bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antifungal stewardship in practice: Insights from a prospective audit and feedback program
Authors: Bio Laura L. , Weng Yingjie , Schwenk Hayden T. 
Published: June 2023

AbstractObjective:To identify characteristics of antifungal prospective audit and feedback (PAF) and to compare rates of PAF recommendation and acceptance between antifungal and antibiotic agents.Design:Retrospective cohort study of antifungal and antibiotic audits by a children’s hospital antimicrobial stewardship program (ASP) from November 1, 2020, to October 31, 2022.Methods:Antimicrobial audit data were retrieved from the ASP data warehouse. We characterized antifungal PAF using descriptive statistics. We then compared the overall rates of PAF recommendation and recommendation acceptance between antifungals and antibiotics. We also compared the differences in antifungal and antibiotic PAF recommendation and acceptance rates across various factors, including infectious problem, medical service, and recommendation type.Results:Of 10,402 antimicrobial audits identified during the study period, 8,599 (83%) were for antibiotics and 1,803 (17%) were for antifungals. The highest antifungal recommendation rates were for liposomal amphotericin B, antifungals used for sepsis or respiratory tract infection, and antifungals prescribed in the cardiovascular intensive care unit. The rate of PAF recommendation was higher for antibiotics than for antifungals (29% vs 21%; P < .001); however, the rates of recommendation acceptance were similar. Recommendations to discontinue or for medication monitoring were more common for antifungals.Conclusions:Our analysis of antifungal PAF identified key opportunities to improve antifungal use, including the optimized use of specific agents and targeted use by certain medical services. Moreover, antifungal PAF, despite identifying fewer recommendations compared to antibiotic PAF, were associated with similarly high rates of acceptance, highlighting a promising opportunity for antifungal stewardship.
Early coronavirus disease 2019 (COVID-19) pandemic effects on individual-level risk for healthcare-associated infections in hospitalized patients
Authors: Farthing Trevor S. , Jolley Ashlan , Nickel Katelin B. , Hill Cherie , Stwalley Dustin , Reske Kimberly A. , Kwon Jennie H. , Olsen Margaret A. , Burnham Jason P. , Dubberke Erik R. , Lanzas Cristina 
Published: June 2023

AbstractObjective:We compared the individual-level risk of hospital-onset infections with multidrug-resistant organisms (MDROs) in hospitalized patients prior to and during the coronavirus disease 2019 (COVID-19) pandemic. We also quantified the effects of COVID-19 diagnoses and intrahospital COVID-19 burden on subsequent MDRO infection risk.Design:Multicenter, retrospective, cohort study.Setting:Patient admission and clinical data were collected from 4 hospitals in the St. Louis area.Patients:Data were collected for patients admitted between January 2017 and August 2020, discharged no later than September 2020, and hospitalized ≥48 hours.Methods:Mixed-effects logistic regression models were fit to the data to estimate patients’ individual-level risk of infection with MDRO pathogens of interest during hospitalization. Adjusted odds ratios were derived from regression models to quantify the effects of the COVID-19 period, COVID-19 diagnosis, and hospital-level COVID-19 burden on individual-level hospital-onset MDRO infection probabilities.Results:We calculated adjusted odds ratios for COVID-19–era hospital-onset Acinetobacter spp., P. aeruginosa and Enterobacteriaceae spp infections. Probabilities increased 2.64 (95% confidence interval [CI], 1.22–5.73) times, 1.44 (95% CI, 1.03–2.02) times, and 1.25 (95% CI, 1.00–1.58) times relative to the prepandemic period, respectively. COVID-19 patients were 4.18 (95% CI, 1.98–8.81) times more likely to acquire hospital-onset MDRO S. aureus infections.Conclusions:Our results support the growing body of evidence indicating that the COVID-19 pandemic has increased hospital-onset MDRO infections.
ON QUADRATIC FIELDS GENERATED BY POLYNOMIALS
Authors: SHPARLINSKI IGOR E. 
Published: June 2023

AbstractLet
$f(X) \in {\mathbb Z}[X]$
be a polynomial of degree
$d \ge 2$
without multiple roots and let
${\mathcal F}(N)$
be the set of Farey fractions of order N. We use bounds for some new character sums and the square-sieve to obtain upper bounds, pointwise and on average, on the number of fields
${\mathbb Q}(\sqrt {f(r)})$
for
$r\in {\mathcal F}(N)$
, with a given discriminant.
Politics of Disaster: Earthquake, Rehousing, and Confronting Colonial Rule in Accra (Gold Coast/Ghana), 1939–45
Authors: Bin-Kasim Waseem-Ahmed 
Published: June 2023

AbstractDespite its destructiveness, disaster clears the way to accomplish a set of goals. That was why the Gold Coast governor and officials welcomed the 1939 earthquake as an opportunity to rebuild Accra. However, mishandling their reconstruction plan proved disadvantageous. The aftermath of the disaster, including an unprecedented rehousing project, exacerbated urban discontent. How everyday urban residents responded to rehousing further exposed the weakness of the colonial state and gave momentum to nationalism. The paper introduces natural disasters and relief programs into the scholarly narratives that have demonstrated that anticolonial nationalism emerged from a chain of grievances from amongst colonial subjects, some of which were unfulfilled social and economic expectations. The experiences of rehousing following the earthquake powerfully informed local perspectives and contributed to the chain of events leading to formal decolonization.
The prevalence of coagulase-negative staphylococcus associated with bovine mastitis in China and its antimicrobial resistance rate: a meta-analysis
Authors: Deng Jianming , Liu Kai , Wang Kuan , Yang Bowen , Xu Hui , Wang Juyu , Dai Feiyan , Xiao Xiao , Gu Xiaolong , Zhang Limei , Qu Weijie 
Published: June 2023

AbstractTo contribute to the treatment decision and optimize coagulase-negative staphylococcus (CNS) control programs, we conducted a meta-analysis to investigate the epidemiology and antimicrobial resistance rates of coagulase-negative staphylococcus associated with bovine mastitis in China. Three databases (PubMed, Google scholar and China National Knowledge Infrastructure database) were utilized to obtain relevant publications. A total of 18 publications were included in our research, and 3 of them included antimicrobial resistant (AMR) test. The pooled prevalence of coagulase-negative staphylococcus was 17.28%. Subgroup analysis revealed that the prevalence was higher in South China than in North China, was higher in 2011–2020 than in 2000–2010 and was higher in clinical bovine mastitis cases than in subclinical cases. The pooled AMR were most resistant to β-lactams, followed by tetracyclines, quinolones, nitrofurans, lincosamides, sulfonamides, amphenicol and aminoglycosides. The pooled AMR rate of coagulase-negative staphylococcus was lower in 2011–2020 than in 2000–2010. Although the prevalence of CNS showed an increasing trend over 20 years, the AMR rate showed a decreasing trend, and the clinical type of mastitis was the most frequent and the prevalence was highest in South China. Finally, CNS was most resistant to β-lactams amongst the eight groups of antimicrobial agents.
Applied linguistics and language education research in Turkey: 2016–2022
Authors: Ortactepe Hart Deniz , Aydınlı Julie 
Published: June 2023

AbstractThis systematic review of 170+ journal articles showcases the current trends and developments in Turkey-based applied linguistics and language education research between 2016–2022. The current review presents similarities to the previous reviews (Alptekin & Tatar, 2011; Aydınlı & Ortaçtepe, 2018) in terms of trends and practices that indicate a vibrant research scene and a community of practice in Turkey within language education and applied linguistics research. While certain research areas such as instructional technologies remain widely popular among Turkey-based scholars, there has been growing interest in multiculturalism, social justice language education, critical pedagogy, and culturally responsive teaching. It was also clear in our analysis that the demands by the Higher Education Council for academic promotion exacerbated some of the already-existing challenges also noted in the previous reviews. Some of the concerns include pre- and post-test study designs that focus on practical concerns and outcomes rather than on processes that would lead to conceptual or theoretical development; and lack of engagement with broader (inter)disciplinary debates. We hope that this review will help establish conversations among fellow scholars in terms of future directions that applied linguistics and language education research in Turkey can take in order to contribute to the larger discussions in the field.
Resolving problems in symbol identification in compilation of electronic navigational charts utilising paper charts
Authors: Fernando P.B.A. , Lewis S.N. , Perera A.N.D. , Gunathilaka M.D.E.K. 
Published: June 2023

AbstractElectronic navigational charts (ENCs) can be compiled using existing paper charts to improve their coverage of the world's oceans. However, in the process of assigning symbols on ENCs, in some cases the software uses the same symbol for different paper chart symbols. This could ultimately compromise maritime safety. Addressing this issue, this paper describes a methodology for developing a new tool that complements the efficient production of ENCs using paper charts. First, the ENC product was produced utilising CARIS S-57 Composer. After considering the difficulties in assigning symbols through the compilation process, a new web application named SYMO EXPERT was introduced. It was developed using Firebase Realtime Database and React app. A questionnaire was prepared to collect data about the time factor and accuracy of using SYMO EXPERT. Results showed that it supports the users in selecting relevant symbols efficiently with an accuracy of up to 98%.
Vitamin E and cardiovascular diseases: an interest to public health?
Authors: Costa Lemos da Silva Ana Gabriella , da Silva Ribeiro Karla Danielly , Alves de Araújo Graciele Eloise , da Silva Oliveira Letícia , de Oliveira Lyra Clélia 
Published: June 2023

AbstractCardiovascular diseases (CVD) are the leading cause of death worldwide. From this perspective, the role of vitamin E and its metabolites in preventing CVD has been studied, being supported by the findings that low vitamin E concentrations are associated with an increased risk of cardiovascular events. Despite this, no studies have analysed the co-existence of vitamin E deficiency (VED) and CVD on the basis of population studies. Facing that, this study summarises information on the relationship between vitamin E status and CVD, providing a basis for understanding the determining and protective factors for its development. VED may be a public health problem since it has been observed to vary from 0·6% to 55·5% worldwide, with higher percentages in Asia and Europe, where CVD mortality rates stand out. Intervention studies with α-tocopherol supplementation do not confirm cardioprotective action of vitamin E, which may reflect that α-tocopherol alone does not provide cardiovascular protection to individuals, but the consumption of all isomers found in food. Considering that low concentrations of α-tocopherol can lead to a higher susceptibility to diseases involving oxidative stress in the population, in addition to the high and growing prevalence of CVD and VED, it is essential to investigate or reinterpret the mechanisms of action of vitamin E and its metabolites in the cardiovascular process to better understand the co-existence of CVD and VED. It is also important to implement public health policies and programmes aimed at promoting the consumption of natural food sources of vitamin E and healthy fats.
Korean named entity recognition based on language-specific features
Authors: Chen Yige , Lim KyungTae , Park Jungyeul 
Published: June 2023

AbstractIn this paper, we propose a novel way of improving named entity recognition (NER) in the Korean language using its language-specific features. While the field of NER has been studied extensively in recent years, the mechanism of efficiently recognizing named entities (NEs) in Korean has hardly been explored. This is because the Korean language has distinct linguistic properties that present challenges for modeling. Therefore, an annotation scheme for Korean corpora by adopting the CoNLL-U format, which decomposes Korean words into morphemes and reduces the ambiguity of NEs in the original segmentation that may contain functional morphemes such as postpositions and particles, is proposed herein. We investigate how the NE tags are best represented in this morpheme-based scheme and implement an algorithm to convert word-based and syllable-based Korean corpora with NEs into the proposed morpheme-based format. Analyses of the results of traditional and neural models reveal that the proposed morpheme-based format is feasible, and the varied performances of the models under the influence of various additional language-specific features are demonstrated. Extrinsic conditions were also considered to observe the variance of the performances of the proposed models, given different types of data, including the original segmentation and different types of tagging formats.
Do Optically Denser Trade‐Wind Cumuli Live Longer?
Authors: Seelig Torsten , Müller Felix , Tesche Matthias 
Published: June 2023

AbstractThis study investigates the lifetime and temporal evolution of physical properties of trade‐wind cumuli based on tracking individual clouds in observations with the Advanced Baseline Imager aboard the geostationary GOES‐16 satellite during the “ElUcidating the RolE of Cloud–Circulation Coupling in ClimAte” (EUREC4A) campaign east of Barbados in winter 2020. A first application of our upgraded cloud‐tracking toolbox to measurements with high spatio‐temporal resolution (2 × 2 km2 and 1 min) provides probability density functions of lifetime and area of clouds that develop as a consequence of meso‐to‐synoptic scale motions. By separately considering clouds that exist during daytime and live in distinct lifetime intervals, we find that shallow marine cumuli live longer when they cover a larger surface area and show higher cloud optical thickness (COT). Besides the effect of COT, the scale of the atmospheric motions with which the clouds interact is also critical to their lifetime.
Lagrangian Characterization of Surface Transport From the Equatorial Atlantic to the Caribbean Sea Using Climatological Lagrangian Coherent Structures and Self‐Organizing Maps
Authors: Allende‐Arandía Ma. Eugenia , Duran Rodrigo , Sanvicente‐Añorve Laura , Appendini Christian M. 
Published: June 2023

AbstractThis study presents an assessment of the transport of suspended material by surface ocean currents, which have a critical role in determining the connectivity and distribution of living and non‐living material. Lagrangian experiments reveal pathways from the Equatorial Atlantic to 10 strategic regions within the Caribbean Sea, determined by considering the space‐time variability of climatological Lagrangian Coherent Structures, which act as recurrent attracting pathways and transport barriers. Due to windage or Stokes drift, wind forcing is a significant factor in determining the spatial locations where particles cluster and the time needed to reach the Caribbean from the Equatorial Atlantic. Pathways shift westward within the Caribbean and take less time to arrive with increasing wind influence. Depending on the wind effect, the particles show higher confluence in different areas of the Caribbean. A case study is presented for the Mexican Caribbean nearshore area, isolated from ocean‐current trajectories. Here, wind weakens the transport barrier responsible for this isolation and causes particle confluence toward that region. Spatial patterns of the Eulerian velocity identified through Self‐Organizing Maps, with time dependence given by their best matching units, can reproduce the characteristic Lagrangian patterns of surface current climate variability. Our study demonstrates the application of tools from dynamical systems and unsupervised neural networks to understand Lagrangian patterns and identify the processes that drive them. These findings improve our understanding of transport mechanisms of suspended material by surface ocean currents in the Western Atlantic and the Caribbean Sea, which is essential for managing and conserving marine ecosystems.
COVID‐19 Impact on the Oil and Gas Industry NO2 Emissions: A Case Study of the Permian Basin
Authors: Serrano‐Calvo Raquel , Veefkind J. Pepijn , Dix Barbara , de Gouw Joost , Levelt Pieternel F. 
Published: June 2023

AbstractCOVID‐19 caused a historic collapse in fossil fuel demand, a general decline in economic activity, and hydrocarbon price volatility. This resulted in an unprecedented scenario to evaluate the contribution of the O&G (Oil and Gas) industry NO2 (nitrogen dioxide) emissions in the Permian basin (United States), currently the second largest hydrocarbon‐bearing area on Earth. TROPOMI (Tropospheric Monitoring Instrument), on board the Sentinel‐5P satellite, has captured the impact of the oil and gas industry emissions during the COVID‐19 lockdown. A generalized drop (∼30%) of NO2 emissions derived using the divergence method in comparison with 2019 was observed following the decline in production and drilling (13% and 68% respectively) during the lockdown. NO2 tropospheric columns were less impacted with a smaller decrease (∼4%) across the basins. This study demonstrates that the impact of the COVID‐19 lockdown on NO2 emissions was not only present in urban areas but also in vast O&G production regions, which shows the potential of TROPOMI to assess future pollution mitigation strategies for this industry.
Antibiotic-degrading resistance changes bacterial community structure via species-specific responses
Authors: Pathak Ayush , Angst Daniel C , León-Sampedro Ricardo , Hall Alex R 
Published: June 2023

Abstract
Some bacterial resistance mechanisms degrade antibiotics, potentially protecting neighbouring susceptible cells from antibiotic exposure. We do not yet understand how such effects influence bacterial communities of more than two species, which are typical in nature. Here, we used experimental multispecies communities to test the effects of clinically important pOXA-48-plasmid-encoded resistance on community-level responses to antibiotics. We found that resistance in one community member reduced antibiotic inhibition of other species, but some benefitted more than others. Further experiments with supernatants and pure-culture growth assays showed the susceptible species profiting most from detoxification were those that grew best at degraded antibiotic concentrations (greater than zero, but lower than the starting concentration). This pattern was also observed on agar surfaces, and the same species also showed relatively high survival compared to most other species during the initial high-antibiotic phase. By contrast, we found no evidence of a role for higher-order interactions or horizontal plasmid transfer in community-level responses to detoxification in our experimental communities. Our findings suggest carriage of an antibiotic-degrading resistance mechanism by one species can drastically alter community-level responses to antibiotics, and the identities of the species that profit most from antibiotic detoxification are predicted by their intrinsic ability to survive and grow at changing antibiotic concentrations.
Arginine regulates HSPA5/BiP translation through ribosome pausing in triple-negative breast cancer cells
Authors: Vidal Christina M. , Ouyang Ching , Qi Yue , Mendez-Dorantes Carlos , Coblentz Alaysia , Alva-Ornelas Jackelyn A. , Stark Jeremy M. , Seewaldt Victoria L. , Ann David K. 
Published: June 2023

Abstract
Background
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with a high mortality rate due to a lack of therapeutic targets. Many TNBC cells are reliant on extracellular arginine for survival and express high levels of binding immunoglobin protein (BiP), a marker of metastasis and endoplasmic reticulum (ER) stress response.

Methods
In this study, the effect of arginine shortage on BiP expression in the TNBC cell line MDA-MB-231 was evaluated. Two stable cell lines were generated in MDA-MB-231 cells: the first expressed wild-type BiP, and the second expressed a mutated BiP free of the two arginine pause-site codons, CCU and CGU, termed G-BiP.

Results
The results showed that arginine shortage induced a non-canonical ER stress response by inhibiting BiP translation via ribosome pausing. Overexpression of G-BiP in MDA-MB-231 cells promoted cell resistance to arginine shortage compared to cells overexpressing wild-type BiP. Additionally, limiting arginine led to decreased levels of the spliced XBP1 in the G-BiP overexpressing cells, potentially contributing to their improved survival compared to the parental WT BiP overexpressing cells.

Conclusion
In conclusion, these findings suggest that the downregulation of BiP disrupts proteostasis during arginine shortage-induced non-canonical ER stress and plays a key role in cell growth inhibition, indicating BiP as a target of codon-specific ribosome pausing upon arginine shortage.
Topology-enhanced mechanical stability of swelling nanoporous electrodes
Authors: Grossman-Ponemon Benjamin E. , Mesgarnejad Ataollah , Karma Alain 
Published: June 2023

AbstractMaterials like silicon and germanium offer a 10-fold improvement in charge capacity over conventional graphite anodes in lithium-ion batteries but experience a roughly threefold volume increase during lithiation, which challenges ensuring battery integrity. Nanoporous silicon, created by liquid-metal-dealloying, is a potentially attractive anode design to mitigate this challenge, exhibiting both higher capacity and extended cycle lifetimes. However, how nanoporous structures accommodate the large volume change is unknown. Here, we address this question by using phase-field modeling to produce nanoporous particles and to investigate their elastoplastic swelling behavior and fracture. Our simulations show that enhanced mechanical stability results from the network topology consisting of ligaments connected by bulbous, sphere-like nodes. The ligaments forcefully resist elongation while the nodes, behaving like isolated spherical particles, experience large stresses driving fracture. However, being smaller compared to a sphere of the same volume as the entire nanoporous particle, the nodes are more protected against fracture.
Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank
Authors: Hofmeister Robin J. , Ribeiro Diogo M. , Rubinacci Simone , Delaneau Olivier 
Published: June 2023

AbstractPhasing involves distinguishing the two parentally inherited copies of each chromosome into haplotypes. Here, we introduce SHAPEIT5, a new phasing method that quickly and accurately processes large sequencing datasets and applied it to UK Biobank (UKB) whole-genome and whole-exome sequencing data. We demonstrate that SHAPEIT5 phases rare variants with low switch error rates of below 5% for variants present in just 1 sample out of 100,000. Furthermore, we outline a method for phasing singletons, which, although less precise, constitutes an important step towards future developments. We then demonstrate that the use of UKB as a reference panel improves the accuracy of genotype imputation, which is even more pronounced when phased with SHAPEIT5 compared with other methods. Finally, we screen the UKB data for loss-of-function compound heterozygous events and identify 549 genes where both gene copies are knocked out. These genes complement current knowledge of gene essentiality in the human genome.