bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability-aware modeling of electrochemical metallization memory cells
Authors: Ahmad Rana Walied , Waser Rainer , Maudet Florian , Toprak Onur , Dubourdieu Catherine , Menzel Stephan 
Published: June 2024

Abstract
Resistively switching electrochemical metallization memory cells are gaining huge interest since they are seen as promising candidates and basic building blocks for future computation-in-memory applications. However, especially filamentary-based memristive devices suffer from inherent variability, originating from their stochastic switching behavior. A variability-aware compact model of electrochemical metallization memory cells is presented in this study and verified by showing a fit to experimental data. It is an extension of the deterministic model. Since this extension consists of several different features allowing for a realistic variability-aware fit, it depicts a unique model comprising physics-based, stochastically and experimentally originating variabilities and reproduces them well. In addition, a physics-based model parameter study is executed, which enables a comprehensive view into the device physics and presents guidelines for the compact model fitting procedure.
Using analogues to predict changes in future UK heatwaves*
Authors: Yule Emma L , Hegerl Gabriele C , Schurer Andrew , Ballinger Andrew , Hawkins Ed 
Published: June 2024

Abstract
The intensity and frequency of extreme heat events is increasing due to climate change, resulting in a range of societal impacts. In this paper, we use temporal analogues to analyse how past UK heatwave events, such as during the summer of 1923, may change if they were to occur under different global warming scenarios. We find that the six most intense early heat events are caused by circulation patterns similar to that of 1923, which can cause intense heat over the UK and parts of NW Europe. Circulation analogues for the 1923 heatwave are also linked to intense heat events in the future, although not all analogues are anomalously hot. At 4 °C of global warming, mean summer temperatures in England over the duration of the 1923 heatwave are between 4.9 and 6.4 degrees warmer than pre-industrial levels across the three models used. At that global mean warming level, future heat events with similar circulation as 1923 over England are estimated to be on average 6.9 °C–10.7 °C hotter than those at pre-industrial levels. Exploring how the intensity of events similar to past events may change in the future could be an effective risk communication tool for adaptation decision making, particularly if past events are stored in society’s memory, for example, due to high impacts.
The forest biodiversity index (FOBI): monitoring forest biodiversity potential over space and time
Authors: Bellamy Chloe , Rattey Andrew , Edwards Colin , Kortland Kenny , Stringer Andrew , Tew Eleanor , Bathgate Stephen , Kerecsenyi Nora , Moseley Darren , Watts Kevin , Broome Alice 
Published: June 2024

Abstract
Public forest agencies are obligated to take steps to conserve and where possible enhance biodiversity, but they often lack information and tools that support and evidence their decision making. To help inform and monitor impact of management actions and policies aimed at improving forest biodiversity, we have co-developed a quantitative, transparent and repeatable approach for assessing the biodiversity potential of the United Kingdom’s (UK) publicly owned forests over space and time. The FOrest Biodiversity Index (FOBI) integrates several forest biodiversity indicators or ‘metrics’, which characterise management-sensitive woodland and landscape features associated with biodiversity. These are measured or modelled annually using spatially comprehensive forest survey data and other well-maintained spatial environmental datasets. Following metric normalisation and a correlation analysis, a statistically robust selection of these metrics is aggregated using a hierarchical procedure to provide composite index scores. The FOBI metric and index results are provided for every individual public forest, and can be summarised across any reporting region of interest. Compared to existing indicators that rely on sample-based forest data, the results thus better support decisions and obligations at a range of scales, from locally targeted action to national, long-term biodiversity monitoring and reporting. We set out how the FOBI approach and associated bespoke online interfaces were co-developed to meet public forest agency needs in two constituent countries of the UK (England and Scotland), whilst providing a conceptual framework that can be adapted and transferred to other geographic areas and private forests. Example results are reported for England’s public forests for four annual timestamps between 2014 and 2021, which indicate improvements to the biodiversity potential of public forests and surrounding landscapes over this time via increases in their diversity, extent, condition and connectivity.
OEDG: Oscillation-eliminating discontinuous Galerkin method for hyperbolic conservation laws
Authors: Peng Manting , Sun Zheng , Wu Kailiang 
Published: June 2024

Suppressing spurious oscillations is crucial for designing reliable high-order numerical schemes for hyperbolic conservation laws, yet it has been a challenge actively investigated over the past several decades. This paper proposes a novel, robust, and efficient oscillation-eliminating discontinuous Galerkin (OEDG) method on general meshes, motivated by the damping technique (see J. Lu, Y. Liu, and C. W. Shu [SIAM J. Numer. Anal. 59 (2021), pp. 1299–1324]). The OEDG method incorporates an oscillation-eliminating (OE) procedure after each Runge–Kutta stage, and it is devised by alternately evolving the conventional semidiscrete discontinuous Galerkin (DG) scheme and a damping equation. A novel damping operator is carefully designed to possess both scale-invariant and evolution-invariant properties. We rigorously prove the optimal error estimates of the fully discrete OEDG method for smooth solutions of linear scalar conservation laws. This might be the first generic fully discrete error estimate for nonlinear DG schemes with an automatic oscillation control mechanism. The OEDG method exhibits many notable advantages. It effectively eliminates spurious oscillations for challenging problems spanning various scales and wave speeds, without necessitating problem-specific parameters for all the tested cases. It also obviates the need for characteristic decomposition in hyperbolic systems. Furthermore, it retains the key properties of the conventional DG method, such as local conservation, optimal convergence rates, and superconvergence. Moreover, the OEDG method maintains stability under the normal Courant–Friedrichs–Lewy (CFL) condition, even in the presence of strong shocks associated with highly stiff damping terms. The OE procedure is nonintrusive, facilitating seamless integration into existing DG codes as an independent module. Its implementation is straightforward and efficient, involving only simple multiplications of modal coefficients by scalars. The OEDG approach provides new insights into the damping mechanism for oscillation control. It reveals the role of the damping operator as a modal filter, establishing close relations between the damping technique and spectral viscosity techniques. Extensive numerical results validate the theoretical analysis and confirm the effectiveness and advantages of the OEDG method.
Explicit formulae for the mean value of products of values of Dirichlet 𝐿-functions at positive integers
Authors: Louboutin Stéphane 
Published: June 2024

Let

m
≥
1

m\ge 1

be a rational integer. We give an explicit formula for the mean value

2

ϕ
(
f
)

∑

χ
(
−
1
)
=
(
−
1

)
m

|
L
(
m
,
χ
)

|
2

,

\begin{equation*} \frac {2}{\phi (f)}\sum _{\chi (-1)=(-1)^m}\vert L(m,\chi )\vert ^2, \end{equation*}

where

χ
\chi

ranges over the

ϕ
(
f
)

/

2

\phi (f)/2

Dirichlet characters modulo

f
>
2

f>2

with the same parity as

m
m

. We then adapt our proof to obtain explicit means values for products of the form

L
(

m
1

,

χ
1

)
⋯
L
(

m

n
−
1

,

χ

n
−
1

)

L
(

m
n

,

χ
1

⋯

χ

n
−
1

)

¯

L(m_1,\chi _1)\cdots L(m_{n-1},\chi _{n-1})\overline {L(m_n,\chi _1\cdots \chi _{n-1})}

.
Who Posts on Instagram? Using Natural Language Processing to Assess the Relationship Between Training Background and Content of 700,000 Posts
Authors: Etebari Cameron A , Braun Sterling E , Vazquez-Machado Maria C , Butterworth James A 
Published: June 2024

Abstract

Background
Instagram (Menlo Park, CA) is a major platform for the dissemination of plastic surgery (PS) information, but the training background of users is difficult to ascertain.

Objectives
We sought to better characterize the source and content of PS-related posts on Instagram.

Methods
Metadata from publicly available Instagram posts containing PS relevant hashtags was collected from December 2018 to August 2020 using Node.js (Node.js Foundation, San Francisco, CA). The data was characterized by account type, and post topics were analyzed using a custom dictionary of PS procedures applied with natural language processing. All data analyses were performed with R (The R Foundation, Vienna, Austria).

Results
Board-certified plastic surgeons account for 38% of posts on Instagram, followed by organizations (31%), nonplastics-trained physicians (19%), facial plastics (5%), oculoplastics (1%), and nonphysician providers (5%). Oculoplastics had the highest engagement rate with their posts (3.7 ± 5.1), whereas plastic surgeons had the lowest (2.7 ± 4.2). Breast aesthetics was the predominant topic posted by plastic surgeons (42%, P &lt; .001), and board certification phrases distinguished their posts from other account types (23%, P &lt; .001). Nonphysician posts focused on nonsurgical aesthetics like Botox and fillers (80%). However, nonplastics-trained physicians and organizations significantly contributed to procedural subcategories in a similar distribution to plastic surgeons.

Conclusions
Board-certified plastic surgeons are not the predominant source of PS content on Instagram. Furthermore, posts by plastic surgeons have the lowest rate of engagement out of all account types studied. Although declarations of board certification distinguish content from plastics disciplines, they are only used in 21% of posts.

Level of Evidence: 4
MolDy: molecular dynamics simulation made easy
Authors: Khan Mohd Imran , Pathania Sheetal , Al-Rabia Mohammed W , Ethayathulla Abdul S , Khan Mohammad Imran , Allemailem Khaled S , Azam Mohd , Hariprasad Gururao , Imran Mohammad Azhar 
Published: June 2024

Abstract

Motivation
Molecular dynamics (MD) is a computational experiment that is crucial for understanding the structure of biological macro and micro molecules, their folding, and the inter-molecular interactions. Accurate knowledge of these structural features is the cornerstone in drug development and elucidating macromolecules functions. The open-source GROMACS biomolecular MD simulation program is recognized as a reliable and frequently used simulation program for its precision. However, the user requires expertise, and scripting skills to carrying out MD simulations.

Results
We have developed an end-to-end interactive MD simulation application, MolDy for Gromacs. This front-end application provides a customizable user interface integrated with the Python and Perl-based logical backend connecting the Linux shell and Gromacs software. The tool performs analysis and provides the user with simulation trajectories and graphical representations of relevant biophysical parameters. The advantages of MolDy are (i) user-friendly, does not requiring the researcher to have prior knowledge of Linux; (ii) easy installation by a single command; (iii) freely available for academic research; (iv) can run with minimum configuration of operating systems; (v) has valid default prefilled parameters for beginners, and at the same time provides scope for modifications for expert users.

Availability and implementation
MolDy is available freely as compressed source code files with user manual for installation and operation on GitHub: https://github.com/AIBResearchMolDy/Moldyv01.git and on https://aibresearch.com/innovations.
Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach
Authors: Jiang Yueyu , McDonald Daniel , Perry Daniela , Knight Rob , Mirarab Siavash 
Published: June 2024

Abstract

Motivation
Phylogenetic placement of a query sequence on a backbone tree is increasingly used across biomedical sciences to identify the content of a sample from its DNA content. The accuracy of such analyses depends on the density of the backbone tree, making it crucial that placement methods scale to very large trees. Moreover, a new paradigm has been recently proposed to place sequences on the species tree using single-gene data. The goal is to better characterize the samples and to enable combined analyses of marker-gene (e.g., 16S rRNA gene amplicon) and genome-wide data. The recent method DEPP enables performing such analyses using metric learning. However, metric learning is hampered by a need to compute and save a quadratically growing matrix of pairwise distances during training. Thus, the training phase of DEPP does not scale to more than roughly 10 000 backbone species, a problem that we faced when trying to use our recently released Greengenes2 (GG2) reference tree containing 331 270 species.

Results
This paper explores divide-and-conquer for training ensembles of DEPP models, culminating in a method called C-DEPP. While divide-and-conquer has been extensively used in phylogenetics, applying divide-and-conquer to data-hungry machine-learning methods needs nuance. C-DEPP uses carefully crafted techniques to enable quasi-linear scaling while maintaining accuracy. C-DEPP enables placing 20 million 16S fragments on the GG2 reference tree in 41 h of computation.

Availability and implementation
The dataset and C-DEPP software are freely available at https://github.com/yueyujiang/dataset_cdepp/.
Piperacillin/tazobactam for surgical prophylaxis during pancreatoduodenectomy: meta-analysis
Authors: Kumar Jayant , Reccia Isabella , Carneiro Adriano , Podda Mauro , Virdis Francesco , Machairas Nikolaos , Nasralla David , Arasaradnam Ramesh P , Poon Kenneth , Gannon Christopher J , Fung John J , Habib Nagy , Llaguna Omar 
Published: June 2024

Abstract

Background
Pancreatoduodenectomy is associated with an increased incidence of surgical-site infections, often leading to a significant rise in morbidity and mortality. This trend underlines the inadequacy of traditional antibiotic prophylaxis strategies. Hence, the aim of this meta-analysis was to assess the outcomes of antimicrobial prophylaxis, comparing piperacillin/tazobactam with traditional antibiotics.

Methods
Upon registering in PROSPERO, the international prospective register of systematic reviews (CRD42023479100), a systematic search of various databases was conducted over the interval 2000–2023. This inclusive search encompassed a wide range of study types, including prospective and retrospective cohorts and RCTs. The subsequent data analysis was carried out utilizing RevMan 5.4.

Results
A total of eight studies involving 2382 patients who underwent pancreatoduodenectomy and received either piperacillin/tazobactam (1196 patients) or traditional antibiotics (1186 patients) as antibiotic prophylaxis during surgery were included in the meta-analysis. Patients in the piperacillin/tazobactam group had significantly reduced incidences of surgical-site infections (OR 0.43 (95% c.i. 0.30 to 0.62); P &lt; 0.00001) and major surgical complications (Clavien–Dindo grade greater than or equal to III) (OR 0.61 (95% c.i. 0.45 to 0.81); P = 0.0008). Subgroup analysis of surgical-site infections highlighted significantly reduced incidences of superficial surgical-site infections (OR 0.34 (95% c.i. 0.14 to 0.84); P = 0.02) and organ/space surgical-site infections (OR 0.47 (95% c.i. 0.28 to 0.78); P = 0.004) in the piperacillin/tazobactam group. Further, the analysis demonstrated significantly lower incidences of clinically relevant postoperative pancreatic fistulas (grades B and C) (OR 0.67 (95% c.i. 0.53 to 0.83); P = 0.0003) and mortality (OR 0.51 (95% c.i. 0.28 to 0.91); P = 0.02) in the piperacillin/tazobactam group.

Conclusion
Piperacillin/tazobactam as antimicrobial prophylaxis significantly lowers the risk of postoperative surgical-site infections, major surgical complications (complications classified as Clavien–Dindo grade greater than or equal to III), clinically relevant postoperative pancreatic fistulas (grades B and C), and mortality, hence supporting the implementation of piperacillin/tazobactam for surgical prophylaxis in current practice.
Protein fibril aggregation on red blood cells: a potential biomarker to distinguish neurodegenerative diseases from healthy aging
Authors: Schneider Thomas Rudolf , Stöckli Luisa , Felbecker Ansgar , Nirmalraj Peter Niraj 
Published: June 2024

Abstract
Neurodegenerative diseases like Alzheimer’s disease are characterized by the accumulation of misfolded proteins into fibrils in the brain. Atomic force microscopy is a nanoscale imaging technique that can be used to resolve and quantify protein aggregates from oligomers to fibrils. Recently, we characterized protein fibrillar aggregates adsorbed on the surface of red blood cells with atomic force microscopy from patients with neurocognitive disorders, suggesting a novel Alzheimer’s disease biomarker. However, the age association of fibril deposits on red blood cells has not yet been studied in detail in healthy adults. Here, we used atomic force microscopy to visualize and quantify fibril coverage on red blood cells in 50 healthy adults and 37 memory clinic patients. Fibrillar protein deposits sporadically appeared in healthy individuals but were much more prevalent in patients with neurodegenerative disease, especially those with Alzheimer’s disease as confirmed by positive CSF amyloid beta 1–42/1–40 ratios. The prevalence of fibrils on the red blood cell surface did not significantly correlate with age in either healthy individuals or Alzheimer’s disease patients. The overlap in fibril prevalence on red blood cells between Alzheimer’s disease and amyloid-negative patients suggests that fibril deposition on red blood cells could occur in various neurodegenerative diseases. Quantifying red blood cell protein fibril morphology and prevalence on red blood cells could serve as a sensitive biomarker for neurodegeneration, distinguishing between healthy individuals and those with neurodegenerative diseases. Future studies that combine atomic force microscopy with immunofluorescence techniques in larger-scale studies could further identify the chemical nature of these fibrils, paving the way for a comprehensive, non-invasive biomarker platform for neurodegenerative diseases.
Disruption in functional networks mediated tau spreading in Alzheimer’s disease
Authors: Nabizadeh Fardin 
Published: June 2024

Abstract
Alzheimer’s disease may be conceptualized as a ‘disconnection syndrome’, characterized by the breakdown of neural connectivity within the brain as a result of amyloid-beta plaques, tau neurofibrillary tangles and other factors leading to progressive degeneration and shrinkage of neurons, along with synaptic dysfunction. It has been suggested that misfolded tau proteins spread through functional connections (known as ‘prion-like’ properties of tau). However, the local effect of tau spreading on the synaptic function and communication between regions is not well understood. I aimed to investigate how the spreading of tau aggregates through connections can locally influence functional connectivity. In total, the imaging data of 211 participants including 117 amyloid-beta-negative non-demented and 94 amyloid-beta-positive non-demented participants were recruited from the Alzheimer’s Disease Neuroimaging Initiative. Furthermore, normative resting-state functional MRI connectomes were used to model tau spreading through functional connections, and functional MRI of the included participants was used to determine the effect of tau spreading on functional connectivity. I found that lower functional connectivity to tau epicentres is associated with tau spreading through functional connections in both amyloid-beta-negative and amyloid-beta-positive participants. Also, amyloid-beta-PET in tau epicentres mediated the association of tau spreading and functional connectivity to epicentres suggesting a partial mediating effect of amyloid-beta deposition in tau epicentres on the local effect of tau spreading on functional connectivity. My findings provide strong support for the notion that tau spreading through connection is locally associated with disrupted functional connectivity between tau epicentre and non-epicentre regions independent of amyloid-beta pathology. Also, I defined several groups based on the relationship between tau spreading and functional disconnection, which provides quantitative assessment to investigate susceptibility or resilience to functional disconnection related to tau spreading. I showed that amyloid-beta, other copathologies and the apolipoprotein E epsilon 4 allele can be a leading factor towards vulnerability to tau relative functional disconnection.
Considerations for legal, ethical, and effective practice in dementia research
Authors: David Michael C B , Del Giovane Martina , Wilson Danielle , Truman Trevor , Huntley Jonathan D , Suleman Mehrunisha , Ruck Keene Alexander , Parker Michael , Sharp David J , Malhotra Paresh A 
Published: June 2024

Abstract
Dementia represents a potentially overwhelming health burden, both for the UK and worldwide. Addressing this fast-growing issue is a key priority for the government, health service and the public. Advances in care including the development of efficacious disease-modifying, and eventually curative, treatments can only be achieved through effective dementia research. Specifically, research directly involving participants with dementia is essential to further understanding. However, working with cognitively impaired participants with and without capacity to consent to research presents unique ethical and legal challenges. For clinicians and scientists on the frontline of dementia research, scenarios frequently arise that pose such challenges. A lack of guidance for a consistent approach in navigating these scenarios limits researchers’ ability to proceed with confidence. This represents a threat to the rights and wishes of research participants as well as the field at large, as it may lead to studies being unnecessarily terminated or, worse, poor practice. In this article, we take a multiprofessional approach, informed by carer input, to these issues. We review the relevant ethical and legal literature relating to the conduct of non-interventional research studies in patients with dementia. This includes a thorough recap of the Mental Capacity Act (2005), which provides a legal framework in England and Wales for conducting research with participants who lack capacity to consent. We also discuss the important, but sometimes incomplete, role of research ethics committees in guiding researchers. We then present and discuss a series of case vignettes designed to highlight areas of incomplete coverage by existing governance. These vignettes describe theoretical scenarios informed by our own real-word experiences of encountering ethical issues when conducting dementia research. They include scenarios in which participants demonstrate varying degrees of understanding of the research they are involved in and ability to communicate their wishes and feelings. Building on these vignettes, we then provide a checklist for researchers to work through when presented with similar scenarios. This checklist covers the key ethical, legal and practical considerations that we have argued for. Taken together, this article can act as a guide, previously lacking in the literature, for colleagues in the field to enable much needed ethical, legal and effective research.