bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishing best practices for modeling multi-day energy storage in deeply decarbonized energy systems
Authors: Mantegna Gabriel , Ricks Wilson , Manocha Aneesha , Patankar Neha , Mallapragada Dharik , Jenkins Jesse 
Published: November 2024

Abstract
Multi-day energy storage (MDS), a subset of long-duration energy storage, may become a critical technology for the decarbonization of the power sector, as current commercially available Lithium-ion battery storage technologies cannot cost-effectively shift energy to address multi-day or seasonal variability in demand and renewable energy availability. MDS is difficult to model in existing energy system planning models (such as electricity system capacity expansion models (CEMs)), as it is much more dependent on an accurate representation of chronology than other resources. Techniques exist for modeling MDS in these planning models; however, it is not known how spatial and temporal resolution affect the performance of these techniques, creating a research gap. In this study we examine what spatial and temporal resolution is necessary to accurately capture the full value of MDS, in the context of a continent-scale CEM. We use the results to draw conclusions and present best practices for modelers seeking to accurately model MDS in a macro-energy systems planning context. Our key findings are: (1) modeling MDS with linked representative periods is crucial to capturing its full value, (2) MDS value is highly sensitive to the cost and availability of other resources, and (3) temporal resolution is more important than spatial resolution for capturing the full value of MDS, although how much temporal resolution is needed will depend on the specific model context.
Understanding and Effectively Utilizing Experiential Therapy
Authors: Laser Julie Anne , Nicotera Nicole 
Published: November 2024

Abstract
This book is about the clinical modality of Experiential Therapy with the addition of mindfulness practices and a trauma-sensitive lens. Experiential Therapy provides hands-on, engaged, holistic experiences aimed at exploring, better understanding, and resolving clinical issues. The experience is a conduit that gives rise to words, thoughts, feelings, and future actions that the client would not have found through traditional talk therapy alone. Experiential Therapy is an alternative to traditional talk therapy because the clients and clinicians are actively and physically engaged in activities that foster introspection, change, well-being, and resilience. Movement and/or being outdoors creates an atmosphere where clinical conversations are often more natural and less forced than in an office or online. Due to this, clients are often more open and willing to do the work of clinical therapy.
Experiential Therapy Activities With Specific Group Characteristics
Authors: Laser Julie Anne , Nicotera Nicole 
Published: November 2024

Abstract
Chapter 11 discusses Experiential Therapy with some of the diverse populations the authors work with: survivors of human trafficking, veterans and military service members, persons with substance use disorders (SUDs), juvenile justice–involved youth, and grief groups. The authors discuss specific issues that each group needs to address in therapy and strategies and considerations for each specific group (survivors of human trafficking, veterans and military service members, persons with substance use disorders (SUDs), juvenile justice–involved youth, and grief groups). They share twelve Experimental Therapy activities for these particular groups. These may not be the specific populations that the reader works with, but the reader can see how versatile Experiential Therapy is for a variety of populations. This also gives the reader more activities that can be modified for their particular clientele.
Locating the Scientific Sublime
Authors: Glauthier Patrick 
Published: November 2024

Abstract
This chapter considers the definition of the sublime and methods for locating it in ancient texts. Important concepts include the sublime subject, greatness of soul, the flight of the mind, and the view from above. The scientific sublime itself emerges as a discourse that configures the study of nature as an exhilarating adventure through which our consciousness expands and our perspective shifts as we leave behind the trivialities of everyday life and approach something that appears truer and more real, something divine. Frequently, images of falling underscore the potentially electrifying proposition that we may not arrive at correct or even consistent answers; this paradigm is related to the idea of flawed sublimity, and an important model for it is Phaethon. The chapter concludes with a survey of philosophical and rhetorical discussions that link natural inquiry with the sublime. Illustrative passages come from Plato, Aristotle, Cicero, Lucretius, Virgil, Ovid, Horace, Longinus, and others.
Thatcher, the New Right, and Rebel Tours in the Early 1980s
Authors: Llewellyn Matthew P , Rider Toby C 
Published: November 2024

Abstract
This chapter begins in 1979 with the election of the Conservative Prime Minister, Margaret Thatcher, and delves into the attitudes of the ‘New Right’ to the sporting boycott throughout the early 1980s. In particular, we focus our attention on the actions of the Tory MP, John Carlisle, a dedicated ‘Thatcherite’ and the most public and persistent critic of the Gleneagles Agreement. Interestingly, as we show, Thatcher struggled to reconcile her instinct to support South Africa with the practical challenges of Gleneagles. Conservative strategists recognized that withdrawing from the Agreement could be a political disaster, so much so that when Thatcher swept to victory in the General Election, she refused to renege on Britain’s obligations to Gleneagles, despite the fact that it ran counter to her broader policy of ‘constructive engagement’ with Pretoria. Carlisle spearheaded a campaign for Britain to break with the Commonwealth consensus and, in so doing, absorbed support from a growing body of Tory MPs and the wider bridge-building community. Using and applying core principles of ‘New Right’ social and economic policy, Carlisle and others reformulated the bridge-builder thesis to a point that it clearly aligned with Thatcher’s own vision on the size, scope, and policies of a British government. For the leaders of the sports boycott in Britain, it soon became clear where Thatcher’s real sympathies lay. As emboldened British teams rebelled against the boycott and thrust British sport back into the dock of international opinion during the early 1980s, the Prime Minister tended to say that she would uphold Gleneagles, rarely that she thought it was right or just.
Interconnected idioblasts in Peltaea polymorpha: a novel component of the mucilage-secretory apparatus in Malvaceae
Authors: Rodrigues Tatiane Maria , de Almeida Aline Rodrigues , de Nicolai Juan , dos Santos Igor Soares , Machado Silvia Rodrigues 
Published: November 2024

Abstract
The anatomical and cytological characteristics of the mucilage-secretory system have been widely studied in Malvaceae. However, conflicting information regarding the morphological nature of secretory structures exists, and some remain poorly understood. In this sense, some secretory structures in Malvaceae are not characterized as typical isolated idioblasts, canals, or cavities. Here, we describe a novel component of the mucilage-secretory apparatus in the Malvaceae family. Samples of the shoot apex, mature stem and fully expanded leaves were obtained from adult Peltaea polymorpha, which grow in the Cerrado (Brazilian savanna). The samples were processed using standard light and transmission electron microscopy methods. Mucilage cells occurred in the cortex and pith of petioles and stems, and in the midrib of leaves. These cells originate early in the stem apex from successive divisions of cells of the fundamental meristem, resulting in a row of interconnected secretory cells enveloped by a sheath of parenchyma cells devoid of secretory activity. Mucilage is stored in both protoplast and apoplast. In the same row, some cells filled with mucilage become very swollen and compress the neighbouring idioblasts that become flattened. This phenomenon results in a sandwich panel structure consisting of the swollen transversal walls of adjacent cells. As the differentiation progresses, the transversal walls of the rowed mucilage cells became very swollen, multilayered, and porous. Cytoplasmic strands cross such transversal walls connecting rowed cells. Mucilage-secreting cells in P. polymorpha are interconnected idioblasts and represent a novel component of the mucilage-secretory apparatus in Malvaceae. These findings open new avenues for understanding the structure and dynamics of mucilage-secreting cells from a functional perspective.
TriTan: an efficient triple nonnegative matrix factorization method for integrative analysis of single-cell multiomics data
Authors: Ma Xin , Lin Lijing , Zhao Qian , Iqbal Mudassar 
Published: November 2024

Abstract
Single-cell multiomics have opened up tremendous opportunities for understanding gene regulatory networks underlying cell states by simultaneously profiling transcriptomes, epigenomes, and proteomes of the same cell. However, existing computational methods for integrative analysis of these high-dimensional multiomics data are either computationally expensive or limited in interpretation. These limitations pose challenges in the implementation of these methods in large-scale studies and hinder a more in-depth understanding of the underlying regulatory mechanisms. Here, we propose TriTan (Triple inTegrative fast non-negative matrix factorization), an efficient joint factorization method for single-cell multiomics data. TriTan implements a highly efficient factorization algorithm, greatly improving its computational performance. Three matrix factorization produced by TriTan helps in clustering cells, identifying signature features for each cell type, and uncovering feature associations across omics, which facilitates the identification of domains of regulatory chromatin and the prediction of cell-type-specific regulatory networks. We applied TriTan to the single-cell multiomics data obtained from different technologies and benchmarked it against the state-of-the-art methods where it shows highly competitive performance. Furthermore, we showed a range of downstream analyses conducted utilizing TriTan outputs, highlighting its capacity to facilitate interpretation in biological discovery.
Keeping it in the family: using protein family templates to rescue low confidence AlphaFold2 models
Authors: Costa Francesco , Blum Matthias , Bateman Alex 
Published: November 2024

Abstract

Motivation
High confidence structure prediction models have become available for nearly all protein sequences. More than 200 million AlphaFold2 models are now publicly available. We observe that there can be significant variability in the prediction confidence as judged by plDDT scores across a protein family. We have explored whether the predictions with lower plDDT in a family can be improved by the use of higher plDDT templates from the family as template structures in AlphaFold2.

Results
Our work shows that about one-third of the time structures with a low plDDT can be “rescued,” moved from low to reasonable confidence. We also find that surprisingly in many cases we get a higher plDDT model when we switch off the multiple sequence alignment (MSA) option in AlphaFold2 and solely rely on a high-quality template. However, we find the best overall strategy is to make predictions both with and without the MSA information and select the model with the highest average plDDT. We also find that using high plDDT models as templates can increase the speed of AlphaFold2 as implemented in ColabFold. Additionally, we try to demonstrate that as well as having increased overall plDDT, the models are likely to have higher quality structures as judged by two metrics.

Availability and implementation
We have implemented our pipeline in NextFlow and it is available in GitHub: https://github.com/FranceCosta/AF2Fix.
Fast polypharmacy side effect prediction using tensor factorization
Authors: Lloyd Oliver , Liu Yi , Gaunt Tom R 
Published: November 2024

Abstract

Motivation
Adverse reactions from drug combinations are increasingly common, making their accurate prediction a crucial challenge in modern medicine. Laboratory-based identification of these reactions is insufficient due to the combinatorial nature of the problem. While many computational approaches have been proposed, tensor factorization (TF) models have shown mixed results, necessitating a thorough investigation of their capabilities when properly optimized.

Results
We demonstrate that TF models can achieve state-of-the-art performance on polypharmacy side effect prediction, with our best model (SimplE) achieving median scores of 0.978 area under receiver-operating characteristic curve, 0.971 area under precision–recall curve, and 1.000 AP@50 across 963 side effects. Notably, this model reaches 98.3% of its maximum performance after just two epochs of training (approximately 4 min), making it substantially faster than existing approaches while maintaining comparable accuracy. We also find that incorporating monopharmacy data as self-looping edges in the graph performs marginally better than using it to initialize embeddings.

Availability and implementation
All code used in the experiments is available in our GitHub repository (https://doi.org/10.5281/zenodo.10684402). The implementation was carried out using Python 3.8.12 with PyTorch 1.7.1, accelerated with CUDA 11.4 on NVIDIA GeForce RTX 2080 Ti GPUs.
lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R
Authors: Khleborodova Asya , Gamboa-Tuz Samuel D , Ramos Marcel , Segata Nicola , Waldron Levi , Oh Sehyun 
Published: November 2024

Abstract

Summary
LEfSe is a widely used Python package and Galaxy module for metagenomic biomarker discovery and visualization, utilizing the Kruskal–Wallis test, Wilcoxon Rank-Sum test, and Linear Discriminant Analysis. R/Bioconductor provides a large collection of tools for metagenomic data analysis but has lacked an implementation of this widely used algorithm, hindering benchmarking against other tools and incorporation into R workflows. We present the lefser package to provide comparable functionality within the R/Bioconductor ecosystem of statistical analysis tools, with improvements to the original algorithm for performance, accuracy, and reproducibility. We benchmark the performance of lefser against the original algorithm using human and mouse metagenomic datasets.

Availability and implementation
Our software, lefser, is distributed through the Bioconductor project (https://www.bioconductor.org/packages/release/bioc/html/lefser.html), and all the source code is available in the GitHub repository https://github.com/waldronlab/lefser.
easySCF: a tool for enhancing interoperability between R and Python for efficient single-cell data analysis
Authors: Zhang Haoyun , Zhang Wentao , Zhao Shuai , Xu Guangyu , Shen Yi , Jiang Feng , Qin An , Cui Lei 
Published: November 2024

Abstract

Summary
This study introduces easySCF, a tool designed to enhance the interoperability of single-cell data between the two major bioinformatics platforms, R and Python. By supporting seamless data exchange, easySCF improves the efficiency and accuracy of single-cell data analysis.

Availability and implementation
easySCF utilizes a unified data format (.h5 format) to facilitate data transfer between R and Python platforms. The tool has been evaluated for data processing speed, memory efficiency, and disk usage, as well as its capability to handle large-scale single-cell datasets. easySCF is available as an open-source package, with implementation details and documentation accessible at https://github.com/xleizi/easySCF.
Imaging and endovascular management of haemoptysis in congenital heart disease
Authors: Chacko Vimal , Radhakrishnan Jayakrishnan , Valakkada Jineesh , Ayyappan Anoop , Kannath Santhosh , Kumar Deepa S , Gopalakrishnan Arun 
Published: November 2024

Abstract
Haemoptysis, a rare but serious complication that can arise in patients with congenital heart disease, necessitates prompt diagnosis and specialized care. The radiologist plays a critical role in this scenario, including identifying the source of haemoptysis, devising treatment plans, and delivering endovascular interventions. This article highlights the importance of imaging techniques, especially computed tomography, in identifying the cause of haemoptysis and the therapeutic value of endovascular interventions. Furthermore, a suggested algorithmic approach is presented to assist with the diagnostic and management process.
Decoupling of motor cortex to movement in Parkinson’s dyskinesia rescued by sub-anaesthetic ketamine
Authors: Vishwanath Abhilasha , Bartlett Mitchell J , Falk Torsten , Cowen Stephen L 
Published: November 2024

Abstract
Gamma band and single-unit neural activity in primary motor cortex (M1) are involved in the control of movement. This activity is disrupted in Parkinson’s disease (PD) and levodopa-induced dyskinesia (LID), a debilitating consequence of dopamine replacement therapy for PD. Physiological features of LID include pathological narrowband gamma oscillations, finely tuned gamma (FTG), and altered M1 firing activity. Since most studies characterize LID through visual scoring, little is known about the relationships between ongoing dyskinetic movements, gamma, and neuronal activity at fast (sub-second) and slow (seconds) timescales. Here, we investigate how motor cortex activity changes with movement at multiple timescales in animal models of PD and LID. Furthermore, sub-anesthetic ketamine has emerged as a possible therapy for LID. How ketamine may reduce LID is not fully understood. Consequently, we investigate how ketamine affects the relationship between motor cortex activity and movement.
To investigate these questions, local-field and single-unit activity from &gt;3000 motor cortex neurons was acquired using a standard model of PD/LID (n = 10 male rats). Data in LID and sham animals was acquired following levodopa (L-DOPA; 12 mg/kg, i.p.) and ketamine (20 mg/kg, i.p.) administration. Movement was assessed using traditional abnormal involuntary movements (AIMs) scores and head-mounted inertial sensors sampled at 200 Hz.
While correlations between movement, gamma, and single-unit activity were high in all animals during control conditions, correlations decreased considerably in animal models of LID following L-DOPA administration. This suggests that M1 can become functionally decoupled from ongoing movements in LID. Interestingly, this effect was observed in both the dopamine depleted and non-depleted hemispheres. Ketamine disrupted FTG, decreased LID, and moderately increased single-unit correlations to movement during LID. Ketamine, however, did not enhance the correlation between gamma-band activity and movement. Finally, ketamine exerted a selective effect on neuronal interactions and ensemble activity in LID animals. Specifically, analysis of cell-pair firing-rate correlations showed that ketamine induced a distinct neural ensemble state in LID by reorganizing the pattern of cell-pair interactions.
These findings provide insight into the role that motor cortex neurons and gamma-band activity play during healthy movement and LID. Results suggest that primary motor cortex does not directly trigger specific dyskinetic movements during LID but, instead, dysregulated motor cortex activity may permit aberrant movements to spontaneously emerge in downstream circuits. These data further support the anti-dyskinetic properties of ketamine and suggest that ketamine acts to reduce LID by disrupting pathological interactions between motor cortex neurons during dyskinesia.
Functional network disruption in cognitively unimpaired autosomal dominant Alzheimer’s disease: a magnetoencephalography study
Authors: van Nifterick Anne M , de Haan Willem , Stam Cornelis J , Hillebrand Arjan , Scheltens Philip , van Kesteren Ronald E , Gouw Alida A 
Published: November 2024

Abstract
Understanding the nature and onset of neurophysiological changes, and the selective vulnerability of central hub regions in the functional network, may aid in managing the growing impact of Alzheimer’s disease on society. However, the precise neurophysiological alterations occurring in the pre-clinical stage of human Alzheimer’s disease remain controversial. This study aims to provide increased insights on quantitative neurophysiological alterations during a true early stage of Alzheimer’s disease. Using high spatial resolution source-reconstructed magnetoencephalography, we investigated regional and whole-brain neurophysiological changes in a unique cohort of 11 cognitively unimpaired individuals with pathogenic mutations in the presenilin-1 or amyloid precursor protein gene and a 1:3 matched control group (n = 33) with a median age of 49 years. We examined several quantitative magnetoencephalography measures that have been shown robust in detecting differences in sporadic Alzheimer’s disease patients and are sensitive to excitation-inhibition imbalance. This includes spectral power and functional connectivity in different frequency bands. We also investigated hub vulnerability using the hub disruption index. To understand how magnetoencephalography measures change as the disease progresses through its pre-clinical stage, correlations between magnetoencephalography outcomes and various clinical variables like age were analysed. A comparison of spectral power between mutation carriers and controls revealed oscillatory slowing, characterized by widespread higher theta (4–8 Hz) power, a lower posterior peak frequency and lower occipital alpha 2 (10–13 Hz) power. Functional connectivity analyses presented a lower whole-brain (amplitude-based) functional connectivity in the alpha (8–13 Hz) and beta (13–30 Hz) bands, predominantly located in parieto-temporal hub regions. Furthermore, we found a significant hub disruption index for (phase-based) functional connectivity in the theta band, attributed to both higher functional connectivity in ‘non-hub’ regions alongside a hub disruption. Neurophysiological changes did not correlate with indicators of pre-clinical disease progression in mutation carriers after multiple comparisons correction. Our findings provide evidence that oscillatory slowing and functional connectivity differences occur before cognitive impairment in individuals with autosomal dominant mutations leading to early onset Alzheimer’s disease. The nature and direction of these alterations are comparable to those observed in the clinical stages of Alzheimer’s disease, suggest an early excitation-inhibition imbalance, and fit with the activity-dependent functional degeneration hypothesis. These insights may prove useful for early diagnosis and intervention in the future.