bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sustained mangrove reproduction despite major turnover in pollinator community composition at expanding range edge
Authors: Nathan Mayda , Gruner Daniel S 
Published: June 2023

Abstract

Background and Aims
How well plants reproduce near their geographic range edge can determine whether distributions will shift in response to changing climate. Reproduction at the range edge can be limiting if pollinator scarcity leads to pollen limitation, or if abiotic stressors affect allocation to reproduction. For many animal-pollinated plants with expanding ranges, the mechanisms by which they have overcome these barriers are poorly understood.

Methods
In this study, we examined plant–pollinator interactions hypothesized to impact reproduction of the black mangrove, Avicennia germinans, which is expanding northward in coastal Florida, USA. We monitored insects visiting A. germinans populations varying in proximity to the geographic range edge, measured the pollen loads of the most common insect taxa and pollen receipt by A. germinans stigmas, and quantified flower and propagule production.

Key Results
We found that despite an 84 % decline in median floral visits by insects at northernmost versus southernmost sites, range-edge pollen receipt remained high. Notably, local floral visitor assemblages exhibited substantial turnover along the study’s latitudinal gradient, with large-bodied bees and hover flies increasingly common at northern sites. We also observed elevated flower production in northern populations and higher per capita reproductive output at the range edge. Furthermore, mean propagule mass in northern populations was 18 % larger than that from the southernmost populations.

Conclusions
These findings reveal no erosion of fecundity in A. germinans populations at range limits, allowing rapid expansion of mangrove cover in the region. These results also illustrate that substantial turnover in the assemblage of flower-visiting insects can occur at an expanding range edge without altering pollen receipt.
Determinants of interspecific variation in season length of perennial herbs
Authors: Koubek Tomáš , Mašková Tereza , Herben Tomáš 
Published: June 2023

Abstract

Background and aims
Perennial plants in seasonal climates need to optimize their carbon balance by adjusting their active season length to avoid risks of tissue loss under adverse conditions. As season length is determined by two processes, namely spring growth and senescence, it is likely to vary in response to several potentially contrasting selective forces. Here we aim to disentangle the cascade of ecological determinants of interspecific differences in season length.

Methods
We measured size trajectories in 231 species in a botanical garden. We examined correlations between their spring and autumn size changes and determined how they make up season length. We used structural equation models (SEMs) to determine how niche parameters and species traits combine in their effect on species-specific season length.

Key results
Interspecific differences in season length were mainly controlled by senescence, while spring growth was highly synchronized across species. SEMs showed that niche parameters (light and moisture) had stronger, and often trait-independent, effects compared to species traits. Several niche (light) and trait variables (plant height, clonal spreading) had opposing effects on spring growth and senescence.

Conclusions
The findings indicate different drivers and potential risks in growth and senescence. The strong role of niche-based predictors implies that shifts in season length due to global change are likely to differ among habitats and will not be uniform across the whole flora.
Molecular and cellular insights into auxin-regulated primary root growth: a comparative study of Arabidopsis and rice
Authors: Nakamura Ayako , Hirota Yuna , Shigihara Masaru , Watanabe Mayu , Sato Akiko , Tsuji Hiroyuki , Shimada Yukihisa 
Published: June 2023

ABSTRACT
Auxin regulation of primary root growth in Arabidopsis and rice was compared by analyzing root growth in response to changes in auxin levels. A bell-shaped root-growth curve was identified in both Arabidopsis and rice in response to change in auxin levels. In Arabidopsis, cell division was the main regulator of root growth in response to auxin; in rice, auxin promoted root growth by regulating cell division and cell length. The expression levels of PLETHORA (PLT) genes in response to change in auxin level followed a bell-shaped curve and closely correlated with cell division in Arabidopsis but not in rice, implying that PLT gene expression plays key role to control root growth in Arabidopsis. The level of auxin in Arabidopsis was optimal for primary root elongation, while in rice it was higher than optimal. These differences may explain the species-dependent development of root systems.
Reference panel-guided super-resolution inference of Hi-C data
Authors: Zhang Yanlin , Blanchette Mathieu 
Published: June 2023

Abstract

Motivation
Accurately assessing contacts between DNA fragments inside the nucleus with Hi-C experiment is crucial for understanding the role of 3D genome organization in gene regulation. This challenging task is due in part to the high sequencing depth of Hi-C libraries required to support high-resolution analyses. Most existing Hi-C data are collected with limited sequencing coverage, leading to poor chromatin interaction frequency estimation. Current computational approaches to enhance Hi-C signals focus on the analysis of individual Hi-C datasets of interest, without taking advantage of the facts that (i) several hundred Hi-C contact maps are publicly available and (ii) the vast majority of local spatial organizations are conserved across multiple cell types.

Results
Here, we present RefHiC-SR, an attention-based deep learning framework that uses a reference panel of Hi-C datasets to facilitate the enhancement of Hi-C data resolution of a given study sample. We compare RefHiC-SR against tools that do not use reference samples and find that RefHiC-SR outperforms other programs across different cell types, and sequencing depths. It also enables high-accuracy mapping of structures such as loops and topologically associating domains.

Availability and implementation
https://github.com/BlanchetteLab/RefHiC.
Ghost Criminology: A Framework for the Discipline’s Spectral Turn
Authors: Fiddler Michael , Linnemann Travis , Kindynis Theo 
Published: June 2023

Abstract
Drawing upon recent criminological scholarship examining spectrality, as well as Jacques Derrida’s notion of hauntology, this article sets out a framework to explore harms experienced as ‘out of joint’. We propose a new sub-discipline of ‘ghost criminology’ as a means to explore and reckon with these afterlives. We identify three strands of the (in)visible, the (in)corporeal and dead space with which to capture phenomena hovering between presence and absence. In doing so, we provide examples of justice being achieved within this sense of time being ‘off its hinges’. A ‘ghost criminology’ provides a means of listening to the voices of the discipline’s dead, as well as the ghosts of its future.
O009 Differential attainment at the Intercollegiate Membership of the Royal Colleges of Surgeons (MRCS) examination according to gender, ethnicity, age and socioeconomic factors
Authors: Ellis R , Brennan PA , Lee AJ , Scrimgeour DSG , Cleland J 
Published: June 2023

Abstract

Introduction
The lack of diversity at senior and leadership positions in surgery highlights concerns that some groups of individuals face barriers to progression in surgical training. This study aimed to investigate whether there is group-level differential attainment (DA) at MRCS, a mandatory postgraduate examination for UK surgical trainees.

Methods
All UK graduates attempting MRCS Part A (n=5,780) and Part B (n=2,600) between 2013–2019 were identified using the UK Medical Education Database. Univariate associations with MRCS performance were identified using chi-squared tests. Multiple logistic regression identified independent predictors of first-attempt MRCS success, adjusted for medical school performance.

Results
We found statistically significant differences in MRCS pass rates according to gender, ethnicity, graduate status, childhood socioeconomic status and educational background (all P&lt;0.05). After adjusting for prior academic attainment, being a non-graduate (odds ratio [OR] 1.98, 95%CI 1.44–2.74) or male (OR 2.34, 95%CI 1.87–2.92) were independent predictors of MRCS Part A success. Being a non-graduate (OR 1.77, 95%CI 1.15–2.71) or having attended a fee-paying school (OR 1.51, 95%CI 1.08–2.10) were independent predictors of MRCS Part B success. Black candidates were significantly less likely to pass MRCS Part B at their first attempt (OR 0.41, 95%CI 0.18–0.92) as were Asian candidates (OR 0.49, 95%CI 0.35–0.69 for) in comparison to White candidates.

Conclusion
We found significant DA at MRCS that cannot be attributed to learner deficit. Royal Colleges and training institutions now need to identify and address the causes of these attainment differences to facilitate equitable career progression for surgical trainees.

Take-home message
We found significant DA at MRCS that cannot be attributed to learner deficit. Royal Colleges and training institutions now need to identify and address the causes of these attainment differences to facilitate equitable career progression for surgical trainees.
O039 Evaluating the influence of risk factors on the development of defaecatory problems: a Delphi study
Authors: Chaichanavichkij P , Hartmann M , McLachlan S , Scott SM , Fenton N , Knowles CH 
Published: June 2023

Abstract

Introduction
The influence of risk factors on the development of defaecatory problems is difficult to ascertain due to heterogeneity of published evidence. An understanding of the impact of these risk factors is important in selecting targets for disease prevention.

Methods
Risk factors for chronic constipation and faecal incontinence were anonymously evaluated using a Delphi technique with 50 experts from the Pelvic Floor Society between May and December 2021. Each risk factor was rated as an independent risk factor, a co-factor, or not a risk factor. The importance of an independent risk factor was rated between 1 (not important) and 10 (critically important) and the mean (± standard deviation) was calculated.

Result
38 risk factors for chronic constipation were evaluated, of which 18 were classed as independent and 16 as co-factors. Opioid analgesia (7.87 ± 2.05), eating disorders (7.80 ± 1.72), and history of abuse (7.70 ± 1.89) were classed as most important. Female gender (6.60 ± 2.02) was an independent risk factor but increasing age was a co-factor. 33 risk factors for faecal incontinence were evaluated, of which 20 were classed as independent and 8 as co-factors. Third- or fourth-degree tear (8.88 ± 1.57), instrumental delivery (8.47 ± 1.58), and grand-multiparity (8.00 ± 1.63) were classed as most important. Increasing age (7.41 ± 2.14) and female gender (7.58 ± 2.05) were independent risk factors.

Conclusion
Several risk factors for chronic constipation and faecal incontinence could be determined by Delphi approach. These factors will feed into Bayesian models of disease development.

Take-home message
Important risk factors for chronic constipation and faecal incontinence could be determined by Delphi approach.
544 Improvement of Skin Quality in Patients Undergoing Nasal Fat Grafting: A Systematic Review Protocol
Authors: Neves P , Ramjeeawon A , Quong W , Bulstrode N , Pitombo V 
Published: June 2023

Abstract

Aim
Primary aims: to understand the effects of adipose tissue or its derivatives on nasal skin quality, and whether lipofilling may improve nasal skin quality. Secondary aims: to understand whether post-lipofilling nasal skin improvement can be observed and quantified in both good quality and scarred nasal skin, to investigate if changes are related to the differing levels of preoperative skin quality (unscarred vs scarred), to review outcomes for different types of fat harvesting and processing techniques prior to grafting and identify complications following nasal lipofilling.

Method
A search strategy will be developed to search MEDLINE, Embase, Web of Science, and the Cochrane Central Register of Controlled Trials, followed by a grey literature search, to identify relevant publications. Two researchers will review titles, abstracts, and full-texts of the resulting publications, against the inclusion and exclusion criteria (a third researcher will decide where there are disagreements), as part of an independent two-person three-stage assessment strategy. Non-English/ Portuguese/ French articles, abstracts, letters, editorials, and expert opinions will be excluded.

Results
This systematic review has been registered on the PROSPERO International Prospective Register of Systematic Reviews (CRD 42021290198).

Conclusion
Adipose tissue has regenerative potential; it has been suggested there may be improvement in nasal skin quality following fat tissue grafting into the nasal region. Primary and secondary rhinoplasty procedures are being increasingly performed and multiple procedures may result in nasal skin damage, which should be addressed during secondary reconstruction. Understanding whether lipofilling improves nasal skin quality in nasal reconstruction could support its use in appropriate patients undergoing rhinoplasty.
Single-cell profiling reveals age-associated immunity in atherosclerosis
Authors: Smit Virginia , de Mol Jill , Schaftenaar Frank H , Depuydt Marie A C , Postel Rimke J , Smeets Diede , Verheijen Fenne W M , Bogers Laurens , van Duijn Janine , Verwilligen Robin A F , Grievink Hendrika W , Bernabé Kleijn Mireia N A , van Ingen Eva , de Jong Maaike J M , Goncalves Lauren , Peeters Judith A H M , Smeets Harm J , Wezel Anouk , Polansky Julia K , de Winther Menno P J , Binder Christoph J , Tsiantoulas Dimitrios , Bot Ilze , Kuiper Johan , Foks Amanda C 
Published: June 2023

Abstract

Aims
Aging is a dominant driver of atherosclerosis and induces a series of immunological alterations, called immunosenescence. Given the demographic shift towards elderly, elucidating the unknown impact of aging on the immunological landscape in atherosclerosis is highly relevant. While the young Western diet-fed Ldlr-deficient (Ldlr−/−) mouse is a widely used model to study atherosclerosis, it does not reflect the gradual plaque progression in the context of an aging immune system as occurs in humans.

Methods and results
Here, we show that aging promotes advanced atherosclerosis in chow diet-fed Ldlr−/− mice, with increased incidence of calcification and cholesterol crystals. We observed systemic immunosenescence, including myeloid skewing and T-cells with more extreme effector phenotypes. Using a combination of single-cell RNA-sequencing and flow cytometry on aortic leucocytes of young vs. aged Ldlr−/− mice, we show age-related shifts in expression of genes involved in atherogenic processes, such as cellular activation and cytokine production. We identified age-associated cells with pro-inflammatory features, including GzmK+CD8+ T-cells and previously in atherosclerosis undefined CD11b+CD11c+T-bet+ age-associated B-cells (ABCs). ABCs of Ldlr−/− mice showed high expression of genes involved in plasma cell differentiation, co-stimulation, and antigen presentation. In vitro studies supported that ABCs are highly potent antigen-presenting cells. In cardiovascular disease patients, we confirmed the presence of these age-associated T- and B-cells in atherosclerotic plaques and blood.

Conclusions
Collectively, we are the first to provide comprehensive profiling of aged immunity in atherosclerotic mice and reveal the emergence of age-associated T- and B-cells in the atherosclerotic aorta. Further research into age-associated immunity may contribute to novel diagnostic and therapeutic tools to combat cardiovascular disease.
Tissue-specific differences in the assembly of mitochondrial Complex I are revealed by a novel ENU mutation in ECSIT
Authors: Nicol Thomas , Falcone Sara , Blease Andrew , Vikhe Pratik , Civiletto Gabriele , Omairi Saleh Salman , Viscomi Carlo , Patel Ketan , Potter Paul K 
Published: June 2023

Abstract

Aims
Mitochondrial Complex I assembly (MCIA) is a multi-step process that necessitates the involvement of a variety of assembly factors and chaperones to ensure that the final active enzyme is correctly assembled. The role of the assembly factor evolutionarily conserved signalling intermediate in the toll (ECSIT) pathway was studied across various murine tissues to determine its role in this process and how this varied between tissues of varying energetic demands. We hypothesized that many of the known functions of ECSIT were unhindered by the introduction of an ENU-induced mutation, while its role in Complex I assembly was affected on a tissue-specific basis.

Methods and results
Here, we describe a mutation in the MCIA factor ECSIT that reveals tissue-specific requirements for ECSIT in Complex I assembly. MCIA is a multi-step process dependent on assembly factors that organize and arrange the individual subunits, allowing for their incorporation into the complete enzyme complex. We have identified an ENU-induced mutation in ECSIT (N209I) that exhibits a profound effect on Complex I component expression and assembly in heart tissue, resulting in hypertrophic cardiomyopathy in the absence of other phenotypes. The dysfunction of Complex I appears to be cardiac specific, leading to a loss of mitochondrial output as measured by Seahorse extracellular flux and various biochemical assays in heart tissue, while mitochondria from other tissues were unaffected.

Conclusions
These data suggest that the mechanisms underlying Complex I assembly and activity may have tissue-specific elements tailored to the specific demands of cells and tissues. Our data suggest that tissues with high-energy demands, such as the heart, may utilize assembly factors in different ways to low-energy tissues in order to improve mitochondrial output. These data have implications for the diagnosis and treatment of various disorders of mitochondrial function as well as cardiac hypertrophy with no identifiable underlying genetic cause.
Evolution of interventional endoscopic ultrasound
Authors: Radlinski Mark J , Strand Daniel S , Shami Vanessa M 
Published: June 2023

Abstract
Endoscopic ultrasound (EUS) has become an indispensable modality for the assessment of the gastrointestinal tract and adjacent structures since its origin in the 1980s. Following the development of the linear echoendoscope, EUS has evolved from a purely diagnostic modality to a sophisticated tool for intervention, with numerous luminal, pancreaticobiliary, and hepatic applications. Broadly, these applications may be subdivided into three categories: transluminal drainage or access procedures, injection therapy, and EUS-guided liver interventions. Transluminal drainage or access procedures include management of pancreatic fluid collection, EUS-guided biliary drainage, EUS-guided bile duct drainage, EUS-guided pancreatic duct drainage, and enteral anastomosis formation. Injection therapies include therapeutic EUS-guided injections for management of malignancies accessible by EUS. EUS-guided liver applications include EUS-guided liver biopsy, EUS-guided portal pressure gradient measurement, and EUS-guided vascular therapies. In this review, we discuss the origins of each of these EUS applications, evolution of techniques leading to the current status, and future directions of EUS-guided interventional therapy.
Transfer Trauma Among Nursing Home Residents: Development of a Composite Measure
Authors: Montoya Ana , Park Pil , Bynum Julie , Chang Chiang-Hua 
Published: June 2023

Abstract

Background and Objectives
Nursing home (NH)-to-NH transfers place NH residents at risk for developing transfer trauma. We aimed to develop a composite measure of transfer trauma and apply it among those transferring before and during the pandemic.

Research Design and Methods
Cross-sectional cohort analysis of long-stay NH residents with a NH-to-NH transfer. Minimum Data Set data (2018–2020) were used to create the cohorts. A composite measure of transfer trauma was developed (2018 cohort) and applied to the 2019 and 2020 cohorts. We analyzed resident characteristics and conducted logistic regression analyses to compare rates of transfer trauma between periods.

Results
In 2018, 794 residents were transferred; 242 (30.5%) met the criteria for transfer trauma. In the 2019 and 2020, 750 residents (2019) and 795 (2020) were transferred. In 2019 cohort, 30.7% met the criteria for transfer trauma, and 21.9% in 2020 cohort. During the pandemic, a higher proportion of transferred residents left the facility before the first quarterly assessment. Among residents who stayed in NH for their quarterly assessment, after adjusting for demographic characteristics, residents in the 2020 cohort were less likely to experience transfer trauma than those in the 2019 cohort (adjusted odds ratio [AOR] = 0.64, 95% confidence interval [CI]: 0.51, 0.81). However, residents in 2020 cohort were two times more likely to die (AOR = 1.94, 95% CI: 1.15, 3.26) and 3 times more likely to discharge within 90 days after transfer (AOR = 2.86, 95% CI: 2.30, 3.56) compared with those in 2019 cohort.

Discussion and Implications
These findings highlight how common transfer trauma is after NH-to-NH transfer and the need for further research to mitigate negative outcomes associated with the transfer in this vulnerable population.
Characterization of an optrA-harbouring unconventional circularizable structure located on a novel ICESa2603 family-like integrative and conjugative element ICESsuHN38 in Streptococcus suis
Authors: Yang Qin , Zhu Yao , Schwarz Stefan , Zhang Wanjiang , Wang Xiumei 
Published: June 2023

Abstract

Objectives
To identify the novel genetic elements involved in the horizontal transfer of the oxazolidinone/phenicol resistance gene optrA in Streptococcus suis.

Methods
Whole-genome DNA of the optrA-positive isolate S. suis HN38 was subjected to WGS via both Illumina HiSeq and Oxford Nanopore platforms. MICs of several antimicrobial agents (erythromycin, linezolid, chloramphenicol, florfenicol, rifampicin and tetracycline) were determined by broth microdilution. PCR assays were performed to identify the circular forms of the novel integrative and conjugative element (ICE) ICESsuHN38, but also the unconventional circularizable structure (UCS) excised from this ICE. The transferability of ICESsuHN38 was evaluated by conjugation assays.

Results
S. suis isolate HN38 harboured the oxazolidinone/phenicol resistance gene optrA. The optrA gene was flanked by two copies of erm(B) genes in the same orientation, located on a novel ICESa2603 family-like ICE, designated ICESsuHN38. PCR assays revealed that a novel UCS carrying the optrA and one copy of erm(B) could be excised from ICESsuHN38. Conjugation assays confirmed that ICESsuHN38 was able to successfully transfer into the recipient strain S. suis BAA.

Conclusions
In this work, a novel optrA-carrying mobile genetic element, a UCS, was identified in S. suis. The optrA gene was flanked by copies of erm(B) and its location on the novel ICESsuHN38 will aid its horizontal dissemination.