bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal collections to study invasion biology
Authors: Kim Amy S. , Kreiner Julia M. , Hernández Fernando , Bock Dan G. , Hodgins Kathryn A. , Rieseberg Loren H. 
Published: October 2023

AbstractBiological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community‐level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.
Long‐term benzodiazepine usage and mortality in patients with chronic non‐cancer musculoskeletal pain: A Nationwide cohort study
Authors: Oh Tak Kyu , Hwang Insung , Song In‐Ae 
Published: October 2023

AbstractObjectivesThe impact of benzodiazepine use on mortality in patients with chronic non‐cancer pain (CNCP) has not been identified. We aimed to examine the factors associated with benzodiazepine use among patients with CNCP and examine whether long‐term benzodiazepine usage is associated with mortality in patients with CNCP.MethodsThis study was conducted using data from the National Health Insurance Service database of South Korea. We selected 2.5% of all adult patients diagnosed with musculoskeletal diseases (MSD) in South Korea from 2010 to 2019 using a stratified random sampling technique and included them in the analysis as patients with CNCP. The risk of 10‐year all‐cause mortality in patients with CNCP was investigated using the 2010 cohort of patients with CNCP.ResultsThe proportion of the study population that used benzodiazepine during the 10‐year study period was 2.1% (390,683/18,770,234). Multivariable logistic regression showed that old age; increased Charlson comorbidity index (CCI); opioid, gabapentin or pregabalin, paracetamol, non‐steroidal anti‐inflammatory drugs, and Z‐drugs usage; and underlying psychiatric comorbidities were associated with increased benzodiazepine use. In addition, benzodiazepine use was associated with increased 10‐year all‐cause mortality (adjusted hazard ratio: 1.03, 95% confidence interval: 1.01, 1.06; p < 0.001).ConclusionsBenzodiazepine was prescribed to 2.1% of the patients with CNCP in South Korea from 2010 to 2019. Old age, increased CCI, underlying psychiatric comorbidities, and use of certain drugs are associated with increased use of benzodiazepines. In addition, benzodiazepine use is associated with 10‐year all‐cause mortality in patients with CNCP.
Innovation and development of the aquaculture nutrition research and feed industry in China
Authors: Bu Xianyong , Li Yueru , Lai Wencong , Yao Chuanwei , Liu Yongtao , Wang Zhen , Zhao Zengqi , Han Shangzhe , Du Jianlong , Yao Xin , Mai Kangsen , Ai Qinghui 
Published: October 2023

AbstractAquaculture in China has undergone significant evolution in recent decades, transitioning from traditional practices to a vital food production industry. Alongside the rapid growth of aquaculture in China, aquafeed production continues to expand swiftly. This review attempts to establish an overview of the history and achievements in aquaculture nutrition research and feed industry in China. The development of scientific concept and methodology, especially the advanced molecular biology technology guarantees the shift from traditional nutrition to molecular nutrition, and subsequently to precision nutrition in aquaculture nutrition research. This evolution has facilitated the formulation of effective strategies to enhance the growth, health and product quality of aquatic animals. The advancements of aquaculture nutrition research and feed industry have also been propelled by innovative research concepts rooted in principles such as the health and safety of aquatic animals, the quality of aquatic products, resource conservation and environmental friendliness, and the advancements in key processing technologies within the aquafeed industry. The future perspectives of the aquaculture nutrition research and feed industry in China are also proposed. The present work aims to provide a reference for promoting the development of aquaculture nutrition research and feed industry in China.
Factors of global change affecting plants act at different levels of the ecological hierarchy
Authors: Rillig Matthias C. , Lehmann Anika , Orr James A. , Rongstock Rebecca 
Published: October 2023

SUMMARYPlants and ecosystems worldwide are exposed to a wide range of chemical, physical, and biological factors of global change, many of which act concurrently. As bringing order to the array of factors is required in order to generate an enhanced understanding of simultaneous impacts, classification schemes have been developed. One such classification scheme is dedicated to capturing the different targets of global change factors along the ecological hierarchy. We build on this pioneering work, and refine the conceptual framework in several ways, focusing on plants and terrestrial systems: (i) we more strictly define the target level of the hierarchy, such that every factor typically has just one target level, and not many; (ii) we include effects above the level of the community, that is, there are effects also at the ecosystem scale that cannot be reduced to any level below this; (iii) we introduce the level of the landscape to capture certain land use change effects while abandoning the level below the individual. We discuss how effects can propagate along the levels of the ecological hierarchy, upwards and downwards, presenting opportunities for explaining non‐additivity of effects of multiple factors. We hope that this updated conceptual framework will help inform the next generation of plant‐focused global change experiments, specifically aimed at non‐additivity of effects at the confluence of many factors.
The directed evolution of NDM-1
Authors: Thomas Caitlyn A. , Cheng Zishuo , Bethel Christopher R. , Hujer Andrea M. , Sturgill Aidan M. , Onuoha Kelechi , Page Richard C. , Bonomo Robert A. , Crowder Michael W. 
Published: October 2023

ABSTRACT

β-Lactam antibiotics are among the most frequently prescribed therapeutic agents. A common mechanism of resistance toward β-lactam antibiotics is the production of β-lactamases. These enzymes are capable of hydrolyzing the β-lactam bond, rendering the drug inactive. Among the four described classes, the metallo- β-lactamases (MBLs, class B) employ one or two zinc ions in the active site for catalysis. One of the three most clinically relevant MBLs is New Delhi Metallo- β-Lactamase (NDM-1). The current study sought to investigate the
in vitro
protein evolution of NDM-1 β-lactamase using error-prone polymerase chain reaction. Evaluation revealed that variants were not found to confer higher levels of resistance toward meropenem based on amino acid substitutions. Thus, we postulate that increases in transcription or changes in zinc transport may be clinically more relevant to meropenem resistance than amino acid substitutions.
Acid adaptation increased the resistance of
Escherichia coli
O157:H7 in bok choy (
Brassica rapa
subsp.
chinensis
) juice to high-pressure processing
Authors: Koo Andrea , Ghate Vinayak , Zhou Weibiao 
Published: October 2023

ABSTRACT

The adaptive response of
Escherichia coli
O157:H7 to acid stress, a major stressor in juice processing environments, has been shown to confer cross-resistance against pasteurization methods such as heat and X-ray. However, whether acid adaptation confers resistance against high-pressure processing (HPP) has not been explored. This study aimed to investigate the effect of acid adaptation on the pressure resistance of
E. coli
O157:H7 in a bok choy vegetable juice matrix. Acid adaptation was performed in tryptone soya broth without dextrose adjusted to pH 5.0 at 37°C for 24 h, while non-adapted cells were prepared in similar conditions, without the pH adjustment (pH 7.3). The C7927 strain was used as it exhibited the greatest increase in pressure resistance after acid adaptation among the three strains tested. Acid adaptation increased the
D
-value at 400 MPa from 0.8 ± 0.1 min in non-adapted cells to 1.2 ± 0.1 min in acid-adapted cells (
P
< 0.05). Furthermore, significantly lower reductions in total viable counts were observed after 72 h of post-HPP refrigerated storage for acid-adapted cells (3.4 ± 0.2 log CFU/mL) as compared to non-adapted cells (5.0 ± 0.1 log CFU/mL). Sublethally injured populations were measured via plating on selective media, as well as differential fluorescent staining and flow cytometry. The levels of damages to membrane, DNA, proteins, and peptidoglycan were significantly lower in acid-adapted cells, suggesting that the acid adaptive response of
E. coli
O157:H7 may protect it against HPP-induced inactivation and injury by modulating the pressure resistance of these cellular targets.

IMPORTANCE

Based on the U.S. Food and Drug Administration regulations,
E. coli
O157:H7 is a pertinent pathogen in high acid juices that needs to be inactivated during the pasteurization process. The results of this study suggest that the effect of acid adaptation should be considered in the selection of HPP parameters for
E. coli
O157:H7 inactivation to ensure that pasteurization objectives are achieved.
Student perceptions of inclusive pedagogy in undergraduate STEM classrooms
Authors: Valdez Caley J. , Kelp Nicole C. 
Published: October 2023

ABSTRACT

In university STEM classrooms, the incorporation of inclusive practices improves student performance, decreases disparities in the academic success of underrepresented students, and increases student retention and persistence in Science, Technology, Engineering, and Mathematics (STEM) programs. Inclusive pedagogical practices include effective instructional choices like active learning, providing rubrics, and other strategies that have been shown to support students from disadvantaged backgrounds. Additionally, explicitly inclusive practices such as addressing microaggressions and sharing pronouns can promote a sense of belonging for students. While a plethora of literature has shown these impacts and faculty have access to resources and training about inclusive pedagogy, we were interested in whether students are noticing these practices and how student identities impact their observations of instructional practices. We surveyed undergraduates (
n
= 74) from diverse STEM disciplines at a large land-grant university regarding their observation of 11 different inclusive pedagogical practices. Overall, students observed inclusive instructional practices more often than they observed explicitly diversity, equity, and inclusion (DEI)-related practices. For explicitly DEI-related practices, white students observed more practices than Students of Color. This suggests that more work needs to be done to train faculty in explicit DEI-related practices, especially with the goal of supporting Students of Color who have been historically excluded from STEM.
Targeted mutations in IFNα2 improve its antiviral activity against various viruses
Authors: Karakoese Zehra , Le-Trilling Vu-Thuy Khanh , Schuhenn Jonas , Francois Sandra , Lu Mengji , Liu Jia , Trilling Mirko , Hoffmann Daniel , Dittmer Ulf , Sutter Kathrin 
Published: October 2023

ABSTRACT
During viral infections, type I interferons (IFN) are induced and play a key role in counteracting initial viral spread. Twelve different human IFNα subtypes exist that bind the same receptor; however, they elicit unique host responses and display distinct potencies of antiviral activities. Our previous studies on human immunodeficiency virus (HIV) and hepatitis B virus (HBV) demonstrated that the clinically used IFNα2 is not the most effective one among the IFNα subtypes. By sequence modeling, we identified a region in helix B with mainly conserved residues at the outside facing IFNAR1, but variable residues at the inside facing the core of IFNα, potentially representing a putative tunable anchor to tune pleiotropic IFN responses. Using site-directed mutagenesis, various mutations were introduced into the IFNα2b backbone targeting sites which are important for binding to IFNAR1 and IFNAR2, the putative tunable anchor, or outside these three regions. Selected mutations were based on sequence differences to high antiviral subtypes IFNα6 and IFNα14. Treatment assays against HBV and HIV identified several critical residues for the antiviral activity of IFNα mainly in the IFNAR1 binding region. Combined mutations of the IFNα2 IFNAR1/2 binding sites or the IFNAR1 binding region plus the putative tunable anchor by those of IFNα14 further augmented activation of different downstream signaling cascades providing a molecular correlate for the enhanced antiviral activity. We describe here important functional residues within IFNα subtype molecules, which enabled us to design novel and innovative drugs that may have the potential to be used in clinical trials against a variety of different viral infections.

IMPORTANCE
The potency of interferon (IFN)α to restrict viruses was already discovered in 1957. However, until today, only IFNα2 out of the 12 distinct human IFNα subtypes has been therapeutically used against chronic viral infections. There is convincing evidence that other IFNα subtypes are far more efficient than IFNα2 against many viruses. In order to identify critical antiviral residues within the IFNα subtype sequence, we designed hybrid molecules based on the IFNα2 backbone with individual sequence motifs from the more potent subtypes IFNα6 and IFNα14. In different antiviral assays with HIV or HBV, residues binding to IFNAR1 as well as combinations of residues in the IFNAR1 binding region, the putative tunable anchor, and residues outside these regions were identified to be crucial for the antiviral activity of IFNα. Thus, we designed artificial IFNα molecules, based on the clinically approved IFNα2 backbone, but with highly improved antiviral activity against several viruses.
Targeted metagenomic assessment reflects critical colonization in battlefield injuries
Authors: Kok Car Reen , Mulakken Nisha , Thissen James B. , Grey Scott F. , Avila-Herrera Aram , Upadhyay Meenu M. , Lisboa Felipe A. , Mabery Shalini , Elster Eric A. , Schobel Seth A. , Be Nicholas A. 
Published: October 2023

ABSTRACT

Current diagnostics and clinical management strategies for combat wounds are based on decisions made by expert clinicians. However, even in the hands of experienced surgeons, wounds from combat injuries can exhibit failed healing and complications related to limitations in the rapid and comprehensive generation of diagnostic information. Previous studies have demonstrated the possible use of genomic sequencing approaches to detect microbial signatures involved in combat casualty care. While effective, whole metagenome sequencing is limited by the depth required to confidently detect all relevant signatures. To address this, we developed a targeted capture sequencing panel to detect microbial signatures relevant to wound healing. These targets include known microbial nosocomial pathogens, wound colonizers, and genes involved in virulence and antimicrobial resistance. A bioinformatics pipeline was built to identify genomic regions of interest and over 8,000 oligonucleotide probes were designed for capture. The panel was synthesized and validated using control reference genomes in human background and on wound-effluent samples from a cohort of combat-injured U.S. service members. Our panel was sensitive against wound-colonizing species,
Acinetobacter baumannii
and
Pseudomonas aeruginosa
, and was specific in detecting corresponding virulence and antimicrobial-resistance genes as well as other pathogenic species present in microflora mixtures. Random forest feature permutation confirmed the prevalence of
Acinetobacter
and
Pseudomonas
in critically colonized wounds and wounds that failed to heal, respectively. Our results demonstrate the capability of targeted sequencing tools and analysis platforms to profile and deliver information on pathogenic factors influencing wound progression, thereby guiding therapeutic intervention.

IMPORTANCE
Microbial contamination in combat wounds can lead to opportunistic infections and adverse outcomes. However, current microbiological detection has a limited ability to capture microbial functional genes. This work describes the application of targeted metagenomic sequencing to profile wound bioburden and capture relevant wound-associated signatures for clinical utility. Ultimately, the ability to detect such signatures will help guide clinical decisions regarding wound care and management and aid in the prediction of wound outcomes.
Developing an implementation intervention for managing acute vertigo in the emergency department
Authors: Herdman David , Ahmad Hena , Antoniades George , Bailur Gokul , Pajaniappane Arun , Moss Phil 
Published: October 2023

BackgroundThere are evidence-based bedside tests for diagnosing acute vertigo, but no evidence-based strategies to support clinicians in implementing them. The purpose of this study was to design an implementation strategy for treating acute vertigo by examining current facilitators and barriers to using these tests in the ED using the principles of implementation science.MethodsA survey was developed using the Theoretical Domains Framework and Consolidated Framework for Implementation Research to examine barriers and facilitators for using HINTS+ (head impulse, nystagmus, test of skew, plus hearing) and Dix-Hallpike tests. The survey was sent to emergency clinicians (ECs) in a teaching hospital in London, UK, between May and September 2022. Semistructured interviews were conducted simultaneously, and data examined using direct content analysis. Implementation strategies were then selected based on the Expert Recommendations for Implementing Change framework.ResultsFifty-one ECs responded to the survey and six ECs volunteered for interview. Less than half reported using the bedside tests to make a diagnosis. The most common barriers were beliefs about complexity, a lack of supporting materials, memory, lack of skills and negative experiences. The interview data revealed negative beliefs about the necessity, validity, safety and practicality. There were also barriers in the ED environment (eg, lack of space). There was a strong perception that the current approach to managing acute vertigo needed to change and ECs view this as part of their professional role and responsibility. Based on clinician input, the authors selected strategies to improve diagnostic efforts, which included guidelines for training, developing vertigo champions, protocols, memory aids, audit and feedback.ConclusionThis study found several barriers to managing acute vertigo such as memory constraints, and inadequate supporting materials and training, although a robust desire for change. The implementation strategy’s initial phase is described, which must now be tested.
Developing a generic business case for an advanced chronic liver disease support service
Authors: Wright Mark , Willmore Sarah , Verma Sumita , Omasta-Martin Anita , Sahota Humraj , Prentice Wendy , Stockley Amelia Jane , Finlay Fiona , Verne Julia , Hudson Ben 
Published: October 2023

IntroductionLiver disease deaths are rising, but specialist palliative care services for hepatology are limited. Expansion across the NHS is required.MethodsWe surveyed clinicians, patients and carers to design an ‘ideal’ service. Using standard NHS tariffs, we calculated the cost of this service. In hospitals where specialist palliative care was available for liver disease, patient-level costs and bed utilisation in last year of life (LYOL) were compared between those seen by specialist palliative care before death and those not.ResultsThe ‘ideal’ service was described. Costs were calculated as whole time equivalent for a minimal service, which could be scaled up. From a hospital with an existing service, patients seen by specialist palliative care had associated costs of £14 728 in LYOL, compared with £18 558 for those dying without. Savings more than balanced the costs of introducing the service. Average bed days per patient in LYOL were reduced (19.4 vs 25.7) also intensive care unit bed days (1.1 vs 1.8). Despite this, time from first admission in LYOL to death was similar in both groups (6 months for the specialist palliative care group vs 5 for those not referred).ConclusionsWe have produced a template business case for an ‘ideal’ advanced liver disease support service, which self-funds and saves many bed days. The model can be easily adapted for local use in other trusts. We describe the methodology for calculating patient-level costs and the required service size. We present a financially compelling argument to expand a service to meet a growing need.
Municipal social expenditures and maternal health disparities: a study of linked birth and hospitalisation records
Authors: Muchomba Felix M , Teitler Julien O , Reichman Nancy E 
Published: October 2023

BackgroundLocal government expenditures provide services and benefits that can affect health but the extent to which they are associated with narrowing or widening of racial/ethnic and socioeconomic disparities in health is unknown. We examined race/ethnicity-stratified and education-stratified associations between municipal social expenditures—those on housing, transportation, education, and other society-wide needs—and serious life-threatening maternal health conditions in a large US state.MethodsIn this cross-sectional study, we used individual birth records for 1 003 974 births in the state of New Jersey from 1 January 2008 to 31 December 2018 linked to individual maternal hospital discharge records and municipality-level characteristics for 564 municipalities. Severe maternal morbidity (SMM) was identified in the discharge records using a measure developed by the US Centers for Disease Control and Prevention. Associations between municipal-level social expenditures per capita and SMM were estimated using multilevel logistic models.ResultsResiding in a municipality with higher social expenditures was associated with lower odds of SMM across all racial/ethnic groups and education levels. Overall, 1% higher annual social expenditures per capita was associated with 0.21% (95% CI −0.29 to –0.13) lower odds of SMM. The associations were greater for individuals with less than a high school education than for those in the other educational groups in both relative (lnOR −0.53; 95% CI −0.74 to –0.31) and absolute (β −0.013; 95% CI −0.019 to –0.008) terms.ConclusionMunicipal-level spending on social services is associated with narrowing socioeconomic disparities in SMM. Narrowing racial/ethnic disparities in maternal health will likely require intervening beyond the provision of services to addressing historical and ongoing structural factors.