bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hybridization and divergent climatic preferences drive divergence of two allopatric Gentiana species on the Qinghai–Tibet Plateau
Authors: Fu Peng-Cheng , Twyford Alex D , Hao Yu-Tong , Zhang Yue , Chen Shi-Long , Sun Shan-Shan 
Published: November 2023

Abstract

Background and Aims
Exploring how species diverge is vital for understanding the drivers of speciation. Factors such as geographical separation and ecological selection, hybridization, polyploidization and shifts in mating system are all major mechanisms of plant speciation, but their contributions to divergence are rarely well understood. Here we test these mechanisms in two plant species, Gentiana lhassica and G. hoae, with the goal of understanding recent allopatric species divergence on the Qinghai–Tibet Plateau (QTP).

Methods
We performed Bayesian clustering, phylogenetic analysis and estimates of hybridization using 561 302 nuclear genomic single nucleotide polymorphisms (SNPs). We performed redundancy analysis, and identified and annotated species-specific SNPs (ssSNPs) to explore the association between climatic preference and genetic divergence. We also estimated genome sizes using flow cytometry to test for overlooked polyploidy.

Key Results
Genomic evidence confirms that G. lhassica and G. hoae are closely related but distinct species, while genome size estimates show divergence occurred without polyploidy. Gentiana hoae has significantly higher average FIS values than G. lhassica. Population clustering based on genomic SNPs shows no signature of recent hybridization, but each species is characterized by a distinct history of hybridization with congeners that has shaped genome-wide variation. Gentiana lhassica has captured the chloroplast and experienced introgression with a divergent gentian species, while G. hoae has experienced recurrent hybridization with related taxa. Species distribution modelling suggested range overlap in the Last Interglacial Period, while redundancy analysis showed that precipitation and temperature are the major climatic differences explaining the separation of the species. The species differ by 2993 ssSNPs, with genome annotation showing missense variants in genes involved in stress resistance.

Conclusions
This study suggests that the distinctiveness of these species on the QTP is driven by a combination of hybridization, geographical isolation, mating system differences and evolution of divergent climatic preferences.
BELMM: Bayesian model selection and random walk smoothing in time-series clustering
Authors: Sarala Olli , Pyhäjärvi Tanja , Sillanpää Mikko J 
Published: November 2023

AbstractMotivationDue to advances in measuring technology, many new phenotype, gene expression, and other omics time-course datasets are now commonly available. Cluster analysis may provide useful information about the structure of such data.ResultsIn this work, we propose BELMM (Bayesian Estimation of Latent Mixture Models): a flexible framework for analysing, clustering, and modelling time-series data in a Bayesian setting. The framework is built on mixture modelling: first, the mean curves of the mixture components are assumed to follow random walk smoothing priors. Second, we choose the most plausible model and the number of mixture components using the Reversible-jump Markov chain Monte Carlo. Last, we assign the individual time series into clusters based on the similarity to the cluster-specific trend curves determined by the latent random walk processes. We demonstrate the use of fast and slow implementations of our approach on both simulated and real time-series data using widely available software R, Stan, and CU-MSDSp.Availability and implementationThe French mortality dataset is available at http://www.mortality.org, the Drosophila melanogaster embryogenesis gene expression data at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121160. Details on our simulated datasets are available in the Supplementary Material, and R scripts and a detailed tutorial on GitHub at https://github.com/ollisa/BELMM. The software CU-MSDSp is available on GitHub at https://github.com/jtchavisIII/CU-MSDSp.
A review of the flortaucipir literature for positron emission tomography imaging of tau neurofibrillary tangles
Authors: Burnham Samantha C , Iaccarino Leonardo , Pontecorvo Michael J , Fleisher Adam S , Lu Ming , Collins Emily C , Devous Michael D 
Published: November 2023

Abstract
Alzheimer’s disease is defined by the presence of β-amyloid plaques and neurofibrillary tau tangles potentially preceding clinical symptoms by many years. Previously only detectable post-mortem, these pathological hallmarks are now identifiable using biomarkers, permitting an in vivo definitive diagnosis of Alzheimer’s disease. 18F-flortaucipir (previously known as 18F-T807; 18F-AV-1451) was the first tau positron emission tomography tracer to be introduced and is the only Food and Drug Administration-approved tau positron emission tomography tracer (Tauvid™). It has been widely adopted and validated in a number of independent research and clinical settings. In this review, we present an overview of the published literature on flortaucipir for positron emission tomography imaging of neurofibrillary tau tangles. We considered all accessible peer-reviewed literature pertaining to flortaucipir through 30 April 2022. We found 474 relevant peer-reviewed publications, which were organized into the following categories based on their primary focus: typical Alzheimer’s disease, mild cognitive impairment and pre-symptomatic populations; atypical Alzheimer’s disease; non-Alzheimer’s disease neurodegenerative conditions; head-to-head comparisons with other Tau positron emission tomography tracers; and technical considerations. The available flortaucipir literature provides substantial evidence for the use of this positron emission tomography tracer in assessing neurofibrillary tau tangles in Alzheimer’s disease and limited support for its use in other neurodegenerative disorders. Visual interpretation and quantitation approaches, although heterogeneous, mostly converge and demonstrate the high diagnostic and prognostic value of flortaucipir in Alzheimer’s disease.
Twenty years of the French Renal Epidemiology and Information Network
Authors: Kazes Isabelle , Solignac Justine , Lassalle Mathilde , Mercadal Lucile , Couchoud Cécile 
Published: November 2023

ABSTRACT

Background
The French Renal Epidemiology and Information Network (REIN) is 20 years old. It is not just a national data registry, but rather an epidemiological and informational network serving patients with chronic kidney disease, nephrology teams and health services.

Methods
The past 10-year trends of the incidence and prevalence of renal replacement therapy by dialysis or kidney transplantation and waitlist activity are presented. To detect potential significant changes in trends from 2012 and 2021, a Joinpoint regression model was used.

Results
The overall incidence of treated end-stage kidney disease (ESKD) was 169 per million population (pmp) in 2021. It was stable despite an increase in the incidence of diabetes. We found a decreasing trend in the proportion of patients starting dialysis in an emergency but an increase in those starting haemodialysis (HD) with a temporary catheter. Peritoneal dialysis decreased by 1.7% each year, whereas home HD, although involving only 1% of dialysis patients, increased by 10% each year. For patients not treated at home, the median time to drive from the patient's home to the dialysis unit was 17 min. The proportion of patients on the transplantation waitlist at the start of dialysis increased from 7% to 12%. Among the 111 263 new ESKD patients from 2012 to 2021, 8% received a first transplant at 1 year and 20% at 5 years. Among kidney transplant recipients, the mean time on the waitlist increased from 13.8 to 22.6 months. Living donor transplants increased in frequency, representing 15% of kidney transplants.

Conclusions
Data from the REIN registry allow for the evaluation of needs and provide a planning tool for French authorities. The progressive implementation of automatic data retrieval from dialysis informatics charts might alleviate the burden of data collection. Furthermore, the research activity the REIN engenders, resulting in renewed confidence by health authorities in the dynamism of French nephrology, allows for an optimistic outlook for the REIN.
Functional traits and drought strategy predict leaf thermal tolerance
Authors: Valliere Justin M , Nelson Kekoa C , Martinez Marco Castañeda 
Published: November 2023

ABSTRACT
Heat stress imposes an important physiological constraint on native plant species—one that will only worsen with human-caused climate change. Indeed, rising temperatures have already contributed to large-scale plant mortality events across the globe. These impacts may be especially severe in cities, where the urban heat island effect amplifies climate warming. Understanding how plant species will respond physiologically to rising temperatures and how these responses differ among plant functional groups is critical for predicting future biodiversity scenarios and making informed land management decisions. In this study, we evaluated the effects of elevated temperatures on a functionally and taxonomically diverse group of woody native plant species in a restored urban nature preserve in southern California using measurements of chlorophyll fluorescence as an indicator of leaf thermotolerance. Our aim was to determine if species’ traits and drought strategies could serve as useful predictors of thermotolerance. We found that leaf thermotolerance differed among species with contrasting drought strategies, and several leaf-level functional traits were significant predictors of thermotolerance thresholds. Drought deciduous species with high specific leaf area, high rates of transpiration and low water use efficiency were the most susceptible to heat damage, while evergreen species with sclerophyllous leaves, high relative water content and high water use efficiency maintained photosynthetic function at higher temperatures. While these native shrubs and trees are physiologically equipped to withstand relatively high temperatures in this Mediterranean-type climate, hotter conditions imposed by climate change and urbanization may exceed the tolerance thresholds of many species. We show that leaf functional traits and plant drought strategies may serve as useful indicators of species’ vulnerabilities to climate change, and this information can be used to guide restoration and conservation in a warmer world.
Impact of ethnicity on antiplatelet treatment regimens for bleeding reduction in acute coronary syndromes: a systematic review and pre-specified subgroup meta-analysis
Authors: Galli Mattia , Laborante Renzo , Occhipinti Giovanni , Zito Andea , Spadafora Luigi , Biondi-Zoccai Giuseppe , Nerla Roberto , Castriota Fausto , D'Amario Domenico , Capodanno Davide , Jeong Young-Hoon , Kimura Takeshi , Mehran Roxana , Angiolillo Dominick J 
Published: November 2023

Abstract

Aims
Randomized controlled trials (RCTs) testing bleeding reduction strategies using antiplatelet treatment regimens (BRATs) in acute coronary syndromes (ACS) have shown promising results, but the generalizability of these findings may be significantly influenced by the ethnicity of the patients enrolled, given that East Asian (EA) patients show different ischaemic-bleeding risk profile compared to non-EA patients.

Methods and results
RCTs comparing a BRAT vs. standard 12-month dual antiplatelet therapy (DAPT) in patients with ACS undergoing percutaneous coronary intervention (PCI) were selected. The primary efficacy endpoint was major adverse cardiovascular events (MACE) as defined in each trial and the primary safety endpoint was minor or major bleeding. Twenty-six RCTs testing seven different BRATs were included. The only strategy associated with a trade-off in MACE was ‘upfront unguided de-escalation’ in the subgroup of non-EAs (risk ratio 1.16, 95% confidence interval 1.09–1.24). All but aspirin monotherapy-based strategies (i.e. ‘short and very short DAPT followed by aspirin’) were associated with reduced bleeding compared with standard DAPT in both EA and non-EA patients. There were no significant differences between subgroups, but the lack of RCTs in some of the included strategies and the difference in the certainty of evidence between EA and non-EA patients revealed that the evidence in support of different BRATs in ACS undergoing PCI is influenced by ethnicity. Moreover, absolute risk reduction estimation revealed that some BRATs might be more effective than others in reducing bleeding according to ethnicity.

Conclusion
The majority of BRATs are associated with reduced bleeding without any trade-off in hard ischaemic endpoints regardless of ethnicity. However, the supporting evidence and relative safety profiles of different BRATs might be significantly affected by ethnicity, which should be taken into account in clinical practice.

Study registration
This study is registered in PROSPERO (CRD42023416710).
What can keep euro area inflation high?
Authors: Reis Ricardo 
Published: November 2023

SUMMARY
A central bank that faces inflation above target may fail to bring it down. This article discusses six ways in which this happens because the central bank is dominated by: misjudgement, expectations, fiscal policy, financial markets, recession fears, or external forces. It applies this approach to the challenge facing the ECB in 2023–24. The hope is that the factors identified can serve as warning signs for what to avoid.
Humanization reveals pervasive incompatibility of yeast and human kinetochore components
Authors: Ólafsson Guðjón , Haase Max A B , Boeke Jef D 
Published: November 2023

Abstract
Kinetochores assemble on centromeres to drive chromosome segregation in eukaryotic cells. Humans and budding yeast share most of the structural subunits of the kinetochore, whereas protein sequences have diverged considerably. The conserved centromeric histone H3 variant, CenH3 (CENP-A in humans and Cse4 in budding yeast), marks the site for kinetochore assembly in most species. A previous effort to complement Cse4 in yeast with human CENP-A was unsuccessful; however, co-complementation with the human core nucleosome was not attempted. Previously, our lab successfully humanized the core nucleosome in yeast; however, this severely affected cellular growth. We hypothesized that yeast Cse4 is incompatible with humanized nucleosomes and that the kinetochore represented a limiting factor for efficient histone humanization. Thus, we argued that including the human CENP-A or a Cse4–CENP-A chimera might improve histone humanization and facilitate kinetochore function in humanized yeast. The opposite was true: CENP-A expression reduced histone humanization efficiency, was toxic to yeast, and disrupted cell cycle progression and kinetochore function in wild-type (WT) cells. Suppressors of CENP-A toxicity included gene deletions of subunits of 3 conserved chromatin remodeling complexes, highlighting their role in CenH3 chromatin positioning. Finally, we attempted to complement the subunits of the NDC80 kinetochore complex, individually and in combination, without success, in contrast to a previous study indicating complementation by the human NDC80/HEC1 gene. Our results suggest that limited protein sequence similarity between yeast and human components in this very complex structure leads to failure of complementation.
Salvage pleurectomy/decortication following immunotherapy for malignant pleural mesothelioma
Authors: Takenaka Masaru , Kuroda Koji , Yoshimatsu Katsuma , Mori Masataka , Kanayama Masatoshi , Taira Akihiro , Kuwata Taiji , Tanaka Fumihiro 
Published: November 2023

Abstract
Salvage surgery following immunotherapy is a promising treatment option for advanced malignant tumour. However, only a few cases of salvage surgery for malignant pleural mesothelioma (MPM) have been reported. This retrospective study was conducted to assess the feasibility of salvage surgery following immunotherapy for initially unresectabele MPM. Among 61 patients who received pleurectomy/decortication (P/D) for MPM, 7 patients received salvage P/D after immunotherapy. Surgical indication of salvage P/D was conversion to resectability in 5 patients and local relapse in 2 patients, and macroscopic complete resection was achieved in all patients. Although salvage P/D was associated with longer operation time (median, 507 min), higher intraoperative blood loss (median, 2573 mL) and higher morbidity (≥ grade 3, 29%), no patient died after surgery. Radiographic response to immunotherapy was well correlated with pathologic response, as all 4 patients with partial response showed significant pathologic response (viable cells, ≤50%). With the median postoperative follow-up duration of 9.0 months, all patients were alive mostly without tumour recurrence as local recurrence developed in 1 patient. To conclude, salvage P/D after immunotherapy may be a feasible treatment option for selected patients with advanced MPM, which should be validated in future multi-institutional studies. In addition, a long-term follow-up is essential to reveal the clinical benefit achieved with salvage P/D following immunotherapy.
Projecting the Clinical and Economic Impacts of Changes to HIV Care Among Adolescents and Young Adults in the United States: Lessons From the COVID-19 Pandemic
Authors: Brenner Isaac Ravi , Simpson Kit N , Flanagan Clare F , Dark Tyra , Dooley Mary , Agwu Allison L , Koay Wei Li Adeline , Freedberg Kenneth A , Ciaranello Andrea L , Neilan Anne M 
Published: November 2023

Abstract

Background
During the COVID-19 pandemic, many US youth with HIV (YHIV) used telehealth services; others experienced disruptions in clinic and antiretroviral therapy (ART) access.

Methods
Using the Cost-effectiveness of Preventing AIDS Complications (CEPAC)-Adolescent HIV microsimulation model, we evaluated 3 scenarios: 1) Clinic: in-person care; 2) Telehealth: virtual visits, without CD4 or viral load monitoring for 12 months, followed by return to usual care; and 3) Interruption: complete care interruption with no ART access or laboratory monitoring for 6 months (maximum clinic closure time), followed by return to usual care for 80%. We assigned higher 1-year retention (87% vs 80%) and lower cost/visit ($49 vs $56) for Telehealth vs Clinic. We modeled 2 YHIV cohorts with non-perinatal (YNPHIV) and perinatal (YPHIV) HIV, which differed by mean age (22 vs 16 years), sex at birth (85% vs 47% male), starting CD4 count (527/μL vs 635/μL), ART, mortality, and HIV-related costs. We projected life months (LMs) and costs/100 YHIV over 10 years.

Results
Over 10 years, LMs in Clinic and Telehealth would be similar (YNPHIV: 11 350 vs 11 360 LMs; YPHIV: 11 680 LMs for both strategies); costs would be $0.3M (YNPHIV) and $0.4M (YPHIV) more for Telehealth than Clinic. Interruption would be less effective (YNPHIV: 11 230 LMs; YPHIV: 11 620 LMs) and less costly (YNPHIV: $1.3M less; YPHIV: $0.2M less) than Clinic. Higher retention in Telehealth led to increased ART use and thus higher costs.

Conclusions
Telehealth could be as effective as in-person care for some YHIV, at slightly increased cost. Short interruptions to ART and laboratory monitoring may have negative long-term clinical implications.
Monitoring broad emission-line components in spectra of the two low-metallicity dwarf compact star-forming galaxies SBS 1420+540 and J1444+4840
Authors: Guseva N G , Thuan T X , Izotov Y I 
Published: November 2023

ABSTRACT
We report the discovery of broad components with P-Cygni profiles of the hydrogen and helium emission lines in the two low-redshift low-metallicity dwarf compact star-forming galaxies SBS 1420+540 and J1444+4840. We found small stellar masses of 106.24 and 106.59 M⊙, low oxygen abundances 12 + log O/H of 7.75 and 7.45, high velocity dispersions reaching σ ∼ 700 and ∼1200 km s−1, high terminal velocities of the stellar wind of ∼1000 and ∼1000–1700 km s−1, respectively, and large EW(H β) of ∼300 Å for both. For SBS 1420+540, we succeeded in capturing an eruption phase by monitoring the variations of the broad-to-narrow component flux ratio. We observe a sharp increase of that ratio by a factor of 4 in 2017 and a decrease by about an order of magnitude in 2023. The peak luminosity of ∼1040 erg s−1 of the broad component in L(H α) lasted for about 6 yr out of a three-decades monitoring. This leads us to conclude that there is probably a luminous blue variable candidate (LBVc) in this galaxy. As for J1444+4840, its very high L(H α) of about 1041 ergs s−1, close to values observed in active galactic nuclei (AGNs) and Type IIn supernovae (SNe), and the variability of no more than 20 per cent of the broad-to-narrow flux ratio of the hydrogen and helium emission lines over a 8 yr monitoring do not allow us to definitively conclude that it contains an LBVc. On the other hand, the possibility that the line variations are due to a long-lived stellar transient of type AGN/SN IIn cannot be ruled out.
Improved models for the near-Earth asteroids (2100) Ra-Shalom, (3103) Eger, (12711) Tukmit, and (161989) Cacus
Authors: Rodríguez Rodríguez Javier , Díez Alonso E , Iglesias Álvarez Santiago , Pérez Fernández Saúl , Licandro Javier , Alarcon Miguel R , Serra-Ricart Miquel , Pinilla-Alonso Noemi , Fernández Susana del Carmen , de Cos Juez Francisco Javier 
Published: November 2023

ABSTRACT
We present 24 new dense light curves of the near-Earth asteroids (3103) Eger, (161989) Cacus, (2100) Ra-Shalom, and (12711) Tukmit, obtained with the Instituto Astrofísico Canarias 80 and Telescopio Abierto Remoto 2 telescopes at the Teide Observatory (Tenerife, Spain) during 2021 and 2022, in the framework of projects visible NEAs observations survey and NEO Rapid Observation, Characterization and Key Simulations. The shape models and rotation state parameters (P, λ, β) were computed by applying the light curve inversion method to the new data altogether with the archival data. For (3013) Eger and (161989) Cacus, our shape models and rotation state parameters agree with previous works, though they have smaller uncertainties. For (2100) Ra-Shalom, our results also agree with previous studies. Still, we find that a Yarkovsky–O’Keefe–Radzievskii–Paddack acceleration of υ = (0.223 ± 0.237) × 10−8 rad d−2 slightly improves the fit of the light curves, suggesting that (2100) Ra-Shalom could be affected by this acceleration. We also present for the first time a shape model for (12711) Tukmit, along with its rotation state parameters (P = 3.484900 ± 0.000031 h, λ = 27° ± 8°, β = 9° ± 15°).