term non-motor outcomes in deep brain stimulation for Parkinson’s disease
Authors: Loehrer Philipp Alexander , Schumacher Wibke , Jost Stefanie T. , Silverdale Monty , Petry-Schmelzer Jan Niklas , Sauerbier Anna , Gronostay Alexandra , Visser-Vandewalle Veerle , Fink Gereon R. , Evans Julian , Krause Max , Rizos Alexandra , Antonini Angelo , Ashkan Keyoumars , Martinez-Martin Pablo , Gaser Christian , Ray Chaudhuri K. , Timmermann Lars , Baldermann Juan Carlos , Dafsari Haidar S. ,   On behalf of EUROPAR and the International Parkinson and Movement Disorders Society Non-Motor Parkinson’s Disease Study Group
Published: April 2024

AbstractDeep brain stimulation of the subthalamic nucleus (STN-DBS) is an established therapy in advanced Parkinson’s disease (PD). Motor and non-motor outcomes, however, show considerable inter-individual variability. Preoperative morphometry-based metrics have recently received increasing attention to explain treatment effects. As evidence for the prediction of non-motor outcomes is limited, we sought to investigate the association between metrics of voxel-based morphometry and short-term non-motor outcomes following STN-DBS in this prospective open-label study. Forty-nine PD patients underwent structural MRI and a comprehensive clinical assessment at preoperative baseline and 6-month follow-up. Voxel-based morphometry was used to assess associations between cerebral volume and non-motor outcomes corrected for multiple comparisons using a permutation-based approach. We replicated existing results associating volume loss of the superior frontal cortex with subpar motor outcomes. Overall non-motor burden, however, was not significantly associated with morphometric features, limiting its use as a marker to inform patient selection and holistic preoperative counselling.
Modelling the impact of different irrigation regimes and mulching on strawberry crop growth and water use in the arsenic-contaminated Bengal basin
Authors: Biswas Benukar , Ghosh Tridiv , Chakraborty Debashis , Banerjee Saon , Mandal Baidya Nath , Saha Sarathi 
Published: April 2024

AbstractReplacement of water-intensive winter rice with strawberry (Fragaria × ananassa Duch.) may restrict groundwater extraction and improve water productivity and sustainability of agricultural production in the arsenic-contaminated Bengal basin. The potential of strawberry cultivation in terms of yield obtained and water use efficiency need to be evaluated under predominant soil types with mulch applications. Water-driven model AquaCrop was used to predict the canopy cover, soil water storage and above-ground biomass of strawberry in an arsenic-contaminated area in the Bengal basin. After successful calibration and validation over three seasons, AquaCrop was used over a range of management scenarios (nine drip-irrigation × three soil types × four mulch materials) to identify the best irrigation options for a drip-irrigated strawberry crop. The most appropriate irrigation of 176 mm for clay loam soil in lowland and 189 mm for sandy clay loam in medium land rice areas and the use of organic mulch from locally available jute agrotextile improved 1.4 times higher yield and 1.7 times higher water productivity than that of without mulch. Strawberry can be introduced as an alternative crop replacing rice in non-traditional upland and medium land areas of the arsenic-contaminated Bengal basin with 88% lower groundwater extraction load and better economic return to farmers.
Construction of a high-density genetic map based on large-scale marker development in Coix lacryma-jobi L. using specific-locus amplified fragment sequencing (slaf-seq)
Authors: Yang Chenglong , Ban Xiuwen , Zhou Mingqiang , Zhou Yu , Luo Kai , Yang Xiaoyu , Li Zhifang , Liu Fanzhi , Li Qing , Luo Yahong , Zhou Xiang , Lei Jing , Long Peilin , Wang Jian , Guo Jianchun 
Published: April 2024

AbstractCoix lacryma-jobi L. is one of the most economically and medicinally important corns. This study constructed a high-density genetic linkage map of C. lacryma-jobi based on a cross between the parents 'Qianyi No. 2' × 'Wenyi No. 2' and their F2 progeny through high-throughput sequencing and the construction of a specific-locus amplified fragment (SLAF) library. After pre-processing, 325.49 GB of raw data containing 1628 M reads were obtained. A total of 22,944 high-quality SLAFs were identified, among which 3952 SLAFs and 3646 polymorphic markers met the requirements for the construction of a genetic linkage map. The integrated map contained 3605 high-quality SLAFs, which were grouped into ten genetic linkage groups. The total length of the map was 1620.39 cM, with an average distance of 0.45 cM and an average of 360.5 markers per linkage group. This report presents the first high-density genetic map of C. lacryma-jobi. This map was constructed using an F2 population and SLAF-seq approach, which allows the development of a large number of polymorphic markers in a short period. These results provide a platform for precise gene/quantitative trait locus (QTL) mapping, map-based gene separation, and molecular breeding in C. lacryma-jobi. They also help identify a target gene for tracking, splitting quantitative traits, and estimating the phenotypic effects of each QTL for QTL mapping. They are of great significance for improving the efficiency of discovering and utilizing excellent gene resources of C. lacryma-jobi.
Anti-Plasmodium vivax merozoite surface protein 3 ϒ (PvMSP3 ϒ) antibodies upon natural infection
Authors: Kuamsab Napaporn , Putaporntip Chaturong , Kakino Azumi , Kosuwin Rattiporn , Songsaigath Sunisa , Tachibana Hiroshi , Jongwutiwes Somchai 
Published: April 2024

AbstractMerozoite surface protein 3 of Plasmodium vivax (PvMSP3) contains a repertoire of protein members with unique sequence organization. While the biological functions of these proteins await elucidation, PvMSP3 has been suggested to be potential vaccine targets. To date, studies on natural immune responses to this protein family have been confined to two members, PvMSP3α and PvMSP3β. This study analyzed natural IgG antibody responses to PvMSP3γ recombinant proteins derived from two variants: one containing insert blocks (CT1230nF) and the other without insert domain (NR25nF). The former variant was also expressed as two subfragment proteins: one encompassing variable domain I and insert block A (CT1230N) and the other spanning from insert block B to conserved block III (CT1230C). Serum samples were obtained from 246 symptomatic vivax malaria patients in Tak (n = 50) and Ubon Ratchathani (n = 196) Provinces. In total, 176 (71.5%) patients could mount antibodies to at least one recombinant PvMSP3γ antigen. IgG antibodies directed against antigens CT1230nF, CT1230N, CT1230C and NR25nF occurred in 96.6%, 61.4%, 71.6% and 68.2% of samples, respectively, suggesting the widespread occurrence of B-cell epitopes across PvMSP3γ. The rates of seropositivity seemed to correlate with the number of previous malaria episodes. Isotype analysis of anti-PvMSP3γ antibodies has shown predominant cytophilic subclass responses, accounting for 75.4–81.7% for IgG1 and 63.6–77.5% for IgG3. Comparing with previous studies in the same cohort, the numbers of serum samples reactive to antigens derived from P. vivax merozoite surface protein 9 (PvMSP9) and thrombospondin-related anonymous protein (PvTRAP) were higher than those to PvMSP3γ, being 92.7% and 87.0% versus 71.5%, respectively. Three (1.22%) serum samples were nonresponsive to all these malarial proteins. Nevertheless, the relevance of naturally acquired antibodies to PvMSP3γ in host protection requires further studies.
A novel customizing knowledge graph evaluation method for incorporating user needs
Authors: Zhang Ying , Xiao Gang 
Published: April 2024

AbstractKnowledge graphs are now widely used in various domains, including Question-and-answer systems, intelligent search and recommendation systems, and intelligent decision-making systems. However, knowledge graphs inevitably contain inaccurate and incomplete knowledge during the creation process, which leads to a reduction in the usefulness of knowledge graphs. Therefore, to assess the usefulness of knowledge graphs based on specific application requirements, quality assessment is particularly important. Among them, accuracy assessment, as a necessary dimension, reflects the degree of correctness of the triples. However, in the actual assessment process, the existing assessment methods do not consider the user’s needs and do not implement the concept of “Fitness for Use”. Meanwhile, it takes a lot of labor cost to evaluate the accuracy of large-scale knowledge graphs. Therefore, to ensure the accuracy of the assessment in a cost-saving way while meeting the needs of users, we propose and implement a novel accuracy assessment method that focuses on the requirements of users by designing an effective sampling method to obtain accurate assessment results that are more practical and instructive for users. Finally, the performance of our proposed method is evaluated by comparing it with the real accuracy rate, and the experimental results show that the accuracy rate obtained by the proposed method is very close to the real accuracy rate, and the sample size is minimized.
Position of Fovea Palatinae relative to the vibrating line in various soft palate classifications among Jordanian edentulous population
Authors: Elmanaseer Wijdan R. , Alamoush Rasha A. , Alsoleihat Firas , AL-Omiri Mahmoud K. 
Published: April 2024

AbstractThis study aims to examine the relationship between the locations of Fovea Palatinae and the posterior vibrating line in different classes of soft palate angulation (House Classification), accordingly determine its reliability as a landmark and a tool for determining the posterior limit of the maxillary complete denture. 280 completely edentulous patients with normal healthy mucosa from both genders were randomly selected. The House classification of the soft palate angulation was identified and recorded as Class I, II, or III. Phonation was used to determine the position of the vibrating line. The Fovea Palatinae was then marked. Then, the distance between the Fovea Palatinae and the vibrating line was measured and recorded. Finally, the relative position of the Fovea Palatinae to the vibrating line was recorded as being anterior, posterior, or on the vibrating line. The Chi Square test, the effect size measures (Eta and Cramer’s V tests), The Spearman’s Rho rank correlation test, and multinominal logistic regression analysis were utilized to analyse the data. House classification percentages were measured among people whose Fovea Palatinae was detectable; Class II palate was the most prevalent (47.14%), followed by Class I (43.93%), and then Class III (8.93%). Based on vibrating line position, 129 (58%) had a vibrating line anterior to Fovea Palatinae, 57 (26%) on the Fovea Palatinae, 36 (16%) posterior to Fovea Palatinae, and in 58 (21%) Fovea Palatinae were not detected. The mean distance between the vibrating line and Fovea Palatinae was 3.66 ± 1.6 mm anteriorly and 2.97 ± 1.36 mm posteriorly. No significant differences were found between males and females in regard to House classification and vibrating line position. The odds of having the fovea posterior to the vibrating line would increase by 5% for each year increase in the age (P = 0.035, odds ratio = 1.050). Class II House classification of the soft palate was found to be the most prevalent among the study participants. Also, the vibrating line was anterior to the Fovea Palatinae in the majority of cases. The odds of having the fovea posterior to the vibrating line would increase by age. The Fovea Palatinae could be considered a useful guide for locating the vibrating line.
Hyper-N-glycosylated SEL1L3 as auto-antigenic B-cell receptor target of primary vitreoretinal lymphomas
Authors: Elbert Michelle , Neumann Frank , Kiefer Maximilian , Christofyllakis Konstantinos , Balensiefer Benedikt , Kos Igor , Carbon Gabi , Kaddu-Mulindwa Dominic , Bittenbring Joerg Thomas , Fadle Natalie , Regitz Evi , Fend Falko , Bonzheim Irina , Thurner Lorenz , Bewarder Moritz 
Published: April 2024

AbstractPrimary vitreoretinal lymphoma (PVRL) is a rare subtype of DLBCL and can progress into primary central nervous system lymphoma (PCNSL). To investigate the role of chronic antigenic stimulation in PVRL, we cloned and expressed B-cell receptors (BCR) from PVRL patients and tested for binding against human auto-antigens. SEL1L3, a protein with multiple glycosylation sites, was identified as the BCR target in 3/20 PVRL cases. SEL1L3 induces proliferation and BCR pathway activation in aggressive lymphoma cell lines. Moreover, SEL1L3 conjugated to a toxin killed exclusively lymphoma cells with respective BCR-reactivity. Western Blot analysis indicates the occurrence of hyper-N-glycosylation of SEL1L3 at aa 527 in PVRL patients with SEL1L3-reactive BCRs. The BCR of a PVRL patient with serum antibodies against SEL1L3 was cloned from a vitreous body biopsy at diagnosis and of a systemic manifestation at relapse. VH4-04*07 was used in both lymphoma manifestations with highly conserved CDR3 regions. Both BCRs showed binding to SEL1L3, suggesting continued dependence of lymphoma cells on antigen stimulation. These results indicate an important role of antigenic stimulation by post-translationally modified auto-antigens in the genesis of PVRL. They also provide the basis for a new treatment approach targeting unique lymphoma BCRs with ultimate specificity.
Multi-stage progressive detection method for water deficit detection in vertical greenery plants
Authors: Deng Fei , Liu Xuan , Zhou Peng , Shen Jianglin , Huang Yuanxiang 
Published: April 2024

AbstractDetecting the water deficit status of vertical greenery plants rapidly and accurately is a significant challenge in the process of cultivating and planting greenery plants. Currently, the mainstream method involves utilizing a single target detection algorithm for this task. However, in complex real-world scenarios, the accuracy of detection is influenced by factors such as image quality and background environment. Therefore, we propose a multi-stage progressive detection method aimed at enhancing detection accuracy by gradually filtering, processing, and detecting images through a multi-stage architecture. Additionally, to reduce the additional computational load brought by multiple stages and improve overall detection efficiency, we introduce a Swin Transformer based on mobile windows and hierarchical representations for feature extraction, along with global feature modeling through a self-attention mechanism. The experimental results demonstrate that our multi-stage detection approach achieves high accuracy in vertical greenery plants detection tasks, with an average precision of 93.5%. This represents an improvement of 19.2%, 17.3%, 13.8%, and 9.2% compared to Mask R-CNN (74.3%), YOLOv7 (76.2%), DETR (79.7%), and Deformable DETR (84.3%), respectively.