bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeographical patterns match the floristic subdivisions: the diversification history of a widespread herb in subtropical China
Authors: Sun Zhixia , Yang Lihua , Kong Hanghui , Kang Ming , Wang Jing 
Published: September 2024

Abstract

Background and Aims
Subtropical China is dominated by evergreen broad-leaved forests (EBLFs) and is acknowledged as a critical region for its high floristic richness and endemism. Our understanding of the evolutionary mechanisms of such global biodiversity hotspots comes almost exclusively from long-lived tree species. Herbaceous plants represent critical biodiversity components in forests, but the diversification history of understorey herbs in subtropical EBLFs remain poorly understood. Here, we investigated the phylogeographical patterns and demographic history of Oreocharis auricula, a widespread perennial herb endemic to the EBLFs of subtropical China.

Methods
Both chloroplast DNA sequences and single-copy nuclear genes were used to investigate the genetic variation among 657 individuals from 68 populations. Evidence from molecular dating, demographic history construction and species distribution modelling was also combined to infer the phylogeography and evolutionary history of O. auricula.

Key Results
Strong phylogeographical signals have been congruently observed using nuclear and plastid DNA markers, with the diversification patterns generally consistent with the recognized floristic subdivisions of subtropical China. Notably, we revealed an important phylogeographical barrier along the Nanling mountain range, which is also around a climatic transition at 24–26°N latitude in subtropical China, separating the south monsoon subtropical EBLFs from the mid-subtropical EBLFs. Demographic expansion and significant niche divergence were detected among the extant lineages, which may have diverged during the early Pleistocene.

Conclusions
The inherent characteristics of understorey herbs with limited dispersal and short generation time intensify the genetic divergence response of O. auricula to abiotic forces, contributing to the profound phylogeographical imprints of mountains and climate in such herbaceous flora. To further substantiate the generality of the identified patterns, it is paramount to extend phylogeographical investigations to other understorey herbaceous taxa in subtropical China. These results have expanded our understanding of the diversification processes of subtropical forests in China.
The impact of breast cancer radiation therapy exposure on the prevalence of breast arterial calcification
Authors: Ramin Seth K , Rubino Jessica , Austin-Strohbehn Judith M , Ali Thara , Jarvis Lesley , diFlorio-Alexander Roberta M 
Published: September 2024

Abstract

Objectives
Mammographic breast arterial calcification (BAC) is an emerging imaging biomarker of cardiovascular disease (CVD) risk in women. The purpose of this study was to assess if breast radiation therapy (RT) exposure impacts the screening utility of this imaging biomarker.

Methods
This cross-sectional study included women ages 40-75 years who underwent index screening mammography between January 1, 2011 and December 31, 2012. Chart review was performed to extract data on the breast cancer RT exposure and CVD risk factors. Mammograms were reviewed for the presence of BAC. Multivariate logistic regression was used to examine breast RT exposure and BAC, with adjustment for age, body mass index, smoking status, hypertension, Type 2 diabetes, statin medication use, and antihypertensive medication use.

Results
Of the 1155 women included in this analysis, 222 (19.2%) had mammographic evidence of BAC, 122 (10.6%) had a history of RT exposure, and 39 (32%) women with RT exposure had mammographic BAC. Women with breast RT exposure had higher odds of BAC compared to women without (odds ratio: 2.18, 95% CI: 1.43, 3.28; P-value = .0008). However, this association became non-significant after multivariable adjustment, with the maximally adjusted model demonstrating an odds ratio of 1.52 (95% CI: 0.95, 2.40; P-value = .07).

Conclusions
Our findings suggest that breast RT exposure does not impact the prevalence of mammographic BAC. Therefore, it does not affect its utility as an imaging biomarker of CVD risk.

Advances in knowledge
This is the first observational study addressing the knowledge gap pertaining to the influence of breast RT exposure on BAC.
Cardiovascular and diabetes outcomes among patients with obesity and type 2 diabetes after metabolic bariatric surgery or glucagon-like peptide 1 receptor agonist treatment
Authors: Stenberg Erik , Ottosson Johan , Cao Yang , Sundbom Magnus , Näslund Erik 
Published: September 2024

Abstract

Background
With the increasing prevalence of obesity and type 2 diabetes, the availability of different treatment options remains essential. Studies comparing the outcomes of glucagon-like peptide 1 receptor agonists with those of metabolic bariatric surgery in patients with type 2 diabetes and obesity are lacking.

Methods
Using propensity score matching, based on data from several nationwide clinical registries, patients who underwent primary metabolic bariatric surgery (Roux-en-Y gastric bypass or sleeve gastrectomy) were matched with patients who received glucagon-like peptide 1 receptor agonists. Outcome measures included the occurrence of major cardiovascular events, microvascular complications, and potential side effects (alcohol/substance abuse, self-harm, and fractures).

Results
Over a mean follow-up of 7 years, major cardiovascular events occurred in 191 of 2039 patients (cumulative incidence 14.5%) in the surgery group compared with 247 of 2039 patients (19.6%) in the glucagon-like peptide 1 receptor agonist group (HR 0.75 (95% c.i. 0.62 to 0.91), P = 0.003). Patients in the surgery group had lower haemoglobin A1c values 5 years after treatment (mean difference 9.82 (95% c.i. 8.51 to 11.14) mmol/mol, P &lt; 0.001) and fewer microvascular complications (retinopathy HR 0.88 (95% c.i. 0.79 to 0.99), P = 0.039; nephropathy HR 0.72 (95% c.i. 0.66 to 0.80), P &lt; 0.001; and neuropathy or leg ulcers HR 0.82 (95% c.i. 0.74 to 0.92), P &lt; 0.001), but a higher risk of alcohol/substance abuse (HR 2.56 (95% c.i. 1.87 to 3.50), P &lt; 0.001), self-harm (HR 1.41 (95% c.i. 1.17 to 1.71), P &lt; 0.001), and fractures (HR 1.86 (95% c.i. 1.11 to 3.12), P = 0.019).

Conclusion
Compared with glucagon-like peptide 1 receptor agonist treatment, metabolic bariatric surgery is associated with superior metabolic outcomes and a lower risk of major cardiovascular events in patients with type 2 diabetes and obesity, but a higher risk of alcohol/substance abuse, self-harm, and fractures.
Global Globin Network and adopting genomic variant database requirements for thalassemia
Authors: Halim-Fikri Hashim , Zulkipli Ninie Nadia , Alauddin Hafiza , Bento Celeste , Lederer Carsten W , Kountouris Petros , Kleanthous Marina , Hernaningsih Yetti , Thong Meow-Keong , Mahmood Muhammad Hamdi , Mohd Yasin Norafiza , Esa Ezalia , Elion Jacques , Coviello Domenico , Raja-Sabudin Raja-Zahratul-Azma , El-Kamah Ghada , Burn John , Mohd Yusoff Narazah , Ramesar Raj , Zilfalil Bin Alwi 
Published: September 2024

Abstract
Thalassemia is one of the most prevalent monogenic disorders in low- and middle-income countries (LMICs). There are an estimated 270 million carriers of hemoglobinopathies (abnormal hemoglobins and/or thalassemia) worldwide, necessitating global methods and solutions for effective and optimal therapy. LMICs are disproportionately impacted by thalassemia, and due to disparities in genomics awareness and diagnostic resources, certain LMICs lag behind high-income countries (HICs). This spurred the establishment of the Global Globin Network (GGN) in 2015 at UNESCO, Paris, as a project-wide endeavor within the Human Variome Project (HVP). Primarily aimed at enhancing thalassemia clinical services, research, and genomic diagnostic capabilities with a focus on LMIC needs, GGN aims to foster data collection in a shared database by all affected nations, thus improving data sharing and thalassemia management. In this paper, we propose a minimum requirement for establishing a genomic database in thalassemia based on the HVP database guidelines. We suggest using an existing platform recommended by HVP, the Leiden Open Variation Database (LOVD) (https://www.lovd.nl/). Adoption of our proposed criteria will assist in improving or supplementing the existing databases, allowing for better-quality services for individuals with thalassemia.
Database URL: https://www.lovd.nl/
The emerging role of SARS-CoV-2 nonstructural protein 1 (nsp1) in epigenetic regulation of host gene expression
Authors: Ivanov Konstantin I , Yang Haibin , Sun Ruixue , Li Chunmei , Guo Deyin 
Published: September 2024

Abstract
Infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes widespread changes in epigenetic modifications and chromatin architecture in the host cell. Recent evidence suggests that SARS-CoV-2 nonstructural protein 1 (nsp1) plays an important role in driving these changes. Previously thought to be primarily involved in host translation shutoff and cellular mRNA degradation, nsp1 has now been shown to be a truly multifunctional protein that affects host gene expression at multiple levels. The functions of nsp1 are surprisingly diverse and include not only the downregulation of cellular mRNA translation and stability, but also the inhibition of mRNA export from the nucleus, the suppression of host immune signaling, and, most recently, the epigenetic regulation of host gene expression. In this review, we first summarize the current knowledge on SARS-CoV-2-induced changes in epigenetic modifications and chromatin structure. We then focus on the role of nsp1 in epigenetic reprogramming, with a particular emphasis on the silencing of immune-related genes. Finally, we discuss potential molecular mechanisms underlying the epigenetic functions of nsp1 based on evidence from SARS-CoV-2 interactome studies.
Applying Ratio-of-Means Estimation for Annualized Components of Volume Change in Forest Resource Monitoring
Authors: Westfall James A , Nelson Mark D , Edgar Christopher B 
Published: September 2024

Abstract
Forest inventory estimates of annualized net growth, removals, and mortality provide a standardized metric for a wide range of management and policy assessments. Commonly, plot-level annualized values are determined by dividing the periodic change by the length of the time interval. Subsequent estimation of means constitutes a mean-of-ratios (MOR) estimation approach. However, due to potential bias concerns for the MOR estimator, the ratio-of-means (ROM) estimator is generally preferred by forestry practitioners. National forest inventory data from six states in the United States were used to compare MOR and ROM annualized change estimation. Generally, MOR and ROM performed similarly when there was little variation among plot measurement intervals. Differences between MOR and ROM increased as variability among measurement intervals increased, with the largest observed differences being in the 3%–4% range. The ROM estimator also resulted in more precise estimates than MOR, although in many cases the differences were trivial. ROM estimation can be negatively affected if the mean of the measurement intervals assigned to unvisited nonforest plots is incongruent with the mean for forested field–visited plots. Nonetheless, if this complication is not present or can be ameliorated, the ROM estimator appears to perform better than MOR across various populations.
Study Implications: Forest inventory volume change results are usually reported on a per-year basis to make them more interpretable by data users. This study compared the use of the typical mean-of-ratios (MOR) approach with an alternative ratio-of-means (ROM) concept. In a simulation study that examined six different populations of forest inventory plots, the ROM method generally had smaller bias and uncertainty statistics than the MOR approach. Thus, the ROM estimation offers forest inventory practitioners a more robust method for calculating annualized change statistics. The use of accurate estimations to inform management and policy decisions is critical to effective stewardship of forest resources.
The Currency Constraint: Explaining the Selective Enforcement of US Financial Sanctions
Authors: Bapat Navin R , Early Bryan R , Grauvogel Julia , Kleinberg Katja B 
Published: September 2024

Abstract
Economic sanctions remain one of the most widely used foreign policy tools. At the same time, their enforcement is often incomplete and selective. If sender states are concerned about sanctions effectiveness, variation in enforcement is counterproductive. We argue that sender states face a trade-off between effective coercion in the present and the ability to use coercion in the future. We develop a formal model to explore the mixed incentives of senders such as the United States in enforcing their financial sanctions against banks. Using data on US enforcement actions taken in support of the Iranian sanctions regime from 2003 to 2014 and three illustrative case examples, we evaluate the hypothesis that sanctions enforcement should be greater when the position of the US dollar is strong relative to alternative settlement mechanisms. Our findings support this contention.
Assessing Mechanisms of Potential Local Adaptation Through a Seascape Genomic Approach in a Marine Gastropod, Littoraria flava
Authors: Cortez Thainá , Sonoda Gabriel G , Santos Camilla A , Andrade Sónia Cristina da Silva 
Published: September 2024

Abstract
Understanding the combined effects of environmental heterogeneity and evolutionary processes on marine populations is a primary goal of seascape genomic approaches. Here, we utilized genomic approaches to identify local adaptation signatures in Littoraria flava, a widely distributed marine gastropod in the tropical West Atlantic population. We also performed molecular evolution analyses to investigate potential selective signals across the genome. After obtaining 6,298 and 16,137 single nucleotide polymorphisms derived from genotyping-by-sequencing and RNA sequencing, respectively, 69 from genotyping-by-sequencing (85 specimens) and four from RNA sequencing (40 specimens) candidate single nucleotide polymorphisms were selected and further evaluated. The correlation analyses support different evolutionary pressures over transcribed and non-transcribed regions. Thus, single nucleotide polymorphisms within transcribed regions could account for the genotypic and possibly phenotypic divergences in periwinkles. Our molecular evolution tests based on synonymous and non-synonymous ratio (kN/kS) showed that genotype divergences containing putative adaptive single nucleotide polymorphisms arose mainly from synonymous and/or UTR substitutions rather than polymorphic proteins. The distribution of genotypes across different localities seems to be influenced by marine currents, pH, and temperature variations, suggesting that these factors may impact the species dispersion. The combination of RNA sequencing and genotyping-by-sequencing derived datasets provides a deeper understanding of the molecular mechanisms underlying selective forces responses on distinct genomic regions and could guide further investigations on seascape genomics for non-model species.
Later-Life Creativity and Successful Aging in Neoliberal Agendas
Authors: Stončikaitė Ieva 
Published: September 2024

Abstract

Background and Objectives
Although the model of successful aging is already well discussed and has received considerable critical responses, its intersection with the growing enthusiasm for creative engagement among older adults needs further exploration. This article contributes to the growing literature on later-life creativity by examining its relationship with the discourse of successful aging.

Research Design and Methods
The study employs critical humanities-based perspectives and the literature on later life to address creativity in older age within contemporary neoliberal imperatives.

Results
Although successful aging is an antithesis to the narrative of decline, it often fails to capture alternative meanings of aging and the creative engagement in later life. The commercialization and commodification of creativity often function to discipline individuals toward a culture of productivity, optimization, and innovation. However, many older individuals challenge these notions as they create their own models of aging well and authentically that do not align with the ideals of successful aging.

Discussion and Implications
Reductionist, individualistic, and capital-driven understandings of later-life creativity can be broadened by employing critical interdisciplinary approaches, which also help rethink the current meanings of old age and aging. The article will be of interest to scholars, policymakers, artists, and practitioners in gerontological scholarship and the humanities.
Haplotype-resolved nonaploid genome provides insights into in vitro flowering in bamboos
Authors: Wang Yu-Jiao , Guo Cen , Zhao Lei , Mao Ling , Hu Xiang-Zhou , Yang Yi-Zhou , Qian Ke-Cheng , Ma Peng-Fei , Guo Zhen-Hua , Li De-Zhu 
Published: September 2024

Abstract
Woody bamboos (Bambusoideae) are renowned for its polyploidy and rare flowering. Bambusa odashimae is one of the bamboo species with the highest chromosome count (104) in the subfamily and has the highest heterozygosity of all sequenced bamboo genomes so far. Compared with other bamboo species, it can efficiently utilize exogenous hormones to regulate in vitro flowering, providing valuable insights into the hormonal regulation of bamboo flowering. Here, we generated the haplotype-resolved genome assembly of B. odashimae, despite the complexity and high chromosome number, supplemented by thirty-three transcriptomes from eleven developmental periods using a tissue culture system. The assembled genome can be divided into Haplotype I, Haplotype II, and Haplotype III, each containing A, B, and C subgenomes. Haplotype I may be derived from Dendrocalamus whereas Haplotypes II and III are closely related to Bambusa, indicating that B. odashimae has an origin involving both intergeneric and interspecific hybridizations. The high heterozygosity renders the possibility to detect abundant allele-specific expression (ASE), with ASE genes enriched in cytokinin-related pathways, likely associated with efficient cytokinin-promoted flowering. Notably, we found that the CONSTANS (CO) genes were potentially key regulators of in vitro flowering in B. odashimae. Overall, based on the in vitro system combined with a high-quality reference genome, our study provides critical insights into the origin of this nonaploid bamboo and links hybridization and in vitro flowering in bamboos.
TOR balances plant growth and cold tolerance by orchestrating amino acid-derived metabolism in tomato
Authors: Li Zihao , Yang Lin , Wu Yanni , Zhang Ran , Yu Sen , Fu Liwen 
Published: September 2024

Abstract
The target of rapamycin (TOR) kinase is a central signaling hub that plays a crucial role in precisely orchestrating plant growth, development, and stress responses. This suggests that TOR is intricately involved in maintaining the balance between plant growth and stress responses. Nevertheless, despite the observed effects, the specific mechanisms through which TOR operates in these processes remain obscure. In this study, we investigated how the tomato (Solanum lycopersicum) TOR (SlTOR) affects plant growth and cold responses. We demonstrated that SlTOR inhibition transcriptionally primes cold stress responses, consequently enhancing tomato cold tolerance. A widely targeted metabolomics analysis revealed the disruption of amino acid metabolism homeostasis under cold stress upon SlTOR inhibition, which led to the accumulation of two important cryoprotective metabolites: salicylic acid (SA) and putrescine (Put). Next, we discovered SlPGH1 (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE 1) as a direct substrate of SlTOR. Inhibiting SlTOR led to increased SlCBF1 (C-REPEAT-BINDING FACTOR 1) expression via SlPGH1, potentially triggering the activation of cold-responsive genes and subsequent metabolic alterations. Our study provides a mechanistic framework that elucidates how SlTOR modulates amino acid-related metabolism to enhance tomato cold tolerance, which sheds light on the complex interplay between growth and stress responses orchestrated by TOR.
Induction of Endoscopic Response, Remission, and Ulcer-Free Endoscopy With Upadacitinib Is Associated With Improved Clinical Outcomes and Quality of Life in Patients With Crohn’s Disease
Authors: Panés Julian , Louis Edouard , Bossuyt Peter , Joshi Namita , Lee Wan-Ju , Lacerda Ana P , Kligys Kristina , Xuan Si , Shukla Nidhi , Loftus Edward V 
Published: September 2024

Abstract

Background
We evaluated the association of achieving endoscopic outcomes at week 12 of induction with improvements in clinical outcomes and quality of life (QoL) at week 52 of maintenance in patients with moderately to severely active Crohn’s disease (CD) treated with upadacitinib (UPA).

Methods
This post hoc analysis evaluated data from 2 phase 3 induction trials (NCT03345836 and NCT03345849) and 1 maintenance (NCT03345823) trial. Clinical responders to 12-week induction therapy with UPA who also received 52-week maintenance treatment with UPA were included. Endoscopic response, remission, healing, and ulcer-free endoscopy were assessed at week 12. Meaningful improvements in clinical and QoL outcomes were evaluated at week 52.

Results
A significantly greater proportion of patients who achieved an endoscopic response at the end of induction, compared with patients who did not, attained Crohn’s Disease Activity Index (CDAI) remission (52.0% vs 34.6%; P ≤ .01), corticosteroid-free CDAI remission (50.0% vs 30.9%), Inflammatory Bowel Disease Questionnaire remission (52.6% vs 30.3%), and meaningful improvements in Functional Assessment of Chronic Illness Therapy—Fatigue response (46.7% vs 25.9%), overall work impairment (47.1% vs 26.5%), and daily activity impairment (53.3% vs 34.1%) (all P &lt; .05) at week 52. Similar findings were observed for patients who achieved endoscopic remission, endoscopic healing, and ulcer-free endoscopy at the end of induction vs those who did not.

Conclusions
Early improvement in endoscopic outcomes after UPA induction treatment was associated with long-term meaningful improvements in clinical outcomes and QoL in patients with CD.

Clinical Registration number
U-EXCEED induction trial (NCT03345836), U-EXCEL induction trial (NCT03345849), and U-ENDURE maintenance trial (NCT03345823).