bluuebunny/crossref_metadata_2025_split huggingface dataset:
PmiREN2.0: from data annotation to functional exploration of plant microRNAs
Authors: Guo Zhonglong , Kuang Zheng , Zhao Yongxin , Deng Yang , He Hao , Wan Miaomiao , Tao Yihan , Wang Dong , Wei Jianhua , Li Lei , Yang Xiaozeng 
Published: September 2021

Abstract
Nearly 200 plant genomes have been sequenced over the last two years, and new functions of plant microRNAs (miRNAs) have been revealed. Therefore, timely update of the plant miRNA databases by incorporating miRNAs from the newly sequenced species and functional information is required to provide useful resources for advancing plant miRNA research. Here we report the update of PmiREN2.0 (https://pmiren.com/) with an addition of 19 363 miRNA entries from 91 plants, doubling the amount of data in the original version. Meanwhile, abundant regulatory information centred on miRNAs was added, including predicted upstream transcription factors through binding motifs scanning and elaborate annotation of miRNA targets. As an example, a genome-wide regulatory network centred on miRNAs was constructed for Arabidopsis. Furthermore, phylogenetic trees of conserved miRNA families were built to expand the understanding of miRNA evolution across the plant lineages. These data are helpful to deduce the regulatory relationships concerning miRNA functions in diverse plants. Beside the new data, a suite of design tools was incorporated to facilitate experimental practice. Finally, a forum named ‘PmiREN Community’ was added for discussion and resource and new discovery sharing. With these upgrades, PmiREN2.0 should serve the community better and accelerate miRNA research in plants.
FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers
Authors: Zhao Linxuan , Xing Pengwei , Polavarapu Vamsi Krishna , Zhao Miao , Valero-Martínez Blanca , Dang Yonglong , Maturi Nagaprathyusha , Mathot Lucy , Neves Inês , Yildirim Irem , Swartling Fredrik Johansson , Sjöblom Tobias , Uhrbom Lene , Chen Xingqi 
Published: September 2021

Abstract
The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide histone modification profiling studies from FFPE samples is either 10–20 tissue sections or whole tissue blocks, which prevents better resolved analyses. But it is desirable to consume a minimal amount of FFPE tissue sections in the analysis as clinical tissues of interest are limited. Here, we present FFPE tissue with antibody-guided chromatin tagmentation with sequencing (FACT-seq), the first highly sensitive method to efficiently profile histone modifications in FFPE tissues by combining a novel fusion protein of hyperactive Tn5 transposase and protein A (T7−pA−Tn5) transposition and T7 in vitro transcription. FACT-seq generates high-quality chromatin profiles from different histone modifications with low number of FFPE nuclei. We proved a very small piece of FFPE tissue section containing ∼4000 nuclei is sufficient to decode H3K27ac modifications with FACT-seq. H3K27ac FACT-seq revealed disease-specific super enhancers in the archived FFPE human colorectal and human glioblastoma cancer tissue. In summary, FACT-seq allows decoding the histone modifications in archival FFPE tissues with high sensitivity and help researchers to better understand epigenetic regulation in cancer and human disease.
Click and Cut: a click chemistry approach to developing oxidative DNA damaging agents
Authors: McStay Natasha , Slator Creina , Singh Vandana , Gibney Alex , Westerlund Fredrik , Kellett Andrew 
Published: September 2021

AbstractMetallodrugs provide important first-line treatment against various forms of human cancer. To overcome chemotherapeutic resistance and widen treatment possibilities, new agents with improved or alternative modes of action are highly sought after. Here, we present a click chemistry strategy for developing DNA damaging metallodrugs. The approach involves the development of a series of polyamine ligands where three primary, secondary or tertiary alkyne-amines were selected and ‘clicked’ using the copper-catalysed azide-alkyne cycloaddition reaction to a 1,3,5-azide mesitylene core to produce a family of compounds we call the ‘Tri-Click’ (TC) series. From the isolated library, one dominant ligand (TC1) emerged as a high-affinity copper(II) binding agent with potent DNA recognition and damaging properties. Using a range of in vitro biophysical and molecular techniques—including free radical scavengers, spin trapping antioxidants and base excision repair (BER) enzymes—the oxidative DNA damaging mechanism of copper-bound TC1 was elucidated. This activity was then compared to intracellular results obtained from peripheral blood mononuclear cells exposed to Cu(II)–TC1 where use of BER enzymes and fluorescently modified dNTPs enabled the characterisation and quantification of genomic DNA lesions produced by the complex. The approach can serve as a new avenue for the design of DNA damaging agents with unique activity profiles.
A dominant-negative SOX18 mutant disrupts multiple regulatory layers essential to transcription factor activity
Authors: McCann Alex J , Lou Jieqiong , Moustaqil Mehdi , Graus Matthew S , Blum Ailisa , Fontaine Frank , Liu Hui , Luu Winnie , Rudolffi-Soto Paulina , Koopman Peter , Sierecki Emma , Gambin Yann , Meunier Frédéric A , Liu Zhe , Hinde Elizabeth , Francois Mathias 
Published: September 2021

Abstract
Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism underlying a dominant-negative form of the SOX18 transcription factor (SOX18RaOp) responsible for both the classical mouse mutant Ragged Opossum and the human genetic disorder Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome. Combining three single-molecule imaging assays in living cells together with genomics and proteomics analysis, we found that SOX18RaOp disrupts the system through an accumulation of molecular interferences which impair several functional properties of the wild-type SOX18 protein, including its target gene selection process. The dominant-negative effect is further amplified by poisoning the interactome of its wild-type counterpart, which perturbs regulatory nodes such as SOX7 and MEF2C. Our findings explain in unprecedented detail the multi-layered process that underpins the molecular aetiology of dominant-negative transcription factor function.
Divergent degeneration ofcreAantitoxin genes from minimal CRISPRs and the convergent strategy of tRNA-sequestering CreT toxins
Authors: Cheng Feiyue , Wang Rui , Yu Haiying , Liu Chao , Yang Jun , Xiang Hua , Li Ming 
Published: September 2021

AbstractAside from providing adaptive immunity, type I CRISPR-Cas was recently unearthed to employ a noncanonical RNA guide (CreA) to transcriptionally repress an RNA toxin (CreT). Here, we report that, for most archaeal and bacterial CreTA modules, the creA gene actually carries two flanking ‘CRISPR repeats’, which are, however, highly divergent and degenerated. By deep sequencing, we show that the two repeats give rise to an 8-nt 5′ handle and a 22-nt 3′ handle, respectively, i.e., the conserved elements of a canonical CRISPR RNA, indicating they both retained critical nucleotides for Cas6 processing during divergent degeneration. We also uncovered a minimal CreT toxin that sequesters the rare transfer RNA for isoleucine, tRNAIleCAU, with a six-codon open reading frame containing two consecutive AUA codons. To fully relieve its toxicity, both tRNAIleCAU overexpression and supply of extra agmatine (modifies the wobble base of tRNAIleCAU to decipher AUA codons) are required. By replacing AUA to AGA/AGG codons, we reprogrammed this toxin to sequester rare arginine tRNAs. These data provide essential information on CreTA origin and for future CreTA prediction, and enrich the knowledge of tRNA-sequestering small RNAs that are employed by CRISPR-Cas to get addictive to the host.
SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients
Authors: Luo Xiaotong , Huang Yuantai , Li Huiqin , Luo Yihai , Zuo Zhixiang , Ren Jian , Xie Yubin 
Published: September 2021

Abstract
As an increasing number of noncoding RNAs (ncRNAs) have been suggested to encode short bioactive peptides in cancer, the exploration of ncRNA-encoded small peptides (ncPEPs) is emerging as a fascinating field in cancer research. To assist in studies on the regulatory mechanisms of ncPEPs, we describe here a database called SPENCER (http://spencer.renlab.org). Currently, SPENCER has collected a total of 2806 mass spectrometry (MS) data points from 55 studies, covering 1007 tumor samples and 719 normal samples. Using an MS-based proteomics analysis pipeline, SPENCER identified 29 526 ncPEPs across 15 different cancer types. Specifically, 22 060 of these ncPEPs were experimentally validated in other studies. By comparing tumor and normal samples, the identified ncPEPs were divided into four expression groups: tumor-specific, upregulated in cancer, downregulated in cancer, and others. Additionally, since ncPEPs are potential targets for neoantigen-based cancer immunotherapy, SPENCER also predicted the immunogenicity of all the identified ncPEPs by assessing their MHC-I binding affinity, stability, and TCR recognition probability. As a result, 4497 ncPEPs curated in SPENCER were predicted to be immunogenic. Overall, SPENCER will be a useful resource for investigating cancer-associated ncPEPs and may boost further research in cancer.
RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation
Authors: Cui Tianyu , Dou Yiying , Tan Puwen , Ni Zhen , Liu Tianyuan , Wang DuoLin , Huang Yan , Cai Kaican , Zhao Xiaoyang , Xu Dong , Lin Hao , Wang Dong 
Published: September 2021

AbstractResolving the spatial distribution of the transcriptome at a subcellular level can increase our understanding of biology and diseases. To facilitate studies of biological functions and molecular mechanisms in the transcriptome, we updated RNALocate, a resource for RNA subcellular localization analysis that is freely accessible at http://www.rnalocate.org/ or http://www.rna-society.org/rnalocate/. Compared to RNALocate v1.0, the new features in version 2.0 include (i) expansion of the data sources and the coverage of species; (ii) incorporation and integration of RNA-seq datasets containing information about subcellular localization; (iii) addition and reorganization of RNA information (RNA subcellular localization conditions and descriptive figures for method, RNA homology information, RNA interaction and ncRNA disease information) and (iv) three additional prediction tools: DM3Loc, iLoc-lncRNA and iLoc-mRNA. Overall, RNALocate v2.0 provides a comprehensive RNA subcellular localization resource for researchers to deconvolute the highly complex architecture of the cell.
Higher-order topology induced by structural buckling
Authors: Huang Huaqing , Liu Feng 
Published: September 2021

Abstract
Higher-order topological insulator (HOTI) states, such as two-dimension (2D) HOTI featured with topologically protected corner modes at the intersection of two gapped crystalline boundaries, have attracted much recent interest. However, the physical mechanism underlying the formation of HOTI states is not fully understood, which has hindered our fundamental understanding and discovery of HOTI materials. Here we propose a mechanistic approach to induce higher-order topological phases via structural buckling of 2D topological crystalline insulators (TCIs). While in-plane mirror symmetry is broken by structural buckling, which destroys the TCI state, the combination of mirror and rotation symmetry is preserved in the buckled system, which gives rise to the HOTI state. We demonstrate that this approach is generally applicable to various 2D lattices with different symmetries and buckling patterns, opening a horizon of possible materials to realize 2D HOTIs. The HOTIs so generated are also shown to be robust against buckling height fluctuation and in-plane displacement. A concrete example is given for the buckled $\beta $-Sb monolayer from first-principles calculations. Our finding not only enriches our fundamental understanding of higher-order topology, but also opens a new route to discovering HOTI materials.
Nutrition as a modifiable factor in the onset and progression of pulmonary function impairment in COPD: a systematic review
Authors: van Iersel Lieke E J , Beijers Rosanne J H C G , Gosker Harry R , Schols Annemie M W J 
Published: September 2021

Abstract

Context
Chronic obstructive lung disease (COPD) is a progressive lung disease characterized by persistent airflow limitation. An increasing amount of evidence suggests an effect of dietary quality on the risk of COPD in the general population and pulmonary function decline in patients with COPD.

Objective
The association of dietary intake and nutrient status with COPD risk and onset, as well as pulmonary function decline (change in forced expiratory volume in 1 second, forced vital capacity, or the ratio of the former to the latter) in patients with COPD was investigated in this systematic review.

Data Sources
The PubMed database was searched by combining terms of pulmonary function or COPD with diet, nutrient status, or nutritional supplementation.

Data Extraction
Original studies and systematic reviews and meta-analyses were included. Articles obtained were independently screened for relevance on the bases of title and abstract by 2 researchers. Eventually, 89 articles were included in the analysis.

Results
The unhealthy Western-style diet is associated with an increased risk of COPD and an accelerated decline of pulmonary function. Intake of fruit, vegetables, dietary fibers, vitamins C and E, polyphenols, and β-carotene were individually associated with lower COPD risk, whereas consumption of processed meat was associated with higher COPD risk. Data on the effect of dietary quality on pulmonary function decline in patients with COPD are limited and inconsistent. Strong evidence for beneficial effects on pulmonary function decline was found only for vitamin D supplementation.

Conclusion
Considering the increasing burden of COPD, more attention should be given to dietary quality as a modifiable factor in disease development and progression in patients with COPD.

Systematic Review Registration
PROSPERO registration no. CRD42021240183.
The association between later eating rhythm and adiposity in children and adolescents: a systematic review and meta-analysis
Authors: Zou Mengxuan , Northstone Kate , Perry Rachel , Johnson Laura , Leary Sam 
Published: September 2021

AbstractContextChildhood adiposity, an important predictor of adult chronic disease, has been rising dramatically. Later eating rhythm, termed night eating, is increasing in adults but rarely studied in younger ages.ObjectiveThe objective of this study was to review the association between later eating rhythm and adiposity in children and adolescents. The aspects of later eating being considered included: energy intake (for evening main meal, evening snack, whole evening period, and around bedtime); timing (any food eaten at later timing); and meal frequency in the evening/night (evening main meal skipping, evening snack consumption).Data SourcesFive databases (the Cochrane Library, CINAHL, Embase, MEDLINE (via OVID), and Web of Science) were searched for eligible articles published prior to and including August 2020.Data ExtractionData extraction and quality assessment were conducted by 2 reviewers independently.Data AnalysisForty-seven studies were included, all of which were observational. Meta-analysis showed positive associations between both higher energy intake around bedtime (odds ratio [OR] 1.19, 95% CI 1.06, 1.33) and evening main meal skipping (OR 1.30, 95% CI 1.14, 1.48), and adiposity. There was evidence to suggest that consuming evening snacks reduced adiposity, but it was very weak (OR 0.80, 95% CI 0.62, 1.05). No association was seen between eating later and adiposity (OR 1.04, 95% CI 0.68, 1.61). In the narrative analysis, approximately half of the studies suggested that there was no association between later eating rhythm and adiposity, either as a whole or within exposure subsets.ConclusionThe magnitude of the relationship between later eating rhythm and adiposity is very small, and may vary depending on which aspects of later eating rhythm are under consideration; however, the evidence for this conclusion is of very low certainty . Further research with a more consistent definition of “later timing”, and longitudinal studies in different populations, may lead to different conclusions.Systematic Review RegistrationPROSPERO registration no. CRD42019134187.
Efficacy and tolerability of the ketogenic diet and its variations for preventing migraine in adolescents and adults: a systematic review
Authors: Caminha Madson C , Moreira Adriana B , Matheus Filipe C , Rieger Débora K , Moreira Júlia D , Dalmarco Eduardo M , Demarchi Izabel G , Lin Katia 
Published: September 2021

Abstract

Context
Migraine is a headache of variable intensity that is associated with focal and systemic symptoms. A ketogenic diet (KD), a very-low-carbohydrate diet with a proportional increase in fat, causes brain metabolic alterations, which could be beneficial for some neurologic conditions.

Objective
A systematic review was conducted to assess the efficacy and tolerability of KD in preventing migraine in adolescents and adults.

Data sources
The Preferred Reporting Items for Systematic Reviews and Meta-Analyses standard was used to review articles found in the PubMed, EMBASE, Scopus, Web of Science, LILACS, LIVIVO, Science Direct, and Cochrane Central Register of Controlled Trials databases. The Google Scholar, DOAJ, ProQuest, and OpenGrey databases were included.

Data Extraction
The population, intervention, comparison, outcome, and study design strategy included assessing the quality of the evidence using Grading of Recommendations Assessment Development and Evaluation and the risk of bias after applying the JBI critical appraisal tools.

Data Analysis
Most of the 10 selected studies reported that KD reduced the number and severity of migraine attacks in patients, with few reported adverse effects. The evidence on the effectiveness of the KD is low, so whether the final effect is due to the treatment remains inconclusive.

Conclusions
This study represents an initial effort to systematize information on the efficacy and tolerability of KD and its variations in the prevention of migraine.

Systematic Review Registration
PROSPERO registration no. CRD42020186253
How cost-effective is nutrition care delivered in primary healthcare settings? A systematic review of trial-based economic evaluations
Authors: Barnes Katelyn A , Szewczyk Zoe , Kelly Jaimon T , Campbell Katrina L , Ball Lauren E 
Published: September 2021

Abstract

Context
Nutrition care is an effective lifestyle intervention for the treatment and prevention of many noncommunicable diseases. Primary care is a high-value setting in which to provide nutrition care.

Objective
The objective of this review was to evaluate the cost-effectiveness of nutrition care interventions provided in primary care settings.

Data Sources
Medline, Embase, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), the Cochrane Central Register of Controlled Trials, EconLit, and the National Health Service Economic Evaluation Database (NHS EED) were searched from inception to May 2021.

Data Extraction
Data extraction was guided by the Consolidated Health Economic Evaluation Reporting Standards (CHEERS) reporting guidelines. Randomized trials of nutrition interventions in primary care settings were included in the analysis if incremental cost-effectiveness ratios were reported. The main outcome variable incremental cost-effectiveness ratios (ICERs) and reported interpretations were used to categorize interventions by the cost-effectiveness plane quadrant.

Results
Of 6837 articles identified, 10 were included (representing 9 studies). Eight of the 9 included studies found nutrition care in primary care settings to be more costly and more effective than usual care. High study heterogeneity limited further conclusions.

Conclusion
Nutrition care in primary care settings is effective, though it requires investment; it should, therefore, be considered in primary care planning. Further studies are needed to evaluate the long-term cost-effectiveness of providing nutrition care in primary care settings.

Systematic review registration
PROSPERO registration no. CRD42020201146.
The persistence of unhappiness: trapped into despair?
Authors:   By, Wilner Lionel 
Published: September 2021

AbstractThis article investigates whether self-assessed states of unhappiness are persistent. To disentangle state dependence from unobserved heterogeneity in life satisfaction, it estimates a dynamic ordered Logit with correlated random effects on longitudinal data in France, the UK, Australia, and Germany. The persistence of life satisfaction is found to be heterogeneous; people already happy with their lives tend to remain happy while unhappiness sounds more transitory. Overall, there is no empirical evidence of unhappiness traps: rather, every individual faces the risk of experiencing some temporary spell of low subjective well-being in her life course.
High Ambient Temperatures Inhibit Ghd7-Mediated Flowering Repression in Rice
Authors: Nagalla Asanga Deshappriya , Nishide Noriko , Hibara Ken-ichiro , Izawa Takeshi 
Published: September 2021

Abstract
The anticipation of changing seasons is crucial for reproduction in plants. Despite the broad cultivation area, the effects of ambient temperature on photoperiodic flowering are largely unknown in rice. Here, we first examined flowering time under four distinct conditions: short-day or long-day and high or low temperature, using cultivars, nearly isogenic lines, and mutants in rice. We also examined gene expression patterns of key flowering-time genes using the same lines under various conditions including temporal dynamics after light pulses. In addition to delayed flowering because of low growth rates, we found that photoperiodic flowering is clearly enhanced by both Hd1 and Ghd7 genes under low-temperature conditions in rice. We also revealed that PhyB can control Ghd7 repressor activity as a temperature sensor to inhibit Ehd1, Hd3a and RFT1 at lower temperatures, likely through a post-transcriptional regulation, despite inductive photoperiod conditions. Furthermore, we found that rapid reduction of Ghd7 messenger RNA (mRNA) under high-temperature conditions can lead to mRNA increase in a rice florigen gene, RFT1. Thus, multiple temperature-sensing mechanisms can affect photoperiodic flowering in rice. The rising of ambient temperatures in early summer likely contributes to the inhibition of Ghd7 repressor activity, resulting in the appropriate floral induction of rice in temperate climates.