bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving the 3D representation of plant architecture and parameterization efficiency of functional–structural tree models using terrestrial LiDAR data
Authors: Bekkers Vera , Evers Jochem , Lau Alvaro 
Published: December 2024

Abstract
Functional–structural plant (FSP) models are useful tools for understanding plant functioning and how plants react to their environment. Developing tree FSP models is data-intensive and measuring tree architecture using conventional measurement tools is a laborious process. Light detection and ranging (LiDAR) could be an alternative nondestructive method to obtain structural information about tree architecture. This research investigated how terrestrial LiDAR (TLS)-derived tree traits could be used in the design and parameterization of tree FSP models. A systematic literature search was performed to create an overview of tree parameters needed for FSP model development. The resulting structural parameters were compared to LiDAR literature to get an overview of the possibilities and limitations. Furthermore, a tropical tree and Scots pine FSP model were selected and parametrized with TLS-derived parameters. Quantitative structural models were used to derive the parameters and a total of 37 TLS-scanned tropical trees and 10 Scots pines were included in the analysis. Ninety papers on FSP tree models were screened and eight papers fulfilled all the selection criteria. From these papers, 50 structural parameters used for FSP model development were identified, from which 28 parameters were found to be derivable from LiDAR. The TLS-derived parameters were compared to measurements, and the accuracy was variable. It was found that branch angle could be used as model input, but internode length was unsuitable. Outputs of the FSP models with TLS-derived branch angle differed from the FSP model outcomes with default branch angle. Results showed that it is possible to use TLS for FSP model inputs, although with caution as this has implications for the model variable outputs. In the future, LiDAR could help improve efficiency in building new FSP models, increase the accuracy of existing models, add metrics for optimization, and open new possibilities to explore previously unobtainable plant traits.
The scalable variant call representation: enabling genetic analysis beyond one million genomes
Authors: Poterba Timothy , Vittal Christopher , King Daniel , Goldstein Daniel , Goldstein Jacqueline I , Schultz Patrick , Karczewski Konrad J , Seed Cotton , Neale Benjamin M 
Published: December 2024

Abstract

Motivation
The Variant Call Format (VCF) is widely used in genome sequencing but scales poorly. For instance, we estimate a 150 000 genome VCF would occupy 900 TiB, making it costly and complicated to produce, analyze, and store. The issue stems from VCF’s requirement to densely represent both reference-genotypes and allele-indexed arrays. These requirements lead to unnecessary data duplication and, ultimately, very large files.

Results
To address these challenges, we introduce the Scalable Variant Call Representation (SVCR). This representation reduces file sizes by ensuring they scale linearly with samples. SVCR’s linear scaling relies on two techniques, both necessary for linearity: local allele indices and reference blocks, which were first introduced by the Genomic Variant Call Format. SVCR is also lossless and mergeable, allowing for N + 1 and N + K incremental joint-calling. We present two implementations of SVCR: SVCR-VCF, which encodes SVCR in VCF format, and VDS, which uses Hail’s native format. Our experiments confirm the linear scalability of SVCR-VCF and VDS, in contrast to the super-linear growth seen with standard VCF files. We also discuss the VDS Combiner, a scalable, open-source tool for producing a VDS from GVCFs and unique features of VDS which enable rapid data analysis. SVCR, and VDS in particular, ensure the scientific community can generate, analyze, and disseminate genetics datasets with millions of samples.

Availability and implementation
https://github.com/hail-is/hail/.
Functional and comparative analysis of the FeII/2-oxoglutarate-dependent dioxygenases without using any substrate
Authors: Das Susmita , Shahnaz Nafeesa , Keerthana Carmel , Ranjan Saumya , Seenivasan Gayathri , Tuti Nikhil , Shaji Unnikrishnan P , Meur Gargi , Anindya Roy 
Published: December 2024

Abstract
Non-haem iron (FeII) and 2-oxoglutarate(2OG)-dependent dioxygenases catalyse various biological reactions. These enzymes couple the oxidative decarboxylation of 2OG to the hydroxylation of the substrates. While some of these enzymes are reported to have multiple substrates, the substrate remains unknown for many of the enzymes. However, in the absence of the substrate, these enzymes catalyse oxidative decarboxylation of 2OG and generate succinate. We have determined succinate level to monitor this uncoupled reaction and compared the uncoupled 2OG turnover of different FeII/2OG-dependent dioxygenases. The uncoupled succinate production was used to verify the NiII-mediated inhibition and functionality of human dioxygenase ALKBH6.
Identification of Pappa and Sall3 as Gli3 direct target genes acting downstream of cilia signaling in corticogenesis
Authors: Basu Shinjini , Mautner Lena , Whiting Kae , Hasenpusch-Theil Kerstin , Borkowska Malgorzata , Theil Thomas 
Published: December 2024

Abstract
The cerebral cortex is critical for advanced cognitive functions and relies on a vast network of neurons to carry out its highly intricate neural tasks. Generating cortical neurons in accurate numbers hinges on cell signaling orchestrated by primary cilia to coordinate the proliferation and differentiation of cortical stem cells. While recent research has shed light on multiple ciliary roles in corticogenesis, specific mechanisms downstream of cilia signaling remain largely unexplored. We previously showed that an excess of early-born cortical neurons in mice mutant for the ciliary gene Inpp5e was rescued by re-introducing Gli3 repressor. By comparing expression profiles between Inpp5e and Gli3 mutants, we here identified novel Gli3 target genes. This approach highlighted the transcription factor gene Sall3 and Pappalysin1 (Pappa), a metalloproteinase involved in IGF signaling, as upregulated genes in both mutants. Further examination revealed that Gli3 directly binds to Sall3 and Pappa enhancers and suppresses their activity in the dorsal telencephalon. Collectively, our analyses provide important mechanistic insights into how primary cilia govern the behavior of neural stem cells, ultimately ensuring the production of adequate numbers of neurons during corticogenesis.
Myocardial bridging resulting in an atypical acute coronary syndrome in a young athlete: a case report
Authors: Coulibaly Sophie , Genet Thibaud , Bisson Arnaud , Bernard Anne , Ivanes Fabrice 
Published: December 2024

Abstract

Background
Myocardial bridging (MB) is considered a frequent and benign condition. However, some patients may experience symptoms. The recent ESC guidelines on sports participation provide guidance on the management of these symptomatic patients with MB but do not provide guidance in the presence of another cardiac pathology.

Case summary
A 14-year-old-male was admitted for ongoing chest pain and palpitations. He practiced rowing at a competitive level and had an episode of exercise-induced paroxysmal atrial fibrillation (AF) a month ago. A 12-lead electrocardiogram and biomarkers orientated toward an acute coronary syndrome. Transthoracic echocardiography was normal. Cardiac magnetic resonance imaging ruled out the hypothesis of myocarditis and showed no ischemic scar. A coronary computed tomography scan showed a significant MB of the left anterior descending coronary artery. We introduced a beta-blocker and monitored the absence of inducible ischaemia with an exercise echocardiography. Our conclusion was a myocardial infarction with non-obstructive coronary arteries due to MB and adrenergic AF. Return to rowing practice including competitions was allowed under beta-blocker therapy. The 6-year follow-up showed no recurrence of AF under treatment. The patient kept on training and competing, though at a lower level.

Discussion
This atypical case demonstrates that the so-called benign MB may become malignant, in particular in conjunction with rapid non-physiologic heart rate, and that dealing with this abnormality in athletes remains difficult despite the latest guidelines. Safe return-to-play and competition remain, however, possible under medical therapy if the patient is asymptomatic and has no inducible ischaemia.
Incidental finding of MELAS in a young woman with decompensated heart failure and end stage kidney disease: a case report
Authors: Sari Novi Yanti , Sia Ching-Hui , Wong Raymond Ching Chiew , Lin Weiqin , Lim Yoke Ching 
Published: December 2024

Abstract

Background
Mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) is a rare and progressive mitochondrial disorder characterized by multi-systemic involvement. This disease manifests in various clinical manifestations, with heart and kidney disorders being among the most common. Accurate diagnosis of MELAS often necessitates a range of complex investigations. Prompt and comprehensive management can significantly improve the prognosis of the disease.

Case summary
A 40-year-old female presented with elevated blood pressure (BP) associated with shortness of breath prior to dialysis. She was found to be hypertensive with a systolic BP of 190 mmHg with prominent signs of congestion. Laboratory examination showed elevated troponin and NT-proBNP. Arterial blood gas revealed severe lactic acidosis, which prompted urgent dialysis. On the latest admission, an echocardiogram showed a left ventricular ejection fraction of 50% with much thickened myocardium compared with the previous study. Linking the past history of hearing impairment, kidney disease, giddiness, and progression of myocardial thickness warranted a genetic test, which revealed the diagnosis of MELAS.

Discussion
This case involved a patient initially diagnosed with hypertensive heart disease based on asymptomatic left ventricular hypertrophy. Further deterioration led to the identification of MELAS syndrome through extensive diagnostic evaluation. This highlights the importance of considering mitochondrial diseases in unexplained cardiac symptoms, especially in younger patients, for timely and appropriate management.
Caval vein obstruction resulting in right to left shunt and desaturation post–endocardial pacing implantation in a 3-year old: a case report
Authors: Poffley Emma , Mortensen Kristian , Starling Luke , Mangat Jasveer , Marek Jan 
Published: December 2024

Abstract

Background
Superior caval vein obstruction is a rare complication of endocardial pacing lead implantation that can result in a right to left shunt.

Case summary
A 3-year-old child with type 2 Brugada syndrome presented with mild cyanosis post–endocardial pacing implantation due to evolutionary right superior caval vein obstruction. This obstruction resulted in a right to left shunt across a previously unrecognized patent levo-atrial cardinal vein associated with partial anomalous pulmonary venous drainage. The patient underwent endocardial pacing explantation, balloon dilation and stenting of the right superior caval vein, banding of the levo-atrial cardinal vein to left upper pulmonary vein venous channel, and implantation of an epicardial pacing system.

Discussion
Levo-atrial cardinal vein and partial anomalous pulmonary venous drainage with dual drainage can go undetected on cardiac imaging and may not ever cause symptoms (high left-to-right shunt or cyanosis). The levo-atrial cardinal vein and associated partial anomalous venous drainage with dual drainage was missed on multiple occasions and with multiple imaging modalities in our patient. Blood flow may not be detected in a small calibre or collapsed levo-atrial cardinal vein with pulmonary venous connection when the pulmonary vein remains widely patent and connected to the left atrium. Detailed comprehensive echocardiography of any child referred for cardiac intervention should include pulsed wave Doppler and colour flow mapping interrogation of the innominate vein from the suprasternal approach.
Monitoring and modulating cardiac bioelectricity: from Einthoven to end-user
Authors: De Coster Tim , Nobacht Arman , Oostendorp Thom , de Vries Antoine A F , Coronel Ruben , Pijnappels Daniël A 
Published: December 2024

Abstract
In 2024, we celebrate the 100th anniversary of Willem Einthoven receiving the Nobel Prize for his discovery of the mechanism of the electrocardiogram (ECG). Building on Einthoven’s legacy, electrocardiography allows the monitoring of cardiac bioelectricity through solutions to the so-called forward and inverse problems. These solutions link local cardiac electrical signals with the morphology of the ECG, offering a reversible connection between the heart’s electrical activity and its representation on the body surface. Inspired by Einthoven’s work, researchers have explored the transition from monitoring to modulation of bioelectrical activity in the heart for the development of new anti-arrhythmic strategies, e.g. via optogenetics. In this review, we demonstrate the lasting influence that Einthoven has on our understanding of cardiac electrophysiology in general, and the diagnosis and treatment of cardiac arrhythmias in particular.
Optimal experimental design for full waveform inversion using a wavenumber sampling criterion—part 1 : 2-D to methodological development
Authors: Abdellaziz Amine , Brossier Romain , Métivier Ludovic , Oudet Édouard 
Published: December 2024

SUMMARY
Due to the complexity of seismic surveys, different strategies have been investigated to optimize characteristics of the acquisition in order to fulfil various criteria, most intuitively those related to the operational and economical aspects of the survey. However the question can also be approached from an imaging perspective. Andrzej Kikjo’s seminal work on the optimal design of seismic stations for earthquake localization, dating back to the seventies, has encouraged several works related to optimal acquisition in exploration geophysics. A common choice for the optimality criterion is the conditioning of the Hessian operator. In our work, we have chosen our optimality criterion to be the regularity of the wavenumber sampling at a specified target: using the theory of diffraction tomography we can estimate the wavenumber sampling at a target point and we note that for a regularly spaced acquisition the corresponding sampling is not regular. In our target-oriented approach, we want to find the best positions of sources and receivers to improve the regularity of this sampling. We develop our work in the context of full waveform inversion, although our approach is more general. Using a simple formula for the estimation of the wavenumber points we are able to get a geometric characterization of the accessible wavenumber space that helps us define its envelope. We describe the problem as finding the geometry for which the sampling points are regular in terms of spacing inside this envelope and to that end we incorporate in our workflow the notion of centroidal Voronoi tessellation, a tool from computational geometry that links the regularity of the sampling to the uniformity of the domain tessellation. To assess the uniformity of the tessellation we utilize an energy function the minimal values of which provide regular samplings. By combining this energy function with a map that estimates the wavenumber content of an acquisition we define a new objective function that assess the quality of such acquisition with regards to our regularity criterion. We then mathematically express our problematic as a minimization problem which we solve using local optimization strategies. In this article we focus on the theoretical aspect of our method and validate it through numerical examples of varying complexities in the 2-D cases: when comparing optimized acquisitions with regular ones the results show a consistent local improvement of the quality of the inversion with the optimized geometries at the target and motivates the exploitation of the method for target-oriented applications such as seismic monitoring. The subsequent extension to 3-D and application to more realistic industrial examples will be discussed in a companion paper.
Dismantling democratic change in Asia: Modalities and weapons of choice
Authors: Shah Dian A H 
Published: December 2024

Abstract
The global phenomenon of democratic decay and constitutional retrogression has garnered intense scrutiny, particularly over the past five years. This article demonstrates that such patterns have also emerged in several Asian countries that have undergone democratic political change in the last twenty-five years or so. Drawing on illustrations from various jurisdictions across South Asia and Southeast Asia, it explores how political actors have assaulted and eroded democratic constitutional commitments following political change, even when—in some cases—they pledged to uphold constitutional democracy. This article thus illustrates that the dismantling of democratic change in Asia is multi-dimensional and that it reflects three main imperatives: consolidation (of political authority), dissolution (of institutional accountability), and suppression (of political competition). It also brings to light the range of actors involved and tools used in the dismantling process. Crucially, this article highlights that constitutional amendments have not been a pervasive “weapon of choice” in targeting democratic commitments; instead, anti-democrats have utilized ordinary legislation, nonjudicial interpretation, and incremental changes in political conventions. Ultimately, as this article shows both explicitly and implicitly, “variety”—in imperatives, actors, tools, and interests at stake—is a key aspect to consider in understanding, identifying, and suppressing efforts to dismantle Asia’s democratic change.
A scoring system to predict resistance to ceftolozane/tazobactam in respiratory isolates of Pseudomonas aeruginosa
Authors: Karadogan Eda , Sertcelik Ahmet , Dizman Gulcin Telli , Uzar Hanife , Hazirolan Gulsen , Cakir Banu , Metan Gokhan 
Published: December 2024

Abstract

Objectives
To develop a scoring system to predict resistance to ceftolozane/tazobactam in Pseudomonas aeruginosa strains isolated from respiratory specimens.

Methods
A case–control study was conducted to evaluate the risk factors associated with resistance to ceftolozane/tazobactam. Patients with P. aeruginosa were defined as cases if they had ceftolozane/tazobactam-resistant strains, whereas those with ceftolozane/tazobactam-susceptible strains were defined as test-negative controls. A predictive scoring system based on binary logistic regression coefficients was formulated to predict resistance to ceftolozane/tazobactam. The score’s performance was assessed using ROC curves and AUC. The sensitivity, specificity and predictive values of the score were determined on the basis of a cut-off point, using the Youden index.

Results
Ceftolozane/tazobactam resistance was detected in 18.4% of P. aeruginosa isolates from 473 patients. In multivariate analysis, a history of bronchoscopy [OR (95% CI) = 2.1 (1.1–4.3), P = 0.035], invasive mechanical ventilation [OR (95% CI) = 2.4 (1.2–4.5), P = 0.009], colistin/polymyxin B use [OR (95% CI) = 3.2 (1.8–5.7), P &lt; 0.001] and fluoroquinolone use [OR (95% CI) = 2.3 (1.1–4.8), P = 0.024] in the preceding month prior to P. aeruginosa isolation were significantly associated with ceftolozane/tazobactam resistance. The AUC (95% CI) of the score was 0.734 (0.675–0.794), with a sensitivity of 69%, specificity of 71.8%, positive predictive value of 35.5% and negative predictive value of 91.1% at the cut-off point of 2, out of a range of 0–5.

Conclusions
In respiratory tract infections caused by P. aeruginosa, use of the proposed scoring system may reduce inappropriate use of ceftolozane/tazobactam in empirical treatment.
A protein corona modulates the function of mineralization-competent matrix vesicles
Authors: Cominal Juçara Gastaldi , Gobbi Sebinelli Heitor , Hayann Larwsk , Nogueira Lucas Fabrício Bahia , Cruz Marcos Antonio Eufrásio , Mello Maryanne Trafanni , da Silva Andrilli Luiz Henrique , Bolean Maytê , Ramos Ana Paula , Mebarek Saida , Bottini Massimo , Millán José Luis , Ciancaglini Pietro 
Published: December 2024

Abstract
Mineralizing cells release a special class of extracellular vesicles known as matrix vesicles (MV), crucial for bone mineralization. Following their release, MV anchor to the extracellular matrix (ECM), where their highly specialized enzymatic machinery facilitates the formation of seed mineral within the MV’s lumen, subsequently releasing it onto the ECM. However, how MV propagate mineral onto the collagenous ECM remains unclear. In this study, we address these questions by exploring the “protein corona” paradigm whereby nanoparticles entering a biological milieu become cloaked by a corona of soluble proteins modifying their biological functions. We isolated native MV from the growth plates of chicken embryos. After removing the protein corona from the native MV using high ionic strength buffer, we obtained shaved MV. Reconstituted MVs were produced by incubating shaved MV with the removed protein corona constituents. Our results show that both the removal and reconstitution of protein corona significantly affect the biochemical and physicochemical properties of MV, resulting in 3 well-defined groups. Shaved MV exhibited an increase in tissue nonspecific alkaline phosphatase (TNAP) activity and a decrease in mineral deposition compared to native MV. Reconstituted MV partially recovered these functions, showing a reduction of TNAP activity and mineral deposition compared to native MV. Furthermore, changes in the protein corona affect the MV ability to anchor to the collagenous ECM, which is crucial for initiating the propagation of the mineral phase within this organic matrix. Proteomic analyses revealed changes in the protein profile of the MV resulting from the removal of the protein corona, indicating that shaved proteins were primarily related to external structural and ECM organization and catabolism. These findings underscore the role of the protein corona in modulating the mineralization capabilities of MV. Understanding these interactions could lead to new therapeutic strategies for enhancing bone repair and regeneration.