bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Political, the Personal, and “The Function of American Literary Criticism at the Present Time,” 1983–2021
Authors: Gillman Susan 
Published: November 2021

Abstract
Focused on the work of Amy Kaplan and Edward Said, two critics known for their engagements with that longtime hot-button slogan, “the personal = the political,” this essay updates Mathew Arnold’s formula of the function of criticism at the present time. In her 2003 ASA presidential address, Kaplan posed the question, what should be the role of American studies scholars today, in the face of American empire today?—and together with Said, she answered it in a series of experiments with form. The essay, the address, and the book, all three reoriented toward making the personal = the political, become their routes to thinking empire as an ongoing historical subject, anarchic and incoherent rather than monolithic. The work on US empire in the 1980s, when Kaplan’s denial thesis on the absence of empire in American studies took hold and inspired so many scholars, is still present but with new terminology in new disciplinary locations. The larger function of criticism appears when we superimpose the timeline of earlier empire work onto other, current confluences of dates (the centenaries 1992/1998, 9/11, BLM, and COVID-19, 2019–2020) and speculate on the why of these still-open-ended key contexts, textual clusters of empire.
Isoform-level quantification for single-cell RNA sequencing
Authors: Pan Lu , Dinh Huy Q , Pawitan Yudi , Vu Trung Nghia 
Published: November 2021

Abstract

Motivation
RNA expression at isoform level is biologically more informative than at gene level and can potentially reveal cellular subsets and corresponding biomarkers that are not visible at gene level. However, due to the strong 3ʹ bias sequencing protocol, mRNA quantification for high-throughput single-cell RNA sequencing such as Chromium Single Cell 3ʹ 10× Genomics is currently performed at the gene level.

Results
We have developed an isoform-level quantification method for high-throughput single-cell RNA sequencing by exploiting the concepts of transcription clusters and isoform paralogs. The method, called Scasa, compares well in simulations against competing approaches including Alevin, Cellranger, Kallisto, Salmon, Terminus and STARsolo at both isoform- and gene-level expression. The reanalysis of a CITE-Seq dataset with isoform-based Scasa reveals a subgroup of CD14 monocytes missed by gene-based methods.

Availability and implementation
Implementation of Scasa including source code, documentation, tutorials and test data supporting this study is available at Github: https://github.com/eudoraleer/scasa and Zenodo: https://doi.org/10.5281/zenodo.5712503.

Supplementary information
Supplementary data are available at Bioinformatics online.
The impact of coronary revascularization on vessel-specific coronary flow capacity and long-term outcomes: a serial [15O]H2O positron emission tomography perfusion imaging study
Authors: de Winter Ruben W , Jukema Ruurt A , van Diemen Pepijn A , Schumacher Stefan P , Driessen Roel S , Stuijfzand Wynand J , Everaars Henk , Bom Michiel J , van Rossum Albert C , van de Ven Peter M , Verouden Niels J , Nap Alexander , Raijmakers Pieter G , Danad Ibrahim , Knaapen Paul 
Published: November 2021

Abstract

Aims
Coronary flow capacity (CFC) integrates quantitative hyperaemic myocardial blood flow (hMBF) and coronary flow reserve (CFR) to comprehensively assess physiological severity of coronary artery disease (CAD). This study evaluated the effects of revascularization on CFC as assessed by serial [15O]H2O positron emission tomography (PET) perfusion imaging.

Methods and results
A total of 314 patients with stable CAD underwent [15O]H2O PET imaging at baseline and after myocardial revascularization to assess changes in hMBF, CFR, and CFC in 415 revascularized vessels. Using thresholds for ischaemia and normal perfusion, vessels were stratified in five CFC categories: myocardial steal, severely reduced CFC, moderately reduced CFC, minimally reduced CFC, and normal flow. Additionally, the association between CFC increase and the composite endpoint of death and non-fatal myocardial infarction (MI) was studied. Vessel-specific CFC improved after revascularization (P &lt; 0.01). Furthermore, baseline CFC was an independent predictor of CFC increase (P &lt; 0.01). The largest changes in ΔhMBF (0.90 ± 0.74, 0.93 ± 0.65, 0.79 ± 0.74, 0.48 ± 0.61, and 0.29 ± 0.66 mL/min/g) and ΔCFR (1.01 ± 0.88, 0.99 ± 0.69, 0.87 ± 0.88, 0.66 ± 0.91, and −0.01 ± 1.06) were observed in vessels with lower baseline CFC (P &lt; 0.01 for both). During a median follow-up of 3.5 (95% CI 3.1–3.9) years, an increase in CFC was independently associated with lower rates of death and non-fatal MI (HR 0.43, 95% CI 0.19–0.98, P = 0.04).

Conclusion
Successful revascularization results in an increase in CFC. Furthermore, baseline CFC was an independent predictor of change in hMBF, CFR, and subsequently CFC. In addition, an increase in CFC was associated with a favourable outcome in terms of death and non-fatal MI.
Gut microbiome status of urban and rural Filipino adults in relation to diet and metabolic disorders
Authors: Watanabe Mai , Sianoya Abraham , Mishima Riko , Therdtatha Phatthanaphong , Rodriguez Abigail , Ramos Donna Christene , Lee Yuan Kun , Dalmacio Leslie Michelle , Nakayama Jiro 
Published: November 2021

ABSTRACT
Here, we aim to understand the condition of the gut microbiome of Filipino adults in relation to their diet and metabolic status. Compared to rural Albay (n = 67), the gut microbiome of subjects living in urban Manila (n = 25) was more colonized by the order Clostridiales, which was negatively correlated with host carbohydrate consumption. Principal component analysis using the genus composition of the 92 total subjects indicated four microbiome types: one type driven by Prevotella, which was associated with high rice consumption and mainly consisted of healthy Albay subjects, one Clostridiales-driven group containing a number of type 2 diabetes mellitus (T2D) subjects from both Manila and Albay who showed lower butyrate levels in association with a decrease in Mediterraneibacter faecis, and the other two types showing dysbiosis-like microbiomes with Lactobacillus and Bifidobacterium overgrowth, with a high ratio of T2D and obese subjects. Multivariate logistic regression analysis suggested high dietary energy intake, and two Veillonellaeae genera, Dialister and Megasphaera, as T2D risk factors, while Prevotella and M. faecis as anti-T2D factors. In conclusion, low-carbohydrate diets restructured the Prevotella-driven gut microbiome, which may predispose Filipino people with high energy diet to T2D.
A Reference Genome Assembly of Hybrid-Derived California Wild Radish (Raphanus sativus × raphanistrum)
Authors: Alexandre Nicolas M , Haji Diler , Bakhtiari Moe , Chatla Kamalakar , Aguilar Jessica M , Arzumanova Ksenia , Whiteman Noah K 
Published: November 2021

AbstractFor agriculturally important plants, pollination and herbivory are 2 ecological factors that play into the success of crop yields. Each is also important in natural environments where invasive plants and their effect on species interactions may alter the native ecology. The California Wild Radish (Raphanus sativus × raphanistrum), a hybrid derived from an agriculturally important crop and a nonnative cultivar, is common in California. Remarkably, it has recently replaced wild populations of both progenitor species. Experiments on phenotypic variation for petal color and antiherbivore defenses suggest both pairs of polymorphisms are maintained as a result of pollinator- and herbivore-mediated natural selection. This species provides an opportunity to understand how natural selection shapes the evolution of ecologically important traits when traits are constrained by 2 opposing forces. Here we provide the genome assembly of the California Wild Radish displaying improvement to currently existing genomes for agronomically important crucifers. This genome sequence provides the tools to dissect the genomic architecture of traits related to herbivory and pollination using natural variation in the wild as well as the ability to infer demographic and selective history in the context of hybridization. Study systems like these will improve our understanding and predictions of evolutionary change for correlated traits.
Evaluation of Discordant Results Between FilmArray Meningitis/Encephalitis Panel and Conventional Testing in Pediatric Patients: A Multisite Retrospective Cohort Study
Authors: Ekambaram Maheswari , Nabower Aleisha , Rajbhandari Prabi , Eisenberg Jaclyn , Goodrich Nathaniel , Ampofo Krow , Gollehon Nathan S , Martin Kimberly C , Lyden Elizabeth , Snowden Jessica 
Published: November 2021

Abstract

Background
The FilmArray Meningitis/Encephalitis panel (MEP) has an 11% false-positive and 2.2% false-negative rate compared with conventional testing. We describe clinical characteristics, treatment decisions, and outcomes in children with discordant results between MEP and conventional testing.

Methods
We conducted a multisite review of patients ≤ 18 years with suspected central nervous system infection and positive results by MEP or conventional testing (cerebrospinal fluid [CSF] culture, herpes simplex virus [HSV] polymerase chain reaction (PCR), and enterovirus [EV] PCR). Descriptive results are provided for patients with discordant results. Comparison between group 1 (MEP and CSF culture positive) and group 2 (MEP positive, CSF culture negative, or showing a different pathogen) was made by Mann-Whitney test for continuous and Fisher’s test for categorical variables.

Results
A total of 355 patients had at least one pathogen identified. More than half of patients with bacterial pathogens identified that are included in the MEP had discordant results (30/52; 58%). There were 28 samples with bacterial pathogen identified on MEP only, 1 with different bacterial pathogens on MEP and culture, and 1 with Escherichia coli identified on CSF culture only. Patients in group 1 were more likely to have CSF pleocytosis, elevated CSF protein, and decreased CSF glucose than group 2 (P &lt; .05). Two patients were HSV positive by MEP while HSV negative by PCR. Ten patients had discordant results between MEP and EV PCR.

Conclusions
Discordant results between MEP and conventional testing are common. Treatment decisions based on a positive MEP should be made in the appropriate clinical context.
Hiatus hernia with gastric volvulus and duodenum component: a case report
Authors: Gimenez F Y , Takahashi L A R , Oliveira G G , Myaki J Y , Inaba M E , Feitosa F P A , Adão D 
Published: November 2021

Abstract
Gastric volvulus is a rare condition defined as an abnormal stomach rotation around its axis, which usually presents in children under a year or in adults in their fifth decade. Cases over 70-year-old are rare and only 30% of cases of this disease present with mesenteric-axial rotation of the stomach.
In this article, we report a rare case of mesenteroaxial gastric volvulus associated with hiatal hernia, in an 88-year-old woman, who presented to the Emergency Department of our institution with bowel obstruction symptoms.
The diagnosis could be difficult due to the rarity of the pathology, the patient's age outside the expected incidence age range and the less common mesenteroaxial presentation.
This report highlights the importance of the differential diagnosis of gastric volvulus as a cause of intestinal obstruction.
Global survey of alternative splicing and gene modules associated with fertility regulation in a thermosensitive genic male sterile wheat
Authors: Bai Jianfang , Wang Yukun , Liu Zihan , Guo Haoyu , Zhang Fengting , Guo Liping , Yuan Shaohua , Duan Wenjing , Li Yanmei , Tan Zhaoguo , Zhao Changping , Zhang Liping 
Published: November 2021

AbstractThermosensitive genic male sterile (TGMS) wheat lines are the core of two-line hybrid systems. Understanding the mechanism that regulates male sterility in TGMS wheat lines is helpful for promoting wheat breeding. Several studies have obtained information regarding the mechanisms associated with male sterility at the transcriptional level, but it is not clear how the post-transcriptional process of alternative splicing might contribute to controlling male sterility. In this study, we performed genome-wide analyses of alternative splicing during the meiosis stage in TGMS line BS366 using PacBio and RNA-Seq hybrid sequencing. Cytological observations indicated that cytoskeleton assembly in pollen cells, calcium deposition in pollen and tapetal cells, and vesicle transport in tapetal cells were deficient in BS366. According to our cytological findings, 49 differentially spliced genes were isolated. Moreover, 25 long non-coding RNA targets and three bHLH transcription factors were identified. Weighted gene co-expression network analysis detected four candidate differentially spliced genes that had strong co-relation with the seed setting percentage, which is the direct representation of male sterility in BS366. In this study, we obtained comprehensive data regarding the alternative splicing-mediated regulation of male sterility in TGMS wheat. The candidates identified may provide the molecular basis for an improved understanding of male sterility.
Investigating the structure of star-forming regions using INDICATE
Authors: Blaylock-Squibbs George A , Parker Richard J , Buckner Anne S M , Güdel Manuel 
Published: November 2021

ABSTRACT
The ability to make meaningful comparisons between theoretical and observational data of star-forming regions is key to understanding the star formation process. In this paper, we test the performance of INDICATE, a new method to quantify the clustering tendencies of individual stars in a region, on synthetic star-forming regions with substructured, and smooth, centrally concentrated distributions. INDICATE quantifies the amount of stellar affiliation of each individual star, and also determines whether this affiliation is above random expectation for the star-forming region in question. We show that INDICATE cannot be used to quantify the overall structure of a region due to a degeneracy when applied to regions with different geometries. We test the ability of INDICATE to detect differences in the local stellar surface density and its ability to detect and quantify mass segregation. We then compare it to other methods such as the mass segregation ratio ΛMSR, the local stellar surface density ratio ΣLDR, and the cumulative distribution of stellar positions. INDICATE detects significant differences in the clustering tendencies of the most massive stars when they are at the centre of a smooth, centrally concentrated distribution, corresponding to areas of greater stellar surface density. When applied to a subset of the 50 most massive stars, we show INDICATE can detect signals of mass segregation. We apply INDICATE to the following nearby star-forming regions: Taurus, ONC, NGC 1333, IC 348, and ρ Ophiuchi and find a diverse range of clustering tendencies in these regions.
Financial Literacy in the Age of Green Investment
Authors: Anderson Anders , Robinson David T 
Published: November 2021

Abstract
We survey a large sample of Swedish households and connect the responses to administrative data to relate pro-environmental attitudes and values to actual investment decisions. Pro-environment households are not more likely to hold pro-environment portfolios. This results from financial disengagement: they are less likely to own stocks, check pension balances, or make green active retirement planning choices. Green financial engagement is stronger in settings where financial literacy is higher or where informational hurdles are lower. Informational barriers appear to prevent financial market prices and returns from fully reflecting household environmental preferences.
Adoption of Best Management Practices for Grapevine Leafroll and Red Blotch Diseases: A Survey of West Coast Growers
Authors: Hobbs Malcolm B. , Vengco Selena M. , Bolton Stephanie L. , Bettiga Larry J. , Moyer Michelle M. , Cooper Monica L. 
Published: November 2021

Grapevine leafroll disease (GLD) and red blotch disease (RBD) threaten the sustainability of the U.S. wine grape industry. To understand the factors influencing the adoption of disease management practices, we surveyed wine grape industry professionals in California, Oregon, and Washington ( n = 154). Economic factors were the fundamental cost of implementing management practices and the ability to sell products from diseased vines (salability). Respondents who encountered reduced salability were more likely to adopt virus testing, replace infected vines, and view these practices as economically favorable. Salability was a strong driver for adoption among Californian respondents but less so in Washington, where wineries appeared more willing to accept infected products. Respondents who had acquired technical knowledge of disease ecology were more likely to adopt management practices and to perceive them as economical. Conversely, when there was a lack of knowledge of GLD ecology, notably that mealybugs transmit the pathogen, adoption was reduced, and practices were considered less economical. Factors affecting adoption were broadly generalizable across diseases. However, knowledge of GLD ecology was more strongly associated with adoption, likely reflecting the remaining knowledge gaps in RBD related to vector ecology and field spread. An emphasis on grower knowledge acquisition and the development of economical disease management practices can improve adoption of best management practices for viral diseases of grapevine. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Lamotrigine may Increase Risk of Arrythmias
Authors: Aschenbrenner Diane S. 
Published: November 2021

The Food and Drug Administration (FDA) is advising health care practitioners that lamotrigine (Lamictal), used in managing seizures and bipolar disorder, may increase the risk of serious and potentially lethal arrythmias.The risk is greater if the patient has underlying cardiac disease or is taking medications that affect heart conduction.The FDA is requiring in vitro studies of other sodium channel blockers to determine if this risk is a class effect or unique to lamotrigine.
Deep learning to estimate gestational age from blind ultrasound sweeps of the gravid abdomen
Authors: Pokaprakarn Teeranan , Prieto Juan C. , Price Joan T. , Kasaro Margaret P. , Sindano Ntazana , Shah Hina R. , Peterson Marc , Akapelwa Mutinta M. , Kapilya Filson M. , Sebastião Yuri V. , Goodnight William , Stringer Elizabeth M. , Freeman Bethany L. , Montoya Lina M. , Chi Benjamin H. , Rouse Dwight J. , Cole Stephen R. , Vwalika Bellington , Kosorok Michael R. , Stringer Jeffrey S. A. 
Published: November 2021

ABSTRACTBackgroundUltrasound is indispensable to gestational age estimation, and thus to quality obstetric care, yet high equipment cost and need for trained sonographers limit its use in low-resource settings.MethodsFrom September 2018 through June 2021, we recruited 4,695 pregnant volunteers in North Carolina and Zambia and obtained blind ultrasound sweeps (cineloops) of the gravid abdomen alongside standard fetal biometry. We trained a neural network to estimate gestational age from the sweeps and, in three test sets, assessed performance of the model and biometry against previously established gestational age.ResultsIn our main test set, model mean absolute error (MAE) was 3.9 days (standard error [SE] 0.12) vs. 4.7 days (SE 0.15) for biometry (difference -0.8 days; 95% CI -1.1, -0.5; p<0.001). Results were similar in North Carolina (difference -0.6 days, 95% CI -0.9, -0.2) and Zambia (−1.0 days, 95% CI -1.5, -0.5). Findings were supported in the test set of women who conceived by in vitro fertilization (model MAE 2.8 days [SE 0.28] vs. 3.6 days [SE 0.53] for biometry; difference -0.8 days, 95% CI -1.7, 0.2), and in the set of women from whom sweeps were collected by untrained users with low-cost, battery-powered devices (model MAE 4.9 days [SE 0.29] vs. 5.4 days [SE 0.28] for biometry; difference -0.6, 95% CI -1.3, 0.1).ConclusionsOur model estimated gestational age more accurately from blindly obtained ultrasound sweeps than did trained sonographers performing fetal biometry. These results presage a future where all pregnant people – not just those in rich countries – can access the diagnostic benefits of sonography.
Modeling on Wastewater Treatment Process in Saudi Arabia: a perspective of Covid-19
Authors: Ahmadini Abdullah , Msmali Ahmed , Mutum Zico , Raghav Yashpal Singh 
Published: November 2021

AbstractThe novel coronavirus disease (COVID-19) pandemic has had devastating effects on healthcare systems and the global economy. Moreover, coronavirus has been found in human feces, sewage, and in wastewater treatment plants. In this paper, we highlight the transmission behavior, occurrence, and persistence of the virus in sewage and wastewater treatment plants. Our approach follows the process of identifying a coronavirus hotspot through existing wastewater plants in major cities of Saudi Arabia. The mathematical distributions, including the log-normal distribution, Gaussian model, and susceptible exposed infected recovery (SEIR) model, are adopted to predict the coronavirus load in wastewater plants. We highlight not only the potential virus removal techniques from wastewater treatment plants, but also methods of tracing SARS-CoV-2 in humans through wastewater treatment plants.