bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aspect-Based Sentiment Analysis Using Interaction Matrix And Global Attention Neural Network
Authors: Wang Xiaodi , Pan Xiaoge , Yang Tian , Xie Jianhua , Tang Mingwei 
Published: February 2022

Abstract
Aspect-based sentiment analysis aims to identify the sentiment polarity of aspects in a given sentence. Although existing neural network models show promising results, they cannot meet the expectations in the case of a single network structure and limited dataset. When an aspect term composes more than one word, many models use the coarse-grained attention mechanism but lead to the unsatisfactory results. Besides, the relative distance between words in a sentence is always out of consideration. In this paper, we propose a model based on the interaction matrix and global attention mechanism to improve the ability of aspect-based sentiment analysis. First of all, the relative distance features of words in a sentence are initialized to enrich word embedding. Second, classic neural networks are applied to extract the essential features of word embedding in a sentence, such as long short-term memory and convolutional neural network. Third, an interaction matrix and global attention mechanism are combined to calculate weighted scores and measure relationships between aspect terms and context words. Finally, sentiment polarity is represented through a softmax layer. Experimental results on restaurant, laptop and twitter datasets show that the performance of the proposed model is superior to other methods.
Zebrafish information network, the knowledgebase for Danio rerio research
Authors: Bradford Yvonne M , Van Slyke Ceri E , Ruzicka Leyla , Singer Amy , Eagle Anne , Fashena David , Howe Douglas G , Frazer Ken , Martin Ryan , Paddock Holly , Pich Christian , Ramachandran Sridhar , Westerfield Monte 
Published: February 2022

Abstract
The Zebrafish Information Network (zfin.org) is the central repository for Danio rerio genetic and genomic data. The Zebrafish Information Network has served the zebrafish research community since 1994, expertly curating, integrating, and displaying zebrafish data. Key data types available at the Zebrafish Information Network include, but are not limited to, genes, alleles, human disease models, gene expression, phenotype, and gene function. The Zebrafish Information Network makes zebrafish research data Findable, Accessible, Interoperable, and Reusable through nomenclature, curatorial and annotation activities, web interfaces, and data downloads. Recently, the Zebrafish Information Network and 6 other model organism knowledgebases have collaborated to form the Alliance of Genome Resources, aiming to develop sustainable genome information resources that enable the use of model organisms to understand the genetic and genomic basis of human biology and disease. Here, we provide an overview of the data available at the Zebrafish Information Network including recent updates to the gene page to provide access to single-cell RNA sequencing data, links to Alliance web pages, ribbon diagrams to summarize the biological systems and Gene Ontology terms that have annotations, and data integration with the Alliance of Genome Resources.
Fully resolved assembly of Cryptosporidium parvum
Authors: Menon Vipin K , Okhuysen Pablo C , Chappell Cynthia L , Mahmoud Medhat , Mahmoud Medhat , Meng Qingchang , Doddapaneni Harsha , Vee Vanesa , Han Yi , Salvi Sejal , Bhamidipati Sravya , Kottapalli Kavya , Weissenberger George , Shen Hua , Ross Matthew C , Hoffman Kristi L , Cregeen Sara Javornik , Muzny Donna M , Metcalf Ginger A , Gibbs Richard A , Petrosino Joseph F , Sedlazeck Fritz J 
Published: February 2022

Abstract

Background
Cryptosporidium parvum is an apicomplexan parasite commonly found across many host species with a global infection prevalence in human populations of 7.6%. Understanding its diversity and genomic makeup can help in fighting established infections and prohibiting further transmission. The basis of every genomic study is a high-quality reference genome that has continuity and completeness, thus enabling comprehensive comparative studies.

Findings
Here, we provide a highly accurate and complete reference genome of Cryptosporidium parvum. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. We also outline how to evaluate and choose from different assembly methods based on 2 main approaches that can be applied to other Cryptosporidium species. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall, the assembly shows a high completion rate with 98.4% single-copy BUSCO genes.

Conclusions
This high-quality reference genome of a zoonotic IIaA17G2R1 C. parvum subtype isolate provides the basis for subsequent comparative genomic studies across the Cryptosporidium clade. This will enable improved understanding of diversity, functional, and association studies.
Central and Eastern European Infrasound Network: contribution to infrasound monitoring
Authors: Bondár István , Šindelářová Tereza , Ghica Daniela , Mitterbauer Ulrike , Liashchuk Alexander , Baše Jiří , Chum Jaroslav , Czanik Csenge , Ionescu Constantin , Neagoe Cristian , Pásztor Marcell , Pichon Alexis Le 
Published: February 2022

SUMMARY
The Central and Eastern European Infrasound Network (CEEIN) has been established in 2018 with the collaboration of four research institutes, the Zentralanstalt für Meteorologie and Geodynamik (ZAMG), Vienna, Austria; the Institute of Atmospheric Physics of the Czech Academy of Sciences (CAS IAP), Prague, Czech Republic; the Research Centre for Astronomy and Earth Sciences of the Eötvös Loránd Research Network (ELKH CSFK), Budapest, Hungary; and the National Institute for Earth Physics (NIEP), Magurele, Romania. The Main Centre of Special Monitoring National Center for Control and Testing of Space Facilities, State Agency of Ukraine joined CEEIN in 2019. We show how the CEEIN infrasound arrays improve the detection capability of the European infrasound network and discuss coherent noise sources observed at CEEIN stations. We present the first CEEIN bulletin (2017–2020) of infrasound-only and seismo-acoustic events and using ground truth events, we demonstrate how adding infrasound observations to seismic data in the location algorithm improves location accuracy.
Are we leaving money on the table in infertility RCTs? Trialists should statistically adjust for prespecified, prognostic covariates to increase power
Authors: Wilkinson J , Showell M , Taxiarchi V P , Lensen S 
Published: February 2022

Abstract
Infertility randomized controlled trials (RCTs) are often too small to detect realistic treatment effects. Large observational studies have been proposed as a solution. However, this strategy threatens to weaken the evidence base further, because non-random assignment to treatments makes it impossible to distinguish effects of treatment from confounding factors. Alternative solutions are required. Power in an RCT can be increased by adjusting for prespecified, prognostic covariates when performing statistical analysis, and if stratified randomization or minimization has been used, it is essential to adjust in order to get the correct answer. We present data showing that this simple, free and frequently necessary strategy for increasing power is seldom employed, even in trials appearing in leading journals. We use this article to motivate a pedagogical discussion and provide a worked example. While covariate adjustment cannot solve the problem of underpowered trials outright, there is an imperative to use sound methodology to maximize the information each trial yields.
Food-Related Quality of Life in Children and Adolescents With Crohn’s Disease
Authors: Brown Stephanie C , Whelan Kevin , Frampton Chris , Wall Catherine L , Gearry Richard B , Day Andrew S 
Published: February 2022

Abstract

Background
Food-related quality of life (FRQoL) encompasses the psychosocial elements of eating and drinking. The FRQoL of children and adolescents with inflammatory bowel disease has not yet been assessed. This study aimed to evaluate the utility of the validated FR-Qol-29 instrument in children with Crohn’s disease (CD).

Methods
Children diagnosed with CD, a shared home environment healthy sibling, and healthy control subjects 6 to 17 years of age were recruited to this single-center, prospective, cross-sectional study. Children or their parent or guardian completed the FR-QoL-29 instrument. Internal consistency was assessed by completing Cronbach’s α. Construct validity was established by correlating the CD FR-QoL-29 sum scores with the Physician Global Assessment and Pediatric Crohn Disease Activity Index scores. The discriminant validity was analyzed using a 1-way analysis of variance, and a Spearman’s correlation coefficient test was completed to identify any correlations associated with FRQoL.

Results
Sixty children or their parent or guardian completed the FR-QoL-29 instrument (10 children in each subgroup). The internal consistency was excellent (Cronbach’s α = 0.938). The mean FR-QoL-29 sum scores were 94.3 ± 27.6 for CD, 107.6 ± 20 for siblings, and 113.7 ± 13.8 for control subjects (P = .005). Those with higher disease activity had worse FRQoL (Physician Global Assessment P = .021 and Pediatric Crohn Disease Activity Index P = .004). Inflammatory bowel disease FR-QoL-29 sum scores correlated with weight (P = .027), height (P = .035), body mass index (P = .023), and age (P = .015).

Conclusions
FRQoL is impaired in children with CD. Healthy siblings also have poorer FRQoL than control subjects. Several clinical factors are associated with poorer FRQoL in children with CD including age and level of nutritional risk (weight, height, and body mass index). Further research is required validate these findings and to develop strategies for the prevention or treatment of impaired FRQoL in children with CD.
Characterization of the Immune Resistance of Severe Acute Respiratory Syndrome Coronavirus 2 Mu Variant and the Robust Immunity Induced by Mu Infection
Authors: Uriu Keiya , Cárdenas Paúl , Muñoz Erika , Barragan Veronica , Kosugi Yusuke , Shirakawa Kotaro , Takaori-Kondo Akifumi ,   Ecuador-COVID19 Consortium, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito Jumpei , Yamasoba Daichi , Kimura Izumi , Suganami Mai , Oide Akiko , Yokoyama Miyabishara , Chiba Mika , Nakagawa So , Wu Jiaqi , Takahashi Miyoko , Kazuma Yasuhiro , Nomura Ryosuke , Horisawa Yoshihito , Nagata Kayoko , Yanagida Yohei , Kawai Yugo , Tashiro Yusuke , Kaneda Atsushi , Nakada Taka-aki , Seki Motoaki , Fujiki Ryoji , Shimada Tadanaga , Hirahara Kiyoshi , Yokote Koutaro , Nakayama Toshinori , Irie Takashi , Kawabata Ryoko , Morizako Nanami , Fukuhara Takasuke , Shimizu Kenta , Tsushima Kana , Kubo Haruko , Ikeda Terumasa , Motozono Chihiro , Nasser Hesham , Shimizu Ryo , Yuan Yue , Kitazato Kazuko , Hasebe Haruyo , Ueno Takamasa , Saito Akatsuki , Butlertanaka Erika P , Tanaka Yuri L , Tokunaga Kenzo , Ozono Seiya , Sadamasu Kenji , Asakura Hiroyuki , Yoshida Isao , Nagashima Mami , Yoshimura Kazuhisa , Márquez Sully , Prado-Vivar Belén , Becerra-Wong Mónica , Carvajal Mateo , Trueba Gabriel , Rojas-Silva Patricio , Grunauer Michelle , Gutierrez Bernardo , Guadalupe Juan José , Fernández-Cadena Juan Carlos , Andrade-Molina Derly , Baldeon Manuel , Pinos Andrea , Sato Kei 
Published: February 2022

Abstract

Background
We have recently revealed that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Mu variant shows a pronounced resistance to antibodies elicited by natural SARS-CoV-2 infection and vaccination.

Methods
However, it remains unclear which mutations determine the resistance of SARS-CoV-2 Mu to antiviral sera. In addition, it is unclear how SARS-CoV-2 Mu infection induces antiviral immunity.

Results
In this study, we reveal that the 2 mutations in the SARS-CoV-2 Mu spike protein, YY144-145TSN and E484K, are responsible for the resistance to coronavirus disease 2019 convalescent sera during early 2020 and vaccine sera.

Conclusions
It is notable that the convalescent sera of SARS-CoV-2 Mu-infected individuals are broadly antiviral against Mu as well as other SARS-CoV-2 variants of concern and interest.
Trends in Rotavirus Laboratory Detections and Internet Search Volume Before and After Rotavirus Vaccine Introduction and in the Context of the Coronavirus Disease 2019 Pandemic—United States, 2000–2021
Authors: Burnett Eleanor , Parashar Umesh D , Winn Amber , Tate Jacqueline E 
Published: February 2022

Abstract

Background
Since rotavirus vaccines became available in the United States in 2006, there have been reductions in rotavirus hospitalizations, changes in seasonality, and the emergence of a biennial trend of rotavirus activity. Reductions in other pathogens have been associated with coronavirus disease 2019 (COVID-19) mitigation measures. We assessed ongoing rotavirus disease trends during the COVID-19 pandemic.

Methods
We report a 3-week moving average of the number of rotavirus tests, positive tests, and the percent positivity from laboratories reporting to the National Respiratory and Enteric Virus Surveillance System (NREVSS) from July 2000 through June 2021. To complement NREVSS data, we analyzed Google internet search interest in “rotavirus” from July 2004 to June 2021.

Results
Declines in rotavirus activity following vaccine introduction and the biennial trend are evident through the 2018–2019 surveillance year. In 2019–2021, rotavirus test positivity was below the historic ranges during the months of typically high rotavirus activity, and precipitous declines were noted in March 2020.

Conclusions
In the 15 years since rotavirus vaccine was introduced, the number of laboratory-detected rotavirus infections has been consistently lower than during the prevaccine era. During the COVID-19 pandemic, rotavirus activity was suppressed. There may be many rotavirus-susceptible children during the 2021–2022 rotavirus season.
Determination of Highly Polar and Ionic Pesticides in Grape and Pomegranate Using Liquid Chromatography Tandem Mass Spectrometry
Authors: Shinde Raviraj , Banerjee Kaushik 
Published: February 2022

Abstract

Background
Residues of polar pesticides cannot be determined by QuEChERS-based multiresidue extractions because of their non-amenability to reverse-phase chromatographic separation and poor recoveries. On the other hand, single-residue methods pose limitations because of the various requirements of sample preparation and LC-MS/MS conditions. A new multiresidue method is thus warranted for rapid and simultaneous analysis of polar pesticides.

Objective
The study developed a multiresidue method for the simultaneous analysis of glyphosate and its metabolite (aminomethylphosphonic acid, AMPA), glufosinate and its metabolites (3-methylphosphinicopropionic acid and N-acetyl-glufosinate), ethephon, fosetyl-aluminum and its metabolite (phosphonic acid), and trimesium in grape and pomegranate by LC-MS/MS.

Method
The homogenized samples (10 g) were extracted with acidified methanol (20 mL). An aliquot of the extract was diluted with acetonitrile (1 + 1) and measured by LC-MS/MS using a Torus DEA column. The performance of a hydrophilic interaction liquid chromatography (HILIC) column and an “anionic polar pesticides” (APP) column was also evaluated.

Results
The method performance on the Torus DEA column was satisfactory for all compounds (recoveries = 77–104%, repeatability-RSD, &lt;11%) at limit of quantification (LOQ) (0.01 mg/kg), and with higher levels in grape and pomegranate. The only exception was AMPA, which had an LOQ of 0.05 mg/kg. In the APP column, AMPA could be determined with an LOQ of 0.01 mg/kg. Trimesium, which had poor retention in Torus DEA, performed better in an XBridge HILIC column (retention time = 4.2 min, LOQ = 0.01 mg/kg). The inter-laboratory validation experiment yielded comparable results with high accuracy and precision.

Conclusions
The method could screen the residues of all compounds on a Torus DEA column. For AMPA and trimesium, the APP and XBridge HILIC columns provided superior method performances. Since isotopically labeled internal standards were not required, the method appeared cost-effective. Considering its compliance with the SANTE/12682/2019 validation guidelines and EU-MRLs, the method can be recommended for regulatory testing purposes.

Highlights
A high-throughput residue analysis method targeting nine polar and ionic compounds in grape and pomegranate involved a single multiresidue extraction, followed by direct analysis using LC-MS/MS. A satisfactory method performance was achieved through intra- and inter-laboratory validation. The method sensitivity met the EU-MRLs and the SANTE/12682/2019 analytical quality control criteria.
Experiences, Difficulties, and Coping Methods of Burn Nurses: An Exploratory-Descriptive Qualitative Study
Authors: Karahan Sabri , Erbas Atiye , Tuncbilek Zahide 
Published: February 2022

Abstract
Caring for burn patients is both physically and emotionally exhausting for nurses. Each nurse can experience different emotions and make different senses of these experiences. This study was conducted to determine the experiences of nurses who care for burn patients. The study conducted as an exploratory-descriptive qualitative study. Six nurses participated in the study who work in the burn units of a university hospital. Data were obtained by the semistructured face-to-face interviews. The transcription of audio records from interviews was performed, and these transcriptions were analyzed using the thematic analysis method. Codes and subthemes were extracted and the main themes were reached. These themes were gathered under two contexts and reported. Under the context of experience, the themes of “emotional challenge,” “physical difficulties,” and “psychological difficulties,” and nine subthemes were created. Under the context of coping, the themes of “coping methods” and “motivation” as well as eight subthemes, were created under these themes. It was found that nurses who provide care to burn patients face emotional and physical difficulties; however, they do not have effective coping methods and adequate support. The biggest source of support for nurses was again seen to be nurses. In line with these results, it is important that nurses experienced in burn care support junior nurses, nurses who work in such clinics are allowed to use coping mechanisms, and professional support should be provided to these nurses.
Humor Reduces Online Incivility
Authors: Elsayed Yomna , Hollingshead Andrea B 
Published: February 2022

Abstract
Online incivility is a persistent issue facing many news and social media platforms. To better understand it, we examined whether humorous content reduced online incivility and whether the (in)civility of another user might mitigate or amplify this effect in two experiments (Study 1, N = 122; Study 2, N = 208). Participants in both experiments read an online opinion article about an instance of negative stereotyping and provided a comment on a simulated online news forum. The first study manipulated article humor (humorous vs. not humorous). The second study manipulated humor and the (in)civility of a previous user’s comment (civil vs. uncivil). In both studies, humor-reduced incivility. Anger mediated this effect. Source liking mediated the positive effect of humor on reducing anger. The (in)civility of a previous comment did not affect these results. Overall, the findings point to the value of humor and anger reduction in managing online incivility.
Lay Summary
Online incivility is a common occurrence in online public forums. This article investigated factors that may reduce incivility in two online experiments. The first experiment tested whether humor reduced anger and subsequently the incivility of participants’ comments towards a negative stereotype-challenging op-ed article. The second experiment tested whether exposure to civil and uncivil previous user comments influenced the civility of participants’ comments. Humor was found to reduce online incivility by reducing feelings of anger and increasing liking towards the author in both experiments. Exposure to another user’s comment, whether civil or uncivil, did not appear to influence the civility of participants’ comments, suggesting that article content is a more likely trigger for online incivility.
The real-world safety of atezolizumab as second-line or later treatment in Japanese patients with non-small-cell lung cancer: a post-marketing surveillance study
Authors: Ohe Yuichiro , Yamazaki Naoya , Yamamoto Nobuyuki , Murakami Haruyasu , Yoh Kiyotaka , Kitano Shigehisa , Hashimoto Hideyuki , Murayama Ayako , Nakane Sayuri , Gemma Akihiko 
Published: February 2022

Abstract

Background
We conducted a post-marketing surveillance study to evaluate the clinical tolerability and safety of atezolizumab in Japanese patients with non-small-cell lung cancer (NSCLC).

Methods
This prospective, observational post-marketing cohort study was conducted in NSCLC patients who received atezolizumab 1200 mg every 3 weeks at 770 facilities in Japan between April 18, 2018, and March 31, 2020 (study number UMIN000031978). Case report forms were completed, recording patient characteristics, treatment details, adverse events, adverse drug reactions (ADRs), their severity, onset and outcomes. Follow-up was for 12 months or until atezolizumab discontinuation.

Results
Overall, 2570 patients were included, median age was 69.0 years, and 69.9% were males. ADRs were reported in 29.1% of patients, most commonly pyrexia (4.2%). Grade ≥ 3 ADRs occurred in 9.7% of patients aged &lt;75 and 9.7% of those aged ≥75 years. The incidence of Grade ≥ 3 ADRs was not affected by the number of lines of previous treatment or the presence or history of an autoimmune disorder. Immune-related ADRs of interest that occurred in &gt;1% of patients were interstitial lung disease (ILD; 4.4%), endocrine disorder (4.3%), and hepatic dysfunction (2.8%). ILD was significantly more common in patients with a history of, or concurrent, ILD versus those without (P ≤ 0.001). Risk factors of Grade ≥ 3 ADRs were a history of, or concurrent, ILD. Grade 5 ADRs occurred in 35 patients, 11 of whom had concurrent ILD.

Conclusions
This large cohort study confirmed the clinical tolerability of atezolizumab in a real-world group of Japanese patients with NSCLC.
Classification for transmission electron microscope images from different amorphous states using persistent homology
Authors: Uesugi Fumihiko , Ishii Masashi 
Published: February 2022

Abstract
It is difficult to discriminate the amorphous state using a transmission electron microscope (TEM). We discriminated different amorphous states on TEM images using persistent homology, which is a mathematical analysis technique that employs the homology concept and focuses on ‘holes’. The structural models of the different amorphous states, that is, amorphous and liquid states, were created using classical molecular dynamic simulation. TEM images in several defocus conditions were simulated by the multi-slice method using the created amorphous and liquid states, and their persistent diagrams were calculated. Finally, logistic regression and support vector classification machine learning algorithms were applied for discrimination. Consequently, we found that the amorphous and liquid phases can be discriminated by more than 85%. Because the contrast of TEM images depends on sample thickness, focus, lens aberration, etc., radial distribution function cannot be classified; however, the persistent homology can discriminate different amorphous states in a wide focus range.