bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quasistatic approximation in neuromodulation
Authors: Wang Boshuo , Peterchev Angel V , Gaugain Gabriel , Ilmoniemi Risto J , Grill Warren M , Bikson Marom , Nikolayev Denys 
Published: July 2024

Abstract
We define and explain the quasistatic approximation (QSA) as applied to field modeling for electrical and magnetic stimulation. Neuromodulation analysis pipelines include discrete stages, and QSA is applied specifically when calculating the electric and magnetic fields generated in tissues by a given stimulation dose. QSA simplifies the modeling equations to support tractable analysis, enhanced understanding, and computational efficiency. The application of QSA in neuromodulation is based on four underlying assumptions: (A1) no wave propagation or self-induction in tissue, (A2) linear tissue properties, (A3) purely resistive tissue, and (A4) non-dispersive tissue. As a consequence of these assumptions, each tissue is assigned a fixed conductivity, and the simplified equations (e.g. Laplace’s equation) are solved for the spatial distribution of the field, which is separated from the field’s temporal waveform. Recognizing that electrical tissue properties may be more complex, we explain how QSA can be embedded in parallel or iterative pipelines to model frequency dependence or nonlinearity of conductivity. We survey the history and validity of QSA across specific applications, such as microstimulation, deep brain stimulation, spinal cord stimulation, transcranial electrical stimulation, and transcranial magnetic stimulation. The precise definition and explanation of QSA in neuromodulation are essential for rigor when using QSA models or testing their limits.
Intentional binding for noninvasive BCI control
Authors: Venot Tristan , Desbois Arthur , Corsi Marie Constance , Hugueville Laurent , Saint-Bauzel Ludovic , De Vico Fallani Fabrizio 
Published: July 2024

Abstract

Objective. Noninvasive brain–computer interfaces (BCIs) allow to interact with the external environment by naturally bypassing the musculoskeletal system. Making BCIs efficient and accurate is paramount to improve the reliability of real-life and clinical applications, from open-loop device control to closed-loop neurorehabilitation. Approach. By promoting sense of agency and embodiment, realistic setups including multimodal channels of communication, such as eye-gaze, and robotic prostheses aim to improve BCI performance. However, how the mental imagery command should be integrated in those hybrid systems so as to ensure the best interaction is still poorly understood. To address this question, we performed a hybrid EEG-based BCI training involving healthy volunteers enrolled in a reach-and-grasp action operated by a robotic arm. Main results. Showed that the hand grasping motor imagery timing significantly affects the BCI accuracy evolution as well as the spatiotemporal brain dynamics. Larger accuracy improvement was obtained when motor imagery is performed just after the robot reaching, as compared to before or during the movement. The proximity with the subsequent robot grasping favored intentional binding, led to stronger motor-related brain activity, and primed the ability of sensorimotor areas to integrate information from regions implicated in higher-order cognitive functions. Significance. Taken together, these findings provided fresh evidence about the effects of intentional binding on human behavior and cortical network dynamics that can be exploited to design a new generation of efficient brain-machine interfaces.
Mean streaming in reciprocating flow in a double bifurcation
Authors: Wanigasekara Chandrika , Jacob Chinthaka , Manasseh Richard , Leontini Justin 
Published: July 2024

Abstract
This paper reports the mean streaming flow generated in a double bifurcation during reciprocating flow calculated using direct numerical simulations. Motivated by the medical ventilation technique of high-frequency ventilation (HFV), we investigate the potential for mean streaming to be maintained in this geometry as the frequency of reciprocation is increased while concurrently reducing the amplitude (and thereby reducing the volume per cycle). We identify four distinct regimes of flow. The first and second occur at low to moderate frequencies and generate significant streaming flows due to the interaction between Dean vortices that are generated during both the in- and out-flows. The third and fourth occur at high frequencies and produce reduced streaming, due to the reduction in formation length of the Dean vortices. Notably, the fourth regime at the highest frequencies investigated appears to show a switch in the direction of the streaming flow at the wall. Considering the motivating application of HFV, we show that currently employed frequencies are low, and much higher frequencies (and subsequently lower volumes per cycle) could potentially be employed.
Analysis of crack propagation of PLA fabricated by the additive manufacturing technique
Authors: Mohd Yusof Ab Aziz Bin , Md Yusop Abdul Hakim Bin , Abu Kasim Haszeme Bin 
Published: July 2024

Abstract
Understanding crack propagation is crucial for evaluating the structural integrity and reliability of additive manufacturing components, as cracks can compromise mechanical properties and potentially lead to catastrophic failures. The study of crack propagation in additive manufacturing components is used to develop strategies for mitigating crack initiation and growth, improving material properties, and optimising the design and manufacturing processes. Crack propagation in additive manufacturing components can be influenced by various factors, including material properties, design considerations, manufacturing defects, and loading conditions. Due to the identified issue, the study was carried out to investigate the crack propagation of the Fused Deposition Modeling (FDM) component using compact tension fracture testing. The experimental work started with fabricating the samples using PLA material, followed by a fracture test based on the compact tension specimen test to get a response of the structure and its crack propagation under tensile. Material properties were also collected using the dog bone tensile test. The material properties of the testing were then imported to Finite Element Analysis for further investigation of fracture mechanics. It was found that the maximum force of the sample was 141.7 ± 28 N at 1.70 ± 0.26 mm displacement, and cracks initiated around the tip and propagated upward or downward based on the initial crack location. The deformation patterns of PLA material have shown it to be brittle plastic deformation and low energy absorption before fracture.
Density of continuous functions in Sobolev spaces with applications to capacity
Authors: Eriksson-Bique Sylvester , Poggi-Corradini Pietro 
Published: July 2024

We show that capacity can be computed with locally Lipschitz functions in locally complete and separable metric spaces. Further, we show that if

(
X
,
d
,
μ
)

(X,d,\mu )

is a locally complete and separable metric measure space, then continuous functions are dense in the Newtonian space

N

1
,
p

(
X
)

N^{1,p}(X)

. Here the measure

μ
\mu

is Borel and is finite and positive on all metric balls. In particular, we don’t assume properness of

X
X

, doubling of

μ
\mu

or any Poincaré inequalities. These resolve, partially or fully, questions posed by a number of authors, including J. Heinonen, A. Björn and J. Björn. In contrast to much of the past work, our results apply to locally complete spaces

X
X

and dispenses with the frequently used regularity assumptions: doubling, properness, Poincaré inequality, Loewner property or quasiconvexity.
Curating BOLD records via Bayesian phylogenetic assignments enables harmonization of regional subgeneric classifications and cryptic species detection within the genus Tachina (Diptera: Tachinidae)
Authors: Stein Frederik , Moura Carina C M , Gailing Oliver 
Published: July 2024

Abstract
DNA barcoding is a popular tool for species identification of insect samples, with important applications for plant protection. However, Barcode of Life Database queries related to tachinid samples can produce ambiguous results due to contradictory species assignments. Therefore, we applied Bayesian phylogenetic inference to 811 Tachina Meigen, 1803 COI-5P sequences containing all contradictory species assignments of Tachina Barcode Index Numbers. Based on phylogenetic assignment, the assemble species by automatic partitioning (ASAP) analysis, the MonoPhy test and analyses of genetic divergence, we identified 805 sequences representing species of the Tachina genus, whereas six sequences were incorrectly assigned to Tachina. The dataset contained 21 described species and at least seven unidentified species. Additionally, we found that the described species Tachina marklini Zetterstedt, 1838, includes two cryptic species based on ASAP partitioning of sequences, phylogenetic inference and geographical metadata. Furthermore, we harmonized conflicting subgeneric classifications of the Palearctic and Nearctic by employing different subgenera assignments from both partitions. We aimed at monophyletic subgenera partitions. We largely confirmed the validity of the Palearctic Tachina subgenera and Nowickia as a subgenus of Tachina. However, Palearctic Nowickia species formerly allocated to the outdated genus Fabriciella appeared to constitute one monophyletic group with the subgenus Rhachogaster. We conclude that this set of bioinformatics tools is suitable for curating COI-5P-based DNA barcode libraries. Although, curation is limited due to possible species introgression, horizontal gene transfer, incomplete lineage sorting and human errors the resulting dataset enabled the revision of subgenera concepts and the unambiguous cryptic species detection.
Heterogeneous effects of increased availability of alcohol on hospitalisation due to external causes. Quasi-experimental evidence from the introduction of Saturday opening at Swedish alcohol retail stores
Authors: Almquist Ylva B , Brännström Lars , Hjorth-Trolle Anders , Rostila Mikael 
Published: July 2024

Abstract
Responses to increased alcohol availability may vary across the population as a function of differential vulnerability. This study therefore aimed to examine the effects of the implementation of Saturday opening at the Swedish alcohol retail monopoly in 2000 on risks of hospitalisation due to external causes (HEC) among different population subgroups. Leveraging the experimental design of the reform, longitudinal difference-in-differences analyses were applied to a register-based cohort of individuals aged 20-40 at the time of implementation. The population was stratified into groups of Swedish, Finnish, and Middle Eastern origin, known to represent different levels of alcohol consumption and rates of alcohol-related morbidity. Results showed a 17.7% increase (p&lt;0.029) in the risk of HEC among individuals of Finnish origin, as jointly caused by both increased prevalence in the experiment area and decreased prevalence in the control area. The increase was primarily driven by younger men with lower levels of education. Those of Swedish origin exhibited largely similar patterns (9.7% increase; p&lt;0.001) while no measurable impact was observed among individuals of Middle Eastern origin (-21.4% decrease; p&lt;0.076). The findings confirm that increasing alcohol availability contributes to the disease burden related to alcohol among population subgroups already susceptible to its effects.
Using quality improvement frameworks to develop, implement, and evaluate a novel ambulatory oncology pharmacy practice model: A descriptive example
Authors: Underhill Hayley , LeBlanc Michael , Macfarlane Robyn , Hutton Lauren 
Published: July 2024

Abstract

Purpose
To describe the application of the Plan-Do-Study-Act quality improvement framework in the development, implementation, and evaluation of a novel pharmacy practice model in ambulatory oncology.

Summary
Four iterations of the Plan-Do-Study-Act framework were completed to develop a patient-facing, pharmacist-led ambulatory oncology clinic program. The clinic provided care to patients with prostate cancer on oral anticancer therapy. Metrics were collected throughout all stages of development to inform target processes for improvement. The pharmacist saw 136 patients between July 2019 and January 2023, resulting in 464 total encounters. The pharmacist provided clinical interventions and counseling to patients newly starting on oral anticancer therapy and those established on therapy using a longitudinal model of care.

Conclusion
Application of the Plan-Do-Study-Act quality improvement framework to a novel pharmacy practice model supported the development, evaluation, and sustainability of a pharmacist-led ambulatory oncology clinic providing care to patients with prostate cancer on oral anticancer therapy.
Comparisons of the amylolytic enzymes and malt starch hydrolysates of two barley cultivars, Hokudai 1 (the first cultivar developed in Japan) and Kitanohoshi (currently used cultivar for beer production)
Authors: Saburi Wataru , Mori Haruhide 
Published: July 2024

Abstract
Starch degradation in malted barley produces yeast-fermentable sugars. In this study, we compared the amylolytic enzymes and composition of the malt starch hydrolysates of two barley cultivars, Hokudai 1 (the first cultivar established in Japan) and Kitanohoshi (the currently used cultivar for beer production). Hokudai 1 malt contained lower activity of amylolytic enzymes than Kitanohoshi malt, although these cultivars contained α-amylase AMY2 and β-amylase Bmy1 as the predominant enzymes. Malt starch hydrolysate of Hokudai 1 contained more limit dextrin and less yeast-fermentable sugars than that of Kitanohoshi. In mixed malt saccharification, a high Hokudai 1 malt ratio increased the limit dextrin levels and decreased the maltotriose and maltose levels. Even though Kitanohoshi malt contained more amylolytic enzymes than Hokudai 1 malt, addition of Kitanohoshi extract containing the amylolytic enzymes did not enhance malt starch degradation of Hokudai 1. Hokudai 1 malt starch was less degradable than Kitanohoshi malt starch.
An overview of key online resources for human genomics: a powerful and open toolbox for in silico research
Authors: Forero Diego A , Bonilla Diego A , González-Giraldo Yeimy , Patrinos George P 
Published: July 2024

Abstract
Recent advances in high-throughput molecular methods have led to an extraordinary volume of genomics data. Simultaneously, the progress in the computational implementation of novel algorithms has facilitated the creation of hundreds of freely available online tools for their advanced analyses. However, a general overview of the most commonly used tools for the in silico analysis of genomics data is still missing. In the current article, we present an overview of commonly used online resources for genomics research, including over 50 tools. This selection will be helpful for scientists with basic or intermediate skills in the in silico analyses of genomics data, such as researchers and students from wet labs seeking to strengthen their computational competencies. In addition, we discuss current needs and future perspectives within this field.
Atypical chemokine receptor 1-positive endothelial cells mediate leucocyte infiltration and synergize with secreted frizzled-related protein 2/asporin-positive fibroblasts to promote skin fibrosis in systemic sclerosis
Authors: Huang Yan , Pu Weilin , Wang Lei , Ma Qianqian , Ma Yanyun , Liu Qingmei , Jiang Shuai , Zhao Xiangyue , Zhang Yuting , He Qiuyu , Tang Yulong , Liu Jing , Lin Jui-Ming , Shi Xiangguang , Tu Wenzhen , Chen Yuanyuan , Lin Jinran , Gong Yiyi , Wu Wenyu , Wang Jiucun 
Published: July 2024

Abstract

Background
Skin fibrosis is the typical pathological manifestation of systemic sclerosis (SSc) and localized scleroderma (LS); it has an unclear aetiology and few effective treatments. Although excessive collagen secretion by fibroblasts is the primary cause of skin fibrosis, evidence has suggested that vascular damage is the initiating event and that various cell types, including fibroblasts, work together to contribute to the pathogenesis of skin fibrosis.

Objectives
To explore the relationship between vascular endothelial cell lesions and immune cell infiltration, along with the interactions between various cell types within the fibrotic skin ecosystem.

Methods
Single-cell RNA sequencing was performed on skin biopsies from three healthy donors and seven patients with SSc. Additional data from three patients with localized scleroderma available in the Gene Expression Omnibus (GSE160536) were integrated by Harmony. CellChat (version 1.5.0) was used to analyse the cell communication network. A Transwell® assay and a bleomycin (BLM) mouse model were used to explore the role of atypical chemokine receptor 1 (ACKR1; ‘Duffy antigen’) in immune cell infiltration. Milo single-cell Western blot was used to show fibroblast subcluster activation.

Results
A total of 62 295 cells were obtained and subpopulations of stromal and immune cells identified. Interaction network analysis found that multiple chemokines secreted by macrophages, pericytes and proinflammatory fibroblasts could bind with ACKR1, which was highly expressed by endothelial cells in lesional skin. The Transwell® assay revealed that overexpression of ACKR1 in human umbilical vein endothelial cells facilitated leucocyte infiltration following treatment with interleukin-8. BLM mice showed enhanced ACKR1 expression, massive immune cell infiltration and skin fibrosis that was attenuated by ACKR1 inhibition. Furthermore, infiltrated macrophages expressing high levels of transforming growth factor (TGF)-β1 or platelet-derived growth factor B (PDGFB) could activate secreted frizzled-related protein 2 (SFRP2)/asporin (ASPN)+ fibroblasts to contribute to the excessive accumulation of extracellular matrix. It was also found that the SOX4–ASPN axis plays an important role in the TGF-β signalling cascade and the aetiology of skin fibrosis.

Conclusions
Our results reveal that high expression of ACKR1 by endothelial cells in fibrotic skin tissue promotes immune cell infiltration and that SFRP2/ASPN+ fibroblasts synergize to exacerbate skin fibrosis.
Large-scale parameters framework with large convolutional kernel for encoding visual fMRI activity information
Authors: Ma Shuxiao , Wang Linyuan , Hou Senbao , Zhang Chi , Yan Bin 
Published: July 2024

Abstract
Visual encoding models often use deep neural networks to describe the brain’s visual cortex response to external stimuli. Inspired by biological findings, researchers found that large receptive fields built with large convolutional kernels improve convolutional encoding model performance. Inspired by scaling laws in recent years, this article investigates the performance of large convolutional kernel encoding models on larger parameter scales. This paper proposes a large-scale parameters framework with a sizeable convolutional kernel for encoding visual functional magnetic resonance imaging activity information. The proposed framework consists of three parts: First, the stimulus image feature extraction module is constructed using a large-kernel convolutional network while increasing channel numbers to expand the parameter size of the framework. Second, enlarging the input data during the training stage through the multi-subject fusion module to accommodate the increase in parameters. Third, the voxel mapping module maps from stimulus image features to functional magnetic resonance imaging signals. Compared to sizeable convolutional kernel visual encoding networks with base parameter scale, our visual encoding framework improves by approximately 7% on the Natural Scenes Dataset, the dedicated dataset for the Algonauts 2023 Challenge. We further analyze that our encoding framework made a trade-off between encoding performance and trainability. This paper confirms that expanding parameters in visual coding can bring performance improvements.
Gender and age related brain structural and functional alterations in children with autism spectrum disorder
Authors: Zhou Di , Hua Ting , Tang Huan , Yang Rong , Huang Linsheng , Gong Yujiao , Zhang Lin , Tang Guangyu 
Published: July 2024

Abstract
To explore the effects of age and gender on the brain in children with autism spectrum disorder using magnetic resonance imaging. 185 patients with autism spectrum disorder and 110 typically developing children were enrolled. In terms of gender, boys with autism spectrum disorder had increased gray matter volumes in the insula and superior frontal gyrus and decreased gray matter volumes in the inferior frontal gyrus and thalamus. The brain regions with functional alterations are mainly distributed in the cerebellum, anterior cingulate gyrus, postcentral gyrus, and putamen. Girls with autism spectrum disorder only had increased gray matter volumes in the right cuneus and showed higher amplitude of low-frequency fluctuation in the paracentral lobule, higher regional homogeneity and degree centrality in the calcarine fissure, and greater right frontoparietal network–default mode network connectivity. In terms of age, preschool-aged children with autism spectrum disorder exhibited hypo-connectivity between and within auditory network, somatomotor network, and visual network. School-aged children with autism spectrum disorder showed increased gray matter volumes in the rectus gyrus, superior temporal gyrus, insula, and suboccipital gyrus, as well as increased amplitude of low-frequency fluctuation and regional homogeneity in the calcarine fissure and precentral gyrus and decreased in the cerebellum and anterior cingulate gyrus. The hyper-connectivity between somatomotor network and left frontoparietal network and within visual network was found. It is essential to consider the impact of age and gender on the neurophysiological alterations in autism spectrum disorder children when analyzing changes in brain structure and function.
pH-dependent interaction between acetaminophen and dioleoylphosphatidylcholine membranes
Authors: Ishikawa Kodai , Nabika Hideki 
Published: July 2024

Abstract
Acetaminophen may cause acute liver failure due to overdose. Understanding the processes of adsorption and incorporation of acetaminophen into cell membranes is crucial for elucidating the mechanisms of action and toxicity of acetaminophen. We investigated the interaction between acetaminophen and a model cell membrane (dioleoylphosphatidylcholine) using surface pressure–area isotherms. Acetaminophen was incorporated into the dioleoylphosphatidylcholine membrane under basic conditions, increasing the dioleoylphosphatidylcholine molecular area. The acetaminophen uptake was explained by the adsorption of hydroxide ions onto the lipid membrane and electrostatic interaction between acetaminophen and lipid molecules under basic conditions.