bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient and Highly Continuous Chromosome-Level Genome Assembly of the First Chameleon Genome
Authors: Xie Hongxin , Chen Zixuan , Pang Shuai , Du Weiguo 
Published: July 2023

Abstract
Most amniote genomes are diploid and moderate in size (∼1–6 Gbp) and contain a large proportion of repetitive sequences. The development of next-generation sequencing technology, especially the emergence of high-fidelity (HiFi) long-read data, has made it feasible to resolve high-quality genome assembly for nonmodel species efficiently. However, reference genomes for squamate reptiles have lagged behind other amniote lineages. Here, we de novo assembled the first genome from the Chameleonidae family, the panther chameleon (Furcifer pardalis). We obtained telomere-to-telomere contigs using only HiFi data, reaching a contig N50 of 158.72 Mbp. The final chromosome-level assembly is 1.61 Gbp in size, and 100% of primary contigs were placed to pseudochromosomes using Hi-C interaction data. We also found that sequencing depth &gt; 30 folds can ensure both the integrity and accuracy of the genome, whereas insufficient depth led to false increase in genome size and proportion of duplicated genes. We provide a high-quality reference genome valuable for evolutionary and ecological studies in chameleons as well as provide comparative genomic resources for squamate reptiles.
Unusually Divergent Ubiquitin Genes and Proteins in Plasmodium Species
Authors: Dalhuisen Thomas , Plenderleith Lindsey J , Ursani Ismail , Philip Nisha , Hahn Beatrice H , Sharp Paul M 
Published: July 2023

Abstract
Ubiquitin is an extraordinarily highly conserved 76 amino acid protein encoded by three different types of gene, where the primary translation products are fusions either of ubiquitin with one of two ribosomal proteins (RPs) or of multiple ubiquitin monomers from head to tail. Here, we investigate the evolution of ubiquitin genes in mammalian malaria parasites (Plasmodium species). The ubiquitin encoded by the RPS27a fusion gene is highly divergent, as previously found in a variety of protists. However, we also find that two other forms of divergent ubiquitin sequence, each previously thought to be extremely rare, have arisen recently during the divergence of Plasmodium subgenera. On two occasions, in two distinct lineages, the ubiquitin encoded by the RPL40 fusion gene has rapidly diverged. In addition, in one of these lineages, the polyubiquitin genes have undergone a single codon insertion, previously considered a unique feature of Rhizaria. There has been disagreement whether the multiple ubiquitin coding repeats within a genome exhibit concerted evolution or undergo a birth-and-death process; the Plasmodium ubiquitin genes show clear signs of concerted evolution, including the spread of this codon insertion to multiple repeats within the polyubiquitin gene.
Suture tie-down forces and cyclic contractile forces after undersized tricuspid annuloplasty using a Tri-Ad Adams tricuspid annuloplasty ring in an ovine model
Authors: Cho Sungkyu , Park Chan Hun , Shin Heean , Lim Jae Hong , Sohn Suk Ho , Kim Ji Seong , Choi Jae Woong , Lee Jung Chan , Kim Woong-Han , Hwang Ho Young 
Published: July 2023

Abstract

OBJECTIVES
This study evaluated suture tie-down forces and cyclic contractile forces (CCFs) after undersized tricuspid annuloplasty using a hybrid band.

METHODS
Downsized tricuspid annuloplasty was planned in adult male sheep using 8 force transducers attached from the septal to the anterior annular areas of the ring (segments 1 and 2, flexible septal; segments 3 and 4, semi-rigid posterior; segments 5 and 6, semi-rigid anterior; segments 7 and 8, flexible anterior). CCFs were analysed at 3 different levels of peak right ventricular pressure (RVP): 30, 50 and 70 mmHg.

RESULTS
Eight 5-year-old male Corriedale sheep (average body weight = 66.8 kg) were used. The average suture tie-down force was 4.42 [standard deviation (SD): 2.32] N. When the forces were compared, it was lowest in the flexible anterior area and highest in the flexible septal area (P &lt; 0.001). With the RVP of 30 mmHg, the average CCFs was lowest at segment 3 [0.07 (SD: 0.07) N] and highest at segment 7 [0.15 (SD: 0.08) N]. The CCFs were 0.12 (SD: 0.1) N, 0.09 (SD: 0.12) N, 0.14 (SD: 0.1) N and 0.13 (SD: 0.09) N in the flexible septal, semi-rigid posterior, semi-rigid anterior and flexible anterior parts, respectively (P = 0.208). As the peak RVP increased to 50 and 70 mmHg, the CCFs of each area increased significantly (P &lt; 0.001). Despite this increase, the CCFs remained low (0.1 and 0.3 N), and differences in CCFs between segments and between annular areas showed similar patterns.

CONCLUSIONS
The flexible end of the hybrid band reduces the CCFs and might prevent annular tears after ring tricuspid annuloplasty, and the risk of tear would be low even in the septal area.
Reasons and predictors of non-participation in a personalized digital prehabilitation care trial for patients undergoing elective cardiothoracic surgery
Authors: Scheenstra Bart , Bongers Bart C , Broeders Britney , Imkamp Maike , Van Susante Lieke , Kietselaer Bas , Maessen Jos , Van ’T Hof Arnoud , Sardari Nia Peyman 
Published: July 2023

Abstract

OBJECTIVES
Prehabilitation through a digital platform could preoperatively improve the physical and mental fitness of patients undergoing cardiothoracic surgery, thereby improving treatment outcomes. This study aimed to describe the reasons and predictors of non-participation in a personalized digital prehabilitation care trial (Digital Cardiac Counseling randomized controlled trial) for patients undergoing elective cardiothoracic surgery.

METHODS
Adult patients scheduled for elective cardiothoracic surgery at the Maastricht University Medical Center+ were approached to participate in a digital prehabilitation care trial, in which patients were informed about their care pathway, monitored for symptom progression and screened for preoperative modifiable risk factors. Baseline characteristics of all eligible patients and reasons of non-participation were registered prospectively. Predictors of non-participation were determined using logistic regression.

RESULTS
Between May 2020 and August 2022, 815 patients were eligible for participation; 421 (52%) did not participate in the personalized digital prehabilitation care trial. Reasons for non-participation were ‘lack of internet access or insufficient digital skills’ (32%), ‘wishing no participation’ (39%) and ‘other reasons’ (30%; e.g. vision or hearing impairments, analphabetism, language barriers). Independent predictors of non-participation were age [odds ratio (OR) 1.024 (1.003–1.046), P = 0.024], socioeconomic status [OR 0.267 (0.133–0.536), P &lt; 0.001], current smoker [OR 1.823 (1.124–2.954), P = 0.015] and EuroSCORE II [OR 1.160 (1.042–1.292), P = 0.007].

CONCLUSIONS
Half of the eligible patients did not participate in a personalized digital prehabilitation care trial. Non-participants were vulnerable patients, with a more unfavourable risk profile and more modifiable risk factors, who could potentially benefit the most from prehabilitation.
Mortality-based indicators for measuring health system performance and population health in high-income countries: a systematic review
Authors: Liang Catherine Y , Kornas Kathy , Bornbaum Catherine , Shuldiner Jennifer , De Prophetis Eric , Buajitti Emmalin , Pach Beata , Rosella Laura C 
Published: July 2023

Abstract

Objectives
Mortality-based indicators are commonly used as measures of population health but less frequently applied to measuring health system performance. This systematic review aimed to identify and describe mortality indicators relevant to the measurement of population health and health system performance in high-income countries.

Methods
We searched peer-reviewed databases (MEDLINE, Embase, CINAHL, Health Business Elite, Health Policy Reference Center, and POPLINE) and grey literature (government agencies, professional associations, and international/non-governmental health organizations). The search was limited to indicators identified for use in high-income countries. We extracted information on indicator characteristics and alignment with dimensions of effectiveness, efficiency, and equity. We assessed the applicability of the indicator to the context of population health, health system, or both settings, alignment with SMART criteria (specific, measurable, actionable, relevant, and timely), and potential for analyses of population subgroups. Health system was defined as encompassing both medical care and public health services and activities.

Results
We extracted 385 mortality-based indicators from 240 sources. Indicators were organized into six major domains: all-cause mortality (n = 12), premature mortality (n = 92), life expectancy (n = 23), cause-specific mortality (n = 127), infant, child, and adolescent mortality (n = 50), and hospital-related mortality (n = 81). The majority of indicators (86%) could be applied to measuring health system performance. Premature mortality indicators showed the most potential to measuring both population health and health system performance.

Conclusions
This review compiled a wide range of mortality indicators relevant to measuring health system performance in high-income countries. Indicators of premature mortality were most relevant to measuring both population health and health system performance.
A Generalization of the Murnaghan–Nakayama Rule for K-k-Schur and k-Schur Functions
Authors: Nguyen Duc-Khanh 
Published: July 2023

Abstract
The $K$-$k$-Schur functions and $k$-Schur functions appeared in the study of $K$-theoretic and affine Schubert Calculus as polynomial representatives of Schubert classes. In this paper, we introduce a new family of symmetric functions $\mathcal {F}_{\lambda }^{(k)}$, that generalizes the constructions via the Pieri rule of $K$-$k$-Schur functions and $ k$-Schur functions. Then we obtain the Murnaghan–Nakayama rule for the generalized functions. The rule is described explicitly in the cases of $K$-$k$-Schur functions and $k$-Schur functions, with concrete descriptions and algorithms for coefficients. Our work recovers the result of Bandlow, Schilling, and Zabrocki for $k$-Schur functions, and explains it as a degeneration of the rule for $K$-$k$-Schur functions. In particular, many other special cases and connections promise to be detailed in the future.
Lung group 2 innate lymphoid cells differentially depend on local IL-7 for their distribution, activation, and maintenance in innate and adaptive immunity-mediated airway inflammation
Authors: Takami Daichi , Abe Shinya , Shimba Akihiro , Asahi Takuma , Cui Guangwei , Tani-ichi Shizue , Hara Takahiro , Miyata Keishi , Ikutani Masashi , Takatsu Kiyoshi , Oike Yuichi , Ikuta Koichi 
Published: July 2023

Abstract
Interleukin-7 (IL-7) is a cytokine critical for the development and maintenance of group 2 innate lymphoid cells (ILC2s). ILC2s are resident in peripheral tissues such as the intestine and lung. However, whether IL-7 produced in the lung plays a role in the maintenance and function of lung ILC2s during airway inflammation remains unknown. IL-7 was expressed in bronchoalveolar epithelial cells and lymphatic endothelial cells (LECs). To investigate the role of local IL-7 in lung ILC2s, we generated two types of IL-7 conditional knockout (IL-7cKO) mice: Sftpc-Cre (SPC-Cre) IL-7cKO mice specific for bronchial epithelial cells and type 2 alveolar epithelial cells and Lyve1-Cre IL-7cKO mice specific for LECs. In steady state, ILC2s were located near airway epithelia, although lung ILC2s were unchanged in the two lines of IL-7cKO mice. In papain-induced airway inflammation dependent on innate immunity, lung ILC2s localized near bronchia via CCR4 expression, and eosinophil infiltration and type 2 cytokine production were reduced in SPC-Cre IL-7cKO mice. In contrast, in house dust mite (HDM)-induced airway inflammation dependent on adaptive immunity, lung ILC2s localized near lymphatic vessels via their CCR2 expression 2 weeks after the last challenge. Furthermore, lung ILC2s were decreased in Lyve1-Cre IL-7cKO mice in the HDM-induced inflammation because of decreased cell survival and proliferation. Finally, administration of anti-IL-7 antibody attenuated papain-induced inflammation by suppressing the activation of ILC2s. Thus, this study demonstrates that IL-7 produced by bronchoalveolar epithelial cells and LECs differentially controls the activation and maintenance of lung ILC2s, where they are localized in airway inflammation.
Advantages and disadvantages of using theory-based versus data-driven models with social and behavioral determinants of health data
Authors: Austin Robin R , McLane Tara M , Pieczkiewicz David S , Adam Terrence , Monsen Karen A 
Published: July 2023

Abstract

Objective
Theory-based research of social and behavioral determinants of health (SBDH) found SBDH-related patterns in interventions and outcomes for pregnant/birthing people. The objectives of this study were to replicate the theory-based SBDH study with a new sample, and to compare these findings to a data-driven SBDH study.

Materials and Methods
Using deidentified public health nurse-generated Omaha System data, 2 SBDH indices were computed separately to create groups based on SBDH (0–5+ signs/symptoms). The data-driven SBDH index used multiple linear regression with backward elimination to identify SBDH factors. Changes in Knowledge, Behavior, and Status (KBS) outcomes, numbers of interventions, and adjusted R-squared statistics were computed for both models.

Results
There were 4109 clients ages 13–40 years. Outcome patterns aligned with the original research: KBS increased from admission to discharge with Knowledge improving the most; discharge KBS decreased as SBDH increased; and interventions increased as SBDH increased. Slopes of the data-driven model were steeper, showing clearer KBS trends for data-driven SBDH groups. The theory-based model adjusted R-squared was 0.54 (SE = 0.38) versus 0.61 (SE = 0.35) for the data-driven model with an entirely different set of SBDH factors.

Conclusions
The theory-based approach provided a framework to identity patterns and relationships and may be applied consistently across studies and populations. In contrast, the data-driven approach can provide insights based on novel patterns for a given dataset and reveal insights and relationships not predicted by existing theories. Data-driven methods may be an advantage if there is sufficiently comprehensive SBDH data upon which to create the data-driven models.
Toward a high-resolution mechanism of intrinsically disordered protein self-assembly
Authors: Sekiyama Naotaka , Kobayashi Ryoga , Kodama Takashi S 
Published: July 2023

Abstract
Membraneless organelles formed via the self-assembly of intrinsically disordered proteins (IDPs) play a crucial role in regulating various physiological functions. Elucidating the mechanisms behind IDP self-assembly is of great interest not only from a biological perspective but also for understanding how amino acid mutations in IDPs contribute to the development of neurodegenerative diseases and other disorders. Currently, two proposed mechanisms explain IDP self-assembly: (1) the sticker-and-spacer framework, which considers amino acid residues as beads to simulate the intermolecular interactions, and (2) the cross-β hypothesis, which focuses on the β-sheet interactions between the molecular surfaces constructed by multiple residues. This review explores the advancement of new models that provide higher resolution insights into the IDP self-assembly mechanism based on new findings obtained from structural studies of IDPs.
Isolated Flat Epithelial Atypia: Upgrade Outcomes After Multidisciplinary Review–Based Management Using Excision or Imaging Surveillance
Authors: Xie Charlies L , Whitman Gary J , Middleton Lavinia P , Bevers Therese B , Bedrosian Isabelle , Chung Hannah L 
Published: July 2023

Abstract

Objective
To compare flat epithelial atypia (FEA) upgrade rates after excision versus surveillance and to identify variables associated with upgrade.

Methods
This single-institution retrospective study identified isolated FEA cases determined by percutaneous biopsy from April 2005 through July 2022 with excision or ≥2 years surveillance. All cases were recommended for excision or surveillance based on multidisciplinary discussion of clinical, imaging, and pathologic variables with emphasis on sampling adequacy and significant atypia. Truth was determined by pathology at excision or the absence of cancer on surveillance. Upgrade was defined as cancer occurring ≤2 cm from the biopsy site. Demographic, imaging, and biopsy variables were compared between those that did and did not upgrade.

Results
Among 112 cases of isolated FEA, imaging findings included calcifications in 81.3% (91/112), MRI lesions in 11.6% (13/112), and distortions or masses in 7.1% (8/112). Excision was recommended in 12.5% (14/112) and surveillance in 87.5% (98/112) of cases. Among those recommended for excision, 28.6% (4/14) of cases were upgraded, all to ductal carcinoma in situ. In those recommended for surveillance, 1.0% (1/98) were upgraded to invasive cancer. Overall, FEA had a 4.5% (5/112) upgrade rate, and 2.7% (3/112) also developed cancer &gt;2 cm from the FEA. There were no significant differences in demographic, imaging, and biopsy variables between those that did and did not upgrade to cancer.

Conclusion
Multidisciplinary management of isolated FEA distinguishes those at higher risk of upgrade to cancer (28.6%) in whom surgery is warranted from those at low risk of upgrade (1.0%) who can be managed non-operatively.
Identification, biology, and management of conifer sawflies (Hymenoptera: Diprioninae) in eastern North America
Authors: Davis Jeremy S , Glover Ashleigh N , Everson Kathryn M , Coyle David R , Linnen Catherine R 
Published: July 2023

Abstract
Pine sawflies (Hymenoptera: Diprionidae) are eruptive herbivores found throughout eastern North America. The Diprionidae family, which contains at least 140 species, constitutes the most persistent threat to conifers as population outbreaks can cause widespread defoliation. Because some species are more prone to large, destructive outbreaks than others, species identification is critical to effective management. Although existing taxonomic keys are primarily based on internal adult morphology, substantial variation among species in larval color traits, geographic location, overwintering strategy, host plant, and egg patterns can be diagnostic at the species level. Here, we focus on the Pinaceae-feeding subfamily Diprioninae, of which there are 25 species in eastern North America. We describe the general biology, life cycle, and host-use ecology of Diprioninae, with an emphasis on the variation among these traits within this subfamily. In addition, we provide tools for species identification, including a taxonomic key that utilizes external diagnostic characteristics. Finally, we discuss available management strategies.
The longest reported survival of a child with McCune–Albright syndrome and a severe early presenting phenotype consisting of neonatal cushing syndrome, cardiac and liver diseases
Authors: Alhalabi Rawan , Elsayed Yasmine , Belsha Dalia , Muad Hussein , Zidan Hanaa , Alhubaishi Laila Y , Ramaiah Sridhar , Ba’ath Muhammad E 
Published: July 2023

Abstract
Neonatal cushing syndrome (NCS) is a rare disease that results from prolonged exposure to high cortisol levels. McCune–Albright syndrome (MAS) is an exceedingly rare genetic disorder characterized by cafe-au-lait skin spots, bone fibrous dysplasia and multiple endocrinopathies. We describe a case of a premature neonate with Intrauterine Growth Retardation who presented with hypercortisolemia, neonatal transaminitis and cardiac dysfunction. Further evaluation revealed significant bilateral adrenal hyperplasia leading to the diagnosis of NCS as part of MAS. Despite maximum medical therapy, including metyrapone, the baby’s refractory hypertension, hyperglycemia and persistent failure to thrive (weight of 1.4 kg at corrected age 38 weeks) necessitated bilateral adrenalectomy. This case did not initially demonstrate the classic MAS triad, notably, the absence of skeletal manifestations. There has been no previous description of a baby who has had all the early life-threatening features present and survived beyond 18 months. This case highlights the severity of the phenotype and the challenges involved in diagnosing and treating NCS and MAS in neonates.
Provincialism at Large: Reading Locality, Scale, and Circulation in Nineteenth-Century Britain
Authors: Livesey Ruth 
Published: July 2023

Abstract
This introduction situates the contributions to the New Agenda in the context of an apparent resurgence of the term ‘provincial’ and ‘provincialism’ in Britain since the Brexit debates and the 2016 United Kingdom European Union membership referendum. It takes the resurgence of provincial thinking as an invitation to explore the cultural history of provincialism in Victorian Britain and the unexpected part it played in the formation of Empire. By revaluing the cultural formation of provincialism through this historical lens the articles in this New Agenda help us see the roots of its power now and the alternative possibilities latent within it. Although provincialism emerged as a fraught and politically charged term during the nineteenth century it was also a means to expand access to print and material cultures to those previously excluded. At the same time as provincialism became a pejorative term in the hands of liberal critics such as Matthew Arnold, nineteenth-century Britain was powered by industry, intellectual enquiry, and newspapers emanating from non-metropolitan towns and cities. The provincial press and provincial fiction are crucial ways in which Victorian Britain represented itself as an entity composed of distinctive constituent regions and imagined itself as an imperial power.
Gut microbiota, immunity, and bile acid metabolism: decoding metabolic disease interactions
Authors: Zhao Qixiang , Wu Jiayu , Ding Yong , Pang Yanli , Jiang Changtao 
Published: July 2023

Abstract
In recent decades, the global prevalence of metabolic syndrome has surged, posing a significant public health challenge. Metabolic disorders, encompassing diabetes, obesity, nonalcoholic fatty liver disease, and polycystic ovarian syndrome, have been linked to alterations in the gut microbiota. Nonetheless, the connection between gut microbiota and host metabolic diseases warrants further investigation. In this review, we delve into the associations between various metabolic disorders and the gut microbiota, focusing on immune responses and bile acid (BA) metabolism. Notably, T helper cells, innate lymphoid cells, macrophages, and dendritic cells have been shown to modulate host metabolism through interactions with intestinal microorganisms and the release of cytokines. Furthermore, secondary BA metabolites, derived from the microbiota, are involved in the pathogenesis of metabolic diseases via the farnesoid X receptor and Takeda G protein-coupled receptor 5. By covering both aspects of this immune system-microorganism axis, we present a comprehensive overview of the roles played by the gut microbiota, microbiota-derived BA metabolites, and immune responses in metabolic diseases, as well as the interplay between these systems.