bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geophysical and Climate Hazards: A Very Short Introduction
Authors: McGuire Bill 
Published: February 2024

Abstract
These are tempestuous times, and barely a day goes by without news of more geophysical mayhem splashed across our Twitter feeds, television screens, and front pages. Earthquakes and volcanic eruptions, floods and storms, and other deadly phenomena have always been with us and have taken a toll on communities for many thousands of years. But now things are changing—and fast. Global heating, unequivocally a consequence of humankind’s carbon-polluting activities, is building rapidly, and in recent years has translated faster than anyone could have imagined into an explosion of extreme weather. As the heat builds and sea levels climb, storms, floods, and wildfires are taking an increasing toll on lives and livelihoods, making our world a far more dangerous place. If we are to cope, we need to better understand the geophysical and climate hazards that now assail us, so as to both limit their impacts and build the resilience needed for people and communities to endure on a hotter and more dynamic planet.
Making mouse transcriptomics deconvolution accessible with immunedeconv
Authors: Merotto Lorenzo , Sturm Gregor , Dietrich Alexander , List Markus , Finotello Francesca 
Published: February 2024

Abstract

Summary
Transcriptome deconvolution has emerged as a reliable technique to estimate cell-type abundances from bulk RNA sequencing data. Unlike their human equivalents, methods to quantify the cellular composition of complex tissues from murine transcriptomics are sparse and sometimes not easy to use. We extended the immunedeconv R package to facilitate the deconvolution of mouse transcriptomics, enabling the quantification of murine immune-cell types using 13 different methods. Through immunedeconv, we further offer the possibility of tweaking cell signatures used by deconvolution methods, providing custom annotations tailored for specific cell types and tissues. These developments strongly facilitate the study of the immune-cell composition of mouse models and further open new avenues in the investigation of the cellular composition of other tissues and organisms.

Availability and implementation
The R package and the documentation are available at https://github.com/omnideconv/immunedeconv.
Associations between inflammatory and angiogenic proteomic biomarkers, and cardiovascular events and mortality in relation to kidney function
Authors: Salzinger Barbara , Lundwall Kristina , Evans Marie , Mörtberg Josefin , Wallén Håkan , Jernberg Tomas , Kahan Thomas , Lundman Pia , Tornvall Per , Erlinge David , Lindahl Bertil , Baron Tomasz , Rezeli Melinda , Spaak Jonas , Jacobson Stefan H 
Published: February 2024

ABSTRACT

Background
The links between chronic kidney disease (CKD) and the high burden of cardiovascular disease remain unclear. We aimed to explore the association between selected inflammatory and angiogenic biomarkers, kidney function and long-term outcome in patients with an acute coronary syndrome (ACS) and to test the hypothesis that CKD status modifies this association.

Methods
A total of 1293 ACS patients hospitalized between 2008 and 2015 were followed until 31 December 2017. Plasma was collected on days 1–3 after admission. A total of 13 biomarkers were a priori identified and analysed with two proteomic methods, proximity extension assay or multiple reaction monitoring mass spectrometry. Boxplots and multiple linear regression models were used to study associations between biomarkers and kidney function and adjusted standardized Cox regression with an interaction term for CKD was used to assess whether CKD modified the association between biomarkers and major adverse cardiovascular events and death (MACE+).

Results
The concentrations of nine biomarkers—endothelial cell-specific molecule-1 (ESM-1), fibroblast growth factor 23 (FGF-23), fractalkine (CX3CL1), interleukin-1 receptor antagonist (IL-1RA), interleukin-18 (IL-18), monocyte chemotactic protein-1 (MCP-1), placenta growth factor (PlGF), transmembrane immunoglobulin 1 (TIM-1) and vascular endothelial growth factor A (VEGFA)—were inversely associated with kidney function. ESM-1, FGF-23 and TIM-1 showed associations with MACE+. Only FGF23 remained independently associated after adjustment for the other biomarkers (hazard ratio per standard deviation increase 1.34; 95% Bonferroni corrected confidence interval 1.19–1.50). None of the biomarkers showed an interaction with CKD.

Conclusions
The concentrations of 9 of the 13 prespecified inflammatory and angiogenic proteomic biomarkers increased when kidney function declined. Only FGF-23 demonstrated an independent association with MACE+, and this association was not modified by CKD status. These findings further support FGF-23 as an independent prognostic marker in ACS patients with and without CKD.
Association between subclinical atherosclerosis burden and unrecognized myocardial infarction detected by cardiac magnetic resonance in middle-aged low-risk adults
Authors: Fernández-Friera Leticia , García-Alvarez Ana , Oliva Belen , García-Lunar Inés , García Iris , Moreno-Arciniegas Andrea , Gómez-Talavera Sandra , Pérez-Herreras Cristina , Sánchez-González Javier , de Vega Vicente Martinez , Rossello Xavier , Bueno Héctor , Fernández-Ortiz Antonio , Ibañez Borja , Sanz Javier , Fuster Valentín 
Published: February 2024

Abstract

Aims
Evidence on the association between subclinical atherosclerosis (SA) and cardiovascular (CV) events in low-risk populations is scant. To study the association between SA burden and an ischaemic scar (IS), identified by cardiac magnetic resonance (CMR), as a surrogate of CV endpoint, in a low-risk population.

Methods and results
A cohort of 712 asymptomatic middle-aged individuals from the Progression of Early SA (PESA-CNIC-Santander) study (median age 51 years, 84% male, median SCORE2 3.37) were evaluated on enrolment and at 3-year follow-up with 2D/3D vascular ultrasound (VUS) and coronary artery calcification scoring (CACS). A cardiac magnetic study (CMR) was subsequently performed and IS defined as the presence of subendocardial or transmural late gadolinium enhancement (LGE). On CMR, 132 (19.1%) participants had positive LGE, and IS was identified in 20 (2.9%) participants. Individuals with IS had significantly higher SCORE2 at baseline and higher CACS and peripheral SA burden (number of plaques by 2DVUS and plaque volume by 3DVUS) at both SA evaluations. High CACS and peripheral SA (number of plaques) burden were independently associated with the presence of IS, after adjusting for SCORE2 [OR for 3rd tertile, 8.31; 95% confidence interval (CI) 2.85–24.2; P &lt; 0.001; and 2.77; 95% CI, 1.02–7.51; P = 0.045, respectively] and provided significant incremental diagnostic value over SCORE2.

Conclusion
In a low-risk middle-aged population, SA burden (CAC and peripheral plaques) was independently associated with a higher prevalence of IS identified by CMR. These findings reinforce the value of SA evaluation to early implement preventive measures.

Clinical Trial Registration
Progression of Early Subclinical Atherosclerosis (PESA) Study Identifier: NCT01410318.
Invasive vs. conservative management of older patients with non-ST-elevation acute coronary syndrome: individual patient data meta-analysis
Authors: Kotanidis Christos P , Mills Gregory B , Bendz Bjørn , Berg Erlend S , Hildick-Smith David , Hirlekar Geir , Milasinovic Dejan , Morici Nuccia , Myat Aung , Tegn Nicolai , Sanchis Juan , Savonitto Stefano , De Servi Stefano , Fox Keith A A , Pocock Stuart , Kunadian Vijay 
Published: February 2024

Abstract

Background and Aims
Older patients with non-ST-elevation acute coronary syndrome (NSTEACS) are less likely to receive guideline-recommended care including coronary angiography and revascularization. Evidence-based recommendations regarding interventional management strategies in this patient cohort are scarce. This meta-analysis aimed to assess the impact of routine invasive vs. conservative management of NSTEACS by using individual patient data (IPD) from all available randomized controlled trials (RCTs) including older patients.

Methods
MEDLINE, Web of Science and Scopus were searched between 1 January 2010 and 11 September 2023. RCTs investigating routine invasive and conservative strategies in persons &gt;70 years old with NSTEACS were included. Observational studies or trials involving populations outside the target range were excluded. The primary endpoint was a composite of all-cause mortality and myocardial infarction (MI) at 1 year. One-stage IPD meta-analyses were adopted by use of random-effects and fixed-effect Cox models. This meta-analysis is registered with PROSPERO (CRD42023379819).

Results
Six eligible studies were identified including 1479 participants. The primary endpoint occurred in 181 of 736 (24.5%) participants in the invasive management group compared with 215 of 743 (28.9%) participants in the conservative management group with a hazard ratio (HR) from random-effects model of 0.87 (95% CI 0.63–1.22; P = .43). The hazard for MI at 1 year was significantly lower in the invasive group compared with the conservative group (HR from random-effects model 0.62, 95% CI 0.44–0.87; P = .006). Similar results were seen for urgent revascularization (HR from random-effects model 0.41, 95% CI 0.18–0.95; P = .037). There was no significant difference in mortality.

Conclusions
No evidence was found that routine invasive treatment for NSTEACS in older patients reduces the risk of a composite of all-cause mortality and MI within 1 year compared with conservative management. However, there is convincing evidence that invasive treatment significantly lowers the risk of repeat MI or urgent revascularisation. Further evidence is needed from ongoing larger clinical trials.
Incorporating fossils into the joint inference of phylogeny and biogeography of the tree fern order Cyatheales
Authors: Ramírez-Barahona Santiago 
Published: February 2024

Abstract
Present-day geographic and phylogenetic patterns often reflect the geological and climatic history of the planet. Neontological distribution data are often sufficient to unravel a lineage’s biogeographic history, yet ancestral range inferences can be at odds with fossil evidence. Here, I use the fossilized birth–death process and the dispersal–extinction cladogenesis model to jointly infer the dated phylogeny and range evolution of the tree fern order Cyatheales. I use data for 101 fossil and 442 extant tree ferns to reconstruct the biogeographic history of the group over the last 220 million years. Fossil-aware reconstructions evince a prolonged occupancy of Laurasia over the Triassic–Cretaceous by Cyathealean tree ferns, which is evident in the fossil record but hidden from analyses relying on neontological data alone. Nonetheless, fossil-aware reconstructions are affected by uncertainty in fossils’ phylogenetic placement, taphonomic biases, and specimen sampling and are sensitive to interpretation of paleodistributions and how these are scored. The present results highlight the need and challenges of incorporating fossils into joint inferences of phylogeny and biogeography to improve the reliability of ancestral geographic range estimation.
The role of proteinaceous toxins secreted by Staphylococcus aureus in interbacterial competition
Authors: Garrett Stephen R , Palmer Tracy 
Published: February 2024

Abstract
Staphylococcus aureus is highly adapted to colonization of the mammalian host. In humans the primary site of colonization is the epithelium of the nasal cavity. A major barrier to colonization is the resident microbiota, which have mechanisms to exclude S. aureus. As such, S. aureus has evolved mechanisms to compete with other bacteria, one of which is through secretion of proteinaceous toxins. S. aureus strains collectively produce a number of well-characterized Class I, II, and IV bacteriocins as well as several bacteriocin-like substances, about which less is known. These bacteriocins have potent antibacterial activity against several Gram-positive organisms, with some also active against Gram-negative species. S. aureus bacteriocins characterized to date are sporadically produced, and often encoded on plasmids. More recently the type VII secretion system (T7SS) of S. aureus has also been shown to play a role in interbacterial competition. The T7SS is encoded by all S. aureus isolates and so may represent a more widespread mechanism of competition used by this species. T7SS antagonism is mediated by the secretion of large protein toxins, three of which have been characterized to date: a nuclease toxin, EsaD; a membrane depolarizing toxin, TspA; and a phospholipase toxin, TslA. Further study is required to decipher the role that these different types of secreted toxins play in interbacterial competition and colonization of the host.
Safety and feasibility of minimally invasive gastrectomy after neoadjuvant immunotherapy for locally advanced gastric cancer: a propensity score-matched analysis in China
Authors: Cui Hao , Liang Wenquan , Cui Jianxin , Song Liqiang , Yuan Zhen , Chen Lin , Wei Bo 
Published: February 2024

Abstract

Background
The effect of neoadjuvant immunotherapy on minimally invasive gastrectomy (MIG) for locally advanced gastric cancer (LAGC) remains controversial. This study aimed to compare short-term outcomes between MIG after neoadjuvant chemo-immunotherapy (NICT-MIG) and MIG after neoadjuvant chemotherapy alone (NCT-MIG), and determine risk factors for post-operative complications (POCs).

Methods
This retrospective study included clinicopathologic data from 193 patients who underwent NCT-MIG or NICT-MIG between January 2020 and February 2023 in the Department of General Surgery, Chinese People’s Liberation Army General Hospital First Medical Center (Beijing, China). Propensity score-matched analysis at a ratio of 1:2 was performed to reduce bias from confounding patient-related variables and short-term outcomes were compared between the two groups.

Results
The baseline characteristics were comparable between 49 patients in the NICT-MIG group and 86 patients in the NCT-MIG group after propensity score matching. Objective and pathologic complete response rates were significantly higher in the NICT-MIG group than in the NCT-MIG group (P &lt; 0.05). The overall incidence of treat-related adverse events, intraoperative bleeding, operation time, number of retrieved lymph nodes, time to the first flatus, post-operative duration of hospitalization, overall morbidity, and severe morbidity were comparable between the NCT-MIG and NICT-MIG groups (P &gt; 0.05). By multivariate logistic analysis, estimated blood loss of &gt;200 mL (P = 0.010) and prognostic nutritional index (PNI) score of &lt;45 (P = 0.003) were independent risk factors for POCs after MIG following neoadjuvant therapy.

Conclusions
Safety and feasibility of NICT were comparable to those of NCT in patients undergoing MIG for LAGC. Patients with an estimated blood loss of &gt;200 mL or a PNI score of &lt;45 should be carefully evaluated for increased POCs risk.
CarFreeMe™-Dementia: Potential Benefits of a Driving Retirement Intervention Supporting Persons With Dementia and Their Families
Authors: Peterson Colleen M , Ingvalson Stephanie , Birkeland Robyn W , Louwagie Katie W , Scott Theresa L , Pachana Nancy A , Liddle Jacki , Gustafsson Louise , Gaugler Joseph E 
Published: February 2024

Abstract

Background and Objectives
Driving retirement can be a necessary but challenging and emotionally complex transition, especially for people living with dementia. This pilot study evaluated the utility of CarFreeMe™-Dementia (CFM™-D), a telehealth intervention providing tailored education and social support to those living with dementia and their care partners, as they prepare for or adjust to driving retirement. Delivered by empathetic health professionals, CFM™-D is a person-centric, flexible program tailored to address challenges specific to the participants’ driving retirement stage and individualized contexts.

Research Design and Methods
A single-arm, mixed-methods design was used to follow participants over a 6-month period. Participants received CFM™-D, a 7–8-module semistructured intervention, including education and planning support for driving retirement (impact of dementia, transportation options) and emotional adjustment (grief and loss, stress management). Surveys evaluated the perceived utility of intervention components as well as changes in well-being and readiness for driving retirement over time. An open-ended survey item and semistructured interviews provided additional feedback and a contextual understanding of the empirical data.

Results
A total of 50 families enrolled (17 care partners, 16 retiring/retired drivers with memory loss, and 17 care partner-retiring/retired driver dyads). Nearly all participants would recommend the intervention. Care partners reported significantly reduced (p &lt; .05) isolation and relationship strain, and retiring drivers reported significant reductions in depressive symptoms. Driving retirement preparedness scores improved. Driving retirement phase, enrolling as a dyad, and retiring driver cognitive/functional impairment were associated with these outcomes. Participants also engaged in more driving retirement activities outside of the intervention (e.g., talking with health professionals).

Discussion and Implications
CFM™-D is a useful intervention for retiring drivers with dementia and their family members, with preliminary data suggesting it supports improved well-being and driving retirement preparedness. A randomized controlled trial is needed to determine the efficacy of the CFM™-D intervention and future translation needs.
Dissection of the spatial dynamics of biosynthesis, transport, and turnover of major amino acids in tea plants (Camellia sinensis)
Authors: Yu Shuwei , Zhu Mingzhi , Li Ping , Zuo Hao , Li Juan , Li Yingying , Peng Anqi , Huang Jianan , Fernie Alisdair R , Liu Zhonghua , Zhao Jian 
Published: February 2024

Abstract
High levels of free amino acids (AAs) in tea leaves are crucial for tea flavor and health function; however, the dynamic AA biosynthesis, transport, and turnover in tea plants remain elusive. Here we dissected whole tea plants for these dynamics by assessing AA profiles and transcriptomes of metabolic pathway genes in tea roots, stems, and leaves and revealing their distinctive features with regard to AA synthesis, transport, and degradation/recycling. Nitrogen assimilation dominated in the roots wherein glutamine (Gln), theanine, and arginine (Arg) were actively synthesized. Arg was transported into trunk roots and stems, together with Glu, Gln, and theanine as the major AAs in the xylem sap for long-distance root-to-leaf transport. Transcriptome analysis revealed that genes involved in Arg synthesis were highly expressed in roots, but those for Arg transport and degradation were highly expressed in stems and young leaves, respectively. CsGSIa transcripts were found in root meristem cells, root, stem and leaf vascular tissues, and leaf mesophyll where it appeared to participate in AA synthesis, transport, and recycling. Overexpression of CsGSIa in tea transgenic hairy roots and knockdown of CsGSIa in transgenic hairy roots and tea leaves produced higher and lower Gln and theanine than wild-type roots and leaves, respectively. This study provides comprehensive and new insights into AA metabolism and transport in the whole tea plant.
Phosphorylation of birch BpNAC90 improves the activation of gene expression to confer drought tolerance
Authors: Wang Zhibo , He Zihang , Gao Caiqiu , Wang Chao , Song Xingshun , Wang Yucheng 
Published: February 2024

Abstract
The NAC transcription factors (TFs) play important roles in mediating abiotic stress tolerance; however, the mechanism is still not fully known. Here, an NAC gene (BpNAC90) from a gene regulatory network of Betula platyphylla (birch) that responded to drought was characterized. Overexpression and knockout of BpNAC90 displayed increased and reduced drought tolerance, respectively, relative to wild-type (WT) birch. BpNAC90 binds to different DNA motifs to regulate target genes in conferring drought tolerance, such as Eomes2, ABRE and Tgif2. BpNAC90 is phosphorylated by drought stress at Ser 205 by birch SNF1-related protein kinase 2 (BpSRK2A). Mutated BpNAC90 (termed S205A) with abolished phosphorylation, was transformed into birch for overexpression. The transgenic S205A plants displayed significantly reduced drought tolerance compared with plants overexpressing BpNAC90, but still showed increased drought tolerance relative to WT birch. At the same time, S205A showed a decreased capability to bind to motifs and reduced activation of target gene expression, which contributed to the reduced drought tolerance. Additionally, BpSRK2A and BpNAC90 can be induced by drought stress and form a complex to phosphorylate BpNAC90. The results together indicated that phosphorylation of BpNAC90 is necessary in conferring drought tolerance in birch.
Segmental analysis of aortic basal ring dimensions in normal and dilated tricuspid aortic roots
Authors: Jelenc Matija , Jelenc Blaž , Habjan Sara , Giebels Christian , Fries Peter , Michelena Hector I , Foley Thomas , Schäfers Hans Joachim 
Published: February 2024

Abstract

OBJECTIVES
In patients with aortic root aneurysm, the aortic basal ring is frequently dilated. It has been speculated that the muscular part of the basal ring dilates most. The purpose of this study was to analyse the segmental dilatation of the basal ring, comparing normal and dilated roots in patients with tricuspid aortic valves.

METHODS
Retrospective analysis of computed tomography studies in patients with normal and dilated aortic roots was performed. Lengths of segments of the basal ring corresponding to each of the 3 sinuses, and to the muscular and fibrous parts were measured. Fractions of these segments relative to the total basal ring perimeter were calculated.

RESULTS
We analysed 152 normal and 126 dilated aortic roots and 86 propensity-matched pairs. Basal ring dilatation was present in all segments of dilated aortic roots with subtle differences between the segments corresponding to the 3 sinuses. The muscular part of the basal ring dilated proportionately to its fibrous part, with no difference in fractions of measured muscular part in normal and dilated roots [42.2% (interquartile range 4.3%) vs 42.1% (interquartile range 6.3%)].

CONCLUSIONS
Basal ring dilatation was present in all segments corresponding to the 3 sinuses in dilated aortic roots. Both muscular and fibrous parts dilated equally, supporting the need to stabilize the entire basal ring when performing aortic valve repair surgery.
Biotic interactions explain seasonal dynamics of the alpine soil microbiome
Authors: Fiore-Donno Anna Maria , Freudenthal Jule , Dahl Mathilde Borg , Rixen Christian , Urich Tim , Bonkowski Michael 
Published: February 2024

Abstract
While it is acknowledged that alpine soil bacterial communities are primarily driven by season and elevation, there is no consensus on the factors influencing fungi and protists. Here we used a holistic approach of the microbiome to investigate the seasonal dynamics in alpine grasslands, focusing on soil food web interactions. We collected 158 soil samples along elevation transects from three mountains in the Alps, in spring during snowmelt and in the following summer. Using metatranscriptomics, we simultaneously assessed prokaryotic and eukaryotic communities, further classified into trophic guilds. Our findings reveal that the consumers’ pressure increases from spring to summer, leading to more diverse and evenly distributed prey communities. Consequently, consumers effectively maintain the diverse soil bacterial and fungal communities essential for ecosystem functioning. Our research highlights the significance of biotic interactions in understanding the distribution and dynamics of alpine microbial communities.