bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mining plant endogenous target mimics from miRNA–lncRNA interactions based on dual-path parallel ensemble pruning method
Authors: Kang Qiang , Meng Jun , Su Chenglin , Luan Yushi 
Published: September 2021

Abstract
The interactions between microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) play important roles in biological activities. Specially, lncRNAs as endogenous target mimics (eTMs) can bind miRNAs to regulate the expressions of target messenger RNAs (mRNAs). A growing number of studies focus on animals, but the studies on plants are scarce and many functions of plant eTMs are unknown. This study proposes a novel ensemble pruning protocol for predicting plant miRNA–lncRNA interactions at first. It adaptively prunes the base models based on dual-path parallel ensemble method to meet the challenge of cross-species prediction. Then potential eTMs are mined from predicted results. The expression levels of RNAs are identified through biological experiment to construct the lncRNA–miRNA–mRNA regulatory network, and the functions of potential eTMs are inferred through enrichment analysis. Experiment results show that the proposed protocol outperforms existing methods and state-of-the-art predictors on various plant species. A total of 17 potential eTMs are verified by biological experiment to involve in 22 regulations, and 14 potential eTMs are inferred by Gene Ontology enrichment analysis to involve in 63 functions, which is significant for further research.
Drug–drug interaction prediction with learnable size-adaptive molecular substructures
Authors: Nyamabo Arnold K , Yu Hui , Liu Zun , Shi Jian-Yu 
Published: September 2021

Abstract
Drug–drug interactions (DDIs) are interactions with adverse effects on the body, manifested when two or more incompatible drugs are taken together. They can be caused by the chemical compositions of the drugs involved. We introduce gated message passing neural network (GMPNN), a message passing neural network which learns chemical substructures with different sizes and shapes from the molecular graph representations of drugs for DDI prediction between a pair of drugs. In GMPNN, edges are considered as gates which control the flow of message passing, and therefore delimiting the substructures in a learnable way. The final DDI prediction between a drug pair is based on the interactions between pairs of their (learned) substructures, each pair weighted by a relevance score to the final DDI prediction output. Our proposed method GMPNN-CS (i.e. GMPNN + prediction module) is evaluated on two real-world datasets, with competitive results on one, and improved performance on the other compared with previous methods. Source code is freely available at https://github.com/kanz76/GMPNN-CS.
Are dropout imputation methods for scRNA-seq effective for scATAC-seq data?
Authors: Liu Yue , Zhang Junfeng , Wang Shulin , Zeng Xiangxiang , Zhang Wei 
Published: September 2021

AbstractThe tremendous progress of single-cell sequencing technology has given researchers the opportunity to study cell development and differentiation processes at single-cell resolution. Assay of Transposase-Accessible Chromatin by deep sequencing (ATAC-seq) was proposed for genome-wide analysis of chromatin accessibility. Due to technical limitations or other reasons, dropout events are almost a common occurrence for extremely sparse single-cell ATAC-seq data, leading to confusion in downstream analysis (such as clustering). Although considerable progress has been made in the estimation of scRNA-seq data, there is currently no specific method for the inference of dropout events in single-cell ATAC-seq data. In this paper, we select several state-of-the-art scRNA-seq imputation methods (including MAGIC, SAVER, scImpute, deepImpute, PRIME, bayNorm and knn-smoothing) in recent years to infer dropout peaks in scATAC-seq data, and perform a systematic evaluation of these methods through several downstream analyses. Specifically, we benchmarked these methods in terms of correlation with meta-cell, clustering, subpopulations distance analysis, imputation performance for corruption datasets, identification of TF motifs and computation time. The experimental results indicated that most of the imputed peaks increased the correlation with the reference meta-cell, while the performance of different methods on different datasets varied greatly in different downstream analyses, thus should be used with caution. In general, MAGIC performed better than the other methods most consistently across all assessments. Our source code is freely available at https://github.com/yueyueliu/scATAC-master.
The advantages of being crepuscular for bees: major pollen gain under low competition during the brief twilight period
Authors: Araújo Priscila de Cássia Souza , de Araujo Fernanda Figueiredo , Mota Theo , Schlindwein Clemens 
Published: September 2021

Abstract
The shift in flight activity from daylight to twilight in crepuscular bees is assumed to have evolved to escape competitors, but quantitative confirmation of this hypothesis has never been demonstrated clearly. Pseudobombax longiflorum is a chiropterophilous plant, with flowers presenting large amounts of pollen throughout anthesis, thus attracting not only nocturnal visitors, but also crepuscular and diurnal bees. In this dynamic system, the fraction of pollen that flows to different visitors and the putative role of bees in pollination remain unknown. We analysed floral biology, the frequency of visitors in periods with different light intensities and the rate of pollen removal by each visitor group. A pollinator-exclusion experiment showed that bees were not pollinators of Pseudobombax longiflorum, although they collected &gt; 60% of the pollen from their flowers. Crepuscular bees gained the greatest amount of pollen in the few minutes when they foraged without either nocturnal or diurnal competitors, confirming the advantage of foraging under low light. During the short twilight period, these bees foraged alone and removed 26.5 and 15 times more pollen per minute than nocturnal and diurnal visitors, respectively. Therefore, pollen removal by crepuscular bees is particularly efficient when they forage in the brief period while competitors are absent.
Single-cell analysis of prostaglandin E2-induced human decidual cell in vitro differentiation: a minimal ancestral deciduogenic signal
Authors: Stadtmauer Daniel J , Wagner Günter P 
Published: September 2021

Abstract
The decidua is a hallmark of reproduction in many placental mammals. Differentiation of decidual stromal cells is known to be induced by progesterone and the cyclic AMP/protein kinase A (cAMP/PKA) pathway. Several candidates have been identified as the physiological stimulus for adenylyl cyclase activation, but their relative importance remains unclear. To bypass this uncertainty, the standard approach for in vitro experiments uses membrane-permeable cAMP and progestin. We phylogenetically infer that prostaglandin E2 (PGE2) likely was the signal that ancestrally induced decidualization in conjunction with progesterone. This suggests that PGE2 and progestin should be able to activate the core gene regulatory network of decidual cells. To test this prediction, we performed a genome-wide study of gene expression in human endometrial fibroblasts decidualized with PGE2 and progestin. Comparison to a cAMP-based protocol revealed shared activation of core decidual genes and decreased induction of senescence-associated genes. Single-cell transcriptomics of PGE2-mediated decidualization revealed a distinct, early-activated state transitioning to a differentiated decidual state. PGE2-mediated decidualization was found to depend upon progestin-dependent induction of PGE2 receptor 2 (PTGER2) which in turn leads to PKA activation upon PGE2 stimulation. Progesterone-dependent induction of PTGER2 is absent in opossum, an outgroup taxon of placental mammals which is incapable of decidualization. Together, these findings suggest that the origin of decidualization involved the evolution of progesterone-dependent activation of the PGE2/PTGER2/PKA axis, facilitating entry into a PKA-dominant rather than AKT-dominant cellular state. We propose the use of PGE2 for in vitro decidualization as an alternative to 8-Br-cAMP.
Domestic Violence Policing of First Nations Women in Australia: ‘Settler’ Frameworks, Consequential Harms and the Promise of Meaningful Self-Determination
Authors: Buxton-Namisnyk Emma 
Published: September 2021

Abstract
This article analyses domestic violence fatality reviews/coronial files for a whole-of-population study of First Nations women killed by male partners across several Australian jurisdictions between 2006 and 2016, alongside yarning/interviews with First Nations domestic violence workers, violence survivors and Elders. Findings show that most women had domestic violence-related police contact before their deaths, and these interactions were frequently harmful. Harms resulted from police inaction, including failures to respond or enforce the law. Harms also resulted from police action, with policing enhancing state surveillance of victims’ families, eroding victims’ autonomy and criminalizing victims. Findings are located in neo-colonial context, emphasizing a policy need for meaningful Indigenous self-determination and reinforcing the importance of inclusive disciplinary and epistemological practices in gender-based violence criminology.
Phylogenetics ofOchna(Ochnaceae) and a new infrageneric classification
Authors: Shah Toral , Mashimba Fandey H , Suleiman Haji O , Mbailwa Yahya S , Schneider Julio V , Zizka Georg , Savolainen Vincent , Larridon Isabel , Darbyshire Iain 
Published: September 2021

AbstractAdvances in high-throughput DNA sequencing are allowing faster and more affordable generation of molecular phylogenetic trees for many organisms. However, resolving relationships at species level is still challenging, particularly for taxonomically difficult groups. Until recently, the classification of Ochna had been based only on morphological data. Here, we present the first comprehensive phylogenomic study for the genus using targeted sequencing with a custom probe kit. We sampled c. 85% of species to evaluate the current infrageneric classification. Our results show that the data generated using the custom probe kit are effective in resolving relationships in the genus, revealing three sections consistent with the current classification and a new section consisting of species from Madagascar and the Mascarene Islands. Our results provide the first insights into the evolutionary relationships of several widespread and morphologically diverse species numerous poorly known and potentially new species to science. We demonstrate that for morphologically challenging groups such as Ochna, an integrated approach to classification is essential. Phylogenomic results are only informative when derived from accurately named samples. There is a symbiotic relationship between molecular phylogenomics and morphology-based taxonomy, with taxonomic expertise a requirement to accurately interpret the phylogenomic results.
Deep genetic structure of a ground-herb along contrasting environments of seasonally dry understories in Amazonia and Cerrado as revealed from targeted genomic sequencing
Authors: André Thiago , Sass Chodon , Yockteng Roxana , Wendt Tânia , Palma-Silva Clarisse , Specht Chelsea D 
Published: September 2021

AbstractCentral South America primarily comprises seasonally dry tropical domains, where a sharp rainy season defines phenological and yearly growth patterns. Here we examine if the genetic structure of the understorey ground-herb Chamaecostus subsessilis species complex, from South American seasonally dry forests, is defined by intrinsic contrasting environments of the Cerrado and southern Amazonia. We analysed a dataset of c. 20 kb of sequence data from targeted capture high-throughput sequencing using PCR-generated probes. We used an admixture model and population pairwise FST comparisons to interpret genetic structure. We also used a Bayesian coalescent approach with a relaxed clock to estimate divergence times between populations and haplotypes. Genetic structure reflects separate populations from Amazonia and from the Cerrado, whereas a haplotype-based phylogenetic tree provides further spatiotemporal evidence of this strong phylogeographical structure. Spatial arrangements among genetic lineages of the C. subsessilis species complex reveal that intraspecific evolution in Central South America seasonally dry understories is closely linked to environmental gradients.
Gynoecium and fruit histology, structure and development in corky-warted representatives of Livistoninae (Trachycarpeae: Coryphoideae: Arecaceae)
Authors: Bobrov Alexey V F C H , Romanov Mikhail S , Zdravchev Nikita S , Dransfield John 
Published: September 2021

AbstractRepresentatives of three genera of Livistoninae (Johannesteijsmannia, Licuala and Pholidocarpus) develop corky-warted fruits in contrast to fruit with smooth surfaces in most other representatives of the ‘apocarpous clade’ of Arecaceae subfamily Coryphoideae. The present developmental study is focused on revealing the anatomical peculiarities of the fruit structure of corky-warted species of Livistoninae and tracing the development of their pericarp. Our study shows that the fruits of Johannesteijsmannia, Licuala bintulensis and Pholidocarpus macrocarpus are drupes of the Rhapis type and that the warts on their fruit surface originate soon after gynoecium pollination as the result of two or three developmental events: (1) suberinization of the exocarp cells; (2) progressive multiplication and growth of the outer zone of the mesocarp; and (3) cracking of the peripheral zone of the pericarp. The warts of taxa of Livistoninae develop at the mid stages of fruit organogenesis and are referred to as either alive, composed of parenchymatous cells and sclereids (species of Licuala and Pholidocarpus), or dead, consisting of cells with suberized walls and sclereids (Johannesteijsmannia). The nests of sclereids comprising the stone of Johannesteijsmannia spp. remain disunited during pericarp development until late developmental stages when the formation of a continuous sclerenchymatous layer occurs, which differs from other representatives of the ‘apocarpous clade’ of Coryphoideae with a continuous layer of sclereids persisting during fruit development (as in L. bintulensis). It is shown that the development of the stone within the drupes of the Rhapis type can be different even in closely related taxa. The recognition of the fruits of studied taxa of Livistoninae as drupes of the Rhapis type like the fruit of many other taxa of Trachycarpeae and the ‘apocarpous clade’ of Coryphoideae suggest this character as a synapomorphy for this tribe and the whole clade.
Primary hyperoxaluria type 1: urologic and therapeutic management
Authors: Kohli Harjivan , Kurtz Michael P 
Published: September 2021

ABSTRACT
While the surgical approaches available in primary hyperoxaluria (PH) are common to all patients requiring intervention for urolithiasis, the indications for treatment and their corresponding toxicities are unique. Being a rare disease, we are guided by case series. This review summarizes the available literature highlighting the important disease-specific considerations. Shockwave lithotripsy (SWL) is of particular interest. It is generally the first-line treatment for stones in children, but here the stones produced will be relatively resistant to fragmentation. In addition, there are concerning reports in children of sudden unilateral decline in function in the treated kidney as measured by nuclear renography. Percutaneous nephrostolithotomy might intuitively seem favorable given the shortest drain duration and the ability to treat larger stones efficiently but, similar to SWL, rapid chronic kidney disease (CKD) progression has been seen postoperatively. Ureteroscopy is therefore generally the safest option, but considerations regarding stent encrustation, the growth of residual fragments and the large volume of stone often faced may limit this approach. The surgeon must balance the above with consideration of the patient's CKD status when considering a plan of monitoring and treating stones in PH.
Genome-wide simple sequence repeat markers in potato: abundance, distribution, composition, and polymorphism
Authors: Jian Yinqiao , Yan Wenyuan , Xu Jianfei , Duan Shaoguang , Li Guangcun , Jin Liping 
Published: September 2021

Abstract
Simple sequence repeats (SSRs) are important sources of genetic diversity and are widely used as markers in genetics and molecular breeding. In this study, we examined four potato genomes of DM1-3 516 R44 (DM) from Solanum phureja, RH89039-16 (RH) from Solanum tuberosum, M6 from Solanum chacoense and Solanum commersonii to determine SSR abundance and distribution and develop a larger list of polymorphic markers for a potentially wide range of uses for the potato community. A total of 1,734,619 SSRs were identified across the four genomes with an average of 433,655 SSRs per genome and 2.31kb per SSR. The most abundant repeat units for mono-, di-, tri-, and tetra-nucleotide SSRs were (A/T)n, (AT/AT)n, (AAT/ATT)n, and (ATAT/ATAT)n, respectively. The SSRs were most abundant (78.79%) in intergenic regions and least abundant (3.68%) in untranslated regions. On average, 168,069 SSRs with unique flanking sequences were identified in the four genomes. Further, we identified 16,245 polymorphic SSR markers among the four genomes. Experimental validation confirmed 99.69% of tested markers could generate target bands. The high-density potato SSR markers developed in this study will undoubtedly facilitate the application of SSR markers for genetic research and marker-pyramiding in potato breeding.
The time is ripe to investigate human centromeres by long-read sequencing
Authors: Suzuki Yuta , Morishita Shinichi 
Published: September 2021

Abstract
The complete sequencing of human centromeres, which are filled with highly repetitive elements, has long been challenging. In human centromeres, α-satellite monomers of about 171 bp in length are the basic repeating units, but α-satellite monomers constitute the higher-order repeat (HOR) units, and thousands of copies of highly homologous HOR units form large arrays, which have hampered sequence assembly of human centromeres. Because most HOR unit occurrences are covered by long reads of about 10 kb, the recent availability of much longer reads is expected to enable observation of individual HOR occurrences in terms of their single-nucleotide or structural variants. The time has come to examine the complete sequence of human centromeres.
Phenology of Lycorma delicatula (Hemiptera: Fulgoridae) in Virginia, USA
Authors: Dechaine Andrew C , Sutphin Mark , Leskey Tracy C , Salom Scott M , Kuhar Thomas P , Pfeiffer Douglas G 
Published: September 2021

Abstract
The spotted lanternfly, Lycorma delicatula (White), is an invasive planthopper that was first discovered in North America in Berks County, Pennsylvania in 2014. Currently, L. delicatula has spread to eight additional states and threatens agricultural, ornamental, and timber commodities throughout the United States. The timing of insect life events is very important in the development of pest management tools and strategies. In 2019 and 2020, L. delicatula phenology was successfully documented in Winchester, Virginia using weekly 5-min observational surveys at established monitoring plots. Each year, L. delicatula were active in the environment from May to November with initial detections of first, second, third, fourth, and adults occurring in May, May, June, June, and July, respectively. Cumulative average growing degree days were also calculated for the onset of each L. delicatula life stage using local weather data and a lower developmental threshold of 10°C. First-instar L. delicatula were initially observed at 135 and 111.5, adults at 835 and 887, and egg masses at 1673.5 and 1611.5 in 2019 and 2020, respectively. Combined, these data can be used by growers and land managers to facilitate timing of effective pest management strategies.
De novo and pre-existing atrial fibrillation in acute coronary syndromes: impact on prognosis and cardiovascular events in long-term follow-up
Authors: Buchta Piotr , Kalarus Zbigniew , Mizia-Stec Katarzyna , Myrda Krzysztof , Skrzypek Michał , Ga˛sior Mariusz 
Published: September 2021

Abstract

Aims
The aim of the study was to compare in-hospital and long-term prognosis in patients with acute coronary syndromes (ACS) and de novo vs. pre-existing atrial fibrillation (AF). Atrial fibrillation increases the risk of serious adverse events including death in patients with ACS. However, it is unclear whether de novo and pre-existing AF portend a different risk.

Methods and results
We analysed the incidence, clinical characteristics, and in-hospital and long-term outcomes in patients with AF and ACS based on combined data from Polish Registry of Acute Coronary Syndrome (PL-ACS) (n = 581 843) and SILICARD (n = 852 063) databases. Atrial fibrillation at admission was diagnosed in of 6.16% patients [de novo: 1129 (2.46%); pre-existing: 1691 (3.7%)]. Groups were compared (N = 1023 vs. 1023) after matching for relevant clinical factors. De novo and pre-existing AF differed in in-hospital diuretic (52% vs. 58%; P = 0.008) and aldosterone inhibitor (27.5% vs. 32.5%; P = 0.02) use, Thrombolysis In Myocardial Infarction (TIMI) flow before percutaneous coronary intervention (P = 0.016), and diuretic (52.1% vs. 58%; P = 0.008) and oral anticoagulant (27.5% vs. 32.5%; P = 0.018) use at discharge. In-hospital mortality in the de novo AF group was significantly higher (13.1% vs. 8.31%; P = 0.0005). Post-discharge 12-month survival was similar between groups (14.5% vs. 15.3%, P = 0.63). Long-term re-hospitalization due to heart failure (22.7% vs. 17.2%; P &lt; 0.005) and medical contact due to AF (48.4% vs. 26.1%, P &lt; 0.0001) rates were higher in the group with pre-existing AF, without the difference of stroke or myocardial infarction occurrence.

Conclusion
De novo AF accounts for 40% of all AF cases in ACS patients and is an unfavourable in-hospital prognostic factor. The occurrence of de novo AF during ACS should require special attention and caution in the treatment of these patients.