bluuebunny/crossref_metadata_2025_split huggingface dataset:
PlantGSAD: a comprehensive gene set annotation database for plant species
Authors: Ma Xuelian , Yan Hengyu , Yang Jiaotong , Liu Yue , Li Zhongqiu , Sheng Minghao , Cao Yaxin , Yu Xinyue , Yi Xin , Xu Wenying , Su Zhen 
Published: September 2021

Abstract
With the accumulation of massive data sets from high-throughput experiments and the rapid emergence of new types of omics data, gene sets have become more diverse and essential for the refinement of gene annotation at multidimensional levels. Accordingly, we collected and defined 236 007 gene sets across different categories for 44 plant species in the Plant Gene Set Annotation Database (PlantGSAD). These gene sets were divided into nine main categories covering many functional subcategories, such as trait ontology, co-expression modules, chromatin states, and liquid-liquid phase separation. The annotations from the collected gene sets covered all of the genes in the Brassicaceae species Arabidopsis and Poaceae species Oryza sativa. Several GSEA tools are implemented in PlantGSAD to improve the efficiency of the analysis, including custom SEA for a flexible strategy based on customized annotations, SEACOMPARE for the cross-comparison of SEA results, and integrated visualization features for ontological analysis that intuitively reflects their parent-child relationships. In summary, PlantGSAD provides numerous gene sets for multiple plant species and highly efficient analysis tools. We believe that PlantGSAD will become a multifunctional analysis platform that can be used to predict and elucidate the functions and mechanisms of genes of interest. PlantGSAD is publicly available at http://systemsbiology.cau.edu.cn/PlantGSEAv2/.
scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution
Authors: Zhu Sheng , Lian Qiwei , Ye Wenbin , Qin Wei , Wu Zhe , Ji Guoli , Wu Xiaohui 
Published: September 2021

Abstract
Alternative polyadenylation (APA) is a widespread regulatory mechanism of transcript diversification in eukaryotes, which is increasingly recognized as an important layer for eukaryotic gene expression. Recent studies based on single-cell RNA-seq (scRNA-seq) have revealed cell-to-cell heterogeneity in APA usage and APA dynamics across different cell types in various tissues, biological processes and diseases. However, currently available APA databases were all collected from bulk 3′-seq and/or RNA-seq data, and no existing database has provided APA information at single-cell resolution. Here, we present a user-friendly database called scAPAdb (http://www.bmibig.cn/scAPAdb), which provides a comprehensive and manually curated atlas of poly(A) sites, APA events and poly(A) signals at the single-cell level. Currently, scAPAdb collects APA information from &gt; 360 scRNA-seq experiments, covering six species including human, mouse and several other plant species. scAPAdb also provides batch download of data, and users can query the database through a variety of keywords such as gene identifier, gene function and accession number. scAPAdb would be a valuable and extendable resource for the study of cell-to-cell heterogeneity in APA isoform usages and APA-mediated gene regulation at the single-cell level under diverse cell types, tissues and species.
Dual targeting of higher-order DNA structures by azacryptands induces DNA junction-mediated DNA damage in cancer cells
Authors: Zell Joanna , Duskova Katerina , Chouh Leïla , Bossaert Madeleine , Chéron Nicolas , Granzhan Anton , Britton Sébastien , Monchaud David 
Published: September 2021

Abstract
DNA is intrinsically dynamic and folds transiently into alternative higher-order structures such as G-quadruplexes (G4s) and three-way DNA junctions (TWJs). G4s and TWJs can be stabilised by small molecules (ligands) that have high chemotherapeutic potential, either as standalone DNA damaging agents or combined in synthetic lethality strategies. While previous approaches have claimed to use ligands that specifically target either G4s or TWJs, we report here on a new approach in which ligands targeting both TWJs and G4s in vitro demonstrate cellular effects distinct from that of G4 ligands, and attributable to TWJ targeting. The DNA binding modes of these new, dual TWJ-/G4-ligands were studied by a panel of in vitro methods and theoretical simulations, and their cellular properties by extensive cell-based assays. We show here that cytotoxic activity of TWJ-/G4-ligands is mitigated by the DNA damage response (DDR) and DNA topoisomerase 2 (TOP2), making them different from typical G4-ligands, and implying a pivotal role of TWJs in cells. We designed and used a clickable ligand, TrisNP-α, to provide unique insights into the TWJ landscape in cells and its modulation upon co-treatments. This wealth of data was exploited to design an efficient synthetic lethality strategy combining dual ligands with clinically relevant DDR inhibitors.
Nano-sandwich composite by kinetic trapping assembly from protein and nucleic acid
Authors: Chen Shi , Xing Li , Zhang Douglas , Monferrer Alba , Hermann Thomas 
Published: September 2021

Abstract
Design and preparation of layered composite materials alternating between nucleic acids and proteins has been elusive due to limitations in occurrence and geometry of interaction sites in natural biomolecules. We report the design and kinetically controlled stepwise synthesis of a nano-sandwich composite by programmed noncovalent association of protein, DNA and RNA modules. A homo-tetramer protein core was introduced to control the self-assembly and precise positioning of two RNA–DNA hybrid nanotriangles in a co-parallel sandwich arrangement. Kinetically favored self-assembly of the circularly closed nanostructures at the protein was driven by the intrinsic fast folding ability of RNA corner modules which were added to precursor complex of DNA bound to the protein. The 3D architecture of this first synthetic protein–RNA–DNA complex was confirmed by fluorescence labeling and cryo-electron microscopy studies. The synthesis strategy for the nano-sandwich composite provides a general blueprint for controlled noncovalent assembly of complex supramolecular architectures from protein, DNA and RNA components, which expand the design repertoire for bottom-up preparation of layered biomaterials.
Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases
Authors: Xu Penghao , Storici Francesca 
Published: September 2021

AbstractRibonucleoside triphosphate (rNTP) incorporation in DNA by DNA polymerases is a frequent phenomenon that results in DNA structural change and genome instability. However, it is unclear whether the rNTP incorporation into DNA follows any specific sequence patterns. We analyzed multiple datasets of ribonucleoside monophosphates (rNMPs) embedded in DNA, generated from three rNMP-sequencing techniques. These rNMP libraries were obtained from Saccharomyces cerevisiae cells expressing wild-type or mutant replicative DNA polymerase and ribonuclease H2 genes. We performed computational analyses of rNMP sites around early and late-firing autonomously replicating sequences (ARSs) of the yeast genome, where leading and lagging DNA synthesis starts bidirectionally. We found the preference of rNTP incorporation on the leading strand in wild-type DNA polymerase yeast cells. The leading/lagging-strand ratio of rNTP incorporation changes dramatically within the first 1,000 nucleotides from ARSs, highlighting the Pol δ - Pol ϵ handoff during early leading-strand synthesis. Furthermore, the pattern of rNTP incorporation is markedly distinct between the leading and lagging strands not only in mutant but also in wild-type polymerase cells. Such specific signatures of Pol δ and Pol ϵ provide a new approach to track the labor of these polymerases.
circMine: a comprehensive database to integrate, analyze and visualize human disease–related circRNA transcriptome
Authors: Zhang Wenliang , Liu Yang , Min Zhuochao , Liang Guodong , Mo Jing , Ju Zhen , Zeng Binghui , Guan Wen , Zhang Yan , Chen Jianliang , Zhang Qianshen , Li Hanguang , Zeng Chunxia , Wei Yanjie , Chan Godfrey Chi-Fung 
Published: September 2021

Abstract
Many circRNA transcriptome data were deposited in public resources, but these data show great heterogeneity. Researchers without bioinformatics skills have difficulty in investigating these invaluable data or their own data. Here, we specifically designed circMine (http://hpcc.siat.ac.cn/circmine and http://www.biomedical-web.com/circmine/) that provides 1 821 448 entries formed by 136 871 circRNAs, 87 diseases and 120 circRNA transcriptome datasets of 1107 samples across 31 human body sites. circMine further provides 13 online analytical functions to comprehensively investigate these datasets to evaluate the clinical and biological significance of circRNA. To improve the data applicability, each dataset was standardized and annotated with relevant clinical information. All of the 13 analytic functions allow users to group samples based on their clinical data and assign different parameters for different analyses, and enable them to perform these analyses using their own circRNA transcriptomes. Moreover, three additional tools were developed in circMine to systematically discover the circRNA–miRNA interaction and circRNA translatability. For example, we systematically discovered five potential translatable circRNAs associated with prostate cancer progression using circMine. In summary, circMine provides user-friendly web interfaces to browse, search, analyze and download data freely, and submit new data for further integration, and it can be an important resource to discover significant circRNA in different diseases.
PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria
Authors: Dai Wei , Li Jiahui , Li Qi , Cai Jiasheng , Su Jianzhong , Stubenrauch Christopher , Wang Jiawei 
Published: September 2021

AbstractFrom industry to food to health, bacteria play an important role in all facets of life. Some of the most important bacteria have been purposely engineered to produce commercial quantities of antibiotics and therapeutics, and non-classical secretion systems are at the forefront of these technologies. Unlike the classical Sec or Tat pathways, non-classically secreted proteins share few common characteristics and use much more diverse secretion pathways for protein transport. Systematically categorizing and investigating the non-classically secreted proteins will enable a deeper understanding of their associated secretion mechanisms and provide a landscape of the Gram-positive secretion pathway distribution. We therefore developed PncsHub (https://pncshub.erc.monash.edu/), the first universal platform for comprehensively annotating and analyzing Gram-positive bacterial non-classically secreted proteins. PncsHub catalogs 4,914 non-classically secreted proteins, which are delicately categorized into 8 subtypes (including the ‘unknown’ subtype) and annotated with data compiled from up to 26 resources and visualisation tools. It incorporates state-of-the-art predictors to identify new and homologous non-classically secreted proteins and includes three analytical modules to visualise the relationships between known and putative non-classically secreted proteins. As such, PncsHub aims to provide integrated services for investigating, predicting and identifying non-classically secreted proteins to promote hypothesis-driven laboratory-based experiments.
The function of twister ribozyme variants in non-LTR retrotransposition in Schistosoma mansoni
Authors: Liu Getong , Jiang Hengyi , Sun Wenxia , Zhang Jun , Chen Dongrong , Murchie Alastair I H 
Published: September 2021

Abstract
The twister ribozyme is widely distributed over numerous organisms and is especially abundant in Schistosoma mansoni, but has no confirmed biological function. Of the 17 non-LTR retrotransposons known in S. mansoni, none have thus far been associated with ribozymes. Here we report the identification of novel twister variant (T-variant) ribozymes and their function in S. mansoni non-LTR retrotransposition. We show that T-variant ribozymes are located at the 5′ end of Perere-3 non-LTR retrotransposons in the S. mansoni genome. T-variant ribozymes were demonstrated to be catalytically active in vitro. In reporter constructs, T-variants were shown to cleave in vivo, and cleavage of T-variants was sufficient for the translation of downstream reporter genes. Our analysis shows that the T-variants and Perere-3 are transcribed together. Target site duplications (TSDs); markers of target-primed reverse transcription (TPRT) and footmarks of retrotransposition, are located adjacent to the T-variant cleavage site and suggest that T-variant cleavage has taken place inS. mansoni. Sequence heterogeneity in the TSDs indicates that Perere-3 retrotransposition is not site-specific. The TSD sequences contribute to the 5′ end of the terminal ribozyme helix (P1 stem). Based on these results we conclude that T-variants have a functional role in Perere-3 retrotransposition.
Genomic impact of stress-induced transposable element mobility in Arabidopsis
Authors: Roquis David , Robertson Marta , Yu Liang , Thieme Michael , Julkowska Magdalena , Bucher Etienne 
Published: September 2021

Abstract
Transposable elements (TEs) have long been known to be major contributors to plant evolution, adaptation and crop domestication. Stress-induced TE mobilization is of particular interest because it may result in novel gene regulatory pathways responding to stresses and thereby contribute to stress adaptation. Here, we investigated the genomic impacts of stress induced TE mobilization in wild type Arabidopsis plants. We find that the heat-stress responsive ONSEN TE displays an insertion site preference that is associated with specific chromatin states, especially those rich in H2A.Z histone variant and H3K27me3 histone mark. In order to better understand how novel ONSEN insertions affect the plant's response to heat stress, we carried out an in-depth transcriptomic analysis. We find that in addition to simple gene knockouts, ONSEN can produce a plethora of gene expression changes such as: constitutive activation of gene expression, alternative splicing, acquisition of heat-responsiveness, exonisation and genesis of novel non-coding and antisense RNAs. This report shows how the mobilization of a single TE-family can lead to a rapid rise of its copy number increasing the host's genome size and contribute to a broad range of transcriptomic novelty on which natural selection can then act.
Operative Treatment of Severe Scoliosis in Symptomatic Adults: Multicenter Assessment of Outcomes and Complications With Minimum 2-Year Follow-up
Authors: Buell Thomas J , Smith Justin S , Shaffrey Christopher I , Kim Han Jo , Klineberg Eric O , Lafage Virginie , Lafage Renaud , Protopsaltis Themistocles S , Passias Peter G , Mundis Gregory M , Eastlack Robert K , Deviren Vedat , Kelly Michael P , Daniels Alan H , Gum Jeff L , Soroceanu Alex , Hamilton D Kojo , Gupta Munish C , Burton Douglas C , Hostin Richard A , Kebaish Khaled M , Hart Robert A , Schwab Frank J , Bess Shay , Ames Christopher P ,   on behalf of The International Spine Study Group (ISSG)
Published: September 2021

Abstract

BACKGROUND
Few reports focus on adults with severe scoliosis.

OBJECTIVE
To report surgical outcomes and complications for adults with severe scoliosis.

METHODS
A multicenter, retrospective review was performed on operatively treated adults with severe scoliosis (minimum coronal Cobb: thoracic [TH] ≥ 75°, thoracolumbar [TL] ≥ 50°, lumbar [L] ≥ 50°).

RESULTS
Of 178 consecutive patients, 146 (82%; TH = 8, TL = 88, L = 50) achieved minimum 2-yr follow-up (mean age = 53.9 ± 13.2 yr, 92% women). Operative details included posterior-only (58%), 3-column osteotomy (14%), iliac fixation (72%), and mean posterior fusion = 13.2 ± 3.7 levels. Global coronal alignment (3.8 to 2.8 cm, P = .001) and maximum coronal Cobb improved significantly (P ≤.020): TH (84º to 57º; correction = 32%), TL (67º to 35º; correction = 48%), L (61º to 29º; correction = 53%). Sagittal alignment improved significantly (P < .001), most notably for L: C7-sagittal vertical axis 6.7 to 2.5 cm, pelvic incidence-lumbar lordosis mismatch 18º to 3º. Health-related quality-of-life (HRQL) improved significantly (P < .001), most notably for L: Oswestry Disability Index (44.4 ± 20.5 to 26.1 ± 18.3), Short Form-36 Physical Component Summary (30.2 ± 10.8 to 39.9 ± 9.8), and Scoliosis Research Society-22r Total (2.9 ± 0.7 to 3.8 ± 0.7). Minimal clinically important difference and substantial clinical benefit thresholds were achieved in 36% to 75% and 29% to 51%, respectively. Ninety-four (64%) patients had ≥1 complication (total = 191, 92 minor/99 major, most common = rod fracture [13.0%]). Fifty-seven reoperations were performed in 37 (25.3%) patients, with most common indications deep wound infection (11) and rod fracture (10).

CONCLUSION
Although results demonstrated high rates of complications, operative treatment of adults with severe scoliosis was associated with significant improvements in mean HRQL outcome measures for the study cohort at minimum 2-yr follow-up.
Formation, Growth, or Rupture of De Novo Intracranial Aneurysms: Long-Term Follow-up Study of Subarachnoid Hemorrhage Survivors
Authors: Han Hyun Jin , Lee Woosung , Kim Junhyung , Park Keun Young , Park Sang Kyu , Chung Joonho , Kim Yong Bae 
Published: September 2021

Abstract

BACKGROUND
The survival rate of aneurysmal subarachnoid hemorrhage (aSAH) has gradually increased, leading to more clinical cases of de novo intracranial aneurysms (DNIAs).

OBJECTIVE
To identify the characteristics of patients with DNIA growth or rupture.

METHODS
We included 1601 patients with aSAH treated by clipping from January 1993 to May 2010. According to the inclusion and exclusion criteria, 233 patients had no DNIAs, and 63 patients had 77 DNIAs. We assessed the incidence rate of DNIAs and risk factors for DNIA formation. After dichotomizing the DNIA group into the heed (patients with DNIA rupture or growth) and stable groups (patients without DNIA growth), we assessed the risk factors for DNIA growth or rupture.

RESULTS
The total follow-up period was 4427.9 patient-years. The incidence rate per patient-year was 1.42%. Age ≤50 yr, family history of aneurysm, and multiplicity at initial aSAH were significant risk factors for DNIA formation. Multivariate regression analysis revealed that female sex (odds ratio [OR], 5.566; 95% confidence interval [CI], 1.241-24.952), duration from initial aSAH to DNIA detection <120 mo (OR, 5.043; 95% CI, 1.362-18.668), multiplicity at initial aSAH (OR, 4.859; 95% CI, 1.207-19.563), and maximum DNIA diameter ≥4 mm (OR, 11.104; 95% CI, 2.337-52.772) were significant risk factors for DNIA growth or rupture.

CONCLUSION
DNIAs had a higher incidence rate than expected. Taking into account the presented incidence rate and risk factors, long-term surveillance in aSAH survivors for more than a decade may be worth considering, at least on a case-by-case basis.
Thrombus Histology as It Relates to Mechanical Thrombectomy: A Meta-Analysis and Systematic Review
Authors: Bhambri Ankur , Adapa Arjun Rohit , Liu Yang , Boeckh-Behrens Tobias , Procházka Václav , Hernández-Fernández Francisco , Barbella-Aponte Rosa Angélica , Hashimoto Tetsuya , Savastano Luis E , Gemmete Joseph J , Chaudhary Neeraj , Shih Albert J , Pandey Aditya S 
Published: September 2021

AbstractBACKGROUNDAppropriate thrombus-device interaction is critical for recanalization. Histology can serve as a proxy for mechanical properties, and thus inform technique selection.OBJECTIVETo investigate the value of histologic characterization, we conducted a systematic review and meta-analysis on the relationship between thrombus histology and recanalization, technique, etiology, procedural efficiency, and imaging findings.METHODSIn this meta-analysis, we identified studies published between March 2010 and March 2020 reporting findings related to the histologic composition of thrombi in large vessel occlusion stroke. Studies with at least 10 patients who underwent mechanical thrombectomy using stent retriever or aspiration were considered. Only studies in which retrieved thrombi were histologically processed were included. Patient-level data were requested when data could not be directly extracted. The primary outcome assessed was the relationship between thrombus histology and angiographic outcome.RESULTSA total of 22 studies encompassing 1623 patients met inclusion criteria. Clots associated with good angiographic outcome had higher red blood cell (RBC) content (mean difference [MD] 9.60%, 95% CI 3.85-15.34,P = .008). Thrombi retrieved by aspiration had less fibrin (MD −11.39, 95% CI −22.50 to −0.27,P = .046) than stent-retrieved thrombi. Fibrin/platelet-rich clots were associated with longer procedure times (MD 13.20, 95% CI 1.30-25.10,P = .037). Hyperdense artery sign was associated with higher RBC content (MD 14.17%, 95% CI 3.07-25.27,P = .027). No relationship was found between composition and etiology.CONCLUSIONRBC-rich thrombi were associated with better recanalization outcomes and shorter procedure times, suggesting that preinterventional compositional characterization may yield important prognostic and therapeutic guidance.
Broadband impedance modulation via non-local acoustic metamaterials
Authors: Zhou Zhiling , Huang Sibo , Li Dongting , Zhu Jie , Li Yong 
Published: September 2021

Abstract
Causality of linear time-invariant systems inherently defines the wave-matter interaction process in wave physics. This principle imposes strict constraints on the interfacial response of materials on various physical platforms. A typical consequence is that a delicate balance has to be struck between the conflicting bandwidth and geometric thickness when constructing a medium with desired impedance, which makes it challenging to realize broadband impedance modulation with compact structures. In pursuit of improvement, the over-damped recipe and the reduced excessive response recipe are creatively presented in this work. As a proof-of-concept demonstration, we construct a metamaterial with intensive mode density that supports strong non-locality over a frequency band from 320 Hz to 6400 Hz. Under the guidelines of the over-damped recipe and the reduced excessive response recipe, the metamaterial realizes impedance matching to air and exhibits broadband near-perfect absorption without evident impedance oscillation and absorption dips in the working frequency band. We further present a dual-functional design capable of frequency-selective absorption and reflection by concentrating the resonance modes in three frequency bands. Our research reveals the significance of over-damped recipe and the strong non-local effect in broadband impedance modulation, which may open up avenues for constructing efficient artificial impedance boundaries for energy absorption and other wave manipulation.