bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advancing apple genetics research: Malus coronaria and Malus ioensis genomes and a gene family-based pangenome of native North American apples
Authors: Švara Anže , Sun Honghe , Fei Zhangjun , Khan Awais 
Published: August 2024

Abstract
Wild Malus species flourished in North America long before Europeans introduced domesticated apples. Malus coronaria and M. ioensis are native to the mid-western and eastern United States, while M. angustifolia and M. fusca grow in the southeast and west, respectively. They offer disease resistance, climate and soil adaptability, and horticultural traits for apple breeding. However, their utilization remains limited due to insufficient genomic resources and specific genetics. We report high-quality phased chromosome-scale assemblies of M. coronaria and M. ioensis, generated using long-read and conformation capture sequencing. Phylogenetic and synteny analysis indicated high relatedness between these 2 genomes and previously published genome of M. angustifolia, and lower relatedness with M. fusca. Gene family-based pangenome of North American Malus identified 60,211 orthogroups containing 340,087 genes. Genes involved in basic cellular and metabolic processes, growth, and development were core to the existence of these species, whereas genes involved in secondary metabolism, stress response, and interactions with other organisms were accessory and are likely associated with adaptation to specific environments. Structural variation hotspots were mostly overlapping with high gene density. This study offers novel native North American Malus genome resources that can be used to identify genes for apple breeding and understand their evolution and adaptation.
Mitral regurgitation evolution after transcatheter tricuspid valve interventions—a sub-analysis of the TriValve registry
Authors: Cannata Francesco , Sticchi Alessandro , Russo Giulio , Stankowski Kamil , Hahn Rebecca T , Alessandrini Hannes , Andreas Martin , Braun Daniel , Connelly Kim A , Denti Paolo , Estevez-Loureiro Rodrigo , Fam Neil , Harr Claudia , Hausleiter Joerg , Himbert Dominique , Kalbacher Daniel , Adamo Marianna , Latib Azeem , Lubos Edith , Ludwig Sebastian , Lurz Philipp , Monivas Vanessa , Nickenig Georg , Pedrazzini Giovanni , Pozzoli Alberto , Praz Fabien , Rodes-Cabau Josep , Rommel Karl-Philipp , Schofer Joachim , Sievert Horst , Tang Gilbert , Thiele Holger , Kresoja Karl-Patrik , Metra Marco , Stephan von Bardeleben Ralph , Webb John , Windecker Stephan , Leon Martin , Maisano Francesco , De Marco Federico , Pontone Gianluca , Taramasso Maurizio 
Published: August 2024

Abstract

Aims
Transcatheter tricuspid valve interventions (TTVI) are increasingly used to treat patients with significant tricuspid regurgitation (TR). The evolution of concurrent mitral regurgitation (MR) severity after TTVI is currently unknown and may be pivotal for clinical decision-making. The aim of this study was to assess the evolution of MR after TTVI and to identify predictors of MR worsening and improvement.

Methods and results
This analysis is a substudy of the TriValve Registry, an international registry designed to collect data on TTVI. This substudy included all patients with echocardiographic data on MR evolution and excluded those with a concomitant tricuspid and mitral transcatheter valve intervention or with a history of mitral valve intervention. The co-primary outcomes were MR improvement and worsening at two timepoints: pre-discharge and 2-month follow-up. This analysis included 359 patients with severe TR, mostly (80%) treated with tricuspid transcatheter edge-to-edge repair (T-TEER). MR improvement was found in 106 (29.5%) and 99 (34%) patients, while MR worsening was observed in 34 (9.5%) and 33 (11%) patients at pre-discharge and 2-month follow-up, respectively. Annuloplasty and heterotopic replacement were associated with MR worsening. Independent predictors of MR improvement were: atrial fibrillation, T-TEER, acute procedural success, TR reduction, left ventricular end-diastolic diameter&gt; 60 mm, and beta-blocker therapy. Patients with moderate-to-severe/severe MR following TTVI showed significantly higher death rates.

Conclusion
MR degree variation is common after TTVI, with most cases showing improvement. Clinical and procedural characteristics may predict the MR evolution, in particular procedural success and T-TEER play key roles in MR outcomes. TTVI may be beneficial, even in the presence of functional MR.
Incidence and outcomes of prosthetic valve thrombosis during peripheral extracorporeal membrane oxygenation
Authors: Danial Pichoy , Zamorano Claudio , Carillion Aude , Barreda Eleodoro , Laali Mojgan , Demondion Pierre , D’Alessandro Cosimo , Bouglé Adrien , Pineton de Chambrun Marc , Combes Alain , Leprince Pascal , Lebreton Guillaume 
Published: August 2024

Abstract

OBJECTIVES
In the context of postcardiotomy cardiogenic shock (PCCS) following valve replacement surgery, it may be necessary to implant a peripheral veno-arterial extracorporeal membrane oxygenation (pVA-ECMO). This procedure, however, carries a risk of prosthetic valve thrombosis. The aim of this retrospective study was to describe the incidence and outcomes of prosthetic valve thrombosis after VA-ECMO support for PCCS and to report the associated risk factors.

METHODS
All consecutive adult patients who received pVA-ECMO for PCCS following a valve replacement procedure between January 2015 and October 2019 in our institution were included in this retrospective study. Outcome variables were prosthetic valve thrombosis, 30-day and hospital survival, pVA-ECMO-associated adverse events and surgery-related adverse events.

RESULTS
During the 4-year study period, 549 patients received pVA-ECMO for PCCS. Among them, 152 had undergone a valve replacement procedure and 9 of these developed prosthetic valve thrombosis. The incidence of valve thrombosis at 30 days was 7.5 ± 2%. The cumulative incidence of prosthetic valve thrombosis was significantly lower with pVA-ECMO + intra-aortic balloon pump versus VA-ECMO alone (1.4 ± 1.4% vs 13.7 ± 4.7%, P = 0.021, respectively). Intra-aortic balloon pump use associated with pVA-ECMO (versus pVA-ECMO alone) was an independent protective factor against hospital death [odds ratio = 0.180 (0.068–0.478), P = 0.001].

CONCLUSIONS
After PCCS following valve replacement surgery, peripheral femoro-femoral VA-ECMO is associated with a low risk of acute valve thrombosis especially when associated with an intra-aortic balloon pump.
Deep learning links localized digital pathology phenotypes with transcriptional subtype and patient outcome in glioblastoma
Authors: Roetzer-Pejrimovsky Thomas , Nenning Karl-Heinz , Kiesel Barbara , Klughammer Johanna , Rajchl Martin , Baumann Bernhard , Langs Georg , Woehrer Adelheid 
Published: August 2024

Abstract

Background
Deep learning has revolutionized medical image analysis in cancer pathology, where it had a substantial clinical impact by supporting the diagnosis and prognostic rating of cancer. Among the first available digital resources in the field of brain cancer is glioblastoma, the most common and fatal brain cancer. At the histologic level, glioblastoma is characterized by abundant phenotypic variability that is poorly linked with patient prognosis. At the transcriptional level, 3 molecular subtypes are distinguished with mesenchymal-subtype tumors being associated with increased immune cell infiltration and worse outcome.

Results
We address genotype–phenotype correlations by applying an Xception convolutional neural network to a discovery set of 276 digital hematozylin and eosin (H&E) slides with molecular subtype annotation and an independent The Cancer Genome Atlas–based validation cohort of 178 cases. Using this approach, we achieve high accuracy in H&E-based mapping of molecular subtypes (area under the curve for classical, mesenchymal, and proneural = 0.84, 0.81, and 0.71, respectively; P &lt; 0.001) and regions associated with worse outcome (univariable survival model P &lt; 0.001, multivariable P = 0.01). The latter were characterized by higher tumor cell density (P &lt; 0.001), phenotypic variability of tumor cells (P &lt; 0.001), and decreased T-cell infiltration (P = 0.017).

Conclusions
We modify a well-known convolutional neural network architecture for glioblastoma digital slides to accurately map the spatial distribution of transcriptional subtypes and regions predictive of worse outcome, thereby showcasing the relevance of artificial intelligence–enabled image mining in brain cancer.
Wildfire impact on soil microbiome life history traits and roles in ecosystem carbon cycling
Authors: Nelson Amelia R , Rhoades Charles C , Fegel Timothy S , Roth Holly K , Caiafa Marcos V , Glassman Sydney I , Borch Thomas , Wilkins Michael J 
Published: August 2024

Abstract
Wildfires, which are increasing in frequency and severity with climate change, reduce soil microbial biomass and alter microbial community composition and function. The soil microbiome plays a vital role in carbon (C) and nitrogen (N) cycling, but its complexity makes it challenging to predict post-wildfire soil microbial dynamics and resulting impacts on ecosystem biogeochemistry. The application of biogeochemically relevant conceptual trait-based frameworks to the soil microbiome can distill this complexity, enabling enhanced predictability of soil microbiome recovery following wildfire and subsequent impacts to biogeochemical cycles. Conceptual frameworks that have direct links to soil C and N cycling have been developed for the soil microbiome; the Y-A-S framework overviews soil microbiome life history strategies that have tradeoffs with one another and others have proposed frameworks specific to wildfire. Here, we aimed to delineate post-wildfire changes of bacterial traits in western US coniferous forests to inform how severe wildfire influences soil microbiome recovery and resultant biogeochemical cycling. We utilized a comprehensive metagenome-assembled genome catalog from post-wildfire soils representing 1 to 11 years following low- and high-severity burning to identify traits that enable the persistence of microbial taxa in burned soils and influence ecosystem C and N cycling. We found that high-severity wildfire initially selects for fast growers and, up to a decade post-fire, taxa that invest in genes for acquiring diverse resources from the external environment, which in combination could increase soil C losses. This work begins to disentangle how climate change–induced shifts in wildfire behavior might alter microbially mediated soil biogeochemical cycling.
Development of resistance monitoring for Helicoverpa armigera (Lepidoptera: Noctuidae) resistance to pyramided Bt cotton in China
Authors: Ruan Jianqiu , Yang Yihua , Carrière Yves , Wu Yidong 
Published: August 2024

Abstract
The cotton bollworm, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae), is a significant cotton pest worldwide. Bacillus thuringiensis (Bt) cotton producing Cry1Ac has been used since 1997 for the control of this pest in China and a significant increase in H. armigera resistance to Cry1Ac has occurred in northern China. To mitigate resistance evolution, it is necessary to develop and plant pyramided 2- and 3-toxin Bt cotton to replace Cry1Ac cotton. For sustainable use of pyramided Bt cotton, we used diet overlay bioassays to measure the baseline susceptibility of H. armigera to Cry2Ab in 33 populations collected in 2017, 2018, and 2021 in 12 locations from major cotton-producing areas of China. The lethal concentration killing 50% (LC50) or 99% (LC99) of individuals from the populations ranged from 0.030 to 0.138 µg/cm2 and 0.365 to 2.964 µg/cm2, respectively. The ratio of the LC50 for the most resistant and susceptible population was 4.6, indicating moderate among-population variability in resistance. The susceptibility of H. armigera to Cry2Ab did not vary significantly over years. A diagnostic concentration of 2 µg/cm2 was calculated as twice the LC99 from an analysis of pooled data for the field-collected populations. This concentration discriminated well between susceptible and resistant individuals, as it killed all larvae from a susceptible laboratory strain and 0%, 0%, and 23% of larvae from 3 laboratory strains with &gt; 100-fold resistance to Cry2Ab. These baseline susceptibility data and diagnostic concentration for Cry2Ab will be useful for monitoring the evolution of H. armigera resistance to pyramided Bt cotton in China.
Land valuation in the metaverse: location matters
Authors: Goldberg Mitchell , Kugler Peter , Schär Fabian 
Published: August 2024

Abstract
In urban economics, transportation costs are a key determinant of land value. However, in virtual worlds, these costs are generally limited by the users’ ability to teleport. Drawing from urban and attention economic literature, we propose a theoretical model microfounded on user behavior. The model suggests that the relative value of land parcels hinges on their potential to attract visitors. Our empirical analysis supports this by demonstrating that location remains crucial in virtual worlds and highlighting the role of the teleportation threshold. We discuss the model’s general applicability, reaffirming the significance of location within most virtual worlds.
Racial and ethnic differences in second primary lung cancer risk among lung cancer survivors
Authors: Choi Eunji , Hua Yue , Su Chloe C , Wu Julie T , Neal Joel W , Leung Ann N , Backhus Leah M , Haiman Christopher , Le Marchand Loïc , Liang Su-Ying , Wakelee Heather A , Cheng Iona , Han Summer S 
Published: August 2024

Abstract

Background
Recent therapeutic advances have improved survival among lung cancer (LC) patients, who are now at high risk of second primary lung cancer (SPLC). Hispanics comprise the largest minority in the United States, who have shown a lower LC incidence and mortality than other races, and yet their SPLC risk is poorly understood. We quantified the SPLC incidence patterns among Hispanics vs other races.

Methods
We used data from the Multiethnic Cohort, a population-based cohort of 5 races (African American, Japanese American, Hispanic, Native Hawaiian, and White), recruited between 1993 and 1996 and followed through 2017. We identified patients diagnosed with initial primary lung cancer (IPLC) and SPLC via linkage to Surveillance, Epidemiology, and End Results registries. We estimated the 10-year cumulative incidence of IPLC (in the entire cohort) and SPLC (among IPLC patients). A standardized incidence ratio (SIR) was calculated as the ratio of SPLC-to-IPLC incidence by race and ethnicity.

Results
Among 202 692 participants, 6788 (3.3%) developed IPLC over 3 871  417 person-years. The 10-year cumulative IPLC incidence was lower among Hispanics (0.80%, 0.72 to 0.88) vs Whites (1.67%, 1.56 to 1.78) or Blacks (2.44%, 2.28 to 2.60). However, the 10-year SPLC incidence following IPLC was higher among Hispanics (3.11%, 1.62 to 4.61) vs Whites (2.80%, 1.94 to 3.66) or Blacks (2.29%, 1.48 to 3.10), resulting in a significantly higher SIR for Hispanics (SIR = 8.27, 5.05 to 12.78) vs Whites (SIR = 5.60, 4.11 to 7.45) or Blacks (SIR = 3.48, 2.42 to 4.84; P &lt; .001).

Conclusion
Hispanics have a higher SPLC incidence following IPLC than other races, which may be potentially due to better survival after IPLC and extended duration for SPLC development. Continuing surveillance is warranted to reduce racial disparities among LC survivors.
Introduction to Guitar Techniques and Genres for the Utilization in Improvised Active Music Therapy
Authors: Kogutek Demian 
Published: August 2024

Abstract
Guitar is a popular instrument for music therapy clinicians and students because it is portable and musically versatile. Guitar training is increasingly shared through music therapy literature, professional conferences, and workshops. However, there is still a lack of literature regarding the use of guitar improvization techniques for beginner and intermediate-level music therapists. The purpose of this manuscript is to provide the first simplified and standardized guitar methodological system for beginner and intermediate-level music therapy students and clinicians for the use in Improvised Active Music Therapy sessions in neurological rehabilitation. Improving guitar skills is important to increase confidence among students and clinicians and to enhance clinical outcomes. The manuscript is divided into two groups of exercises. The first group consists of four exercises with chord progressions. The second group consists of six strumming exercises. The strumming exercises should be combined with the chord progressions in the first group to expand upon the first position and aesthetic qualities. The exercises incorporate extended, chromatic, and suspended chords in Rock & Roll, Blues, Hip-Hop and rap, Reggae, folk, country, Latin American, and Spanish styles in key of E major. The goal is to stimulate the skill of music therapy students and clinicians, and perhaps add some extra motivation and ideas for guitar improvization skills to enhance clinical outcomes.
Toll-like receptor agonists promote the formation of tertiary lymphoid structure and improve anti-glioma immunity
Authors: Shen Shaoping , Cui Yong , Li Mingxiao , Yu Kefu , Zhu Qinghui , Zhang Xiaokang , Shen Weicheng , Li Haoyi , Jiang Haihui , Li Ming , Wang Xijie , Zhao Xuzhe , Ren Xiaohui , Lin Song 
Published: August 2024

Abstract

Background
Glioma, characterized by limited lymphocytic infiltration, constitutes an “immune-desert” tumor displaying insensitivity to various immunotherapies. This study aims to explore therapeutic strategies for inducing tertiary lymphoid structure (TLS) formation within the glioma microenvironment (GME) to transition it from an immune resistant to an activated state.

Methods
TLS formation in GME was successfully induced by intracranial administration of Toll-like receptor (TLR) agonists (OK-432, TLR2/4/9 agonist) and glioma antigens (i.c. αTLR-mix). We employed staining analysis, antibody neutralization, single-cell RNA sequencing (scRNA-Seq), and BCR/TCR sequencing to investigate the underlying mechanisms of TLS formation and its role in anti-glioma immunity. Additionally, a preliminary translational clinical study was conducted.

Results
TLS formation correlated with increased lymphocyte infiltration in GME and led to improved prognosis in glioma-bearing mice. In the study of TLS induction mechanisms, certain macrophages/microglia and Th17 displayed markers of “LTo” and “LTi” cells, respectively, interaction through LTα/β-LTβR promoted TLS induction. Post-TLS formation, CD4 + and CD8 + T cells but not CD19 + B cells contributed to anti-glioma immunity. Comparative analysis of B/T cells between brain and lymph node showed that brain B/T cells unveiled the switch from naïve to mature, some B cells highlighted an enrichment of class switch recombination (CSR)-associated genes, V gene usage, and clonotype bias were observed. In related clinical studies, i.c. αTLR-mix treatment exhibited tolerability, and chemokines/cytokines assay provided preliminary evidence supporting TLS formation in GME.

Conclusions
TLS induction in GME enhanced anti-glioma immunity, improved the immune microenvironment, and controlled glioma growth, suggesting potential therapeutic avenues for treating glioma in the future.
Impact of the Coronavirus Disease 2019 Pandemic on Substance Use Disorder Risk Among People Living With Human Immunodeficiency Virus (HIV) Enrolled in HIV Care in the United States: An Interrupted Time Series Analysis
Authors: Jain Jennifer P , Heise Megan J , Lisha Nadra E , Moreira Carlos H , Glidden David V , Burkholder Greer A , Crane Heidi M , Jacobson Jeffrey M , Cachay Edward R , Mayer Kenneth H , Napravnik Sonia , Moore Richard D , Dawson-Rose Carol , Johnson Mallory O , Christopoulos Katerina A , Gandhi Monica , Spinelli Matthew A 
Published: August 2024

Abstract

Background
Rising overdose deaths globally and increased social isolation during the coronavirus disease 2019 (COVID-19) pandemic may have disproportionately impacted people with human immunodeficiency virus (PWH) with substance use disorders (SUD). We examined trends in SUD risk among PWH before and after the COVID-19 shelter-in-place (SIP) mandate.

Methods
Data were collected between 2018 and 2022 among PWH enrolled across 8 US sites in the Centers for AIDS Research Network of Integrated Clinical Systems cohort. We evaluated changes in moderate/high SUD risk after SIP using interrupted time series analyses.

Results
There were 7126 participants, including 21 741 SUD assessments. The median age was 51 (interquartile range, 39–58) years; 12% identified as Hispanic or Latino/Latina, 46% Black/African American, and 46% White. Moderate/high SUD risk increased continuously after the pandemic's onset, with 43% (95% confidence interval [CI], 40%–46%) endorsing moderate/high SUD risk post-SIP, compared to 24% (95% CI, 22%–26%) pre-SIP (P &lt; .001). There were increases in the use of heroin, methamphetamine, and fentanyl, and decreases in prescription opioids and sedatives post-SIP. Further, there was a decrease in reported substance use treatment post-SIP compared to pre-SIP (P = .025).

Conclusions
The rising prevalence of SUD through late 2022 could be related to an increase in isolation and reduced access to substance use and HIV treatment caused by disruptions due to COVID-19. A renewed investment in integrated substance use treatment is vital to address the combined epidemics of substance use and HIV following the COVID-19 pandemic and to support resilience in the face of future disruptions.
Antibacterial activity of microwave-hydroxyapatite and cellulose blend
Authors: Kyeremeh Sheila Priscilla , Asimeng Bernard Owusu , Paemka Lily , Kojo Michael Ainooson , Annan Ebenezer , Tiburu Elvis K 
Published: August 2024

Abstract
The aim of the work was to synthesize a microwave-hydroxyapatite and cellulose nanocrystal (HApM/CNC) blend and investigate it for its antibacterial efficacy in water treatment applications. The blend was synthesized at varying ratios (100 : 0, 80 : 20, 60 : 40, and 40 : 60) and evaluated using disc diffusion, optical density (OD), and colony-forming unit (CFU) tests. Structural, functional group, and morphological analyses were conducted using X-ray diffraction (XRD), Fourier-transform infrared (FTIR) spectroscopy, and scanning electron microscopy (SEM). Antibacterial activity tests revealed enhanced antibacterial efficacy in the HApM/CNC blend. The inhibition zones for the blend measured 13.6 mm for E. coli and 17 mm for S. aureus, surpassing the 7.5 and 9.5 mm zones for pure HApM and the 10.5 and 10 mm zones for pure CNC, respectively. OD and CFU tests further corroborated these results, indicating a consistent pattern of increased antibacterial activity in the blends. XRD analysis revealed a calcium pyrophosphate phase associated with the employed microwave technique, further validated by FTIR spectra. SEM mophology confirmed the blend’s surface roughness, which improved antibacterial efficacy. The microwaved combustion created possible radical species thought to be the cause of the increased antibacterial activity seen. This study highlights the potential of HApM/CNC blends for effective antibacterial applications in water treatment.