bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collapsible tree: interactive web app to present collapsible hierarchies
Authors: Gao Yuan , Patro Rob , Jiang Peng 
Published: October 2024

Abstract

Motivation
A crucial component of intuitive data visualization is presenting a hierarchical tree structure with interactive functions. For example, single-cell transcriptomics studies may generate gene expression values with developmental trajectories or cell lineage structures. Two common visualization methods, t-Distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP), require two separate figures to depict the distribution of cell types and gene expression data, with low-dimension projections that may not capture the hierarchical structures among cells.

Results
Here, we present a JavaScript framework and an interactive web app named Collapsible Tree, which presents values jointly with interactive, expandable, and collapsible lineage structures. For example, the Collapsible Tree presents cellular states and gene expression from single-cell transcriptomics within a single hierarchical plot, enabling comparisons of gene expression across lineages and subtle patterns between sub-lineages. Our framework can facilitate the exploration of complicated value patterns that are not evident in UMAP or t-SNE plots.

Availability and implementation
The Collapsible Tree web interface is available at https://collapsibletree.data2in.net. The JavaScript library source code is available at https://github.com/data2intelligence/collapsible_tree.
Genital coupling and copulatory wounding in the Drosophila rufa species complex: comparison with the D. auraria species complex (Diptera: Drosophilidae)
Authors: Omiya Haruka , Onuma Moe , Awasaki Takeshi , Kamimura Yoshitaka , Sawamura Kyoichi 
Published: October 2024

Abstract
In sexually reproducing animals, genital morphology is usually divergent among closely related species, which can lead to a mismatch of genital coupling (i.e. mechanical isolation). The montium species group of the subgenus Sophophora is the largest clade in Drosophila and is a useful model in which to study the evolution of genital morphology. This group includes a pair of sister clades, i.e. the Drosophila auraria and Drosophila rufa species complexes. The former includes four species with overlapping distributions, and the latter consists of five species that are almost allopatric. The previous study on the D. auraria complex suggested genital co-evolution between sexes (female structures accepting for or protecting from male structures). To test the generality, we analysed the D. rufa complex and three outgroup species. In the D. rufa complex, we detected genital structures corresponding between sexes, and copulatory wounds with species-specific positions. Given that approximately the same number of evolutionary changes in the genital traits were detected in both sexes of the two clades, we conclude that selection pressure to avoid interspecific mating (reproductive character displacement) is not a prerequisite for rapid genital co-evolution.
A rapid and inexpensive 96-well DNA-extraction method from blood using silicon dioxide powder (Glassmilk)
Authors: Vásquez Bonilla Maria Mercedes , Guerrero-Freire Mónica Salome , Ledesma Yanua , Laglaguano Juan Carlos , de Waard Jacobus H 
Published: October 2024

Abstract
We present a rapid high-throughput DNA extraction method for use with EDTA-anticoagulated blood using silicon dioxide (SiO2) powder in a guanidine–HCl solution, hereinafter referred to as “Glassmilk.” The method utilizes a 96-well deep-well plate, enabling DNA extraction from 96 samples in under 3 h. The method integrates cell lysis, washing, elution, and DNA storage within the same well, eliminating the need for DNA transfer. The Glassmilk extraction method is cost-effective and fast, and it avoids expensive or toxic reagents by using only basic lab equipment. The method yielded approximately 40 μg of high-quality DNA from 200 μl of blood. The DNA yield of the Glassmilk method was about 50% higher, and the purity of the DNA was comparable to those obtained using two commercial column-based extraction kits that were used for comparison. The cost per sample was around $1, with the most expensive item being the filter pipette tips, which account for about $0.80 per sample. As we show, the extracted DNA is suitable for downstream applications such as polymerase chain reaction (PCR), PCR-restriction fragment length polymorphism analysis, and qPCR. The method can be adapted for various sample types, including biopsies, fecal samples, cultured cells, and bacteria (see “subprotocols” section), and can also be applied in individual Eppendorf tubes. Our protocol may be useful for basic molecular research in laboratories having limited funds.
Telecoupling cannot be ignored for the forest-based carbon market
Authors: Williams Brooke A , Metzger Jean-Paul , Cho Frankie , Phelan Anya , López-Cubillos Sofía , Bentley Lily K , Fu Bojie , Zhang Yangjian , Liu Yanxu , Johnson Justin , Rhodes Jonathan R 
Published: October 2024

Abstract
Telecoupling interactions between social–ecological systems across large, often global distances drive negative impacts from the forest-based carbon market. However, these negative impacts have been underreported and, therefore, have likely been vastly underestimated. We identify how these unintended negative impacts may occur and provide recommendations for the forest-based carbon market to better account for externalities by prioritizing positive social impact, expanding comprehensive ecological outcomes, and improving the transparency of investments. We call for a carbon market that is designed to account for its global interconnectedness.
An update on pancreatic cancer imaging, staging, and use of the PACT-UK radiology template pre- and post-neoadjuvant treatment
Authors: Corallo Carmelo , Al-Adhami Abdullah S , Jamieson Nigel , Valle Juan , Radhakrishna Ganesh , Moir John , Albazaz Raneem 
Published: October 2024

Abstract
Pancreatic ductal adenocarcinoma continues to have a poor prognosis, although recent advances in neoadjuvant treatments (NATs) have provided some hope. Imaging assessment of suspected tumours can be challenging and requires a specific approach, with pancreas protocol CT being the primary imaging modality for staging with other modalities used as problem-solving tools to facilitate appropriate management. Imaging assessment post NAT can be particularly difficult due to a current lack of robust radiological criteria to predict response and differentiate treatment induced fibrosis/inflammation from residual tumour. This review aims to provide an update of pancreatic ductal adenocarcinoma with particular focus on three points: tumour staging pre- and post-NAT including vascular assessment, structured reporting with introduction of the PAncreatic Cancer reporting Template—UK (PACT-UK) radiology template, and the potential future role of artificial intelligence in the diagnosis and staging of pancreatic cancer.
CACNA1A haploinsufficiency leads to reduced synaptic function and increased intrinsic excitability
Authors: Hommersom Marina P , Doorn Nina , Puvogel Sofía , Lewerissa Elly I , Mordelt Annika , Ciptasari Ummi , Kampshoff Franziska , Dillen Lieke , van Beusekom Ellen , Oudakker Astrid , Kogo Naoki , Dolga Amalia M , Frega Monica , Schubert Dirk , van de Warrenburg Bart P C , Nadif Kasri Nael , van Bokhoven Hans 
Published: October 2024

Abstract
Haploinsufficiency of CACNA1A, encoding the pore-forming α1 subunit of P/Q-type voltage-gated calcium channels, is associated with a clinically variable phenotype ranging from cerebellar ataxia to neurodevelopmental syndromes with epilepsy and intellectual disability.
To understand the pathological mechanisms of CACNA1A loss-of-function variants, we characterized a human neuronal model for CACNA1A haploinsufficiency by differentiating isogenic induced pluripotent stem cell lines into glutamatergic neurons and investigated the effect of CACNA1A haploinsufficiency on mature neuronal networks through a combination of electrophysiology, gene expression analysis and in silico modelling.
We observed an altered network synchronization in CACNA1A+/− networks alongside synaptic deficits, notably marked by an augmented contribution of GluA2 subunit-lacking α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. Intriguingly, these synaptic perturbations coexisted with increased non-synaptically driven activity, as characterized by inhibition of N-methyl-D-aspartate and AMPA receptors on micro-electrode arrays. Single-cell electrophysiology and gene expression analysis corroborated this increased intrinsic excitability through reduced potassium channel function and expression. Moreover, we observed partial mitigation of the CACNA1A+/− network phenotype by 4-aminopyridine, a therapeutic intervention for episodic ataxia type 2. Positive modulation of small conductance calcium-activated potassium channels could reverse the CACNA1A+/− network electrophysiological phenotype.
In summary, our study pioneers the characterization of a human induced pluripotent stem cell-derived neuronal model for CACNA1A haploinsufficiency and has unveiled new mechanistic insights. Beyond showcasing synaptic deficits, this neuronal model exhibited increased intrinsic excitability mediated by diminished potassium channel function, underscoring its potential as a therapeutic discovery platform with predictive validity.
The Substantial Role of Sleep, Stress, and Physical Activity in Persistent High Levels of Fatigue in Patients With Inflammatory Bowel Disease: A Longitudinal Trajectory Study
Authors: Bredero Quirine M , Fleer Joke , Blom Denise M , Bourgonje Arno R , Dijkstra Gerard , Schroevers Maya J 
Published: October 2024

Abstract

Background and Aims
Fatigue is a common and burdensome problem for patients with inflammatory bowel disease (IBD). Previous studies lack insight into the individual variability in fatigue severity and course over time, and the characteristics of patients at risk of severe and persistent fatigue. This study aimed to identify distinct groups of IBD patients based on their level and course of fatigue over 5 years. Subsequently, we examined the relationship between these trajectories, patient characteristics, and trajectories of perceived stress, sleep, and physical activity.

Methods
This longitudinal cohort study used prospectively collected data from the myIBDcoach telemedicine monitoring tool, including 320 IBD patients who completed 3 or more online consultations between 2016 and 2021. Latent class growth analyses were performed to identify distinct trajectories.

Results
We found 5 subgroups with distinct trajectories of fatigue, differing in level and course over time, with 33% of patients experiencing chronic stable and high levels of fatigue. Few differences in patient characteristics were found between trajectories, yet the chronic high fatigue subgroup was more likely to report persistent stable sleep problems, perceived stress, and little physical activity over time compared to the other groups.

Conclusions
Distinct subgroups of IBD patients can be identified based on longitudinal fatigue trajectories. The relatively stable levels of fatigue, stress, sleep, and physical activity suggest that a one-time screening of patients on these topics may be sufficient to identify those at risk. Interventions aiming to reduce fatigue should target persistent stress, sleep problems, and low levels of physical activity.
Response of hibiscus mealybug (Hemiptera: Pseudococcidae) to citrus volatiles induced by mechanical injury
Authors: Olabiyi David , Diepenbrock Lauren M , Martini Xavier , Stelinski Lukasz L 
Published: October 2024

Abstract
Hibiscus mealybug, Nipaecoccus viridis (Newstead) (Hemiptera: Pseudococcidae), is a recent invasive pest of citrus and many other crops in Florida. Nipaecoccus viridis attacks all above ground parts of citrus trees and heavy infestation can cause leaf drop and premature abortion of developing fruits. We quantified greater captures of N. viridis in cardboard band traps on areas of citrus trees that were intentionally injured by mechanical rasping of epidermal tissues as compared with similar but uninjured citrus branches. Direct field collection of headspace volatiles from mechanically injured or intact citrus branches revealed both qualitative and quantitative differences. Certain volatiles (γ-terpinene, citronellal, citronellyl acetate, β-E-farnesene, α-humulene, and α-E-E-farnesene) were only present in samples from damaged citrus branches. Behavioral assays using a laboratory Y-tube olfactometer revealed attraction of N. viridis to volatiles associated with mechanical damage of citrus including synthetic β-ocimene, γ-terpinene, sabinene, isomers of farnesene, and citronellal when loaded into lures at either of 2 concentrations (0.01 or 0.1 µg/µl). Subsequent field trapping experiments confirmed increased captures of various life stages of N. viridis in cardboard band traps baited with a 10.0 µg/µl concentration of farnesene:ocimene:sabinene blend (in 7:13:17 ratio), as well as those releasing either farnesene or ocimene alone at this same concentration, as compared with the mineral oil (diluent) negative control. Our results indicate that common plant related terpenes released by citrus following mechanical damage may be useful for development of an effective monitoring trap for N. viridis.
Entrepreneurial Reluctance: Talent and Firm Creation in China
Authors: Bai Chong-En , Jia Ruixue , Li Hongbin , Wang Xin 
Published: October 2024

Abstract
This paper examines the correlation between cognitive ability and firm creation. Drawing on administrative college admission data and firm registration records in China, we investigate who had created firms by their mid-thirties. We find a clear pattern of entrepreneurial reluctance: given the same backgrounds, individuals with higher college entrance exam scores are less likely to create firms. Through an exploration of firm performance, alternative career trajectories and variations across regions, we propose an explanation: the ability represented by exam scores is useful across occupations, yet higher-scoring individuals are attracted to waged jobs, particularly those of the state sector.
Fully automated measurements of echocardiographic mechanical dispersion using deep learning: enhanced prediction of ventricular arrhythmias in a large heart failure cohort
Authors: Melichova D , Nyberg J , Nguyen T M , Salte I M , Brunvand H , Haugaa K , Edvardsen T , Dalen H , Lovstakken L , Ostvik A , Grenne B 
Published: October 2024

Abstract

Background
Assessment of left ventricular (LV) myocardial deformation by strain echocardiography has shown improved prognostic value over LV ejection fraction (LVEF). Mechanical dispersion (MD) by strain reflects deformation heterogeneity. Also, MD is a marker of ventricular arrhythmia (VA) that improves risk prediction independently of LVEF in patients with heart failure. However, to analyze MD is time consuming and operator-dependent, and clinical use remains limited.

Purpose
We aimed to investigate the performance of a novel deep learning (DL) based method for fully automated measurements of MD and evaluate its prognostic utility in patients with heart failure compared to a conventional speckle tracking application.

Methods
In this prospective multicenter follow up study, the IMPROVE study, we consecutively included patients with recently diagnosed heart failure of all cause with LVEF ≤ 40%. Echocardiograms, ECG, blood samples and clinical data were acquired during index hospitalization. All patients were treated according to contemporary guidelines with optimal medical therapy and revascularization if necessary. Two experienced cardiologists recorded all echocardiograms using Vivid E9 or E95 scanners. We obtained data regarding sudden cardiac death, ventricular arrhythmia and appropriate shock from the ICD from medical records and ICD recordings. The primary endpoint was sudden cardiac death or ventricular arrhythmia (SCD/VA) during follow-up. The prognostic value of DL-based and reference MD measurements was assessed through survival statistics.

Results
We included 492 patients (mean ± SD 73 ± 13 years old, 32% females). Follow-up time was median (IQR) 5 (3) years. The incidence of SCD/VA was 9% (n=45). Patients with MD ≥70ms had increased risk of SCD/VA both by DL-based and reference measurements (both p &lt;0.001). Furthermore, automated MD measurements using DL had higher prognostic value (HR 4.3) compared to manual reference measurements (HR 3.1) (p &lt;0.001).

Conclusion
Fully automated measurements of MD using a novel DL method was fast, feasible, and improved prediction of SCD/VA in patients with heart failure and reduced LVEF. The integration of DL measurements may facilitate the clinical implementation of MD assessment and improve risk prediction in echocardiography.
Serial changes in left atrial strain in symptomatic obstructive hypertrophic cardiomyopathy treated with mavacamten: insights from VALOR-HCM trial
Authors: Desai M , Okushi Y , Popovic Z , Wolski K , Owens A , Geske J , Saberi S , Wang A , Cremer P , Lakdawala N , Tower-Rader A , Fermin D , Naidu S , Lampl K , Sehnert A 
Published: October 2024

Abstract

Background
In severely symptomatic patients with obstructive hypertrophic cardiomyopathy (HCM), the VALOR-HCM phase 3 randomized, double-blind, placebo-controlled clinical trial demonstrated that mavacamten, a cardiac myosin inhibitor, reduces the eligibility for septal reduction therapy with sustained improvement in left ventricular (LV) outflow tract gradients and symptoms. Mavacamten also resulted in favorable cardiac remodeling, including improvement in left atrial volume index (LAVI), LV diastolic function, and biomarkers (NT-proBNP and troponin T). However, the impact of mavacamten on LA function is not known.

Objective
We sought to assess serial changes in LA strain measures in patients enrolled in the VALOR-HCM trial.

Methods
VALOR-HCM included 112 symptomatic obstructive HCM patients (mean age 60 years, 51% male). Patients assigned to mavacamten at baseline (n=56) continued therapy for 56 weeks and those assigned to placebo crossed over to mavacamten (n=52) from week 16-56 (40-week exposure). Echocardiographic LA strain assessment was performed according to the current American and European guideline recommendations, using a vendor-neutral post processing software. For assessment of LA strain components (reservoir, conduit, and contraction), the non-foreshortened apical 4-chamber view was utilized. The zero reference was set at end-diastole.

Results
Serial changes in LAVI and all components of mean LA strain from baseline to week 56 are shown in the Figure. At baseline, LAVI and all mean LA strain values were worse than reported normal mean thresholds. There was a continued and significant improvement in all 3 LA strain values, from baseline to week 56, along with a significant reduction in LAVI. Improvement in LAVI was seen earlier than improvements in LA strain. There was a significant inverse correlation between change in mean LAVI and LA reservoir strain from baseline to week 56 (r= -0.42, p&lt;0.001).

Conclusions
In the VALOR-HCM trial, average LAVI and baseline LA strain values were significantly worse than reported normal thresholds. Treatment with mavacamten resulted in an improvement in LAVI and LA strain values from baseline through week 56 suggesting a sustained favorable impact on cardiac remodeling. The advantageous cardiac remodeling associated with long-term treatment with mavacamten may in turn have a favorable impact on the observed high burden of atrial tachyarrhythmias in HCM.Serial changes in LA strain in VALOR-HCM
Atrial cardiomyopathy in postmenopausal female healthcare professionals- a single-center study
Authors: Borizanova-Petkova A , Kinova E , Goudev A 
Published: October 2024

Abstract

Background
Atrial cardiomyopathy (ACM) is a new clinical entity with significant importance, because of its potential to be a determinant of heart failure, atrial fibrillation and thromboembolic complications¹. Defining different atrial phenotypes is challenging, because of the lack of consensus for the diagnosis of ACM²'³. Menopausal transition is associated with adverse changes in women’s health such as obesity and hypertension, both known risk factors for ACM⁴.

Aim
To investigate left atrial (LA) structural and functional echocardiographic parameters in postmenopausal female healthcare professionals and to define atrial phenotype in this population.

Methods
Consecutive asymptomatic, postmenopausal, middle-age women (n=105), healthcare professionals from our hospital, were separated in 3 groups according to co-morbidities : with obesity (n=50), obesity and hypertension (n=24), healthy control (n=31). All patients underwent 2D echocardiographic examination with volumetric and speckle tracking analysis of LA.

Results
There were significant differences in LA structural and functional indices between 3 groups- table 1. Higher body mass index was associated with increased LA volume index (p&lt;0.001, r= 0.56), reduced LA total emptying fraction- LATEF (p&lt;0.001, r= -0.62), Peak atrial longitudinal strain-PALS (p&lt;0.001, r= -0.59 ) and Peak atrial contractile strain- PACS (p&lt;0.001, r= 0.56 ). ROC analysis was performed for identifying atrial phenotype of obese women with hypertension: LAVi 16.5ml/m2,(sensitivity 0.833, specificity 0.839, AUC 0.875), PALS 46.55% (sensitivity 0.903, specificity 0.875, AUC 0.951), PACS -20.75% (sensitivity 0.806, specificity 0.708, AUC 0.855), LATEF 69% (sensitivity 0.903, specificity 0.792, AUC 0.920)- figure 1.

Conclusion
Postmenopausal women with obesity and hypertension are at risk for asymptomatic ACM. Further investigations are needed to confirm this concept.
Comparison of left atrial and left atrial appendage mechanics in patients with ischaemic strokes of different aetiologies
Authors: Mao Y K , Yang Y , Ma M M , Yu C , Wang Y , Jiang R H , Jiang C Y 
Published: October 2024

Abstract

Background
Left atrial (LA) and left atrial appendage (LAA) mechanical dysfunction account for an increase in cardioembolic stroke risk in atrial fibrillation (AF), and more recently in individuals in sinus rhythm (SR). However, the exact contribution of LA and LAA to the pathogenesis of thromboembolic events is not fully understood. Here, we aimed to assess the alterations of LA and LAA mechanics in different stroke subtypes.

Methods
We recruited three groups of participants: patients with paroxysmal or persistent AF with a history of stroke (AF-stroke, n=69,respectively), individuals in SR with no history of AF but with acute ischaemic stroke(non-AF stroke,n=46); individuals with no history of AF or stroke(control group,n=17). Patients with AF were further categorized into sinus rhythm group (AF-stroke-SR,n=24) and AF rhythm group(AF-stroke-AF, n=45) according to the rhythm at the time of echocardiography. Using speckle-tracking echocardiography, global longitudinal strain (GLS) and mechanical dispersion (MD) of LA and LAA were measured in all patients. Mechanical dispersion was defined as the standard deviation of the time to peak of the regional strain corrected by R-R interval.

Results
Patients with AF-stroke demonstrated prominently impaired LA and LAA mechanics(LA GLS: 20±6%(AF-stroke-SR),11±4%(AF-stroke-AF); LA MD: 9±3%,11±3%; LAA GLS: 15±3%,11±4% ; LAA MD: 11±4%,12±3% ,respectively) compare with those with non-AF stroke and controls (LA GLS:35±8%, 41±11%;LA MD,6±2%, 4±2%; LAA GLS:21±5%, 23±7%; LAA MD:8±4%, 7±3%,respectively) (all p&lt;0.01). Interestingly, LA and LAA mechanical function was not significantly different between patients with non-AF strokes and the control group. In multivariable analysis, only AF-strokes were independently associated with LA and LAA GLS after adjusting for age and comorbidities (both P&lt;0.01).

Conclusions
Mechanical dysfunction of LA and LAA might play a greater role in pathogenesis of strokes related to AF rather than non-AF strokes.