bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasound-Based Noncontrast Microvascular Imaging for Evaluation of Breast Lesions: Imaging Techniques and Review of Diagnostic Criteria
Authors: Mohindra Namita , Soni Neetu 
Published: March 2024

AbstractVascularity plays a pivotal role in the progression of breast lesions and may be associated with their aggressiveness and likelihood of being malignant. Contrast-enhanced imaging techniques are necessary to evaluate vascularity due to the limited sensitivity of conventional color Doppler techniques, in which motion artifacts are eliminated using wall filters. However, in this process, low-flow signals from small vessels also get removed unintentionally. Advancements in technology have revolutionized the way ultrasound images are generated, resulting in tremendous improvements in Doppler imaging techniques. The new, ultrasound-based noncontrast microvascular imaging techniques overcome the limitations of conventional Doppler, and are highly sensitive for detecting microvessels and low flow. The resultant high Doppler sensitivity leads to detection of vascularity in more breast lesions. It is important for radiologists to understand the imaging principles and the clinical implications of the new techniques, to optimally utilize them and aid correct diagnosis. Angio-PLUS is one such recent advancement, which uses unfocused or plane waves and three-dimensional wall filtering to analyze tissue motion in time, space, and amplitude domains that effectively distinguish between blood flow and tissue. The information is beneficial for assessing the lesion vascularity without using contrast. This article aims to explain the Doppler imaging techniques, their clinical applications, scanning methods, and review the common Doppler-based diagnostic criteria used in the evaluation of breast lesions.
Deep unrolling networks with recurrent momentum acceleration for nonlinear inverse problems
Authors: Zhou Qingping , Qian Jiayu , Tang Junqi , Li Jinglai 
Published: March 2024

Abstract
Combining the strengths of model-based iterative algorithms and data-driven deep learning solutions, deep unrolling networks (DuNets) have become a popular tool to solve inverse imaging problems. Although DuNets have been successfully applied to many linear inverse problems, their performance tends to be impaired by nonlinear problems. Inspired by momentum acceleration techniques that are often used in optimization algorithms, we propose a recurrent momentum acceleration (RMA) framework that uses a long short-term memory recurrent neural network (LSTM-RNN) to simulate the momentum acceleration process. The RMA module leverages the ability of the LSTM-RNN to learn and retain knowledge from the previous gradients. We apply RMA to two popular DuNets—the learned proximal gradient descent (LPGD) and the learned primal-dual (LPD) methods, resulting in LPGD-RMA and LPD-RMA, respectively. We provide experimental results on two nonlinear inverse problems: a nonlinear deconvolution problem, and an electrical impedance tomography problem with limited boundary measurements. In the first experiment we have observed that the improvement due to RMA largely increases with respect to the nonlinearity of the problem. The results of the second example further demonstrate that the RMA schemes can significantly improve the performance of DuNets in strongly ill-posed problems.
Occupational skin dose from radionuclide contamination: one country’s approach at standardising skin dose estimates using Varskin+
Authors: Sharpe Katherine , McCallum Stephen , O’Neill Janice , Paterson Carolyn , McCormick Jennifer , Sexton Kate 
Published: March 2024

Abstract
The manipulation of unsealed radiopharmaceuticals by healthcare workers can cause accidental personal contamination leading to occupational radiation skin dose. The UK Ionising Radiations Regulations 2017 require that potential skin doses arising from reasonably foreseeable accident scenarios are included in risk assessments. Workers must be designated as classified if these dose estimates exceed 150 mSv equivalent dose averaged over 1 cm2. Updates from the UK Health and Safety Executive recently prompted many in the UK to review the classification of workers in Nuclear Medicine. Skin dose from contamination cannot be measured, it must be estimated. Varskin+ is a code that is widely recommended for estimating skin dose. The subjective choices made by users when defining modelled scenarios in Varskin+ lead to significant variation in the calculated skin doses. At the time of writing there is no definitive calculation method and all calculations rely on theoretical models. NHS Health Boards in Scotland have adopted a standardised framework for performing skin dose estimates for risk assessments. The parametric sensitivity of Varskin+ inputs were examined and the available evidence was reviewed. Generic, reasonably forseeable, worst-case accident scenarios were decided upon for: direct skin contamination, glove contamination and needlestick injury. Standardised inputs and assumptions for each scenario were compiled in a protocol that has been adopted by the Scottish Health Boards. The protocol allows for differences in practice between departments, but standardises most inputs. While significant uncertainty remains in the estimated skin doses, this approach reduces variation and enables the comparison of estimated skin doses between departments. The framework facilitates continuous improvement as more evidence is gathered to refine the standardised assumptions. Task by task skin dose estimates were made for workers in Nuclear Medicine in Scotland and many workers were designated classified as a result.
When should PIC simulations be applied to atmospheric pressure plasmas? Impact of correlation heating
Authors: Acciarri M D , Moore C , Beving L P , Baalrud S D 
Published: March 2024

Abstract
Molecular dynamics simulations are used to test when the particle-in-cell (PIC) method applies to atmospheric pressure plasmas. It is found that PIC applies only when the plasma density and macroparticle weight are sufficiently small because of two effects associated with correlation heating. The first is the physical effect of disorder-induced heating (DIH). This occurs if the plasma density is large enough that a species (typically ions) is strongly correlated in the sense that the Coulomb coupling parameter exceeds one. In this situation, DIH causes ions to rapidly heat following ionization. PIC is not well suited to capture DIH because doing so requires using a macroparticle weight of one and a grid that well resolves the physical interparticle spacing. These criteria render PIC intractable for macroscale domains. The second effect is a numerical error due to artificial correlation heating (ACH). ACH is like DIH in that it is caused by the Coulomb repulsion between particles, but differs in that it is a numerical effect caused by a macroparticle weight larger than one. Like DIH, it is associated with strong correlations. However, here the macroparticle coupling strength is found to scale as

Γ

w

2

/

3

, where Γ is the physical coupling strength and w is the macroparticle weight. So even if the physical coupling strength of a species is small, as is expected for electrons in atmospheric pressure plasmas, a sufficiently large macroparticle weight can cause the macroparticles to be strongly coupled and therefore heat due to ACH. Furthermore, it is shown that simulations in reduced dimensions exacerbate these issues.
Bogoliubov corner excitations in a conventional s-wave superfluid
Authors: Tu Wei , Wu Ya-Jie , Li Ning , Guo Miaodi , Hou Junpeng 
Published: March 2024

Abstract
Higher-order topological superconductors and superfluids have triggered a great deal of interest in recent years. While Majorana zero-energy corner or hinge states have been studied intensively, whether superconductors and superfluids host higher-order topological Bogoliubov excitations with finite energies remain elusive. In this work, we propose that Bogoliubov corner excitations with finite energies can be induced through only mirror-symmetric local potentials from a trivial conventional s-wave superfluid. The topological Bogoliubov excited modes originate from the nontrivial Bogoliubov excitation bands. These modes are protected by the mirror symmetry and are robust against mirror-symmetric perturbations as long as the Bogoliubov energy gap remains open. Our work provides a new insight into higher-order topological excitation states in superfluids and superconductors.
Suppression of the m/n = 2/1 tearing mode by electron cyclotron resonance heating on J-TEXT
Authors: FANG 方 Jiangang 建港 , CHEN 陈 Zhongyong 忠勇 , YAN 严 Wei 伟 , WANG 王 Nengchao 能超 , MAO 毛 Feiyue 飞越 , LUO 罗 Qiang 蔷 , XUAN 玄 Zijian 子健 , CHEN 陈 Xixuan 曦璇 , REN 任 Zhengkang 正康 , ZHANG 张 Feng 峰 , HUANG 黄 Mei 梅 , XIA 夏 Donghui 冬辉 , YANG 杨 Zhoujun 州军 , CHEN 陈 Zhipeng 志鹏 , DING 丁 Yonghua 永华 , Team the J-TEXT 
Published: March 2024

Abstract
Stabilization of tearing modes and neoclassical tearing modes is of great importance for tokamak operation. Electron cyclotron waves (ECWs) have been extensively used to stabilize the tearing modes with the virtue of highly localized power deposition. Complete suppression of the m/n = 2/1 tearing mode (TM) by electron cyclotron resonance heating (ECRH) has been achieved successfully on the J-TEXT tokamak. The effects of ECW deposition location and power amplitude on the 2/1 TM suppression have been investigated. It is found that the suppression is more effective when the ECW power is deposited closer to the rational surface. As the ECW power increases to approximately 230 kW, the 2/1 TM can be completely suppressed. The island rotation frequency is increased when the island width is reduced. The experimental results show that the local heating inside the magnetic island and the resulting temperature perturbation increase at the O-point of the island play dominant roles in TM suppression. As the ECW power increases, the 2/1 island is suppressed to smaller island width, and the flow shear also plays a stabilizing effect on small magnetic islands. With the stabilizing contribution of heating and flow shear, the 2/1 TM can be completely suppressed.
Oh, Rats!
Authors: Sarkar Natasha 
Published: March 2024

Abstract
Part of what came to be known as the ‘pioneer phase’ in modern plague research, that of eventual acceptance of the rat flea as the plague vector, is discussed in this chapter. All attention was directed to the termination of rats as a means of combating plague. The chapter surveys the varied experiments aimed at killing rats that were devised and tested in Bombay, Punjab, Calcutta, Central Provinces, and Madras. Measures especially for destroying rat fleas came to be instituted much later, only in 1911, while experiments for devising successful methods to exterminate rats were well underway. The chapter also looks at the various changes introduced in plague policy at the turn of the century, when Lord Curzon took over as the Viceroy and Governor-General of India. The final section of the chapter engages with the complexities of seasonal variations and their influence of the intensity and diffusion of plague.
Imaginative Exhibition in Morality
Authors: Matherne Samantha 
Published: March 2024

Abstract
This chapter aims to show that in Kant’s framework one of the main ways in which we morally use our imagination is as the faculty of exhibition. After addressing some initial reasons to worry that Kant can accord imagination, as the faculty of exhibition, a substantive role in our moral lives, it makes the case for why he nevertheless regards imaginative exhibition as something that is morally valuable. To this end, the chapter canvasses various ways in which Kant thinks our imagination morally serves us by making moral ideas sensible through indirect and direct modes of exhibition. In the indirect vein, it considers the moral value of the exhibition of moral ideas in our aesthetic engagement with beauty, art, and sublimity. And in the direct vein, it discusses the moral value of the exhibition of moral ideas through moral ideals, moral examples, and moral perception.
Clinical decision support to improve CBC and differential ordering
Authors: Mahowald Grace K , Lewandrowski Kent B , Dighe Anand S 
Published: March 2024

Abstract

Objectives
Complete blood count and differential (CBC diff) is a common laboratory test that may be overused or misordered, particularly in an inpatient setting. We assessed the ability of a clinical decision support (CDS) alert to decrease unnecessary orders for CBC diff and analyzed its impact in the laboratory.

Methods
We designed 3 CDS alerts to provide guidance to providers ordering CBC diff on inpatients at frequencies of daily, greater than once daily, or as needed.

Results
The 3 alerts were highly effective in reducing orders for CBC diff at the frequencies targeted by the alert. Overall, test volume for CBC diff decreased by 32% (mean of 5257 tests per month) after implementation of the alerts, with a corresponding decrease of 22% in manual differentials performed (mean of 898 per month). Turnaround time for manual differentials decreased by a mean of 41.5 minutes, with a mean decrease of up to 90 minutes during peak morning hours.

Conclusions
The 3 CDS alerts successfully decreased inpatient orders for CBC diff and improved the quality of patient care by decreasing turnaround time for manual differentials.
The rise of taxon-specific epitope predictors
Authors: Campelo Felipe , Lobo Francisco P 
Published: March 2024

Abstract
Computational predictors of immunogenic peptides, or epitopes, are traditionally built based on data from a broad range of pathogens without consideration for taxonomic information. While this approach may be reasonable if one aims to develop one-size-fits-all models, it may be counterproductive if the proteins for which the model is expected to generalize are known to come from a specific subset of phylogenetically related pathogens. There is mounting evidence that, for these cases, taxon-specific models can outperform generalist ones, even when trained with substantially smaller amounts of data. In this comment, we provide some perspective on the current state of taxon-specific modelling for the prediction of linear B-cell epitopes, and the challenges faced when building and deploying these predictors.
DeTox: a pipeline for the detection of toxins in venomous organisms
Authors: Ringeval Allan , Farhat Sarah , Fedosov Alexander , Gerdol Marco , Greco Samuele , Mary Lou , Modica Maria Vittoria , Puillandre Nicolas 
Published: March 2024

Abstract
Venomous organisms have independently evolved the ability to produce toxins 101 times during their evolutionary history, resulting in over 200 000 venomous species. Collectively, these species produce millions of toxins, making them a valuable resource for bioprospecting and understanding the evolutionary mechanisms underlying genetic diversification. RNA-seq is the preferred method for characterizing toxin repertoires, but the analysis of the resulting data remains challenging. While early approaches relied on similarity-based mapping to known toxin databases, recent studies have highlighted the importance of structural features for toxin detection. The few existing pipelines lack an integration between these complementary approaches, and tend to be difficult to run for non-experienced users. To address these issues, we developed DeTox, a comprehensive and user-friendly tool for toxin research. It combines fast execution, parallelization and customization of parameters. DeTox was tested on published transcriptomes from gastropod mollusks, cnidarians and snakes, retrieving most putative toxins from the original articles and identifying additional peptides as potential toxins to be confirmed through manual annotation and eventually proteomic analysis. By integrating a structure-based search with similarity-based approaches, DeTox allows the comprehensive characterization of toxin repertoire in poorly-known taxa. The effect of the taxonomic bias in existing databases is minimized in DeTox, as mirrored in the detection of unique and divergent toxins that would have been overlooked by similarity-based methods. DeTox streamlines toxin annotation, providing a valuable tool for efficient identification of venom components that will enhance venom research in neglected taxa.
scMLC: an accurate and robust multiplex community detection method for single-cell multi-omics data
Authors: Chen Yuxuan , Zheng Ruiqing , Liu Jin , Li Min 
Published: March 2024

Abstract
Clustering cells based on single-cell multi-modal sequencing technologies provides an unprecedented opportunity to create high-resolution cell atlas, reveal cellular critical states and study health and diseases. However, effectively integrating different sequencing data for cell clustering remains a challenging task. Motivated by the successful application of Louvain in scRNA-seq data, we propose a single-cell multi-modal Louvain clustering framework, called scMLC, to tackle this problem. scMLC builds multiplex single- and cross-modal cell-to-cell networks to capture modal-specific and consistent information between modalities and then adopts a robust multiplex community detection method to obtain the reliable cell clusters. In comparison with 15 state-of-the-art clustering methods on seven real datasets simultaneously measuring gene expression and chromatin accessibility, scMLC achieves better accuracy and stability in most datasets. Synthetic results also indicate that the cell-network-based integration strategy of multi-omics data is superior to other strategies in terms of generalization. Moreover, scMLC is flexible and can be extended to single-cell sequencing data with more than two modalities.
Effective multi-modal clustering method via skip aggregation network for parallel scRNA-seq and scATAC-seq data
Authors: Hu Dayu , Liang Ke , Dong Zhibin , Wang Jun , Zhao Yawei , He Kunlun 
Published: March 2024

Abstract
In recent years, there has been a growing trend in the realm of parallel clustering analysis for single-cell RNA-seq (scRNA) and single-cell Assay of Transposase Accessible Chromatin (scATAC) data. However, prevailing methods often treat these two data modalities as equals, neglecting the fact that the scRNA mode holds significantly richer information compared to the scATAC. This disregard hinders the model benefits from the insights derived from multiple modalities, compromising the overall clustering performance. To this end, we propose an effective multi-modal clustering model scEMC for parallel scRNA and Assay of Transposase Accessible Chromatin data. Concretely, we have devised a skip aggregation network to simultaneously learn global structural information among cells and integrate data from diverse modalities. To safeguard the quality of integrated cell representation against the influence stemming from sparse scATAC data, we connect the scRNA data with the aggregated representation via skip connection. Moreover, to effectively fit the real distribution of cells, we introduced a Zero Inflated Negative Binomial-based denoising autoencoder that accommodates corrupted data containing synthetic noise, concurrently integrating a joint optimization module that employs multiple losses. Extensive experiments serve to underscore the effectiveness of our model. This work contributes significantly to the ongoing exploration of cell subpopulations and tumor microenvironments, and the code of our work will be public at https://github.com/DayuHuu/scEMC.
Coarse-grained molecular dynamics simulation of the effect of cross-linking on the wear mechanism of polymer brush
Authors: Liu Zhongmin , Ootani Yusuke , Uehara Shuichi , Zhang Jing , Chen Qian , Wang Yang , Ozawa Nobuki , Kubo Momoji 
Published: March 2024

Abstract
The effects of a cross-linking layer on the wear resistance of polymer brush were investigated by using molecular dynamics-based sliding simulations. We found that a cross-linking layer improved wear resistance. The cross-linking layer suppressed the interpenetration of polymer chains on the counter surface and thus lowered the frictional force and wear. The degrees of interpenetration decreased as the cross-linking layer closed to the tip of the chain. A cross-linking layer in the tip of the polymer chains was thus found to improve wear resistance most effectively.
Computed tomography pericoronary adipose tissue density predicts coronary allograft vasculopathy and adverse clinical outcomes after cardiac transplantation
Authors: Wall Christopher , Weir-McCall Jonathan , Tweed Katharine , Hoole Stephen P , Gopalan Deepa , Huang Yuan , Corovic Andrej , Peverelli Marta , Dey Damini , Bennett Martin R , Rudd James H F , Kydd Anna , Bhagra Sai , Tarkin Jason M 
Published: March 2024

Abstract

Aims
To assess pericoronary adipose tissue (PCAT) density on coronary computed tomography angiography (CCTA) as a marker of inflammatory disease activity in coronary allograft vasculopathy (CAV).

Methods and results
PCAT density, lesion volumes, and total vessel volume-to-myocardial mass ratio (V/M) were retrospectively measured in 126 CCTAs from 94 heart transplant patients [mean age 49 (SD 14.5) years, 40% female] who underwent imaging between 2010 and 2021; age- and sex-matched controls; and patients with atherosclerosis. PCAT density was higher in transplant patients with CAV [n = 40; −73.0 HU (SD 9.3)] than without CAV [n = 86; −77.9 HU (SD 8.2)], and controls [n = 12; −86.2 HU (SD 5.4)], P &lt; 0.01 for both. Unlike patients with atherosclerotic coronary artery disease (n = 32), CAV lesions were predominantly non-calcified and comprised of mostly fibrous or fibrofatty tissue. V/M was lower in patients with CAV than without [32.4 mm3/g (SD 9.7) vs. 41.4 mm3/g (SD 12.3), P &lt; 0.0001]. PCAT density and V/M improved the ability to predict CAV from area under the receiver operating characteristic curve (AUC) 0.75–0.85 when added to donor age and donor hypertension status (P &lt; 0.0001). PCAT density above −66 HU was associated with a greater incidence of all-cause mortality {odds ratio [OR] 18.0 [95% confidence interval (CI) 3.25–99.6], P &lt; 0.01} and the composite endpoint of death, CAV progression, acute rejection, and coronary revascularization [OR 7.47 (95% CI 1.8–31.6), P = 0.01] over 5.3 (SD 2.1) years.

Conclusion
Heart transplant patients with CAV have higher PCAT density and lower V/M than those without. Increased PCAT density is associated with adverse clinical outcomes. These CCTA metrics could be useful for the diagnosis and monitoring of CAV severity.