bluuebunny/crossref_metadata_2025_split huggingface dataset:
Front Matter
Authors: Li Wei , Ji Leilei , Agarwal Ramesh , Shi Weidong , Zhou Ling 
Published: June 2024

This frontmatter contains the Wiley-ASME Press Series, Contents, Preface, Acknowledgments, List of Acronyms and List of Symbols. It is available for access by clicking on the PDF icon below.
eBook keywords: mixed-flow pumps, agricultural applications of pumps, industrial applications of pumps, computational fluid dynamics, hydrodynamics, pump performance analysis methods, fluid transport, centrifugal pumps, axial pumps, radial pumps.
Draft genome sequences of a

bla
CTX

-M-15
-harboring and an atypical enteropathogenic
Escherichia coli
isolate recovered from slaughterhouses in Nigeria
Authors: Beshiru Abeni , Igbinosa Etinosa O. , Al Dahouk Sascha , Dieckmann Ralf , Neuhaus Szilvia 
Published: June 2024

ABSTRACT

We present the draft genome sequences of two
Escherichia coli
strains isolated from slaughterhouses in Edo State, Nigeria, in 2019. The isolates were identified as

bla
CTX-

M-15
-harboring (19-47-58) and atypical enteropathogenic
E. coli
(aEPEC) (19-47-66), belonging to multilocus sequence types (MLST) ST46 and ST2089, respectively.
Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost
Authors: Li Yaoming , Xue Yaxin , Roy Chowdhury Taniya , Graham David E. , Tringe Susannah G. , Jansson Janet K. , Taş Neslihan 
Published: June 2024

ABSTRACT

Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative
Firmicutes
and
Bacteroidota
taking over from
Actinobacteria
and
Proteobacteria
over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.

IMPORTANCE

As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like
Firmicutes
and
Bacteroidota
taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.
Integrated OMICs approach reveals energy metabolism pathway is vital for
Salmonella
Pullorum survival within the egg white
Authors: Kang Xiamei , An Hongli , Wang Baikui , Huang Linlin , Huang Chenghu , Huang Yingying , Wang Zining , He Fang , Li Yan , Yue Min 
Published: June 2024

ABSTRACT

Eggs, an important part of a healthy daily diet, can protect chicken embryo development due to the shell barrier and various antibacterial components within the egg white. Our previous study demonstrated that
Salmonella
Pullorum, highly adapted to chickens, can survive in the egg white and, therefore, be passed to newly hatched chicks. However, the survival strategy of
Salmonella
Pullorum in antibacterial conditions remains unknown. The overall transcripts in the egg white showed a large-scale shift compared to LB broth. The expression of common response genes and pathways, such as those involved in iron uptake, biotin biosynthesis, and virulence, was significantly changed, consistent with the other transovarial transmission serovar Enteritidis. Notably, membrane stress response, amino acid metabolism, and carbohydrate metabolism were specifically affected. Additional upregulated functionally relevant genes (JI728_13095, JI728_13100, JI728_17960, JI728_10085, JI728_15605, and
nhaA
) as mutants confirmed the susceptible phenotype. Furthermore,
fim
deletion resulted in an increased survival capacity in the egg white, consistent with the downregulated expression. The second-round RNA-Seq analysis of the Δ
fim
mutant in the egg white revealed significantly upregulated genes compared with the wild type in the egg white responsible for energy metabolism located on the
hyc
and
hyp
operons regulated by FhlA, indicating the Δ
fim
mutant cannot receive enough oxygen and switched to fermentative growth due to its inability to attach to the albumen surface. Together, this study provides a first estimate of the global transcriptional response of
Salmonella
Pullorum under antibacterial egg white and highlights the new potential role of
fim
deletion in optimizing energy metabolism pathways that may assist vertical transmission.

IMPORTANCE

Pullorum disease, causing serious embryo death and chick mortality, results in substantial economic losses worldwide due to transovarial transmission. Egg-borne outbreaks are frequently reported in many countries. The present study has filled the knowledge gap regarding how the specific chicken-adapted pathogen
Salmonella
Pullorum behaves within the challenging environment of egg white. The deletion of the
fim
fimbrial system can increase survival in the albumen, possibly by reprogramming metabolism-related gene products, which reveals a new adaptive strategy of pathogens. Moreover, the comparison, including previous research on
Salmonella
Enteritidis, capable of vertical transmission, aims to provide diversified data sets in the field and further help to implement reasonable and effective measures to improve both food safety and animal health.
Tenecteplase versus alteplase for acute ischaemic stroke in the elderly patients: a post hoc analysis of the TRACE-2 trial
Authors: Xiong Yunyun , Wang Liyuan , Pan Yuesong , Wang Mengxing , Schwamm Lee H , Duan Chunmiao , Campbell Bruce C V , Li Shuya , Hao Manjun , Wu Na , Cao Zhixin , Wu Shuangzhe , Li Zixiao , Wang Yongjun 
Published: June 2024

BackgroundThe benefit–risk profile of tenecteplase in the elderly patients with acute ischaemic stroke (AIS) is uncertain. We sought to investigate the efficacy and safety of 0.25 mg/kg tenecteplase compared with alteplase for AIS patients aged ≥80 years.MethodsWe performed a post hoc analysis of the Tenecteplase Reperfusion Therapy in Acute Ischaemic Cerebrovascular Events-2 Trial, a randomised, phase 3, non-inferiority clinical trial. Disabling AIS patients aged ≥80 years who initiated intravenous thrombolytics within 4.5 hours of symptom onset were enrolled from June 2021 to May 2022 across 53 centres in China and were randomly allocated to receive 0.25 mg/kg tenecteplase or 0.9 mg/kg alteplase. The primary efficacy outcome was the proportion of participants with a modified Rankin Scale (mRS) score of 0–1 at 90 days. Symptomatic intracranial haemorrhage (sICH) within 36 hours was the safety outcome.ResultsOf 137 participants, mRS 0–1 at 90 days occurred in 37 (49.3%) of 75 in the tenecteplase group vs 20 (33.9%) of 59 in the alteplase group (risk ratio (RR) 1.47, 95% CI 0.96 to 2.23). sICH within 36 hours was observed in 3 (4.0%) of 76 in the tenecteplase group and two (3.3%) of 61 in the alteplase group (RR 1.30, 95% CI 0.20 to 8.41).ConclusionsThe risk–benefit profile of tenecteplase thrombolysis was preserved in the elderly patients, which lends further support to intravenous 0.25 mg/kg tenecteplase as an alternative to alteplase in these patients.
Pregnancy Outcomes Among Teenagers at a National Referral Hospital in Uganda
Authors: Kagawa Mike Nantamu , Owori Otto Alex , Nakalembe Miriam 
Published: June 2024

Introduction: Teenage pregnancy is a global public health challenge, and it is a major contributor to the high maternal and neonatal morbidity and mortality rates reported in sub‐Saharan Africa and Uganda. However, there is a paucity of data regarding pregnancy outcomes and their associated factors among teenagers in Uganda. The purpose of this study was to determine the prevalence and factors associated with pregnancy outcomes among teenagers who delivered at a National Referral Hospital in Kampala, Uganda.Materials and Methods: This cross‐sectional study was conducted among teenage mothers who delivered at a National Referral Hospital in Kampala, Uganda. Consecutive participant recruitment was done for those who fulfilled the eligibility criteria. The outcomes of interest included adverse maternal outcome with obstructed labor being used as a proxy and adverse fetal outcomes with birth asphyxia used as a proxy. Logistic regression analysis was used to determine the association between independent and dependent variables with a 5% level of statistical significance (α = 0.05).Results: Teenage pregnancy was associated with adverse maternal outcomes which included obstructed labor (18%) and preterm labor (5.5%). There were no maternal deaths during the study period. Adverse fetal outcomes observed in this study population included low birth weight (83%), birth asphyxia (18%), and stillbirth (4%). The only factor associated with adverse maternal outcome was gestational age where teenage mothers had 4 times likelihood of delivering before 37 weeks. Relatedly, teenage mothers had an 81% chance of having a preterm birth.Conclusion: Teenage pregnancy was generally not associated with adverse maternal or fetal outcomes except for preterm birth. The reasons for adverse pregnancy outcomes may reflect a combination of gynecological and biological immaturity, as well as adverse socioeconomic pressures.
Clinical Updates and Surveillance Recommendations for DNA Replication Repair Deficiency Syndromes in Children and Young Adults
Authors: Das Anirban , MacFarland Suzanne P. , Meade Julia , Hansford Jordan R. , Schneider Kami W. , Kuiper Roland P. , Jongmans Marjolijn C.J. , Lesmana Harry , Schultz Kris Ann P. , Nichols Kim E. , Durno Carol , Zelley Kristin , Porter Christopher C. , States Lisa J. , Ben-Shachar Shay , Savage Sharon A. , Kalish Jennifer M. , Walsh Michael F. , Scott Hamish S. , Plon Sharon E. , Tabori Uri 
Published: June 2024

Abstract
Replication repair deficiency (RRD) is a pan-cancer mechanism characterized by abnormalities in the DNA mismatch repair (MMR) system due to pathogenic variants in the PMS2, MSH6, MSH2, or MLH1 genes, and/or in the polymerase-proofreading genes POLE and POLD1. RRD predisposition syndromes (constitutional MMR deficiency, Lynch, and polymerase proofreading–associated polyposis) share overlapping phenotypic and biological characteristics. Moreover, cancers stemming from germline defects of one mechanism can acquire somatic defects in another, leading to complete RRD. Here we describe the recent advances in the diagnostics, surveillance, and clinical management for children with RRD syndromes. For patients with constitutional MMR deficiency, new data combining clinical insights and cancer genomics have revealed genotype–phenotype associations and helped in the development of novel functional assays, diagnostic guidelines, and surveillance recommendations. Recognition of non-gastrointestinal/genitourinary malignancies, particularly aggressive brain tumors, in select children with Lynch and polymerase proofreading–associated polyposis syndromes harboring an RRD biology have led to new management considerations. Additionally, universal hypermutation and microsatellite instability have allowed immunotherapy to be a paradigm shift in the treatment of RRD cancers independent of their germline etiology. These advances have also stimulated a need for expert recommendations about genetic counseling for these patients and their families. Future collaborative work will focus on newer technologies such as quantitative measurement of circulating tumor DNA and functional genomics to tailor surveillance and clinical care, improving immune surveillance; develop prevention strategies; and deliver these novel discoveries to resource-limited settings to maximize benefits for patients globally.
Carotid Ultrasound‐Based Plaque Score for the Allocation of Aspirin for the Primary Prevention of Cardiovascular Disease Events: The Multi‐Ethnic Study of Atherosclerosis and the Atherosclerosis Risk in Communities Study
Authors: Dzaye Omar , Razavi Alexander C. , Dardari Zeina A. , Nasir Khurram , Matsushita Kunihiro , Mok Yejin , Santilli Francesca , Cobo Augusto María Lavalle , Johri Amer M. , Albrecht Gerhard , Blaha Michael J. 
Published: June 2024

Background
Coronary artery calcium testing using noncontrast cardiac computed tomography is a guideline‐indicated test to help refine eligibility for aspirin in primary prevention. However, access to cardiac computed tomography remains limited, with carotid ultrasound used much more often internationally. We sought to update the role of aspirin allocation in primary prevention as a function of subclinical carotid atherosclerosis.

Methods and Results
The study included 11 379 participants from the MESA (Multi‐Ethnic Study of Atherosclerosis) and ARIC (Atherosclerosis Risk in Communities) studies. A harmonized carotid plaque score (range, 0–6) was derived using the number of anatomic sites with plaque from the left and right common, bifurcation, and internal carotid artery on ultrasound. The 5‐year number needed to treat and number needed to harm as a function of the carotid plaque score were calculated by applying a 12% relative risk reduction in atherosclerotic cardiovascular disease (ASCVD) events and 42% relative increase in major bleeding events related to aspirin use, respectively. The mean age was 57 years, 57% were women, 23% were Black, and the median 10‐year ASCVD risk was 12.8%. The 5‐year incidence rates (per 1000 person‐years) were 5.5 (4.9–6.2) for ASCVD and 1.8 (1.5–2.2) for major bleeding events. The overall 5‐year number needed to treat with aspirin was 306 but was 2‐fold lower for individuals with carotid plaque versus those without carotid plaque (212 versus 448). The 5‐year number needed to treat was less than the 5‐year number needed to harm when the carotid plaque score was ≥2 for individuals with ASCVD risk 5% to 20%, whereas the presence of any carotid plaque demarcated a favorable risk–benefit for individuals with ASCVD risk >20%.

Conclusions
Quantification of subclinical carotid atherosclerosis can help improve the allocation of aspirin therapy.
Bias and Fairness in Large Language Models: A Survey
Authors: Gallegos Isabel O. , Rossi Ryan A. , Barrow Joe , Tanjim Md Mehrab , Kim Sungchul , Dernoncourt Franck , Yu Tong , Zhang Ruiyi , Ahmed Nesreen K. 
Published: June 2024

Abstract
Rapid advancements of large language models (LLMs) have enabled the processing, understanding, and generation of human-like text, with increasing integration into systems that touch our social sphere. Despite this success, these models can learn, perpetuate, and amplify harmful social biases. In this article, we present a comprehensive survey of bias evaluation and mitigation techniques for LLMs. We first consolidate, formalize, and expand notions of social bias and fairness in natural language processing, defining distinct facets of harm and introducing several desiderata to operationalize fairness for LLMs. We then unify the literature by proposing three intuitive taxonomies, two for bias evaluation, namely, metrics and datasets, and one for mitigation. Our first taxonomy of metrics for bias evaluation disambiguates the relationship between metrics and evaluation datasets, and organizes metrics by the different levels at which they operate in a model: embeddings, probabilities, and generated text. Our second taxonomy of datasets for bias evaluation categorizes datasets by their structure as counterfactual inputs or prompts, and identifies the targeted harms and social groups; we also release a consolidation of publicly available datasets for improved access. Our third taxonomy of techniques for bias mitigation classifies methods by their intervention during pre-processing, in-training, intra-processing, and post-processing, with granular subcategories that elucidate research trends. Finally, we identify open problems and challenges for future work. Synthesizing a wide range of recent research, we aim to provide a clear guide of the existing literature that empowers researchers and practitioners to better understand and prevent the propagation of bias in LLMs.
Observed Relationships between Supercell Mesocyclone Intensity and Evolution, Background Environmental Characteristics, and Cell Mergers
Authors: Flournoy Matthew D. , Lyza Anthony W. , Wade Andrew R. , Fischer Jannick 
Published: June 2024

Abstract
Cell mergers with supercells are relatively common, but much remains unknown about how they may influence subsequent supercell hazards. Furthermore, many outstanding questions regarding mesocyclone evolution exist despite numerous studies linking supercell hazards with the background environments in which they occur. In this study, we analyze the Multi-Year Reanalysis of Remotely Sensed Storms dataset along with hundreds of observed supercell tracks to begin addressing these ideas. In line with recent studies, the outcome of a supercell–cell merger (specifically the final strength of the low-level supercell mesocyclone) is not strongly related to the background environment. Of the parameters that we tested, mixed-layer (ML) LCL exhibited the largest correlation, but the very small coefficient of determination suggests limited operational use. More significantly, the incorporation of Storm Prediction Center objective analyses yields novel quantification of observed mesocyclone strengths in different environments. Of the environmental characteristics tested, kinematic parameters like 0–3-km storm-relative helicity (SRH) and 0–3-km bulk wind difference are more correlated with peak mesocyclone intensity than thermodynamic variables like CAPE and CIN. 0–3-km SRH exhibits the largest correlation, and its variability explains roughly one-third of the variance of peak azimuthal shear. We show trends in peak mesocyclone intensity across notable environmental parameter spaces, as well as how low-level mesocyclone strength fluctuates as background environmental characteristics evolve. Environmental trends during and preceding the times of peak mesocyclone strength are quantified. These analyses may be useful for predicting short-term mesocyclone intensity changes in real time.

Significance Statement
This study addresses open research questions related to how storms merging with supercell thunderstorms may influence supercell evolution and how supercells tend to evolve in different background environments. We find that an environmental measure of cloud-base height is statistically correlated with whether a supercell–cell merger will yield a strengthening or weakening supercell, but the strength of this correlation is quite weak. We find stronger correlations between peak supercell strength across storm lifetimes and some environmental characteristics, particularly parameters related to the change in the wind with height in the lowest few kilometers above ground level. These relationships may be useful for predicting short-term changes in supercell strength in real time.
Influence of surface modifications on interfacial and mechanical properties in fibre-reinforced composites
Authors: Saka Dinç Zaide , Eren Semiha , Öz Yahya , Eren Hüseyin Aksel 
Published: June 2024

Carbon fibres play a crucial role in fibre-reinforced composite materials. Properties of these composites are not solely determined by the fibre and matrix. In contrast, the interface between fibre and matrix also plays a pivotal role. The presence of sufficient van der Waals and hydrogen bonds between carbon fibre and matrix is vital for achieving strong interfacial adhesion during the composite fabrication. However, due to the chemical inertness and hydrophobic nature of carbon fibre surfaces, establishing effective interfacial bonding with the matrix poses a challenge. To address this, a range of methods has been developed to modify the carbon fibre surface and facilitate the formation of functional groups. Combined methods, such as sized carbon fibre and ozone treatment, have gained widespread usage in overcoming these challenges. In this study, a detailed examination was conducted to compare differences between ozonation of desized and sized carbon fibres by X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), Raman spectroscopy and scanning electron microscopy (SEM). XPS results distinctly demonstrated the transformation of epoxy groups into hydroxyl and carboxyl functional groups following the ozonation process. Notably, in the 60 min ozone treatment with 5 L/min (ozone-5), carboxyl groups increased from 1.27 to 8.12 %. In addition, in ozone-5 conditions, hydroxyl groups increased by 28.37 %. An escalation in graphite regions was also identified during the ozonation of the desized carbon fibre sample. Conversely, there was no significant alteration observed in the Raman value of sized carbon fibre samples. Furthermore, mechanical test results for both desized and sized carbon fibres after ozonation were compared. Ozone treatment of carbon fibres, regardless of whether sizing is present or not, leads to an increase in the interlaminar shear strength (ILSS). ILSS values for sized carbon fibres were initially 41 MPa. However, following ozone treatment, ILSS values of sized carbon fibres increased to 64 MPa. The tensile strength of sized carbon fibres increased from 772 to 831 MPa. This behaviour can be attributed to the increased amount of functional groups detected by XPS, Raman spectroscopy and the increase in roughness.