bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defoliation severity is positively related to soil solution nitrogen availability and negatively related to soil nitrogen concentrations following a multi-year invasive insect irruption
Authors: Conrad-Rooney Emma , Barker Plotkin Audrey , Pasquarella Valerie J , Elkinton Joseph , Chandler Jennifer L , Matthes Jaclyn Hatala 
Published: November 2020

Abstract
Understanding connections between ecosystem nitrogen (N) cycling and invasive insect defoliation could facilitate the prediction of disturbance impacts across a range of spatial scales. In this study we investigated relationships between ecosystem N cycling and tree defoliation during a recent 2015–18 irruption of invasive gypsy moth caterpillars (Lymantria dispar), which can cause tree stress and sometimes mortality following multiple years of defoliation. Nitrogen is a critical nutrient that limits the growth of caterpillars and plants in temperate forests. In this study, we assessed the associations among N concentrations, soil solution N availability and defoliation intensity by L. dispar at the scale of individual trees and forest plots. We measured leaf and soil N concentrations and soil solution inorganic N availability among individual red oak trees (Quercus rubra) in Amherst, MA and across a network of forest plots in Central Massachusetts. We combined these field data with estimated defoliation severity derived from Landsat imagery to assess relationships between plot-scale defoliation and ecosystem N cycling. We found that trees in soil with lower N concentrations experienced more herbivory than trees in soil with higher N concentrations. Additionally, forest plots with lower N soil were correlated with more severe L. dispar defoliation, which matched the tree-level relationship. The amount of inorganic N in soil solution was strongly positively correlated with defoliation intensity and the number of sequential years of defoliation. These results suggested that higher ecosystem N pools might promote the resistance of oak trees to L. dispar defoliation and that defoliation severity across multiple years is associated with a linear increase in soil solution inorganic N.
MetaADEDB 2.0: a comprehensive database on adverse drug events
Authors: Yu Zhuohang , Wu Zengrui , Li Weihua , Liu Guixia , Tang Yun 
Published: November 2020

ABSTRACT

Summary
MetaADEDB is an online database we developed to integrate comprehensive information on adverse drug events (ADEs). The first version of MetaADEDB was released in 2013 and has been widely used by researchers. However, it has not been updated for more than seven years. Here, we reported its second version by collecting more and newer data from the U.S. FDA Adverse Event Reporting System (FAERS) and Canada Vigilance Adverse Reaction Online Database, in addition to the original three sources. The new version consists of 744 709 drug–ADE associations between 8498 drugs and 13 193 ADEs, which has an over 40% increase in drug–ADE associations compared to the previous version. Meanwhile, we developed a new and user-friendly web interface for data search and analysis. We hope that MetaADEDB 2.0 could provide a useful tool for drug safety assessment and related studies in drug discovery and development.

Availability and implementation
The database is freely available at: http://lmmd.ecust.edu.cn/metaadedb/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Satellite open data to monitor forest damage caused by extreme climate-induced events: a case study of the Vaia storm in Northern Italy
Authors: Vaglio Laurin Gaia , Francini Saverio , Luti Tania , Chirici Gherardo , Pirotti Francesco , Papale Dario 
Published: November 2020

Abstract
The frequency of extreme storm events has significantly increased in the past decades, causing significant damage to European forests. To mitigate the impacts of extreme events, a rapid assessment of forest damage is crucial, and satellite data are an optimal candidate for this task. The integration of satellite data in the operational phase of monitoring forest damage can exploit the complementarity of optical and Synthetic Aperture Radar (SAR) open datasets from the Copernicus programme. This study illustrates the testing of Sentinel 1 and Sentinel 2 data for the detection of areas impacted by the Vaia storm in Northern Italy. The use of multispectral Sentinel 2 provided the best performance, with classification overall accuracy (OA) values up to 86 percent; however, optical data use is seriously hampered by cloud cover that can persist for months after the event and in most cases cannot be considered an appropriate tool if a fast response is required. The results obtained using SAR Sentinel 1 were slightly less accurate (OA up to 68 percent), but the method was able to provide valuable information rapidly, mainly because the acquisition of this dataset is weather independent. Overall, for a fast assessment Sentinel 1 is the better of the two methods where multispectral and ground data are able to further refine the initial SAR-based assessment.
Development of Multimorbidity Over Time: An Analysis of Belgium Primary Care Data Using Markov Chains and Weighted Association Rule Mining
Authors: Shi Xi , Nikolic Gorana , Van Pottelbergh Gijs , van den Akker Marjan , Vos Rein , De Moor Bart 
Published: November 2020

Abstract

Background
The prevalence of multimorbidity is increasing in recent years, and patients with multimorbidity often have a decrease in quality of life and require more health care. The aim of this study was to explore the evolution of multimorbidity taking the sequence of diseases into consideration.

Methods
We used a Belgian database collected by extracting coded parameters and more than 100 chronic conditions from the Electronic Health Records of general practitioners to study patients older than 40 years with multiple diagnoses between 1991 and 2015 (N = 65 939). We applied Markov chains to estimate the probability of developing another condition in the next state after a diagnosis. The results of Weighted Association Rule Mining (WARM) allow us to show strong associations among multiple conditions.

Results
About 66.9% of the selected patients had multimorbidity. Conditions with high prevalence, such as hypertension and depressive disorder, were likely to occur after the diagnosis of most conditions. Patterns in several disease groups were apparent based on the results of both Markov chain and WARM, such as musculoskeletal diseases and psychological diseases. Psychological diseases were frequently followed by irritable bowel syndrome.

Conclusions
Our study used Markov chains and WARM for the first time to provide a comprehensive view of the relations among 103 chronic conditions, taking sequential chronology into consideration. Some strong associations among specific conditions were detected and the results were consistent with current knowledge in literature, meaning the approaches were valid to be used on larger data sets, such as National Health care Systems or private insurers.
Daily Stress Processes in a Pandemic: The Effects of Worry, Age, and Affect
Authors: Nelson Niccole A , Bergeman Cindy S 
Published: November 2020

Abstract

Background and Objectives
In March 2020, the World Health Organization declared the coronavirus disease 2019 (COVID-19) a pandemic. Given that such a global event might affect day-to-day stress processes, the current study examined individuals’ daily stress reactivity and its moderators early in the COVID-19 pandemic.

Research Design and Methods
Two-level, multilevel models examined the daily relationship between perceived stress and negative affect, or stress reactivity, as well as the moderating effects of daily pandemic worry, age, and daily positive affect on this process. Participants included 349 individuals (age range = 26–89) from the Notre Dame Study of Health & Well-being who completed a 28-day, daily diary study at the beginning of the COVID-19 pandemic.

Results
Older individuals were less stress-reactive than younger individuals. Within individuals, however, stress reactivity was buffered by daily positive affect and exacerbated by daily pandemic worry. Finally, although daily positive affect buffered daily stress reactivity, this effect was weaker on days individuals were more worried about the COVID-19 pandemic.

Discussion and Implications
The mobilization of positive emotion may be a promising avenue for buffering stress reactivity during the COVID-19 pandemic, although this may be limited on days individuals are particularly concerned about the pandemic.
Association between preconception paternal health and pregnancy loss in the USA: an analysis of US claims data
Authors: Kasman Alex M , Zhang Chiyuan A , Li Shufeng , Lu Ying , Lathi Ruth B , Stevenson David K , Shaw Gary M , Eisenberg Michael L 
Published: November 2020

Abstract

STUDY QUESTION
Is preconception paternal health associated with pregnancy loss?

SUMMARY ANSWER
Poor preconception paternal health is associated with a higher risk of pregnancy loss as confirmed in sensitivity analyses accounting for maternal age and health.

WHAT IS KNOWN ALREADY
Preconception paternal health can negatively impact perinatal outcomes.

STUDY DESIGN, SIZE, DURATION
Retrospective cohort study of US insurance claims database from 2009 to 2016 covering 958 804 pregnancies.

PARTICIPANTS/MATERIALS, SETTING, METHODS
US insurance claims database including women, men and pregnancies within the USA between 2007 and 2016. Paternal preconception health status (e.g. metabolic syndrome diagnoses (MetS), Charlson comorbidity index (CCI) and individual chronic disease diagnoses) was examined in relation to pregnancy loss (e.g. ectopic pregnancy, miscarriage and stillbirth).

MAIN RESULTS AND THE ROLE OF CHANCE
In all, 958 804 pregnancies were analyzed. The average paternal age was 35.3 years (SD 5.3) and maternal age was 33.1 years (SD 4.4). Twenty-two percent of all pregnancies ended in a loss. After adjusting for maternal factors, the risk of pregnancy loss increased with increasing paternal comorbidity. For example, compared to men with no components of MetS, the risk of pregnancy loss increased for men with one (relative risk (RR) 1.10, 95% CI 1.09–1.12), two (RR 1.15, 95% CI 1.13–1.17) or three or more (RR 1.19, 95% CI 1.14–1.24) components. Specifically, less healthy men had a higher risk of siring a pregnancy ending in spontaneous abortion, stillbirth and ectopic pregnancies. Similar patterns remained with other measures of paternal health (e.g. CCI, chronic diseases, etc.). When stratifying by maternal age as well as maternal health, a similar pattern of increasing pregnancy loss risk for men with 1, 2 or 3+ MetS was observed. A statistically significant but weak association between timing of pregnancy loss and paternal health was found.

LIMITATIONS, REASONS FOR CAUTION
Retrospective study design covering only employer insured individuals may limit generalizability

WIDER IMPLICATIONS OF THE FINDINGS
Optimization of a father’s health may improve pregnancy outcomes.

STUDY FUNDING/COMPETING INTERESTS
National Institutes of Health National Center for Advancing Translational Science Clinical and Translational Science Award (UL1 TR001085). M.L.E. is an advisor for Sandstone Diagnostics, Dadi, Hannah and Underdog. No other competing interests were declared.

TRIAL REGISTRATION NUMBER
N/A
Supplementing Yucca schidigera extract to mitigate frothy bloat in beef cattle receiving a high-concentrate diet
Authors: Rett Bruna , Cooke Reinaldo F , Brandão Alice P , Ferreira Vitor S M , Colombo Eduardo A , Wiegand Jacob B , Pohler Ky G , Rincker Michael J , Schubach Kelsey M 
Published: November 2020

Abstract
This experiment compared incidence of frothy bloat, as well as ruminal, physiological, and performance responses of beef heifers receiving a bloat-provoking diet and supplemented with Yucca schidigera extract. Sixteen ruminally cannulated Angus-influenced heifers were ranked by body weight (BW) and assigned to 4 groups of 4 heifers each. Groups were enrolled in a replicated 4 × 4 Latin square design containing 4 periods of 28 d, and a 21-d washout interval between periods. Groups were assigned to receive no Y. schidigera extract (CON), or Y. schidigera extract at (as-fed basis) 1 g/heifer daily (YS1), 2 g/heifer daily (YS2), or 4 g/heifer daily (YS4). During each period, heifers (n = 16/treatment) were housed in individual pens, and fed a sorghum (Sorghum bicolor L.)-based bloat-provocative diet at 2% of their BW. Diet and treatments were individually fed to heifers, twice daily in equal proportions (0700 and 1600 hours). Heifers were assessed for bloat score (0 to 5 scale, increasing according to bloat severity) 3 hr after the morning feeding. Blood samples were collected on days 0, 7, 14, 21, and 28 prior to (0 hr) and at 3, 6, and 9 hr relative to the morning feeding. Rumen fluid samples were collected at the same time points on days 0 and 28. Orthogonal contrasts were tested to determine whether inclusion of Y. schidigera extract (0, 1, 2, or 4 g/heifer daily) yielded linear or quadratic effects, and explore an overall effect of Y. schidigera extract supplementation (CON vs. YS1 + YS2 + YS4). Rumen fluid viscosity was impacted quadratically by Y. schidigera extract inclusion (P = 0.02), being greatest in YS1, followed by YS2, and equivalent between CON and YS4 heifers. Heifers receiving Y. schidigera extract had greater (P ≤ 0.05) rumen propionate, iso-valerate, and valerate concentrations, as well as less (P &lt; 0.01) acetate : propionate ratio compared with CON heifers. Inclusion of Y. schidigera extract linearly increased (P ≤ 0.04) average daily gain and feed efficiency. No other treatment effects were noted (P ≥ 0.19) including bloat score (1.07 ± 0.03 across treatments), ruminal protozoa count, plasma concentrations of cortisol, haptoglobin, urea N, total protein, and rumen concentration of total volatile fatty acids. Supplementing Y. schidigera extract up to 4 g/d favored rumen propionate concentrations and linearly increased growth and feed efficiency but failed to mitigate incidence of frothy bloat in beef heifers consuming a grain-based bloat-provocative diet.
RNA-seq Analysis Reveals Mitochondrial and Cuticular Protein Genes Are Associated with Phosphine Resistance in the Rusty Grain Beetle (Coleoptera:Laemophloeidae)
Authors: Chen Er-Hu , Duan Jin-Yan , Song Wei , Wang Dian-Xuan , Tang Pei-An 
Published: November 2020

AbstractThe rusty grain beetle, Cryptolestes ferrugineus (Stephens), is a serious pest of stored grain, which has developed high levels of resistance to phosphine. In this study, five geographically distant populations of C. ferrugineus had been collected in China, specifically in granaries where phosphine fumigant is used for pest control, and they showed a high resistance ratio up to 1,907 (LC50 = 21.0 mg/liter). Then, a reference transcriptome was constructed to use as a basis for investigating the molecular mechanisms of phosphine resistance in this species, which consisted of 47,006 unigenes with a mean length of 1,090. Subsequently, the RNA-Seq analysis of individuals from the most susceptible and resistant populations led to the identification of 54 genes that are differentially expressed. GO and KEGG analysis demonstrated that genes associated with mitochondrial and respiration functions were significantly enriched. Also, the ‘structural constituent of cuticle’ term was annotated in the GO enrichment analysis and further qRT-PCR confirmed that the expression levels of nine cuticular protein genes were significantly increased in the resistant population. In conclusion, we present here a transcriptome-wide overview of gene expression changes between resistant and susceptible populations of C. ferrugineus, and this in turn documents that mitochondria and cuticular protein genes may play together a crucial role in phosphine resistance. Further gene function analysis should enable the provision of advice to expedite resistance management decisions.
Visualizing textual similarity of Shakespearean suspect texts: An examination of the Henry VI plays
Authors: Kim Heejin 
Published: November 2020

Abstract
The relationship between Shakespeare’s First Folio and early printings, published in his lifetime, has been a matter of dispute for centuries. A computer program that I have developed visualizes the fluctuating quality of textual correspondences between Folio texts, Henry the Sixth, Part Two and Three, and texts that have been suspected as memorial reconstructions of the Folio, The First Part of the Contention and The True Tragedy of Richard Duke of York. The memorial reconstruction hypothesis assumes increased similarity between the two texts when an alleged actor–reporter is on the stage or speaking and vice versa. The visualization of similarity between two texts, based on the Dice similarity metric, does not show a strong association between the fluctuation of similarity and actor–reporter factors, which challenges the memorial reconstruction hypothesis on statistical grounds. In addition, the distribution of line-by-line similarity scores suggests scene division is a considerable explanatory factor for fluctuating similarity, which is not inexplicable, considering the practice of collaborative writing in the early modern playhouse.
The transcriptional repressors VAL1 and VAL2 recruit PRC2 for genome-wide Polycomb silencing in Arabidopsis
Authors: Yuan Liangbing , Song Xin , Zhang Lu , Yu Yaoguang , Liang Zhenwei , Lei Yawen , Ruan Jiuxiao , Tan Bin , Liu Jun , Li Chenlong 
Published: November 2020

Abstract
The Polycomb repressive complex 2 (PRC2) catalyzes histone H3 Lys27 trimethylation (H3K27me3) to repress gene transcription in multicellular eukaryotes. Despite its importance in gene silencing and cellular differentiation, how PRC2 is recruited to target loci is still not fully understood. Here, we report genome-wide evidence for the recruitment of PRC2 by the transcriptional repressors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 in Arabidopsis thaliana. We show that the val1 val2 double mutant possesses somatic embryonic phenotypes and a transcriptome strikingly similar to those of the swn clf double mutant, which lacks the PRC2 catalytic subunits SWINGER (SWN) and CURLY LEAF (CLF). We further show that VAL1 and VAL2 physically interact with SWN and CLF in vivo. Genome-wide binding profiling demonstrated that they colocalize with SWN and CLF at PRC2 target loci. Loss of VAL1/2 significantly reduces SWN and CLF enrichment at PRC2 target loci and leads to a genome-wide redistribution of H3K27me3 that strongly affects transcription. Finally, we provide evidence that the VAL1/VAL2–RY regulatory system is largely independent of previously identified modules for Polycomb silencing in plants. Together, our work demonstrates an extensive genome-wide interaction between VAL1/2 and PRC2 and provides mechanistic insights into the establishment of Polycomb silencing in plants.
Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins
Authors: Ren Xiangle , Zhou Yang , Xue Zhaoyu , Hao Ning , Li Yuanyuan , Guo Xiaohuan , Wang Daliang , Shi Xiaobing , Li Haitao 
Published: November 2020

Abstract
Histone modifications and their functional readout serve as an important mechanism for gene regulation. Lysine benzoylation (Kbz) on histones is a recently identified acylation mark associated with active transcription. However, it remains to be explored whether putative readers exist to recognize this epigenetic mark. Here, our systematic binding studies demonstrated that the DPF and YEATS, but not the Bromodomain family members, are readers for histone Kbz. Co-crystal structural analyses revealed a ‘hydrophobic encapsulation’ and a ‘tip-sensor’ mechanism for Kbz readout by DPF and YEATS, respectively. Moreover, the DPF and YEATS family members display subtle yet unique features to create somewhat flexible engagements of different acylation marks. For instance, YEATS2 but not the other YEATS proteins exhibits best preference for Kbz than lysine acetylation and crotonylation due to its wider ‘tip-sensor’ pocket. The levels of histone benzoylation in cultured cells or in mice are upregulated upon sodium benzoate treatment, highlighting its dynamic regulation. In summary, our work identifies the first readers for histone Kbz and reveals the molecular basis underlying Kbz recognition, thus paving the way for further functional dissections of histone benzoylation.
An RNA pseudoknot is essential for standby-mediated translation of thetisBtoxin mRNA inEscherichia coli
Authors: Romilly Cédric , Lippegaus Anne , Wagner E Gerhart H 
Published: November 2020

AbstractIn response to DNA damage, Escherichia coli cells activate the expression of the toxin gene tisB of the toxin–antitoxin system tisB-istR1. Of three isoforms, only the processed, highly structured +42 tisB mRNA is active. Translation requires a standby site, composed of two essential elements: a single-stranded region located 100 nucleotides upstream of the sequestered RBS, and a structure near the 5′-end of the active mRNA. Here, we propose that this 5′-structure is an RNA pseudoknot which is required for 30S and protein S1-alone binding to the mRNA. Point mutations that prevent formation of this pseudoknot inhibit formation of translation initiation complexes, impair S1 and 30S binding to the mRNA, and render the tisB mRNA non-toxic in vivo. A set of mutations created in either the left or right arm of stem 2 of the pseudoknot entailed loss of toxicity upon overexpression of the corresponding mRNA variants. Combining the matching right-left arm mutations entirely restored toxicity levels to that of the wild-type, active mRNA. Finally, since many pseudoknots have high affinity for S1, we predicted similar pseudoknots in non-homologous type I toxin–antitoxin systems that exhibit features similar to that of tisB-IstR1, suggesting a shared requirement for standby acting at great distances.
A fast and robust iterative genome-editing method based on a Rock-Paper-Scissors strategy
Authors: Wang Jichao , Sui Xinyue , Ding Yamei , Fu Yingxin , Feng Xinjun , Liu Min , Zhang Youming , Xian Mo , Zhao Guang 
Published: November 2020

Abstract
The production of optimized strains of a specific phenotype requires the construction and testing of a large number of genome modifications and combinations thereof. Most bacterial iterative genome-editing methods include essential steps to eliminate selection markers, or to cure plasmids. Additionally, the presence of escapers leads to time-consuming separate single clone picking and subsequent cultivation steps. Herein, we report a genome-editing method based on a Rock-Paper-Scissors (RPS) strategy. Each of three constructed sgRNA plasmids can cure, or be cured by, the other two plasmids in the system; plasmids from a previous round of editing can be cured while the current round of editing takes place. Due to the enhanced curing efficiency and embedded double check mechanism, separate steps for plasmid curing or confirmation are not necessary, and only two times of cultivation are needed per genome-editing round. This method was successfully demonstrated in Escherichia coli and Klebsiella pneumoniae with both gene deletions and replacements. To the best of our knowledge, this is the fastest and most robust iterative genome-editing method, with the least times of cultivation decreasing the possibilities of spontaneous genome mutations.