bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mixed-stock analysis of Atlantic herring (Clupea harengus): a tool for identifying management units and complex migration dynamics
Authors: Bekkevold Dorte , Berg Florian , Polte Patrick , Bartolino Valerio , Ojaveer Henn , Mosegaard Henrik , Farrell Edward D , Fedotova Jelena , Hemmer-Hansen Jakob , Huwer Bastian , Trijoulet Vanessa , Albertsen Christoffer Moesgaard , Fuentes-Pardo Angela P , Gröhsler Tomas , Pettersson Mats , Jansen Teunis , Folkvord Arild , Andersson Leif 
Published: January 2023

AbstractWe developed and validated a mixed-stock analysis (MSA) method with 59 single-nucleotide polymorphisms selected from genome-wide data to assign individuals to populations in mixed-stock samples of Atlantic herring from the North and Baltic seas. We analysed 3734 herring from spawning locations and scientific catches of mixed feeding stocks to demonstrate a “one-fits-all” tool with unprecedented accuracy for monitoring spatio-temporal dynamics throughout a large geographical range with complex stock mixing. We re-analysed time-series data (2002–2021) and compared inferences about stock composition with estimates from morphological data. We show that contributions from the western Baltic spring-spawning stock complex, which is under management concern, have likely been overestimated. We also show that a genetically distinctive population of western Baltic autumn spawners, ascribed low fisheries importance, contributes non-negligible and potentially temporally increasing proportions to mixed-stock aggregations, calling for a re-evaluation of stock definitions. MSA data can be implemented in stock assessment and in a variety of applications, including marine ecosystem description, impact assessment of specific fleets, and stock-rebuilding plans.
Incorporating distribution shifts and spatio-temporal variation when estimating weight-at-age for stock assessments: a case study involving the Bering Sea pollock (Gadus chalcogrammus)
Authors: Indivero Julia , Essington Timothy E , Ianelli James N , Thorson James T 
Published: January 2023

AbstractEnvironmental conditions can create spatial and temporal variability in growth and distribution processes, yet contemporary stock assessment methods often do not explicitly address the consequences of these patterns. For example, stock assessments often assume that body weight-at-age (i.e. size) is constant across the stocks’ range, and may thereby miss important spatio-temporal patterns. This is becoming increasingly relevant given climate-driven distributional shifts, because samples for estimating size-at-age can be spatially unbalanced and lead to biases when extrapolating into unsampled areas. Here, we jointly analysed data on the local abundance and size of walleye pollock (Gadus chalcogrammus) in the Bering Sea, to demonstrate a tractable first step in expanding spatially unbalanced size-at-age samples, while incorporating fine-scale spatial and temporal variation for inclusion in stock assessments. The data come from NOAA’s bottom trawl survey data and were evaluated using a multivariate spatio-temporal statistical model. We found extensive variation in size-at-age at fine spatial scales, though specific patterns differed between age classes. In addition to persistent spatial patterns, we also documented year-to-year differences in the spatial patterning of size-at-age. Intra-annual variation in the population-level size-at-age (used to generate the size-at-age matrix in the stock assessment) was largely driven by localized changes in fish size, while shifts in species distribution had a smaller effect. The spatio-temporal size-at-age matrix led to marginal improvement in the stock assessment fit to the survey biomass index. Results from our case study suggest that accounting for spatially unbalanced sampling improved stock assessment consistency. Additionally, it improved our understanding on the dynamics of how local and population-level demographic processes interact. As climate change affects fish distribution and growth, integrating spatiotemporally explicit size-at-age processes with anticipated environmental conditions may improve stock-assessment forecasts used to set annual harvest limits.
China’s Foreign Policies and Attitudes toward Chinese Diaspora: A Direct Link?
Authors: Sumaktoyo Nathanael Gratias , Muhtadi Burhanuddin 
Published: January 2023

Abstract
Do China’s foreign policies and actions as a state directly influence public opinion toward Chinese diaspora? Notwithstanding the multitude of studies and commentaries on the rise of China and its consequences on the regional and global orders, evidence, and insights on the topic have been lacking. We answer this question through two original, nationally representative survey experiments in Indonesia and by leveraging both contemporary dynamics related to China’s growing influence in Southeast Asia and historical discrimination against ethnic Chinese minorities in the country. We examine whether information about a positive (negative) international issue related to China as a state leads to more positive (negative) attitudes toward Chinese Indonesians. Our findings, consistently replicated in the two surveys, show that information about positive or negative international issues concerning China has only little impacts on attitudes toward ethnic Chinese. To the extent that these issues matter, they mostly affect perceptions toward China itself, not toward ethnic Chinese.
Characterizing the Spectrum of LatentMycobacterium tuberculosisin the Cynomolgus Macaque Model: Clinical, Immunologic, and Imaging Features of Evolution
Authors: Medrano Jessica Marie , Maiello Pauline , Rutledge Tara , Tomko Jaime , Rodgers Mark A , Fillmore Daniel , Frye L James , Janssen Christopher , Klein Edwin , Flynn JoAnne L , Lin Philana Ling 
Published: January 2023

AbstractMycobacterium tuberculosis infection outcomes have been described as active tuberculosis or latent infection but a spectrum of outcomes is now recognized. We used a nonhuman primate model, which recapitulates human infection, to characterize the clinical, microbiologic, and radiographic patterns associated with developing latent M. tuberculosis infection. Four patterns were identified. “Controllers” had normal erythrocyte sedimentation rate (ESR) without M. tuberculosis growth in bronchoalveolar lavage or gastric aspirate (BAL/GA). “Early subclinicals” showed transient ESR elevation and/or M. tuberculosis growth on BAL/GA for 60 days postinfection, “mid subclinicals” were positive for 90 days, and “late subclinicals” were positive intermittently, despite the absence of clinical disease. Variability was noted regarding granuloma formation, lung/lymph node metabolic activity, lung/lymph node bacterial burden, gross pathology, and extrapulmonary disease. Like human M. tuberculosis infection, this highlights the heterogeneity associated with the establishment of latent infection, underscoring the need to understand the clinical spectrum and risk factors associated with severe disease.
Development of a Corticosteroid-Immunosuppressed Mouse Model to Study the Pathogenesis and Therapy of Influenza-Associated Pulmonary Aspergillosis
Authors: Wurster Sebastian , Pantaleón García Jezreel , Albert Nathaniel D , Jiang Ying , Bhoda Keerthi , Kulkarni Vikram V , Wang Yongxing , Walsh Thomas J , Evans Scott , Kontoyiannis Dimitrios P 
Published: January 2023

Abstract
Influenza-associated pulmonary aspergillosis (IAPA) is a feared complication in patients with influenza tracheobronchitis, especially those receiving corticosteroids. Herein, we established a novel IAPA mouse model with low-inoculum Aspergillus infection and compared outcomes in mice with and without cortisone acetate (CA) immunosuppression. CA was an independent predictor of increased morbidity/mortality in mice with IAPA. Early antifungal treatment with liposomal amphotericin B was pivotal to improve IAPA outcomes in CA-immunosuppressed mice, even after prior antiviral therapy with oseltamivir. In summary, our model recapitulates key clinical features of IAPA and provides a robust preclinical platform to study the pathogenesis and treatment of IAPA.
Aesthetic Cognitivism and Serialized Television Fiction
Authors: Vidmar Jovanović Iris 
Published: January 2023

AbstractIn this article, I defend the cognitive value of certain generic television series. Unlike media and television scholars, who have been appreciative of the informative capacity of television fiction, philosophers have been less willing to acknowledge the way in which these works contribute to our understanding of our social reality. My aim here is to provide one such account, grounded in aesthetic cognitivism, that is, the view that fiction is a source of knowledge. Focusing on crime and courtroom dramas, I start by offering some examples of the cognitive benefits available in some of these series and I argue that the more beneficial cases establish superior mimetic relations with reality, enhancing their capacity to present ethically challenging issues. I then examine whether the fictional dimension of these works presents an obstacle to their informative potential and I conclude that it does not. A central aspect of my account is the claim that the degree of cognitive benefit depends on the underlying narrative strategy of the series. Specifically, there are clues in any given show, including the treatment of ongoing characters, which signal the extent to which it can be taken as mimetically reliable and thus, cognitively valuable. I complete my account by addressing anti-cognitivists’ arguments which call to doubt the informative aspect of television series and their capacity to address ethical concerns.
Big Tent Aesthetics
Authors: Lopes Dominic McIver 
Published: January 2023

AbstractTheoretical work on aesthetic value has taken off in the past 5 or 10 years. Since work on artistic value dates at least as far back as the first debates about the interaction between artistic and other values, aesthetic value presumably differs from artistic value. Unlike artistic value, aesthetic value is found in art, but also in nature, design, and intellectual material, even philosophy (Lopes 2022a). Indeed, continued use of “aesthetic” as a synonym for “artistic” has held up work on aesthetic value, as has the hegemony of aesthetic hedonism (Van der Berg 2020). Now a raft of new ideas are on offer, and each has something going for it. We should not be too quick to winnow: we can build a tent that is big enough to house them all.
Effect of sulfadoxine-pyrimethamine chemoprophylaxis in pregnant women on selection of the newP. falciparum dhpsquintuple mutant carrying the I431V mutation
Authors: Cohen Olivia , Guemas Emilie , Menard Sandie , Tsague Kenfack Martial , Talom Ngassa Carine , Iriart Xavier , Bidzogo Lebobo Marlise , Ondobo Ekae Celestin , Eboumbou Carole , Tiyou Kenmeni Calvin , Berry Antoine 
Published: January 2023

AbstractBackgroundA new mutation in the Plasmodium falciparum dihydropteroate synthetase gene (pfdhps), I431V, has been identified in several countries of Central and West Africa. This mutation is mostly found in association with four other SNPs on pfdhps (S436A, A437G, A581G and A613S), forming a quintuple mutant (vagKgs) and almost always associated with the Plasmodium falciparum dihydrofolate reductase gene (pfdhfr) CirnI (C50R, N51I, S108N) triple mutant. To date, nothing is known about the impact of this new pfdhps genotype on sulfadoxine-pyrimethamine (SP) resistance.ObjectivesWe sought to assess the prevalence of this pfdhps vagKgs quintuple mutant in two groups of pregnant women with malaria, one that took intermittent preventive treatment with sulfadoxine-pyrimethamine (IPTp-SP) and one that did not.MethodsThe pfdhfr and pfdhps genes from Plasmodium falciparum isolates collected in Yaoundé (Cameroon) from pregnant women with symptomatic malaria under IPTp-SP or not, were sequenced.ResultsOf 159 patients evaluated, 70 had already taken SP during pregnancy and 89 had never taken SP. Only the vagKgs allele was significantly overrepresented in the SP+ group (21.4% versus 3.4%; P &lt; 0.001), whereas the ISgKAA mutant, widely distributed in this area and known to be less susceptible to SP, tended to be less abundant in this group (48.6% versus 64.0%; P = 0.0503).ConclusionsWe found a strong overrepresentation of the CirnI/vagKgs haplotype in the IPTp-SP pregnant group, suggesting a high level of resistance of this mutant to SP. This could compromise not only the effectiveness of IPTp-SP but also the seasonal malaria chemoprevention of young children, now widely implemented.
Evaluation of publication bias for 12 clinical trials of molnupiravir to treat SARS-CoV-2 infection in 13 694 patients with meta-analysis
Authors: Lawrence Jack M , Mirchandani Manya , Hill Andrew 
Published: January 2023

AbstractIn response to the COVID-19 pandemic, Merck Sharp & Dohme (MSD) acquired the global licensing rights for the antiviral molnupiravir, promising affordable access via licensing deals. Numerous Indian pharmaceutical companies subsequently conducted trials of the drug. Registered trials of molnupiravir were searched on the Clinical Trials Registry–India (CTRI) and efforts made to detect resulting public data. Per the CTRI, 12 randomized trials of molnupiravir were conducted in 13 694 Indian patients, from mid-2021. By August 2022, only a preprint and medical conference presentation had resulted. Additionally, two trials were mentioned in press releases suggesting failure of treatment. The available data contain unexplained results that differ significantly from both the PANORAMIC and MSD MOVe-OUT trials. Approximately one-third of the global data on molnupiravir remain unpublished. We conducted a meta-analysis with four studies that provided results and observed that molnupiravir does not have a significant benefit for hospitalizations.
Utility of the BioFire® FilmArray® Pneumonia Panel plus assay for syndromic testing of lower respiratory tract infections in a low/middle-income setting
Authors: Van Der Westhuyzen M , Samodien N , Brink A J , Moodley C 
Published: January 2023

Abstract

Background
Determining lower respiratory tract infection (LRTI) aetiology is complex. Culture-based methods are laborious with poor sensitivity. Molecular assays improve detection of potential pathogens, but incorrect interpretation of results may lead to inappropriate antimicrobial therapy.

Methods
The utility of the BioFire® FilmArray® Pneumonia Panel plus (FA-PP) to detect LRTI pathogens, and the potential impact on antimicrobial stewardship in a low-resource setting, were assessed. Routine LRT samples were included from adult patients with clinically suspected LRTI or with a concomitant blood culture at Groote Schuur Hospital and referring facilities. Culture and FA-PP results were compared, and pharmacy data analysed to determine appropriateness of antibiotic therapy.

Results
There was an 80% correlation between cultured LRTI pathogens and the FA-PP bin ≥107 results. Compared with culture, the FA-PP detected substantially more pathogens (86.6% versus 17.9%) and produced a combined 100% positive percent agreement, and 88% negative percent agreement. The FA-PP detected bacterial/viral coinfections in 27% of samples. Correlation of FA-PP results with pharmacy data (n = 69) indicated a potential antibiotic change in 75% of cases, but this is difficult to accurately characterize without a ‘gold standard’ for treatment or complete clinical data.

Conclusions
The FA-PP increased the number of positive samples with typical bacteria, but the semi-quantitative reporting algorithm does not describe the correlation between the different bin values and colonization versus infection. This complicates result interpretation and may lead to inappropriate antimicrobial treatment. This study highlights the potential positive impact of rapid molecular assays for routine care in lower-income settings, but also underscores the interpretive challenges associated with these tests.
Point prevalence survey of antibiotic use among hospitalized patients across 41 hospitals in Thailand
Authors: Anugulruengkitt Suvaporn , Charoenpong Lantharita , Kulthanmanusorn Anond , Thienthong Varaporn , Usayaporn Sang , Kaewkhankhaeng Wanwisa , Rueangna Oranat , Sophonphan Jiratchaya , Moolasart Visal , Manosuthi Weerawat , Tangcharoensathien Viroj 
Published: January 2023

Abstract

Objectives
To describe the antibiotic use among hospitalized patients in Thailand.

Methods
A standardized cross-sectional point prevalence survey (PPS) modified from the WHO PPS protocol was conducted in 41 selected hospitals in Thailand. All inpatients who received an antibiotic at 9 a.m. on the survey date were enrolled. The total number of inpatients on that day was the denominator.

Results
Between March and May 2021, a total of 8958 inpatients were enumerated; 4745 inpatients received antibiotics on the day of the survey and there were 6619 prescriptions of antibiotics. The prevalence of antibiotic use was 53.0% (95% CI 51.1%–54.0%), ranging from 14.3% to 73.4%. The antibiotic use was highest among adults aged &gt;65 years (57.1%; 95% CI 55.3%–58.9%). From 6619 antibiotics prescribed, 68.6% were used to treat infection, 26.7% for prophylaxis and 4.7% for other or unknown indications. Overall, the top three commonly used antibiotics were third-generation cephalosporins (1993; 30.1%), followed by first-generation cephalosporins (737; 11.1%) and carbapenems (703; 10.6%). The most frequently used antibiotics for community-acquired infections were third-generation cephalosporins (36.8%), followed by β-lactam/β-lactamase inhibitors (11.8%) and carbapenems (11.3%) whereas for the patients with hospital-acquired infections, the most common antibiotics used were carbapenems (32.7%), followed by β-lactam/β-lactamase inhibitors (15.7%), third-generation cephalosporins (11.7%) and colistin (11.7%). The first-generation cephalosporins were the most commonly used antibiotics (37.7%) for surgical prophylaxis. Seventy percent of the patients received surgical prophylaxis for more than 1 day post surgery.

Conclusions
The prevalence of antibiotic use among hospitalized patients in Thailand is high and one-quarter of these antibiotics were used for prophylaxis. The majority of surgical prophylaxis was inappropriately used for a long duration post operation. Therefore, it is recommended that local guidelines should be developed and implemented.
Firm Size Distribution in African Manufacturing Firms: Revisiting the ‘Missing Middle’
Authors: Tsaedu Kahsay G , Chen Zhihong , Azmete Hana W 
Published: January 2023

AbstractThere has been a widespread view that firm size distribution (FSD) in developing countries has been characterised as having a ‘missing middle’. We have investigated this question using evidence from the entire population of Ethiopian manufacturing firms, including small informal firms. Based on the analysis, we have documented the following four facts. First, there is no evidence of a bimodal distribution in the FSD. Second, small firms overwhelmingly, and increasingly, dominate the distribution. Third, the distribution of the average product of factor input is neither bimodal nor an inverted U-shaped. Fourth, we have investigated the potential regulatory notches of employment sizes of the sort often thought to discourage firm growth and have found no unusual bunching of firms near the notch points. More recently it has been argued by Tybout that instead of looking at the actual FSD to capture a ‘missing middle’, the actual should be compared with an undistorted one, which could be characterised as Paretian. We show, using this approach, that there is a ‘missing middle’ when using employment shares. However, when we look at firm share, by size category, over time large firms have been missing as well.
Potential Impact of Pharmacogenomic Single Nucleotide Variants in a Rural Caucasian Population
Authors: Williams Grace R , Tsongalis Gregory J , Lewis Lionel D , Barney Rachael E , Cook Leanne J , Aaron Geno K , Nerenz Robert D 
Published: January 2023

Abstract

Background
In the US adverse drug reactions (ADRs) are estimated to cause 100 000 fatalities and cost over $136 billion annually. A patient’s genes play a significant role in their response to a drug. Pharmacogenomics aims to optimize drug choice and dose for individual patients by characterizing patients’ pharmacologically relevant genes to identify variants of known impact.

Methods
DNA was extracted from randomly selected remnant whole blood samples from Caucasian patients with previously performed complete blood counts. Samples were genotyped by mass spectrometry using a customized pharmacogenomics panel. A third-party result interpretation service used genotypic results to predict likely individual responses to frequently prescribed drugs.

Results
Complete genotypic and phenotypic calls for all tested Cytochrome P450 isoenzymes and other genes were obtained from 152 DNA samples. Of these 152 unique genomic DNA samples, 140 had genetic variants suggesting dose adjustment for at least one drug. Cardiovascular and psychiatry drugs had the highest number of recommendations, which included United States Food and Drug Administration warnings for highly prescribed drugs metabolized by CYP2C19, CYP2C9, CYP2D6, HLA-A, and VKORC1.

Conclusions
Risk for each drug:gene pairing primarily depends upon the degree of predicted enzyme impairment or activation, width of the therapeutic window, and whether parent compound or metabolite is pharmacologically active. The resulting metabolic variations range from risk of toxicity to therapeutic failure. Pharmacogenomic profiling likely reduces ADR potential by allowing up front drug/dose selection to fit a patient’s unique drug-response profile.
Validation of the Reveal® 3-D for Gluten Assay for Detection of Gluten in Clean-in-Place Rinses and Stainless Steel Environmental Surfaces: AOAC Performance Tested MethodSM 122201
Authors: Le Quynh-Nhi , Beck Nancy , Schwingel Zack , Roman Brooke , Mozola Mark , Sperry Amanda , Almy Dave , Donofrio Robert 
Published: January 2023

Abstract

Background
Reveal® 3-D for Gluten is an immunochromatographic assay for the qualitative detection of gluten in environmental samples. The test uses monoclonal antibodies reactive to prolamins in wheat.

Objective
The objective of the study was to validate the Reveal 3-D test for detection of gluten in clean-in-place rinse and swabs from a stainless steel surface.

Methods
Elements of the study included food selectivity and interference testing, matrix testing, an assay robustness study, and reagent stability/lot-to-lot consistency testing. Wheat flour was used as the spiking material for all matrixes.

Results
In selectivity and interference testing, nine target matrixes all tested positive and 36 of 39 non-target matrixes tested negative. Almond flour, sesame flour, and cornstarch produced positive results as 100% commodities; reactivity can be eliminated with dilution or by testing without use of food extraction buffer, which is not a standard part of the environmental testing method. With a gluten spike at 9.3 mg/kg, chestnut flour, guar gum, and xanthan gum as 100% commodities inhibited the ability of the assay to detect gluten when tested without dilution. In quaternary ammonium clean-in-place rinse and swabs from stainless steel, 100% positive results were obtained at levels of 2.8 mg/kg and 4.7 µg/100 cm2, respectively. Results of independent laboratory testing of swabs from stainless steel supported those of internal trials. Robustness testing showed that introducing variations to three operating parameters simultaneously had no adverse effect on assay performance. In the reagent stability study, data supported kit expiration dating of 11 months.

Conclusion
Results of the current study show that the Reveal test is an accurate and reliable method for qualitative detection of gluten in select clean-in-place rinse and environmental samples.

Highlights
The Reveal test was able to detect gluten at levels of 2.8 ppm in clean-in-place rinse and 4.7 µg/100 cm2 in swabs from stainless steel.