bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of Soft Rock Anisotropy Based on Three-point Bending Experiments
Authors: Yao Guoming , Li Weiguo , Lu Yunhui , Song Xinhong , Yu Zhehan , Chen Jiancheng , Yu Wenhai , Wu Yonghong 
Published: November 2024

Abstract
Under the influence of its layered structure, soft rock exhibits significant non-homogeneity in its mechanical properties and a certain degree of anisotropy in its fracture characteristics. In this paper, we utilize GDEM-Pdyna to conduct numerical simulations of three-point bending experiments on soft rocks with various layered structures. The research focuses on examining the mechanical properties and anisotropic characteristics of soft rocks subjected to three-point bending tests with different prefabricated fracture angles and layered angles. The experimental results indicate that as the prefabricated crack angle increases, the peak strength required for the failure of the soft rock gradually increases. The load-displacement curves and deformation field maps for soft rocks with horizontal and vertical grain layers under three-point bending loading show a certain degree of consistency. Additionally, with an increase in the angle of the laminae, both the peak load and peak displacement during the loading process gradually decrease, along with a corresponding decrease in fracture toughness. This study provides valuable insights into the mechanical behavior and anisotropic characteristics of soft rocks, contributing to a better understanding of their response under different loading conditions and structural configurations.
Study of Collaborative Space in Rebar Tying Robotic Systems
Authors: He Jun , Niu Yuqian , Qin Ze , Yin Hao , Yang Xingyu 
Published: November 2024

Abstract
In the process of rebar tying operations conducted by multiple robots, the flexibility and operability of the robot’s end effector directly influence the overall performance of the rebar tying system. This reflects the crucial role of the coordinated working capability of multiple robots in the trajectory planning of the rebar tying system. Utilizing an eight degrees of freedom rebar tying system composed of two collaborative robots and a truss structure, the D-H (Denavit-Hartenberg) dynamic model for each robotic arm is established. The working area of the system is ascertained via Monte Carlo methods. Flexibility and operability are adopted as metrics to evaluate the system’s performance, subsequently leading to the formulation of a mathematical model for assessing the system’s flexibility. MATLAB is employed to delineate the robotic working range and simulate analysis of flexibility and operability when operating on the rebar tying plane, yielding an intuitive distribution of system flexibility. By analysing the distribution of flexibility and operability across the working plane at varying robot spacing intervals, an optimal robot movement distance can be determined. This ensures that during operational tasks, the rebar tying system not only possesses a larger total working area but also maintains a high level of flexibility and operability within the collaborative region, thereby fulfilling the objective of enhancing workspace utilization and improving rebar tying efficiency.
A review of potential biological controls for Ailanthus altissima
Authors: Miles Harrison H , Salom Scott , Shively Timothy J , Bielski Jason T , McAvoy Thomas J , Fearer Carrie J 
Published: November 2024

Abstract
Ailanthus altissima (Mill.) Swingle (Sapindales: Simaroubaceae) (tree-of-heaven) is an invasive tree species first introduced to the United States in 1784. With high rates of sexual reproduction, rapid growth, and prolific vegetative sprouting, A. altissima is an aggressive competitor that reduces native plant diversity and is difficult to manage beyond small-scale infestations. In the United States, the issues associated with Ailanthus management were compounded by the 2014 arrival of Lycorma delicatula (spotted lanternfly). Lycorma delicatula coevolved with A. altissima, its primary host, in eastern Asia. Suppression of A. altissima is recommended as an important strategy to slow the spread of L. delicatula. Due to the inadequacy of traditional control methods to manage A. altissima, biological controls are desired. Several potential biological control agents have been proposed for A. altissima. This review discusses current research on several promising candidates, specifically a native fungus, Verticillium nonalfalfae Inderb. et al. (Hypocreales: Plectosphaerellaceae); a trunk-boring beetle, Eucryptorrhynchus brandti (Harold) (Coleoptera: Curculionidae: Cryptorrhynchinae); and an eriophyid mite, Aculops ailanthi (Lin-Fuping, Jin-Changle & Kuang-Haiya) (Arachnida: Eriphyidae). A list of other possible biological control agents is also provided. We discuss unanswered questions for each species, the limits of biological controls in this system, and call for further research on integrated pest management practices for managing A. altissima.
SIngle cell level Genotyping Using scRna Data (SIGURD)
Authors: Grasshoff Martin , Kalmer Milena , Chatain Nicolas , Kricheldorf Kim , Maurer Angela , Weiskirchen Ralf , Koschmieder Steffen , Costa Ivan G 
Published: November 2024

Abstract
Motivation: By accounting for variants within measured transcripts, it is possible to evaluate the status of somatic variants using single-cell RNA-sequencing (scRNA-seq) and to characterize their clonality. However, the sparsity (very few reads per transcript) or bias in protocols (favoring 3’ ends of the transcripts) makes the chance of capturing somatic variants very unlikely. This can be overcome by targeted sequencing or the use of mitochondrial variants as natural barcodes for clone identification. Currently, available computational tools focus on genotyping, but do not provide functionality for combined analysis of somatic and mitochondrial variants and functional analysis such as characterization of gene expression changes in detected clones. Results: Here, we propose SIGURD (SIngle cell level Genotyping Using scRna Data) (SIGURD), which is an R-based pipeline for the clonal analysis of scRNA-seq data. This allows the quantification of clones by leveraging both somatic and mitochondrial variants. SIGURD also allows for functional analysis after clonal detection: association of clones with cell populations, detection of differentially expressed genes across clones, and association of somatic and mitochondrial variants. Here, we demonstrate the power of SIGURD by analyzing single-cell data of colony-forming cells derived from patients with myeloproliferative neoplasms.
The ISCB competency framework v. 3: a revised and extended standard for bioinformatics education and training
Authors: Brooksbank Cath , Brazas Michelle D , Mulder Nicola , Schwartz Russell , Ras Verena , Morgan Sarah L , Lloret Llinares Marta , Carvajal López Patricia , Larcombe Lee , Ghouila Amel , Hancocks Tom , Satagopam Venkata , De Las Rivas Javier , Mazandu Gaston , Gaeta Bruno 
Published: November 2024

Abstract

Motivation
Developing competency in the broad area of bioinformatics is challenging globally, owing to the breadth of the field and the diversity of its audiences for education and training. Course design can be facilitated by the use of a competency framework—a set of competency requirements that define the knowledge, skills and attitudes needed by individuals in (or aspiring to be in) a particular profession or role. These competency requirements can help to define curricula as they can inform both the content and level to which competency needs to be developed. The International Society for Computational Biology (ISCB) developed a list of bioinformatics competencies in 2014, and these have undergone several rounds of improvement. In consultation with a broad bioinformatics training community, these have now been further refined and extended to include knowledge skills and attitudes, and mappings to previous and other existing competency frameworks.

Results
Here, we present version 3 of the ISCB competency framework. We describe how it was developed and how to access it, as well as providing some examples of how it has been used.

Availability and implementation
The framework is openly accessible at https://competency.ebi.ac.uk/framework/iscb/3.0/competencies.
Dynamic modelling of signalling pathways when ordinary differential equations are not feasible
Authors: Rachel Timo , Brombacher Eva , Wöhrle Svenja , Groß Olaf , Kreutz Clemens 
Published: November 2024

Abstract

Motivation
Mathematical modelling plays a crucial role in understanding inter- and intracellular signalling processes. Currently, ordinary differential equations (ODEs) are the predominant approach in systems biology for modelling such pathways. While ODE models offer mechanistic interpretability, they also suffer from limitations, including the need to consider all relevant compounds, resulting in large models difficult to handle numerically and requiring extensive data.

Results
In previous work, we introduced the retarded transient function (RTF) as an alternative method for modelling temporal responses of signalling pathways. Here, we extend the RTF approach to integrate concentration or dose-dependencies into the modelling of dynamics. With this advancement, RTF modelling now fully encompasses the application range of ODE models, which comprises predictions in both time and concentration domains. Moreover, characterizing dose-dependencies provides an intuitive way to investigate and characterize signalling differences between biological conditions or cell types based on their response to stimulating inputs. To demonstrate the applicability of our extended approach, we employ data from time- and dose-dependent inflammasome activation in bone marrow-derived macrophages treated with nigericin sodium salt. Our results show the effectiveness of the extended RTF approach as a generic framework for modelling dose-dependent kinetics in cellular signalling. The approach results in intuitively interpretable parameters that describe signal dynamics and enables predictive modelling of time- and dose-dependencies even if only individual cellular components are quantified.

Availability and implementation
The presented approach is available within the MATLAB-based Data2Dynamics modelling toolbox at https://github.com/Data2Dynamics and https://zenodo.org/records/14008247 and as R code at https://github.com/kreutz-lab/RTF.
Damsel: analysis and visualisation of DamID sequencing in R
Authors: Page Caitlin G , Lonsdale Andrew , Mitchell Katrina A , Schröder Jan , Harvey Kieran F , Oshlack Alicia 
Published: November 2024

Abstract

Summary
DamID sequencing is a technique to map the genome-wide interaction of a protein with DNA. Damsel is the first Bioconductor package to provide an end to end analysis for DamID sequencing data within R. Damsel performs quantification and testing of significant binding sites along with exploratory and visual analysis. Damsel produces results consistent with previous analysis approaches.

Availability and implementation
The R package Damsel is available for install through the Bioconductor project https://bioconductor.org/packages/release/bioc/html/Damsel.html and the code is available on GitHub https://github.com/Oshlack/Damsel/.
Democracy, Egalitarianism and the Homicide Rate: An Empirical Test of a Variety of Democracies, 1990–2019
Authors: de Soysa Indra 
Published: November 2024

Abstract
Democracy and the level of economic development correlate tightly. While some argue that egalitarian conditions inherent in democracies reduce homicide, others suggest that it is economic development that matters. This study evaluates competing theory and tests the democracy—homicide link using homicide data defined as death due to interpersonal violence and novel data on a variety of democracies. The results show that democracies associate positively with homicide, and egalitarian democracy shows the strongest effect. The level of economic development is negative on homicide and substantively large. The basic results are robust to alternative data, estimating method, and to omitted variables bias.
Rituximab as a first-line therapy in children with new-onset idiopathic nephrotic syndrome
Authors: Zhang Xiaojing , Jin Yanyan , Liu Fei , Li Qiuyu , Xie Yi , Huang Guoping , chen Junyi , He Xue , He Siyi , Fu Haidong , Wang Jingjing , Shen Huijun , Mao Jianhua 
Published: November 2024

ABSTRACT

Background
Idiopathic nephrotic syndrome (INS) in children, commonly treated with steroids, poses challenges due to associated side effects. Rituximab, known for its efficacy in reducing relapse frequency in difficult-to-treat cases, emerges a potential first-line therapy for pediatric new-onset INS.

Method
This is a single-center, retrospective, observational study to evaluate the efficacy and safety of rituximab as a first-line therapy for pediatric INS. The complete treatment strategy was weekly injections at a dose of 375 mg/m2 for four doses. Children with new-onset INS who received rituximab as a first-line monotherapy from 1 January 2022 to 31 December 2023 were included and followed until 31 May 2024.

Results
Seventeen patients (median age at diagnosis 4.8 years) were included. Twelve patients achieved complete remission within a median time of 19 days. Over a follow-up period ranging from 41 to 112 weeks, 11 patients maintained remission even after B-cell reconstitution, with one patient experiencing a relapse at 85 weeks. Three patients, who presented with hematuria, hypocomplementemia or renal injury at initial diagnosis, exhibited resistance to rituximab. No severe adverse events were noted.

Conclusion
Rituximab may be an effective and safe option as a first-line therapy for inducing and maintaining remission in newly diagnosed INS.
MUC1-associated autosomal dominant tubulointerstitial kidney disease: prevalence in kidney failure of undetermined aetiology and clinical insights from Danish families
Authors: Granhøj Jeff , Lildballe Dorte L , Pedersen Katja V , Tougaard Birgitte G , Sokol Martin , Aagaard Mads M , Petersen Annabeth H , Kristensen Tilde , Djursby Malene , Birn Henrik , Rasmussen Maria 
Published: November 2024

ABSTRACT

Background
Frameshift variants in the variable number tandem repeat region of mucin-1 (MUC1) cause autosomal dominant tubulointerstitial kidney disease (ADTKD-MUC1) but are challenging to detect. We investigated the prevalence in patients with kidney failure of undetermined aetiology and compared Danish families with ADTKD-MUC1.

Methods
We recruited patients with suspected kidney failure of undetermined aetiology at ≤50 years and excluded those with a clear-cut clinical or histopathological kidney diagnoses or established genetic kidney diseases identified thorough medical record review. MUC1 genotyping was performed by SNaPshot analysis, detecting the most common pathogenic cytosine duplication, followed by bioinformatics pipeline VNtyper analysis of short-read sequencing data.

Results
Of 172 recruited patients, 123 underwent SNaPshot analyses, which were abnormal in 5/123 patients (4%). Next, VNtyper genotyping was performed in all patients, including the five with abnormal SNaPshot analysis. VNtyper re-identified the common cytosine duplication in all five patients and revealed novel frameshift variants in two additional patients, while the analyses were normal in the remaining 116 patients. All patients carrying frameshift variants in MUC1 fulfilled ADTKD criteria and had a family history of kidney failure. A considerable inter- and intrafamilial variability of chronic kidney disease stage relative to age was observed in families with ADTKD-MUC1.

Conclusions
ADTKD-MUC1 was identified in 7/123 patients (6%) in a selected cohort of kidney failure of undetermined aetiology ≤50 years, and VNtyper effectively identified all pathogenic MUC1 variants.
Variation in reproductive photosynthetic compensation of distinct germplasm varieties of a native rangeland grass, Pseudoroegneria spicata, following floral defoliation
Authors: Quigley Kathleen M , O’Connor Rory C , Monaco Thomas A , Hamerlynck Erik P 
Published: November 2024

Abstract
Understanding plant ecophysiological functioning is critical in formulating effective ecologically based strategies to conserve and enhance resiliency and resistance in sagebrush steppe, as well as improving their restoration following degradation by interactive effects of climate change, wildland fire and invasive annual grasses. Recent research has shown increased reproductive photosynthesis following floral defoliation can be important to reproductive potential, yet how this is expressed in plant material selected for different functional attributes is unknown. To address this, we measured photosynthetic gas exchange in clipped and unclipped basal florets and flag leaves of two germplasms of the native perennial bunchgrass, bluebunch wheatgrass, var. Anatone and var. Columbia, selected for higher reproductive culm production. Clipping induced a stronger direct compensatory reproductive photosynthetic response in basal florets of Anatone compared to Columbia germplasm individuals, with no indirect compensatory response apparent in unaffected distal florets of either germplasm. Flag-leaf photosynthesis did not differ between the germplasm lines, but Columbia flag leaves did show evidence of increased photosynthesis on culms with clipped basal florets. These findings suggest selection for increased flowering culms may alter reproductive herbivory tolerance, a feature important in the convergence of herbivory and drought tolerance traits. Such information could help in planning effective seed mixes to enhance population stability across highly variable sagebrush steppe ecosystems, as well as directing future plant material selection to improve restoration success in these economically important rangelands.
Device-related adverse events and flow capacity of percutaneous ventricular assist devices
Authors: Ikeda Yuki , Ishii Shunsuke , Nakahara Shohei , Iikura Saeko , Fujita Teppei , Iida Yuichiro , Nabeta Takeru , Sato Nobuhiro , Ako Junya 
Published: November 2024

Abstract

Aims
Complication management is crucial in patients receiving mechanical circulatory devices. However, there are limited data on the association between the risks of complications and device type in patients with percutaneous ventricular assist devices (PVAD).

Methods and results
The Japanese registry for PVAD (J-PVAD) is a nationwide ongoing registry that enrols consecutive patients with cardiogenic shock treated with PVAD. We analysed 5717 patients in the J-PVAD from 1 February 2020 to 31 December 2022, to compare the incident risks of device-related problems and all-cause mortality within 30 days after PVAD introduction based on flow capacities of first-line PVAD (low: Impella 2.5/CP, n = 5375; high: Impella 5.0/5.5, n = 342). The overall incidence of major device-related problems, including haemolysis, major bleeding, kidney injury, sepsis, and pump stop, was 13%, 21%, 7%, 3%, and 1%, respectively. The all-cause mortality rate was 34%. The incident risks of haemolysis [hazard ratio (HR) 0.38, 95% confidence interval (CI) 0.24–0.58], kidney injury (HR 0.32, 95% CI 0.18–0.57), and pump stop (HR 0.38, 95% CI 0.16–0.91) were lower in patients with high-flow PVAD compared with those with low-flow PVAD. The risks of major bleeding or sepsis did not differ significantly between groups. The risk of all-cause mortality was lower in patients with high-flow PVAD compared with those with low-flow PVAD (HR 0.79, 95% CI 0.65–0.96).

Conclusion
Compared with those with low-flow PVAD, patients with high-flow PVAD had lower incident risks of device-related problems, including haemolysis, kidney injury, and pump stop, as well as lower risk of all-cause mortality.
Adaptation During the Shift from Entomopathogen to Endosymbiont Is Accompanied by Gene Loss and Intensified Selection
Authors: Ward Chris M , Onetto Cristobal A , Borneman Anthony R 
Published: November 2024

Abstract
Fungi have been found to be associated with many insect species, with some species transitioning to reside within insects as symbionts. However, the evolutionary pressures and genomic consequences associated with this transition are not well understood. Pathogenic fungi of the genus Ophiocordyceps have undergone multiple, independent transitions from pathogen to endosymbiont lifestyles, where they reside within the fatty tissues of infected soft-scale insects transgenerationally without killing their hosts. To gain an understanding of the genomic adaptations underlying this life history shift, long-read sequencing was utilized to assemble the genomes of both the soft-scale insect Parthenolecanium corni and its Ophiocordyceps endosymbiont from a single insect. Assembly and metagenomic-based binning produced a highly contiguous genome for Pa. corni and a chromosome-level assembly for the Ophiocordyceps endosymbiont. The endosymbiont genome was characterized by 524 gene loss events compared to free-living pathogenic Ophiocordyceps relatives, with predicted roles in hyphal growth, cell wall integrity, metabolism, gene regulation, and toxin production. Contrasting patterns of selection were observed between the nuclear and mitochondrial genomes specific to the endosymbiont lineage. Intensified selection was most frequently observed across orthologs in the nuclear genome, whereas selection on most mitochondrial genes was found to be relaxed. Scans for positive selection were enriched within the fatty acid metabolism pathway with endosymbiont specific selection within three adjacent enzymes catalyzing the conversion of acetoacetate to acetyl-coenzyme A, suggesting that the endosymbiont lineage is under selective pressure to effectively exploit the lipid rich environment of the insect fat bodies in which it is found.
Bayesian hierarchical hypothesis testing in large-scale genome-wide association analysis
Authors: Samaddar Anirban , Maiti Tapabrata , de los Campos Gustavo 
Published: November 2024

Abstract
Variable selection and large-scale hypothesis testing are techniques commonly used to analyze high-dimensional genomic data. Despite recent advances in theory and methodology, variable selection and inference with highly collinear features remain challenging. For instance, collinearity poses a great challenge in genome-wide association studies involving millions of variants, many of which may be in high linkage disequilibrium. In such settings, collinearity can significantly reduce the power of variable selection methods to identify individual variants associated with an outcome. To address such challenges, we developed a Bayesian hierarchical hypothesis testing (BHHT)—a novel multiresolution testing procedure that offers high power with adequate error control and fine-mapping resolution. We demonstrate through simulations that the proposed methodology has a power-FDR performance that is competitive with (and in many scenarios better than) state-of-the-art methods. Finally, we demonstrate the feasibility of using BHHT with large sample size (n∼ 300,000) and ultra dimensional genotypes (∼ 15 million single-nucleotide polymorphisms or SNPs) by applying it to eight complex traits using data from the UK-Biobank. Our results show that the proposed methodology leads to many more discoveries than those obtained using traditional SNP-centered inference procedures. The article is accompanied by open-source software that implements the methods described in this study using algorithms that scale to biobank-size ultra-high-dimensional data.