bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of fluid salinity using coseismic electric signal generated by an earthquake
Authors: Ma Xinpeng , Liu Yunhe , Yin Changchun , Zhang Bo , Ren Xiuyan 
Published: November 2022

SUMMARY
The seismoelectric effect is a coupling phenomenon between the seismic wavefield and electromagnetic field caused by the electric double layer in a fluid-saturated porous medium. As seismoelectric signals are sensitive to porous medium properties, such as the water saturation, salinity, porosity and permeability, they have good potential for imaging the structure and estimating underground parameters. In this study, we proposed an inversion method for estimating the salinity using coseismic electric fields generated by electrokinetic effects. The method was established by waveform matching between synthetic and observed coseismic electric signals based on a horizontally layered model. We used an L1 norm measure to construct the regularization term and achieve a high-resolution layer interface. Subsequently, we applied the first-order Taylor expansion to estimate the sensitivity and used logarithm transformation to constrain the range of parameters and reduce the solution space. Finally, we used an iteratively reweighted least-squares method to solve the final Gauss–Newton-type inversion function in each iteration to obtain the model update until the inversion converged. Numerical experiments were conducted to test the resolution, anti-noise ability and stability of the inversion algorithm. These results demonstrate that the proposed method can effectively recover the salinity structure, which broadens the application of seismoelectric effects. We further applied the method to the Mw 6.5 Jiuzhaigou earthquake in 2017 and used the observed coseismic electric field to estimate the salinity and conductivity beneath the station.
Genome-wide identification of copy neutral loss of heterozygosity reveals its possible association with spatial positioning of chromosomes
Authors: Kim Hyeonjeong , Suyama Mikita 
Published: November 2022

AbstractLoss of heterozygosity (LOH) is a genetic alteration that results from the loss of one allele at a heterozygous locus. In particular, copy neutral LOH (CN-LOH) events are generated, for example, by mitotic homologous recombination after monoallelic defection or gene conversion, resulting in novel homozygous locus having two copies of the normal counterpart allele. This phenomenon can serve as a source of genome diversity and is associated with various diseases. To clarify the nature of the CN-LOH such as the frequency, genomic distribution and inheritance pattern, we made use of whole-genome sequencing data of the three-generation CEPH/Utah family cohort, with the pedigree consisting of grandparents, parents and offspring. We identified an average of 40.7 CN-LOH events per individual taking advantage of 285 healthy individuals from 33 families in the cohort. On average 65% of them were classified as gonosomal-mosaicism-associated CN-LOH, which exists in both germline and somatic cells. We also confirmed that the incidence of the CN-LOH has little to do with the parents’ age and sex. Furthermore, through the analysis of the genomic region including the CN-LOH, we found that the chance of the occurrence of the CN-LOH tends to increase at the GC-rich locus and/or on the chromosome having a relatively close inter-homolog distance. We expect that these results provide significant insights into the association between genetic alteration and spatial position of chromosomes as well as the intrinsic genetic property of the CN-LOH.
Laughter of the Oppressor: Humour, Whiteness and Masculinity in Late Rhodesia
Authors: Ginsburgh Nicola 
Published: November 2022

Abstract
In the 1960s and 1970s Rhodesian settlers engaged in a violent struggle to maintain white minority rule. Humour and jokes offer insights into how different sections of the settler population attempted to articulate a distinct Rhodesian-ness in this historical situation. I argue that jokes told by white men, for white men, both expressed an idealized white masculinity and engaged fears over its impossibility. In exploring these dynamics I show how humour can be used to explore the production and regulation of social identities and the symbiotic, unnerving relations between white power and white anxiety.
Evaluating lleal Pouch Anal Anastomosis Function: Time to Expand Our ARM-amentarium
Authors: Luo Yuying , Schmidt Natalia , Dubinsky Marla C , Jaffin Barry , Kayal Maia 
Published: November 2022

Abstract

Background
Total proctocolectomy with ileal pouch anal anastomosis (IPAA) for medically refractory ulcerative colitis or dysplasia may be associated with structural and inflammatory complications. However, even in their absence, defecatory symptoms secondary to dyssynergic defecation or fecal incontinence may occur. Although anorectal manometry is well established as the diagnostic test of choice for defecatory symptoms, its utility in the assessment of patients with IPAA is less established. In this systematic review, we critically evaluate the existing evidence for anopouch manometry (APM).

Methods
A total of 393 studies were identified, of which 6 studies met all inclusion criteria. Studies were not pooled given different modalities of testing with varying outcome measures.

Results
Overall, less than 10% of symptomatic patients post-IPAA were referred to APM. The prevalence of dyssynergic defecation as defined by the Rome IV criteria in symptomatic patients with IPAA ranged from 47.0% to 100%. Fecal incontinence in patients with IPAA was characterized by decreased mean and maximal resting anal pressure on APM, as well as pouch hyposensitivity. The recto-anal inhibitory reflex was absent in most patients with and without incontinence.

Conclusion
Manometry alone is an imperfect assessment of pouch function in patients with defecatory symptoms, and confirmatory testing may need to be performed with dynamic imaging.
The effect of financial literacy on policy preferences: evidence from Argentina
Authors: Petrachkova Alexandra 
Published: November 2022

Abstract
In this article, I study the role of economic knowledge in economic policy preferences. I find that this domain-specific knowledge has a direct effect on attitudes toward economic issues. Using evidence from two surveys of 7,565 of Argentines, I demonstrate that people who score higher on the financial literacy and economic knowledge tests are more supportive of pro-market economic policies, such as the elimination of trade barriers and subsidies, and integration into the global financial markets. These results are independent of partisan ties, self-interest, or personal investment in financial literacy.
Complementarity or substitution? The interaction effects between knowledge and trust on public attitudes toward genetic modification
Authors: Zhu Yina , He Guangxi , Gao Lu 
Published: November 2022

Abstract
Knowledge and trust are generally viewed as key drivers of favorable attitudes toward technology, but it remains uncertain whether and how different types of knowledge and trust interact with each other in predicting public acceptance. To address this gap, the present study hypothesized that knowledge and trust would exert both main and interaction effects on public opinion. Data from a national survey of public attitudes toward genetic modification (GM) in China were used to test an interactive model of attitudes. We have found that factual knowledge of and perceived familiarity with GM and trust in university scientists interacted as complements, with knowledge impacting positive attitudes more strongly for people who had high levels of trust; while we found no such interaction for knowledge/familiarity and trust in industry scientists and governmental officials. The implications of these findings for future research and policymaking in the domain of science and risk communication are discussed.
Determination of Ethanol in Food by Enzymatic Method Enzytec™ Liquid Ethanol, Collaborative Study: Final Action 2017.07
Authors: Lacorn Markus , Heßler-Noll Michaela , Wehling Paul , Hektor Thomas 
Published: November 2022

Abstract

Background
Enzytec™ Liquid Ethanol was approved as AOAC Official MethodSM2017.07 First Action in September 2017 and is now further characterized by a collaborative study using the manual and automated version of the test.

Method
It is applicable to quantify ethanol in diluted or undiluted kombucha, fruit juices, vegetable juices, and alcohol-free beer samples around 0.5% ABV within 20 min using two ready-to-use reagents and measurement of absorbance at 340 nm.

Results
The overall relative reproducibility standard deviation across a wide concentration range for kombucha was calculated to be 6.99% by modeling the reproducibility standard deviation by the mean concentration for each of the six kombucha pairs by a linear regression. Analysis of juices and beer showed an overall higher variation with an estimated overall RSD(R) value by regression of 10.1%. Mean recovery of aqueous ethanol reference solutions tested by each participant was between 100 and 103%.

Conclusions
The data obtained by this collaborative study show that the EnzytecTMLiquid Ethanol is suitable to quantify ethanol from matrices representing important alcohol-free liquid food categories.

Highlights
The EnzytecTMLiquid Ethanol was approved as AOAC Method 2017.07 Final Action.
Shifts in global mobility dictate the synchrony of SARS-CoV-2 epidemic waves
Authors: Tegally Houriiyah , Khan Kamran , Huber Carmen , de Oliveira Tulio , Kraemer Moritz U G 
Published: November 2022

Abstract

Background
Human mobility changed in unprecedented ways during the SARS-CoV-2 pandemic. In March and April 2020, when lockdowns and large travel restrictions began in most countries, global air-travel almost entirely halted (92% decrease in commercial global air travel in the months between February and April 2020). Initial recovery in global air travel started around July 2020 and subsequently nearly tripled between May and July 2021. Here, we aim to establish a preliminary link between global mobility patterns and the synchrony of SARS-CoV-2 epidemic waves across the world.

Methods
We compare epidemic peaks and human global mobility in two time periods: November 2020 to February 2021 (when just over 70 million passengers travelled) and November 2021 to February 2022 (when more than 200 million passengers travelled). We calculate the time interval during which continental epidemic peaks occurred for both of these time periods, and we calculate the pairwise correlations of epidemic waves between all pairs of countries for the same time periods.

Results
We find that as air travel increases at the end of 2021, epidemic peaks around the world are more synchronous with one another, both globally and regionally. Continental epidemic peaks occur globally within a 20 day interval at the end of 2021 compared with 73 days at the end of 2020, and epidemic waves globally are more correlated with one another at the end of 2021.

Conclusions
This suggests that the rebound in human mobility dictates the synchrony of global and regional epidemic waves. In line with theoretical work, we show that in a more connected world, epidemic dynamics are more synchronized.
Use of YEARS Algorithm in Military Health Care Beneficiaries to Evaluate Use of Computed Tomography Pulmonary Angiography
Authors: Meaney Colleen , Stroer Kenneth , Perdue Matthew , Walker Jerimiah , Umar Mohamad , Mitchell Christopher 
Published: November 2022

ABSTRACT

Introduction
Pulmonary embolism (PE) can be difficult to rule out without computed tomography pulmonary angiograms (CTPAs), as presentations vary. Multiple clinical decision rules (CDRs) exist to risk-stratify patients to avoid unnecessary CTPAs. However, the currently used CDRs are complex, and research has shown low compliance with their usage. The YEARS algorithm is less complex and excludes patients from CTPA if PE is not the most likely diagnosis, they do not have a history of hemoptysis, and no clinical signs of deep vein thrombosis, is less complex. However, no studies have evaluated YEARS in the U.S. Military health care beneficiary population. Therefore, this study sought to determine if implementing the YEARS algorithm could decrease the number of CTPAs ordered to rule out PE in low-risk patients.

Methods
This retrospective, single-center cohort study applied the YEARS algorithm to low-risk military beneficiaries presenting to the emergency department in the calendar year 2020 at a single U.S. Army MTF. The primary outcome was the number of CTPAs indicated by the YEARS algorithm versus the number ordered via standard practice. We used chi-square testing to compare the number of subjects in whom YEARS indicated CTPA (meets criteria/does not meet criteria) versus the actual number of subjects who underwent CTPA (meets criteria/does not meet criteria). The secondary outcomes included applying YEARS similarly to the number of subjects &gt;50 years of age (as opposed to age-adjusted d-dimer), determining the number of pregnant patients who could have avoided CTPA via application of YEARS, and assessing possible cost savings via reduction of CTPA.

Results
We included 353 subjects during the study period, 271 of whom underwent CTPA. YEARS would have only indicated 25 of them, P = .018. In patients &gt;50 years of age, 164 underwent CTPA versus nine who met YEARS criteria, P = .014. Among pregnant patients, six underwent CTPA versus one who YEARS would have indicated, P = .130. Application of the YEARS algorithm would have led to a 90.8% reduction in CTPAs ordered with an overall known missed PE rate of 1.1%. Applying the YEARS algorithm in 2020 could have led to 246 fewer CTPAs at a minimum cost savings of $38,762.22 for the MTF based on the coded billing cost of $157.57 per CTPA when local staff radiologists performed image interpretation. This estimate does not consider the additional undisclosed cost of contracted radiologists interpreting after regular duty hours.

Conclusions
For our military beneficiaries, our study indicates that the YEARS algorithm would have reduced CTPA utilization in all age ranges and potentially among pregnant patients with a known missed PE rate of 1.1%.
NLRscape: an atlas of plant NLR proteins
Authors: Martin Eliza C , Ion Catalin F , Ifrimescu Florin , Spiridon Laurentiu , Bakker Jaap , Goverse Aska , Petrescu Andrei-J 
Published: November 2022

AbstractNLRscape is a webserver that curates a collection of over 80 000 plant protein sequences identified in UniProtKB to contain NOD-like receptor signatures, and hosts in addition a number of tools aimed at the exploration of the complex sequence landscape of this class of plant proteins. Each entry gathers sequence information, domain and motif annotations from multiple third-party sources but also in-house advanced annotations aimed at addressing caveats of the existing broad-based annotations. NLRscape provides a top-down perspective of the NLR sequence landscape but also services for assisting a bottom-up approach starting from a given input sequence. Sequences are clustered by their domain organization layout, global homology and taxonomic spread—in order to allow analysis of how particular traits of an NLR family are scattered within the plant kingdom. Tools are provided for users to locate their own protein of interest in the overall NLR landscape, generate custom clusters centered around it and perform a large number of sequence and structural analyses using included interactive online instruments. Amongst these, we mention: taxonomy distribution plots, homology cluster graphs, identity matrices and interactive MSA synchronizing secondary structure and motif predictions. NLRscape can be found at: https://nlrscape.biochim.ro/.
GWAS Central: an expanding resource for finding and visualising genotype and phenotype data from genome-wide association studies
Authors: Beck Tim , Rowlands Thomas , Shorter Tom , Brookes Anthony J 
Published: November 2022

Abstract
The GWAS Central resource gathers and curates extensive summary-level genome-wide association study (GWAS) data and puts a range of user-friendly but powerful website tools for the comparison and visualisation of GWAS data at the fingertips of researchers. Through our continued efforts to harmonise and import data received from GWAS authors and consortia, and data sets actively collected from public sources, the database now contains over 72.5 million P-values for over 5000 studies testing over 7.4 million unique genetic markers investigating over 1700 unique phenotypes. Here, we describe an update to integrate this extensive data collection with mouse disease model data to support insights into the functional impact of human genetic variation. GWAS Central has expanded to include mouse gene–phenotype associations observed during mouse gene knockout screens. To allow similar cross-species phenotypes to be compared, terms from mammalian and human phenotype ontologies have been mapped. New interactive interfaces to find, correlate and view human and mouse genotype–phenotype associations are included in the website toolkit. Additionally, the integrated browser for interrogating multiple association data sets has been updated and a GA4GH Beacon API endpoint has been added for discovering variants tested in GWAS. The GWAS Central resource is accessible at https://www.gwascentral.org/.
Type I arginine methyltransferases are intervention points to unveil the oncogenic Epstein-Barr virus to the immune system
Authors: Angrand Gaelle , Quillévéré Alicia , Loaëc Nadège , Dinh Van-Trang , Le Sénéchal Ronan , Chennoufi Rahima , Duchambon Patricia , Keruzoré Marc , Martins Rodrigo Prado , Teulade-Fichou Marie-Paule , Fåhraeus Robin , Blondel Marc 
Published: November 2022

Abstract
The oncogenic Epstein-Barr virus (EBV) evades the immune system but has an Achilles heel: its genome maintenance protein EBNA1. Indeed, EBNA1 is essential for viral genome maintenance but is also highly antigenic. Hence, EBV seemingly evolved a system in which the glycine–alanine repeat (GAr) of EBNA1 limits the translation of its own mRNA to the minimal level to ensure its essential function, thereby, at the same time, minimizing immune recognition. Therefore, defining intervention points at which to interfere with GAr-based inhibition of translation is an important step to trigger an immune response against EBV-carrying cancers. The host protein nucleolin (NCL) plays a critical role in this process via a direct interaction with G-quadruplexes (G4) formed in the GAr-encoding sequence of the viral EBNA1 mRNA. Here we show that the C-terminal arginine–glycine-rich (RGG) motif of NCL is crucial for its role in GAr-based inhibition of translation by mediating interaction of NCL with G4 of EBNA1 mRNA. We also show that this interaction depends on the type I arginine methyltransferase family, notably PRMT1 and PRMT3: drugs or small interfering RNA that target these enzymes prevent efficient binding of NCL on G4 of EBNA1 mRNA and relieve GAr-based inhibition of translation and of antigen presentation. Hence, this work defines type I arginine methyltransferases as therapeutic targets to interfere with EBNA1 and EBV immune evasion.
PARP1 proximity proteomics reveals interaction partners at stressed replication forks
Authors: Mosler Thorsten , Baymaz H Irem , Gräf Justus F , Mikicic Ivan , Blattner Georges , Bartlett Edward , Ostermaier Matthias , Piccinno Rossana , Yang Jiwen , Voigt Andrea , Gatti Marco , Pellegrino Stefania , Altmeyer Matthias , Luck Katja , Ahel Ivan , Roukos Vassilis , Beli Petra 
Published: November 2022

Abstract
PARP1 mediates poly-ADP-ribosylation of proteins on chromatin in response to different types of DNA lesions. PARP inhibitors are used for the treatment of BRCA1/2-deficient breast, ovarian, and prostate cancer. Loss of DNA replication fork protection is proposed as one mechanism that contributes to the vulnerability of BRCA1/2-deficient cells to PARP inhibitors. However, the mechanisms that regulate PARP1 activity at stressed replication forks remain poorly understood. Here, we performed proximity proteomics of PARP1 and isolation of proteins on stressed replication forks to map putative PARP1 regulators. We identified TPX2 as a direct PARP1-binding protein that regulates the auto-ADP-ribosylation activity of PARP1. TPX2 interacts with DNA damage response proteins and promotes homology-directed repair of DNA double-strand breaks. Moreover, TPX2 mRNA levels are increased in BRCA1/2-mutated breast and prostate cancers, and high TPX2 expression levels correlate with the sensitivity of cancer cells to PARP-trapping inhibitors. We propose that TPX2 confers a mitosis-independent function in the cellular response to replication stress by interacting with PARP1.
Annotation and evaluation of base editing outcomes in multiple cell types using CRISPRbase
Authors: Fan Jibiao , Shi Leisheng , Liu Qi , Zhu Zhipeng , Wang Fan , Song Runxian , Su Jimeng , Zhou Degui , Chen Xiao , Li Kailong , Xue Lixiang , Sun Lichao , Mao Fengbiao 
Published: November 2022

Abstract
CRISPR-Cas base editing (BE) system is a powerful tool to expand the scope and efficiency of genome editing with single-nucleotide resolution. The editing efficiency, product purity, and off-target effect differ among various BE systems. Herein, we developed CRISPRbase (http://crisprbase.maolab.org), by integrating 1 252 935 records of base editing outcomes in more than 50 cell types from 17 species. CRISPRbase helps to evaluate the putative editing precision of different BE systems by integrating multiple annotations, functional predictions and a blasting system for single-guide RNA sequences. We systematically assessed the editing window, editing efficiency and product purity of various BE systems. Intensive efforts were focused on increasing the editing efficiency and product purity of base editors since the byproduct could be detrimental in certain applications. Remarkably, more than half of cancer-related off-target mutations were non-synonymous and extremely damaging to protein functions in most common tumor types. Luckily, most of these cancer-related mutations were passenger mutations (4840/5703, 84.87%) rather than cancer driver mutations (863/5703, 15.13%), indicating a weak effect of off-target mutations on carcinogenesis. In summary, CRISPRbase is a powerful and convenient tool to study the outcomes of different base editors and help researchers choose appropriate BE designs for functional studies.
COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations
Authors: Obayashi Takeshi , Kodate Shun , Hibara Himiko , Kagaya Yuki , Kinoshita Kengo 
Published: November 2022

Abstract
Gene coexpression is synchronization of gene expression across many cellular and environmental conditions and is widely used to infer the biological function of genes. Gene coexpression information is complex, comprising a complete graph of all genes in the genome, and requires appropriate visualization and analysis tools. Since its initial release in 2007, the animal gene expression database COXPRESdb (https://coxpresdb.jp) has been continuously improved by adding new gene coexpression data and analysis tools. Here, we report COXPRESdb version 8, which has been enhanced with new features for an overview, summary, and individual examination of coexpression relationships: CoexMap to display coexpression on a genome scale, pathway enrichment analysis to summarize the function of coexpressed genes, and CoexPub to bridges coexpression and existing knowledge. COXPRESdb also facilitates downstream analyses such as interspecies comparisons by integrating RNAseq and microarray coexpression data in a union-type gene coexpression. COXPRESdb strongly support users with the new coexpression data and enhanced functionality.