bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semiparametric inference of effective reproduction number dynamics from wastewater pathogen surveillance data
Authors: Goldstein Isaac H , Parker Daniel M , Jiang Sunny , Minin Volodymyr M 
Published: August 2024

ABSTRACT
Concentrations of pathogen genomes measured in wastewater have recently become available as a new data source to use when modeling the spread of infectious diseases. One promising use for this data source is inference of the effective reproduction number, the average number of individuals a newly infected person will infect. We propose a model where new infections arrive according to a time-varying immigration rate which can be interpreted as an average number of secondary infections produced by one infectious individual per unit time. This model allows us to estimate the effective reproduction number from concentrations of pathogen genomes, while avoiding difficulty to verify assumptions about the dynamics of the susceptible population. As a byproduct of our primary goal, we also produce a new model for estimating the effective reproduction number from case data using the same framework. We test this modeling framework in an agent-based simulation study with a realistic data generating mechanism which accounts for the time-varying dynamics of pathogen shedding. Finally, we apply our new model to estimating the effective reproduction number of SARS-CoV-2, the causative agent of COVID-19, in Los Angeles, CA, using pathogen RNA concentrations collected from a large wastewater treatment facility.
Coronary computed tomography angiography-derived fat attenuation index predict future percutaneous coronary intervention
Authors: He Wei , Lu Yige , Yin Jiasheng , He Furong , Zhang Yaoyi , Qiao Guanyu , Luan Jingyang , Yao Zhifeng , Li Chenguang , Yang Shan , Zhao Shihai , Shen Li , Guo Weifeng , Zeng Mengsu 
Published: August 2024

Abstract

Objectives
This study aims to investigate the differences in plaque characteristics and fat attenuation index (FAI) between in patients who received revascularization versus those who did not receive revascularization and examine whether the machine learning (ML)-based model constructed by plaque characteristics and FAI can predict revascularization.

Methods
This study was a post hoc analysis of a prospective single-centre registry of sequential patients undergoing coronary computed tomography angiography, referred from inpatient and emergency department settings (n = 261, 63 years ± 8; 188 men). The primary outcome was revascularization by percutaneous coronary revascularization. The computed tomography angiography (CTA) images were analysed by experienced radiologists using a dedicated workstation in a blinded fashion. The ML-based model was automatically computed.

Results
The study cohort consisted of 261 subjects. Revascularization was performed in 105 subjects. Patients receiving revascularization had higher FAI value (67.35 ± 5.49 vs −80.10 ± 7.75 Hu, P &lt; .001) as well as higher plaque length, calcified, lipid, and fibrous plaque burden and volume. When FAI was incorporated into an ML risk model based on plaque characteristics to predict revascularization, the area under the curve increased from 0.84 (95% CI, 0.68-0.99) to 0.95 (95% CI, 0.88-1.00).

Conclusions
ML algorithms based on FAI and characteristics could help improve the prediction of future revascularization and identify patients likely to receive revascularization.

Advances in knowledge
Pre-procedural FAI could help guide revascularization in symptomatic coronary artery disease patients.
Development of organic photoreactions utilizing the characteristics of elements with low electronegativity
Authors: Nagashima Yuki 
Published: August 2024

AbstractOrganic photoreactions have received much attention as unique tools to access kinetically and/or thermodynamically prohibited products in the ground state. These photoreactions have been based mainly on using elements with high electronegativity such as carbon (C), oxygen (O), nitrogen (N), halogens (F, Cl, Br, and I) as well as transition metals. On the other hand, we have been interested in the characteristics of elements with low electronegativity, such as boron (B), silicon (Si), and tin (Sn), in the excited state, enabling highly reactive and/or selective photoinduced borylations, silylations, and stannylations. In this account, we highlight our latest findings concerning diverse organic photoreactions utilizing B, Si, and Sn elements, which are challenging when using conventional strategies.
One-month DAPT after biodegradable-polymer everolimus-eluting stent implantation in patients at high-bleeding risk: an individual patient data pooled analysis of the SENIOR and POEM trials
Authors: Pivato Carlo A , Stefanini Giulio , Giacoppo Daniele , Sideris Georgios , Testa Luca , Paunovic Dragica , Briguori Carlo , Indolfi Ciro , Reimers Bernhard , Sinnaeve Peter , Varenne Olivier 
Published: August 2024

Abstract

Aims
Dual antiplatelet therapy (DAPT) can be shortened up to 1 month in high-bleeding risk (HBR) patients receiving a contemporary biodegradable-polymer sirolimus-eluting stent. We aimed to summarize the evidence on a similar DAPT regimen after biodegradable-polymer everolimus-eluting stent (EES) implantation in patients at HBR.

Methods and results
We pooled the individual participant data from the available trials evaluating this strategy, namely, the SENIOR and the POEM trials. Inclusion criteria were ≥1 biodegradable-polymer EES implantation and ≤1-month duration of DAPT. The primary endpoint was the 1-year composite of cardiovascular death, myocardial infarction, or stroke. Major bleeding was defined as Bleeding Academic Research Consortium (BARC) type 3–5 bleeding. Landmark analyses were performed at 1 month, the time point for intended DAPT interruption. We included 766 participants (age 77.5 ± 8.2 years, women 31.9%), 323 from the SENIOR and 443 from the POEM trial. The primary endpoint occurred in 45 participants (6.0%; 95% confidence interval [CI], 4.3–7.7%) through 1 year of follow-up, with 21 (2.8%; 95% CI, 1.6–3.9%) events during the first month and 24 (3.4%; 95% CI, 2.0–4.7%) thereafter. The incidences of cardiovascular death, myocardial infarction, and stroke were 2.2% (95% CI, 0.36–2.50%), 3.1% (95% CI, 1.8–4.3%), and 1.2% (95% CI, 0.4–2.0%), respectively. BARC type 3–5 bleeding ocuurred in 1.1% (95% CI, 0.3–1.8%) at 1 month and 2.9% (95% CI, 1.6–4.1%) at 1 year.

Conclusion
HBR patients receiving biodegradable-polymer EES had few ischemic and bleeding events when given 1 month of DAPT. One-month DAPT after biodegradable-polymer EES implantation seems safe in patients at HBR.
Gender gap in cardiothoracic surgery randomized controlled trial and post-hoc analysis of randomized controlled trial authorship from 2014 to 2020
Authors: Shariff Mariam , Kumar Ashish , Stulak John , Naumann Kathryn E , Blackmon Shanda H , Saddoughi Sahar A 
Published: August 2024

Abstract

OBJECTIVES
To estimate gender disparities among first and last authorships in cardiothoracic randomized controlled trials (RCTs) and association of gender with publications in high-impact journals.

METHODS
PubMed/MEDLINE database was searched from 1 January 2014 to 31 December 2020 using R statistical software via the ‘easyPubMed’ package to retrieve pertinent data. The ‘gender’ package was utilized to determine gender using the United States Social Security Administration Baby Name Data. The percentage of female first and last authors were computed along with determining the uniqueness of the names. The association of gender and publication in high-impact peer-reviewed journals was delineated. Jonckheere’s trend was computed.

RESULTS
The database search retrieved a total of 4820 RCTs, of which gender was encoded for the first author in 3247 (67%) RCTs, among which 911 (28%) studies had women as first authors, with a similar trend across 7 years (P = 0.23). Gender was encoded for the last author of 3204 (66%) RCTs, of which 622 (19%) studies had women as last authors, with a similar trend across 7 years (P = 0.45). A total of 627 studies were published in high-impact-factor journals, among which 79 (16%) studies had female first authors and 67 (13%) studies had female last authors.

CONCLUSIONS
There is an obvious gender disparity of first and last authors in cardiothoracic surgery-related RCTs, with a similar trend across 7 years. However, the post-hoc analysis did demonstrate a positive trend with an increase in the number of female first authors, demonstrating progress.
Impact of chitin-derived β-N-acetyl-d-glucosaminyl-(1,4)-d-glucosamine on chitinase upregulation in Shewanella baltica
Authors: Hirano Takako , Yokoyama Masahiro , Ikejima Masafumi , Shiraishi Haruka , Hakamata Wataru , Nishio Toshiyuki 
Published: August 2024

Abstract
The first steps in chitin degradation in marine bacteria involve chitinase, which produces N,N′-diacetylchitobiose (GlcNAc)2 from chitin. Moreover, in Vibrio bacteria, chitinase activity is enhanced by heterodisaccharide β-N-acetyl-d-glucosaminyl-(1,4)-d-glucosamine (GlcNAc–GlcN) produced from (GlcNAc)2 by chitin oligosaccharide deacetylase (COD). However, the role of COD in other marine bacteria, such as Shewanella, remains unexplored. This study investigates GlcNAc–GlcN’s impact on chitinase gene expression and enzyme production in S. baltica ATCC BAA-1091, drawing parallels with Vibrio parahaemolyticus RIMD2210633. Using real-time quantitative PCR, the study assesses the upregulation of chitinase gene expression in S. baltica in response to GlcNAc–GlcN, informed by COD’s known ability to produce GlcNAc–GlcN from (GlcNAc)2. In Vibrio, GlcNAc–GlcN considerably upregulates chitinase gene expression. This study posits a similar regulatory mechanism in S. baltica, with preliminary investigations indicating COD’s capacity to produce GlcNAc–GlcN. This study highlights the importance of exploring GlcNAc–GlcN’s regulatory role in chitin metabolism across diverse marine bacteria. The potential induction of chitinase production in S. baltica suggests broader ecological implications. Further research is crucial for a comprehensive understanding of chitin utilization and regulatory pathways in marine bacterial genera.
The role of uncertainty and negative feedback loops in the evolution of induced immune defenses
Authors: Asgari Danial , Stewart Alexander J , Meisel Richard P 
Published: August 2024

Abstract
Organisms use constitutive or induced defenses against pathogens and other external threats. Constitutive defenses are constantly on, whereas induced defenses are activated when needed. Each of these strategies has costs and benefits, which can affect the type of defense that evolves in response to pathogens. In addition, induced defenses are usually regulated by multiple negative feedback mechanisms that prevent overactivation of the immune response. However, it is unclear how negative feedback affects the costs, benefits, and evolution of induced responses. To address this gap, we developed a mechanistic model of the well-characterized Drosophila melanogaster immune signaling network that includes 3 separate mechanisms of negative feedback as a representative of the widespread phenomenon of multilevel regulation of induced responses. We show that, under stochastic fly–bacteria encounters, an induced defense is favored when bacterial encounters are rare or uncertain, but in ways that depend on the bacterial proliferation rate. Our model also predicts that the specific negative regulators that optimize the induced response depend on the bacterial proliferation rate, linking negative feedback mechanisms to the factors that favor induction.
A hybrid genome assembly of the endangered aye-aye (Daubentonia madagascariensis)
Authors: Versoza Cyril J , Pfeifer Susanne P 
Published: August 2024

Abstract
The aye-aye (Daubentonia madagascariensis) is the only extant member of the Daubentoniidae primate family. Although several reference genomes exist for this endangered strepsirrhine primate, the predominant usage of short-read sequencing has resulted in limited assembly contiguity and completeness, and no protein-coding gene annotations have yet been released. Here, we present a novel, fully annotated, chromosome-level hybrid de novo assembly for the species based on a combination of Oxford Nanopore Technologies long reads and Illumina short reads and scaffolded using genome-wide chromatin interaction data—a community resource that will improve future conservation efforts as well as primate comparative analyses.
Characterization of the rainbow trout (Oncorhynchus mykiss) mucosal glycosphingolipid repertoire and Aeromonas salmonicida binding to neutral glycosphingolipids
Authors: Benktander John , Sundh Henrik , Sundell Kristina , Sharba Sinan , Teneberg Susann , Lindén Sara K 
Published: August 2024

Abstract
Infections pose a challenge for the fast growing aquaculture sector. Glycosphingolipids are cell membrane components that pathogens utilize for attachment to the host to initiate infection. Here, we characterized rainbow trout glycosphingolipids from five mucosal tissues using mass spectrometry and nuclear magnetic resonance and investigated binding of radiolabeled Aeromonas salmonicida to the glycosphingolipids on thin-layer chromatograms. 12 neutral and 14 acidic glycosphingolipids were identified. The glycosphingolipids isolated from the stomach and intestine were mainly neutral, whereas glycosphingolipids isolated from the skin, gills and pyloric caeca were largely acidic. Many of the acidic structures were poly-sialylated with shorter glycan structures in the skin compared to the other tissues. The sialic acids found were Neu5Ac and Neu5Gc. Most of the glycosphingolipids had isoglobo and ganglio core chains, or a combination of these. The epitopes on the rainbow trout glycosphingolipid glycans differed between epithelial sites leading to differences in pathogen binding. A major terminal epitope was fucose, that occurred attached to GalNAc in a α1-3 linkage but also in the form of HexNAc-(Fuc-)HexNAc-R. A. salmonicida were shown to bind to neutral glycosphingolipids from the gill and intestine. This study is the first to do a comprehensive investigation of the rainbow trout glycosphingolipids and analyze binding of A. salmonicida to glycosphingolipids. The structural information paves the way for identification of ways of interfering in pathogen colonization processes to protect against infections in aquaculture and contributes towards understanding A. salmonicida infection mechanisms.
CaMYB80 enhances the cold tolerance of pepper by directly targeting CaPOA1
Authors: Xiao Jiachang , Wang Dong , Liang Le , Xie Minghui , Tang Yi , Lai Yun-Song , Sun Bo , Huang Zhi , Zheng Yangxia , Li Huanxiu 
Published: August 2024

Abstract
Cold temperatures negatively impact crop yield and quality, posing significant limitations to the advancement of the vegetable industry. MYB transcription factors are pivotal in enhancing plant resilience against various abiotic stresses, including low-temperature stress. Pepper (Capsicum annuum L.) is a nutrient-rich vegetable crop sensitive to low temperatures. This study aimed to determine the function of CaMYB80 in the cold stress response of pepper through virus-induced silencing. The study also conducted heterologous expression of CaMYB80 in Arabidopsis and tomato plants. The results showed that CaMYB80 could respond to low-temperature stress in pepper. CaMYB80 was localized in the nucleus and cytoplasm and exhibited transcriptional activation ability. Moreover, CaMYB80 silencing decreased cold tolerance in pepper, while its heterologous overexpression increased cold tolerance in Arabidopsis and tomato. Further analysis showed that CaMYB80 interacted with CaPOA1 (peroxidase N1-like). Similarly, the expression of CaPOA1 also responded to low-temperature stress. Overexpression of CaPOA1 enhanced freezing tolerance in Arabidopsis, while its silencing reduced cold stress tolerance in pepper. Furthermore, overexpression of CaMYB80 in Arabidopsis and tomato could increase the activity of peroxidases and the expression levels of genes in the ICE-CBF-COR (inducer of CBF expression, C-repeat binding factor, cold-responsive) regulatory network. In conclusion, our research results indicate that CaMYB80 enhances pepper cold tolerance by interacting with CaPOA1 to increase peroxidase activity and influence the expression of ICE-CBF-COR related genes.
A comparative study of home healthcare quality in urban and rural home health agencies throughout the USA (2010–22)
Authors: Zhang Yili , Koru Güneş 
Published: August 2024

Abstract
Urban–rural disparities in medical care, including in home healthcare, persist globally. With aging populations and medical advancements, demand for home health services rises, warranting investigation into home healthcare disparities. Our study aimed to (i) investigate the impact of rurality on home healthcare quality, and (ii) assess the temporal disparities and the changes in disparities in home healthcare quality between urban and rural home health agencies (HHAs), incorporating an analysis of geospatial distribution to visualize the underlying patterns. This study analyzed data from HHAs listed on the Centers for Medicare and Medicaid Services website, covering the period from 2010 to 2022. Data were classified into urban and rural categories for each HHA. We employed panel data analysis to examine the impact of rurality on home healthcare quality, specifically focusing on hospital admission and emergency room (ER) visit rates. Disparities between urban and rural HHAs were assessed using the Wilcoxon test, with results visualized through line and dot plots and heat maps to illustrate trends and differences comprehensively. Rurality is demonstrated as the most significant variable in hospital admission and ER visit rates in the panel data analysis. Urban HHAs consistently exhibit significantly lower hospital admission rates and ER visit rates compared to rural HHAs from 2010 to 2022. Longitudinally, the gap in hospital admission rates between urban and rural HHAs is shrinking, while there is an increasing gap in ER visit rates. In 2022, HHAs in Mountain areas, which are characterized by a higher proportion of rural regions, exhibited higher hospital admission and ER visit rates than other areas. This study underscores the persistent urban–rural disparities in home healthcare quality. The analysis emphasizes the ongoing need for targeted interventions to address disparities in home healthcare delivery and ensure equitable access to quality care across urban and rural regions. Our findings have the potential to inform policy and practice, promoting equity and efficiency in the long-term care system, for better health outcomes throughout the USA.
A Disputed Hegemony: Negotiating Neurosurgical Patient Care in the Netherlands, 1930–1952
Authors: Lutters Bart 
Published: August 2024

Abstract
The emergence of the neurosurgical patient as a novel clinical entity in the Netherlands was marked by a lingering conflict between neurologists and neurosurgeons, in which both types of specialists sought to assume the clinical and institutional leadership of neurosurgical patient care. In the 1920s and 1930s, neurologists had facilitated the establishment of the first generation of neurosurgeons in the country, and in the process, had managed to clinically and institutionally subordinate neurosurgery to neurology. As the demand for neurosurgical patient care grew, the neurosurgeons began to challenge this hegemonic relationship. The neurologists, however, were unwilling to give up their control, fearing that they would be bypassed in the diagnosis of patients eligible to neurosurgery. These conflicting aims and interests resulted in an intricate demarcation battle, in which the boundary work between neurologists and neurosurgeons was directly played out at the local workplace and at the meetings of the Study Club for Neuro-Surgery, and indirectly at various other sites of contestation, such as medical journals and academic lecture halls, as both parties sought to rally external stakeholders to their cause. During these negotiations, local, national, and international forces increasingly intertwined to shape the particular organization of Dutch neurosurgery in the middle of the twentieth century. By analyzing this multilayered demarcation process, this article draws attention to the complexity of medical boundary work, and to the way in which, despite pervasive international influences, specialist practice was ultimately negotiated at the local and national levels.
Equality, Diversity and Inclusion within Ireland’s Police Service, An Garda Síochána: Bridging the Gap between Commitments and Reality
Authors: Sweeney Caroline 
Published: August 2024

Abstract
The Black Lives Matter movement highlighted the importance of equality, diversity and inclusion (EDI) in a policing context. Using the Irish police service, An Garda Síochána, as a case study, this article critically evaluates efforts to promote EDI within a policing organization that has been characterized as resistant to change. It focuses primarily on the implementation of relevant recommendations contained in the landmark 2018 Report of the Commission on the Future of Policing in Ireland. It demonstrates that while building a culture that respects and promotes EDI within any organization is a challenging process, it can be even more difficult in policing organizations due to police sub-culture. It submits that laws, policies and commitments, while necessary, are insufficient of themselves to achieve transformative change. Strong and committed leadership is also required, as well as measures to recruit and retain a diverse workforce at all levels, sufficient resourcing for EDI initiatives, EDI training that accords with international best practice, efforts to improve relationships with marginalized communities, measures to combat hate crime and racial profiling, effective mechanisms for collecting EDI data and evaluating EDI policies, and a robust governance, oversight and accountability framework. While identifying and welcoming measures undertaken to date by An Garda Síochána to convert EDI policy commitments into reality, the article also highlights areas where improvements are necessary. Finally, aligning with several theorists of police sub-culture, the article concludes that any efforts to promote EDI within An Garda Síochána will need to be accompanied by efforts to combat structural inequality in wider society.
Combinators as presheaves
Authors: Gangle Rocco , Tohmé Fernando , Caterina Gianluca 
Published: August 2024

Abstract
Computer scientists, logicians and other researchers have recently paid renewed attention to the model of computation based on the logic of combinators. We develop a new formalization of the syntax of combinators employing the ‘generic figures’ approach to the categories of presheaves that provides an intuitive and easily interpreted diagrammatic syntax for combinators, one that eschews the need to label proper combinators with variable names. Furthermore, we show that this formal framework provides the possibility of representing choices of operand from among given alternatives at each level of a combinatory term, allowing for a more general type of combinatory expression, which we call a multi-combinator.