bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of viscoelasticity in the adhesion of mushroom-shaped pillars
Authors: Violano Guido , Dibitonto Savino , Afferrante Luciano
Published: October 2024

The contact behaviour of mushroom-shaped pillars has been extensively studied for their superior adhesive properties, often inspired by natural attachment systems observed in insects. Typically, pillars are modeled with linear elastic materials in the literature; in reality, the soft materials used for their fabrication exhibit a rate-dependent constitutive behaviour. Additionally, conventional models focus solely on the detachment phase of the pillar, overlooking the analysis of the attachment phase. As a result, they are unable to estimate the energy loss during a complete loading-unloading cycle. This study investigates the role of viscoelasticity in the adhesion between a mushroom-shaped pillar and a rigid flat countersurface. Interactions at the interface are assumed to be governed by van der Waals forces, and the material is modeled using a standard linear solid model. Normal push and release contact cycles are simulated at different approaching and retracting speeds. Results reveal that, in the presence of an interfacial defect, a monotonically increasing trend in the pull-off force with pulling speed is observed. The corresponding change in the contact pressure distribution suggests a transition from short-range to long-range adhesion, corroborating recent experimental and theoretical investigations. Moreover, the pull-off force remains invariant to the loading history due to our assumption of a flat–flat contact interface. Conversely, in the absence of defects and under the parameters used in this study, detachment occurs after reaching the theoretical contact strength, and the corresponding pull-off force is found to be rate independent. Notably, the hysteretic loss exhibits a peak at intermediate detachment speeds, where viscous dissipation occurs, which holds true in both the presence and absence of a defect. However, the presence of a defect shifts the region where the majority of viscous dissipation takes place.
The first global catalogue of gas flaring sources derived from a multi-temporal time series of OLI and MSI daytime data: the DAFI v2 algorithm
Authors: Faruolo Mariapia , Genzano Nicola , Pergola Nicola , Marchese Francesco
Published: October 2024

Gas flaring (GF) is an industrial phenomenon requiring a special attention for the serious impacts on environment, climate and human health. To analyses and map GF sites (GFs), the Daytime Approach for GF Investigation (DAFI), which is based on daytime data from the Operational Land Imager (OLI) aboard the Landsat-8 satellite, has recently been developed. The GFs catalogue from the DAFI system, spanning over the years 2013–2021, represents the first worldwide GF product generated from mid-high spatial resolution data (30 m). The DAFI version 2 (v2), also including information from the Multispectral Instrument (MSI) aboard Sentinel-2 satellites, already showed an improved capacity in the mapping of GFs over Iran and Iraq. In this work, the new catalogue arising from the porting of DAFI v2 at global scale is presented and discussed. By using a parallel workflow, based on a loop tiling scheme running in Google Earth Engine, DAFI v2 allowed us to extend the GF inventory globally up to 2023, by analyzing ∼4 million of OLI/OLI-2 (Collection 2) and MSI imagery. Results of this study show: (i) an increased DAFI v2 capacity, of about 41%, in detecting GFs compared to the previous DAFI version; (ii) a downward trend (∼4.6%) in terms of GF sites detected from 2021 to 2023. These findings demonstrated that DAFI v2, which will also include the estimates of radiative power at different spatial scales, may contribute in assessing and monitoring the GFs activities and in evaluating the effectiveness of the greenhouse gas-emission reduction strategies at global, continental, national and local scales.
Assessment of the Climate Trace global powerplant CO2 emissions
Authors: Gurney Kevin R , Aslam Bilal , Dass Pawlok , Gawuc Lech , Hocking Toby , Barber Jarrett J , Kato Anna
Published: October 2024

Accurate estimation of planetary greenhouse gas (GHG) emissions at the scale of individual emitting activities is a critical need for both scientific and policy applications. Powerplants represent the single largest and most concentrated form of global GHG emissions. Climate Trace, co-founded and promoted by former U.S. Vice President Al Gore, is a new effort using, in part, artificial intelligence (AI) approaches to estimate asset-scale GHG emissions. Climate Trace recently released a database of global powerplant CO2 emissions at the facility-scale that uses both AI and non-AI estimation approaches. However, no independent peer-reviewed assessment has been made of this important global emissions database. Here, we compare the Climate Trace powerplant CO2 emissions to an atmospherically calibrated, multi-constraint estimate of powerplant CO2 emissions in the United States. The 3.7% (65) of compared facilities that used an AI-based approach show a mean relative difference (MRD) of −1.1% (SD: 46.4%) in the year 2019. The 96.3% (1726) of the facilities that used a non-AI-based approach show a MRD of −50.0% (SD: 117.7%). Of the non-AI estimated facilities, 151 (8.7%) facilities agree to within ±20%. The large differences between Climate Trace and Vulcan-power emission estimates for these facilities is primarily caused by Climate Trace’ use of a national-mean power plant capacity factor (CF) which is a poor representation of the reported power plant CFs of individual US facilities and leads to very large errors at those same 1726 facilities.
The impact of IPOD on boreal midsummer extratropical cyclones accompanied by torrential rains in Central and Eastern China
Authors: Zhang Meng , Luo Jing-Jia , Xie Tiejun , Song Jianing , Fu Jing
Published: October 2024

In recent years, extratropical cyclones accompanied by torrential rains (ETCTRs) have caused an increasing number of disasters in Central and Eastern China. However, our understanding of climatic mechanisms remains inadequate for operational prediction. By analyzing the atmospheric circulation of ETCTRs occurring in Central and Eastern China during the boreal midsummer period (July–August) from 1981 to 2020, this study found that these boreal midsummer ETCTRs may be influenced by the Indo-Pacific Warm Pool and North Pacific Ocean Dipole (IPOD). Diagnostic analysis and Linear Baroclinic Model experiments indicated that negative IPOD-type sea surface temperature anomalies can trigger positive geopotential height anomalies in the mid-upper troposphere over the subtropical region and negative geopotential height anomalies from the Western North Pacific to Northeastern and Northern China. This circulation pattern and moisture transport conditions are conducive to the formation of ETCTRs during boreal midsummer in Central and Eastern China and vice versa for the positive IPOD case. This study provides useful evidence for short-range climate prediction of boreal midsummer ETCTRs in Central and Eastern China.
A prototype early warning system for diarrhoeal disease to combat health threats of climate change in the asia-pacific region
Authors: Cruz Cano Raul , He Hao , Aryal Samyam , Dhimal Megnath , Thu Dang Thi Anh , Zhang Linus , Ma Tianzhou , Liang Xin-Zhong , Murtugudde Raghu , Gao Chuansi , Sharma Ayushi , Andhikaputra Gerry , Wang Yu-Chun , Sapkota Amir
Published: October 2024

Ongoing climate variability and change are increasing the burden of diarrhoeal disease worldwide. Meaningful early warning systems with adequate lead times (weeks to months) are needed to guide public health decision–making and enhance community resilience against health threats posed by climate change. Toward this goal, we trained various machine-learning models to predict diarrhoeal disease rates in Nepal (2002–2014), Taiwan (2008–2019), and Vietnam (2000–2015) using temperature, precipitation, previous disease rates, and El Niño Southern Oscillation phases. We also compared the performance of shallow time-series neural network (NN), Random Forest Regressor, artificial nn, gradient boosting regressor, and long short-term memory–based methods for their effectiveness in predicting diarrhoeal disease burden across multiple countries. We evaluated model performance using a test dataset and assessed the accuracy of predicted diarrhoeal disease incidence rates for the last year of available data in each district. Our results suggest that even in the absence of the most recent disease surveillance data, a likely scenario in most low- and middle-income countries, our NN-based early warning system using historical data performs reasonably well. However, future studies are needed to perform prospective evaluations of such early warning systems in real-world settings.
Exploring the impact of population agglomeration on ecosystem services: an empirical study based on Fenhe River Basin
Authors: Li Qiang , Cao An , Shi Xueyi , Zhao Zhongqiu , Wu Qingqing
Published: October 2024

Since the 21st century, cities have experienced rapid expansion, posing serious threats to the health of non-urban ecosystems. It is generally believed that continued urbanization will put increasing pressure on ecosystems. However, in recent decades, the degree of population agglomeration and ecological environment have simultaneously increased in China. This paper takes Fenhe River Basin as the study area, measures the spatial Gini coefficient of population distribution (Gini) and ecosystem services in 165 sub-basins from 2000 to 2020, and adopts two-way fixed effects model to study the impacts of population agglomeration on ecosystem services and its mechanism. The results show that population agglomeration is positively correlated with the overall benefit (OB) of ecosystem services, and the effect is moderated by vegetation coverage, slope and distance from market centre, only when the values are greater than 0.198, less than 6.62° and 17.90 km, respectively, will the positive effects become apparent. The phenomenon of ‘people withdrawing and vegetation entering’ makes population agglomeration have significant impacts on individual ecosystem services and trade-offs and synergies. In order to give better play to the positive effect, the population needs to migrate from areas with worse geographical conditions and farther away from market centres to better places, and the return of farmland to forests should be accelerated in areas with population concentration. Following the laws of nature to promote population agglomeration and vegetation restoration, so as to achieve a ‘win–win’ situation between economic development and ecological civilization construction through the optimization of resource allocation.
3D bioprinting of an intervertebral disc tissue analogue with a highly aligned annulus fibrosus via suspended layer additive manufacture
Authors: Moxon S R , McMurran Z , Kibble M J , Domingos M , Gough J E , Richardson S M
Published: October 2024

Intervertebral disc (IVD) function is achieved through integration of its two component regions: the nucleus pulposus (NP) and the annulus fibrosus (AF). The NP is soft (0.3–5 kPa), gelatinous and populated by spherical NP cells in a polysaccharide-rich extracellular matrix (ECM). The AF is much stiffer (∼100 kPa) and contains layers of elongated AF cells in an aligned, fibrous ECM. Degeneration of the disc is a common problem with age being a major risk factor. Progression of IVD degeneration leads to chronic pain and can result in permanent disability. The development of therapeutic solutions for IVD degeneration is impaired by a lack of in vitro models of the disc that are capable of replicating the fundamental structure and biology of the tissue. This study aims to investigate if a newly developed suspended hydrogel bioprinting system (termed SLAM) could be employed to fabricate IVD analogues with integrated structural and compositional features similar to native tissue. Bioprinted IVD analogues were fabricated to recapitulate structural, morphological and biological components present in the native tissue. The constructs replicated key structural components of native tissue with the presence of a central, polysaccharide-rich NP surrounded by organised, aligned collagen fibres in the AF. Cell tracking, actin and matrix staining demonstrated that embedded NP and AF cells exhibited morphologies and phenotypes analogous to what is observed in vivo with elongated, aligned AF cells and spherical NP cells that deposited HA into the surrounding environment. Critically, it was also observed that the NP and AF regions contained a defined cellular and material interface and segregated regions of the two cell types, thus mimicking the highly regulated structure of the IVD.
Solar light-induced degradation of hazardous organic pollutants using Diospyros kaki mediated green synthesized zirconium doped nickel oxide-zinc oxide nanocomposite
Authors: Haq Sirajul , Raja Aqsa Waheed , Rehman Sadiq Ur , Sadiq Muhammad Usman , Alsaiari Ahad Amer , Razzokov Jamoliddin , Gulzar Faisal
Published: October 2024

This study explores an eco-friendly route using Diospyros kaki leaves extract as a stabilizing and reducing agent for the fabrication of 0.5% and 1% Zr-NiO/ZnO NCs. The fabricated samples were characterized using x-ray diffraction (XRD), fourier transform infrared spectroscopy (FTIR), diffuse reflectance spectroscopy (DRS), scanning electron microscopy (SEM), energy-dispersive x-ray (EDX) and transmission electron microscopy (TEM). The physicochemical analysis confirmed the successful fabrication of zirconium-doped NiO/ZnO (Zr-NiO/ZnO NCs) NCs. UV-DRS study showed the widening of the band gap from 3.43 eV to 3.66 eV with the increase in the amount of dopant from 0.5% to 1%. The SEM and TEM micrographs revealed the formation of nanostructures having irregular morphologies which were unevenly distributed. Furthermore, EDX results showed the characteristic signal of zirconium, nickel, zinc, and oxygen in the sample which confirmed the successful formation of Zr-NiO/ZnO NCs. The photocatalytic activity of Zr-NiO/ZnO NCs was evaluated by performing degradation of brilliant green (BG) and 4-nitrophenol (4-NP) under direct solar light, which showed enhanced photocatalytic performance. The 0.5%Zr-NiO/ZnO NC demonstrated enhanced performance (86.4% degradation of BG and 89% degradation of 4-NP) as compared to 1% Zr-NiO/ZnO NC (67% and 51% of BG and 4-NP respectively) which can be related to lower band gap and less agglomeration of nanostructures.
Convergence of a stabilized parametric finite element method of the Barrett–Garcke–Nürnberg type for curve shortening flow
Authors: Bai Genming , Li Buyang
Published: October 2024

The parametric finite element methods of the Barrett–Garcke–Nürnberg (BGN) type have been successful in preventing mesh distortion/ degeneration in approximating the evolution of surfaces under various geometric flows, including mean curvature flow, Willmore flow, Helfrich flow, surface diffusion, and so on. However, the rigorous justification of convergence of the BGN-type methods and the characeterization of the particle trajectories produced by these methods still remain open since this class of methods was proposed in 2007. The main difficulty lies in the stability of the artificial tangential velocity implicitly determined by the BGN methods. In this paper, we give the first proof of convergence of a stabilized BGN method for curve shortening flow, with optimal-order convergence in

L
2

L^2

norm for finite elements of degree

k
≥
2

k \geq 2

under the stepsize condition

τ
≤
c

h

k
+
1

\tau \leq c h^{k+1}

(for any fixed constant

c
c

). Moreover, we give the first rigorous characterization of the particle trajectories produced by the BGN-type methods for one-dimensional curves, i.e., we prove that the particle trajectories produced by the stabilized BGN methods converge to the particle trajectories determined by a system of geometric partial differential equations which differs from the standard curve shortening flow by a tangential motion. The characterization of the particle trajectories also rigorously explains, for one-dimensional curves, why the BGN-type methods could maintain the quality of the underlying evolving mesh.
A convex dual problem for the rational minimax approximation and Lawson’s iteration
Authors: Zhang Lei-Hong , Yang Linyi , Yang Wei Hong , Zhang Ya-Nan
Published: October 2024

Computing the discrete rational minimax approximation in the complex plane is challenging. Apart from Ruttan’s sufficient condition, there are few other sufficient conditions for global optimality. The state-of-the-art rational approximation algorithms, such as the adaptive Antoulas-Anderson (AAA), AAA-Lawson, and the rational Krylov fitting method, perform highly efficiently, but the computed rational approximations may not be minimax solutions. In this paper, we propose a convex programming approach, the solution of which is guaranteed to be the rational minimax approximation under Ruttan’s sufficient condition. Furthermore, we present a new version of Lawson’s iteration for solving this convex programming problem. The computed solution can be easily verified as the rational minimax approximation. Our numerical experiments demonstrate that this updated version of Lawson’s iteration generally converges monotonically with respect to the objective function of the convex optimization. It is an effective competitive approach for computing the rational minimax approximation, compared to the highly efficient AAA, AAA-Lawson, and the stabilized Sanathanan-Koerner iteration.
On the stability of the dnoidal waves for the Schrödinger-KdV system
Authors: Hakkaev Sevdzhan , Stefanov Atanas
Published: October 2024

We study the periodic Schrödinger-Korteweg de Vries system. We describe the two-parametetric family of

2
T

2T

periodic traveling waves of dnoidal type. The main objective of the paper is to establish their spectral stability with respect to co-periodic perturbations. In the limit

T
→
∞

T\to \infty

, we recover the results of Chen, [J. Partial Differential Equations 12 (1999), pp. 11–25] for the stability of the soliton solutions of this system on the real line.
Continuous and discrete universality of zeta-functions: Two sides of the same coin?
Authors: Sourmelidis Athanasios
Published: October 2024

In 1975 Voronin proved the universality theorem for the Riemann zeta-function

ζ
(
s
)

\zeta (s)

which roughly says that any admissible function

f
(
s
)

f(s)

is approximated by

ζ
(
s
)

\zeta (s)

. A few years later Reich proved a discrete analogue of this result. The proofs of these theorems are almost identical but it is not known whether one of them implies the other. We will see that if we translate the question in the language of linear dynamics then there is a link which we exploit to obtain in a straightforward way a big variety of discrete universality results appearing in the literature.
Noncommutative Hardy algebras associated with 𝒰-twisted polyballs and functional calculus
Authors: Popescu Gelu
Published: October 2024

The main goal of the paper is to introduce the twisted noncommutative Hardy algebra

F
∞

(

U

,

S

)

F^\infty (\mathcal {U}, \mathbf {S})

associated with the standard

U

\mathcal {U}

-twisted multi-shift

S

\mathbf {S}

, describe some of its basic properties, and develop a

w
∗

w^*

-continuous functional calculus for the pure (resp. completely non-coisometric) elements in the regular

U

\mathcal {U}

-twisted polyball

B

U

(

H

)

\mathbf {B}_\mathcal {U}(\mathcal {H})

. In addition, we introduce the twisted noncommutative polyball algebra

A

(

U

,

S

)

\mathcal {A}(\mathcal {U}, \mathbf {S})

and present the corresponding functional calculus for the elements in

B

U

(

H

)

\mathbf {B}_\mathcal {U}(\mathcal {H})

.
Fractal percolation on statistically self-affine carpets
Authors: Falconer Kenneth , Feng Tianyi
Published: October 2024

We consider a random self-affine carpet

F
F

based on an

n
×
m

n\times m

subdivision of rectangles and a probability

0
>
p
>
1

0>p>1

. Starting by dividing

[
0
,
1

]
2

[0,1]^2

into an

n
×
m

n\times m

grid of rectangles and selecting these independently with probability

p
p

, we then divide the selected rectangles into

n
×
m

n\times m

subrectangles which are again selected with probability

p
p

; we continue in this way to obtain a statistically self-affine set

F
F

. We are particularly interested in topological properties of

F
F

. We show that the critical value of

p
p

above which there is a positive probability that

F
F

connects the left and right edges of

[
0
,
1

]
2

[0,1]^2

is the same as the critical value for

F
F

to connect the top and bottom edges of

[
0
,
1

]
2

[0,1]^2

. Once this is established we derive various topological properties of

F
F

analogous to those known for self-similar carpets.
On Fourier multipliers with rapidly oscillating symbols
Authors: Stolyarov D.
Published: October 2024

Asymptotically sharp bounds are provided for the 

L
p

L_p

norms of the Fourier multipliers with symbols 

e

i
λ
φ
(
ξ

/

|

ξ

|

)

e^{i\lambda \varphi (\xi /|\xi |)}

, where 

λ
∈

R

\lambda \in \mathbb {R}

is a large parameter.
Probabilistic method to fundamental gap problems on the sphere
Authors: Cho Gunhee , Wei Guofang , Yang Guang
Published: October 2024

We provide a probabilistic proof of the fundamental gap estimate for Schrödinger operators in convex domains on the sphere, which extends the probabilistic proof of F. Gong, H. Li, and D. Luo [Potential Anal. 44 (2016), pp. 423–442] for the Euclidean case. Our results further generalize the results achieved for the Laplacian by S. Seto, L. Wang, and G. Wei [J. Differential Geom. 112 (2019), pp. 347–389], as well as by C. He, G. Wei, and Qi S. Zhang [Amer. J. Math. 142 (2020), pp. 1161–1191]. The essential ingredient in our analysis is the reflection coupling method on Riemannian manifolds.
On 𝑝-adic Simpson and Riemann–Hilbert correspondences in the imperfect residue field case
Authors: Gao Hui
Published: October 2024

Let

K
K

be a mixed characteristic complete discrete valuation field with residue field admitting a finite

p
p

-basis, and let

G
K

G_K

be the Galois group. Inspired by Liu and Zhu’s construction of

p
p

-adic Simpson and Riemann–Hilbert correspondences over rigid analytic varieties, we construct such correspondences for representations of

G
K

G_K

. As an application, we prove a Hodge–Tate (resp. de Rham) “rigidity” theorem for

p
p

-adic representations of

G
K

G_K

, generalizing a result of Morita.
Decausativization, reflexivization, reciprocalization, and middle voices
Authors: Creissels Denis
Published: October 2024

In reflexive and reciprocal constructions, discussed in Sections 11.2 and 11.3 of this chapter, the relationship between participants in the event and participant roles implied by the lexical meaning of the verb is not one-to-one, but the set of participant roles implied by the lexical meaning of transitive verbs is not affected. By contrast, decausativization, discussed in section 11.1, modifies the set of participant roles implied by the lexical meaning of transitive verbs. However, dedicated decausative voices are less common than multifunctional detransitivizing voices, commonly designated as middle voices, used to encode not only decausativization, but also various semantic types of valency operations that involve detransitivization without modifying the set of participant roles. The possible functions and historical origins of middle voices are discussed in Sections 11.4 to 11.11.
The State of Firearm Policy Research in the United States
Authors: Crifasi Cassandra K , Ward Julie A , Fitch Kate Vinita , Ranapurwala Shabbar I
Published: October 2024

Firearm-related deaths lead to the most person-years of life lost in the US. There were 48,830 deaths from homicides and suicides in 2021 alone. Firearm access remains at an all-time high in most states - indicated by record manufacturing, sales, employment in firearm industry, taxes collected from sales, and the number of federal background check applications in 2020 and 2021. Yet, firearm injury is a politically contentious topic to the point of stalling progress on an important public health topic. This politicization led to nearly three decades of federal disinvestment in firearm research; reduced surveillance of firearm-related crime, injury, and death; and degraded data quality. This left generations of researchers with limited epidemiologic tools to conduct firearm policy research, jeopardizing the amount and quality of research conducted. Despite these limitations, research has persisted and promising approaches to reduce firearm morbidity and mortality have been identified. Yet the field has struggled to keep pace with methodological advancements and conceptualizations of racial and ethnic disparities as products of systemic racism. In this commentary, we highlight some existing evidence-informed policies, explicate some limitations in the field, and identify opportunities to address the limitations of prior work to strengthen future capacity for evidence-informed prevention.
Invited commentary: thirty-five years of leaky vaccines
Authors: Halloran M Elizabeth , Struchiner Claudio J
Published: October 2024

Over the past 35 years, the term “leaky vaccine” has gained widespread use in both mathematical modeling and epidemiologic methods for evaluating vaccines. Here, we present a short history, as we recall it, of how the term was coined in the context of the history of sporozoite malaria vaccines that were thought in the 1980s to be possibly leaky. We draw a contrast with the all-or-none vaccine mechanism and review a few consequences for study design and population-level effects. We invite readers to contribute information covering the period preceding our memories in the 1980s, because we may have overlooked something.
High metabolic rates drive tiny genomes in plants (and birds): a commentary on ‘The smallest angiosperm genomes may be the price for effective traps of bladderworts’
Authors: Givnish Thomas J
Published: October 2024

This article comments on:

František Zedek, Jakub Šmerda, Aneta Halasová, Lubomír Adamec, Adam Veleba, Klára Plačková and Petr Bureš, The smallest angiosperm genomes may be the price for effective traps of bladderworts, Annals of Botany, Volume 134, Issue 7, 31 December 2024, Pages 1131–1138, https://doi.org/10.1093/aob/mcae107
Clutch attendance and call parameters are linked to mating success in a glassfrog with paternal care
Authors: Garrido-Priego Marina , Tószeghi Moric , Angiolani-Larrea Francesca N , Valencia-Aguilar Anyelet , Bégué Lauriane , Núñez Raby , Culebras Jaime , Ringler Max , Stynoski Jennifer L , Ringler Eva
Published: October 2024

Females of some species improve their reproductive success not only by being choosy and selecting males with certain traits, but also by sequentially mating with multiple males within one reproductive season. However, it is relatively unknown whether females also evaluate parental care during mate choice and, if they do, whether males actively communicate their care status to approaching females. We monitored a natural population of the glassfrog Hyalinobatrachium valerioi, a species with sequential polyandry and paternal care, to assess the role of parental care and advertisement calling on male mating success. Using field observations and acoustic analysis, we found that even in this species which has single-note calls, variations in call parameters allow for individual discrimination. Calling was strongly associated with mating success in H. valerioi males. Males with longer calls achieved the highest total mating success over the entire study period, indicating that females might have a preference for longer calls. Moreover, active calling and the presence of clutches were both linked to male mating success on a given night, although we cannot fully exclude that the link between presence of clutches and mating success is due to attractive call features alone. Call parameters differed between males when they were calling on top of their clutches, compared to sitting on the leaf directly, which might provide reliable cues about parental state to approaching females. These findings demonstrate the prominent role of acoustic communication and female choice in a species with male parental care and sequential polyandry.
A modern multi-omics data exploration experience with Panomicon
Authors: Allendes Osorio Rodolfo S , Kosugi Yuji , Nyström-Persson Johan T , Mizuguchi Kenji , Natsume-Kitatani Yayoi
Published: October 2024

To address the challenges of the storage, sharing, and analysis of multi-omics data, here we introduce the newest version of Panomicon, which includes the improvement of the underlying data model, the introduction of new registration and control access service, together with the seamless integration with other services (like TargetMine for data enrichment analysis), integrated in a completely new, more user friendly web application.

Availability and implementation

Panomicon is available online at https://panomicon.nibiohn.go.jp. Unregistered users can access the publicly available data uploaded to Panomicon using the following account: user: guest, password: anonymous. Source code for the application is also freely available under a GNU license at https://github.com/Toxygates/Panomicon/. A brief user guide for the new features of Panomicon is provided as supplementary material online.
ABodyBuilder3: improved and scalable antibody structure predictions
Authors: Kenlay Henry , Dreyer Frédéric A , Cutting Daniel , Nissley Daniel , Deane Charlotte M
Published: October 2024

In this article, we introduce ABodyBuilder3, an improved and scalable antibody structure prediction model based on ABodyBuilder2. We achieve a new state-of-the-art accuracy in the modelling of CDR loops by leveraging language model embeddings, and show how predicted structures can be further improved through careful relaxation strategies. Finally, we incorporate a predicted Local Distance Difference Test into the model output to allow for a more accurate estimation of uncertainties.

Availability and implementation

The software package is available at https://github.com/Exscientia/ABodyBuilder3 with model weights and data at https://zenodo.org/records/11354577.
BatchFLEX: feature-level equalization of X-batch
Authors: Davis Joshua T , Obermayer Alyssa N , Soupir Alex C , Hesterberg Rebecca S , Duong Thac , Yang Ching-Yao , Dao Ken Phong , Manley Brandon J , Grass G Daniel , Avram Dorina , Rodriguez Paulo C , Fridley Brooke L , Yu Xiaoqing , Teng Mingxiang , Wang Xuefeng , Shaw Timothy I
Published: October 2024

Motivation

Integrative analysis of heterogeneous expression data remains challenging due to variations in platform, RNA quality, sample processing, and other unknown technical effects. Selecting the approach for removing unwanted batch effects can be a time-consuming and tedious process, especially for more biologically focused investigators.

Results

Here, we present BatchFLEX, a Shiny app that can facilitate visualization and correction of batch effects using several established methods. BatchFLEX can visualize the variance contribution of a factor before and after correction. As an example, we have analyzed ImmGen microarray data and enhanced its expression signals that distinguishes each immune cell type. Moreover, our analysis revealed the impact of the batch correction in altering the gene expression rank and single-sample GSEA pathway scores in immune cell types, highlighting the importance of real-time assessment of the batch correction for optimal downstream analysis.

Availability and implementation

Our tool is available through Github https://github.com/shawlab-moffitt/BATCH-FLEX-ShinyApp with an online example on Shiny.io https://shawlab-moffitt.shinyapps.io/batch_flex/.
Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data
Authors: Mayne Richard , Secret Shannah , Geoghegan Cyndi , Trebes Amy , Kean Kai , Reid Kaitlin , Lin Gu-Lung , Ansari M Azim , de Cesare Mariateresa , Bonsall David , Elliott Ivo , Piazza Paolo , Brown Anthony , Bray James , Knight Julian C , Harvala Heli , Breuer Judith , Simmonds Peter , Bowden Rory J , Golubchik Tanya
Published: October 2024

Motivation

Target enrichment strategies generate genomic data from multiple pathogens in a single process, greatly improving sensitivity over metagenomic sequencing and enabling cost-effective, high-throughput surveillance and clinical applications. However, uptake by research and clinical laboratories is constrained by an absence of computational tools that are specifically designed for the analysis of multi-pathogen enrichment sequence data. Here we present an analysis pipeline, Castanet, for use with multi-pathogen enrichment sequencing data. Castanet is designed to work with short-read data produced by existing targeted enrichment strategies, but can be readily deployed on any BAM file generated by another methodology. Also included are an optional graphical interface and installer script.

Results

In addition to genome reconstruction, Castanet reports method-specific metrics that enable quantification of capture efficiency, estimation of pathogen load, differentiation of low-level positives from contamination, and assessment of sequencing quality. Castanet can be used as a traditional end-to-end pipeline for consensus generation, but its strength lies in the ability to process a flexible, pre-defined set of pathogens of interest directly from multi-pathogen enrichment experiments. In our tests, Castanet consensus sequences were accurate reconstructions of reference sequences, including in instances where multiple strains of the same pathogen were present. Castanet performs effectively on standard computers and can process the entire output of a 96-sample enrichment sequencing run (50M reads) using a single batch process command, in $<$2 h.

Availability and implementation

Source code freely available under GPL-3 license at https://github.com/MultipathogenGenomics/castanet, implemented in Python 3.10 and supported in Ubuntu Linux 22.04. The data underlying this article are available in Europe Nucleotide Archives, at https://www.ebi.ac.uk/ena/browser/view/PRJEB77004.
Pediatric wrist fractures: variations in management across countries. An evidence-based summary of evidence
Authors: Labianca Luca , Calderaro Cosma , Maffulli Nicola
Published: October 2024

Introduction

Fractures of the distal radius are common in pediatric population, with considerable variation in the management of pediatric wrist fractures across different countries. It is crucial to consider the different approaches to conservative management and surgical intervention. The decision on the appropriate treatment method often depends on the type and severity of the fracture, as well as the available healthcare resources and expertise in each country. This article tries to identify these variations, so the various healthcare systems can work toward implementing best practices in the management of pediatric wrist fractures on a global scale.

Source of data

Published peer-reviewed articles identified in electronic databases, including PubMed Scopus and Google Scholar.

Areas of agreement

The management of pediatric wrist fractures can differ significantly among countries given the high variability in healthcare resources and cultural practices.

Areas of controversy

The management of pediatric wrist fractures can be challenging in certain countries, especially in developing regions with limited resources.

Growing points

Challenges such as long therapeutic delays, lack of appropriate anesthesia, and the absence of fluoroscopy can complicate the treatment process. Randomized controlled clinical trials (RCTs) are vital in providing high-quality evidence to guide clinical decision-making, especially in the field of pediatric wrist fractures.

Areas timely for developing research

Efforts to support and prioritize the conduct and dissemination of RCTs in pediatric wrist fracture management can ultimately lead to more consistent, effective, and evidence-based care for children with wrist fractures worldwide.
Extraordinary 99Mo adsorption: utilizing spray-dried mesoporous alumina for clinical-grade generator development
Authors: Alowasheeir Azhar , Eguchi Miharu , Fujita Yoshitaka , Tsuchiya Kunihiko , Wakabayashi Ryutaro , Kimura Tatsuo , Ariga Katsuhiko , Hatano Kentaro , Fukumitsu Nobuyoshi , Yamauchi Yusuke
Published: October 2024

Mesoporous alumina spherical particles, synthesized via spray-drying with the self-assembly of EOnPOmEOn, have been utilized for the development of clinical-grade molybdenum-99/technetium-99 m (99Mo/99mTc) generators. When evaluated as molybdenum (Mo) adsorbents, the mesoporous alumina spherical particles are useful for effective adsorption of Mo ions rather than commercially available particulate alumina. The effects of surfactant removal methods on the Mo adsorption property are also systematically investigated using the batch method. Batch adsorption studies reveal practical adsorption capacities ranging from 45.9 to 91.2 mg Mo g−1 in a Mo solution (1000 mg Mo L−1) at pH 3. The experimental results indicate the following trend in Mo adsorption capacity: solvent extraction >calcination (400 °C and 800 °C) >commercially available alumina (Medical Al2O3 used as is). To explore the feasibility of developing a clinical-scale generator, a novel tandem column generator concept is employed. Using the spray-dried and extracted mesoporous alumina, 99mTc eluted from the generator exhibits high radionuclidic, radiochemical, and chemical purity, making it suitable for the preparation of 99mTc-labeled radiopharmaceuticals.
Expert opinion on characteristics of vulval lichen sclerosus: initial identification of important clinical features through an international electronic Delphi consensus study
Authors: Simpson Rosalind C , Birchall­­ Michael , Daniels Jane , Gran Sonia , Kirtschig Gudula , Thomas Kim S
Published: October 2024

Background

Lichen sclerosus (LS) is a chronic inflammatory condition that mainly affects genital skin. It causes distressing symptoms that impact daily quality of life, as well as progressive anatomical changes and a potential risk of cancer. Vulval LS is often misdiagnosed and treatment delayed. If nonexperts can be supported to identify clinical features of LS, they may diagnose the condition sooner and commence timely treatment or refer a patient for assessment and confirmatory biopsy.

Objectives

To reach international expert consensus on clinical diagnostic features for vulval LS.

Methods

Between March and May 2023, a four-stage electronic Delphi consensus exercise was conducted. In the first three rounds, participants were asked to rate the importance of a list of clinical features. Responses from round 1 were summarized and presented in rounds 2 and 3, along with additional features suggested by participants. Any items rated as ‘very important/critical’ or ‘not important’ that met the definition of consensus were removed from subsequent rounds. In round 4, items that were rated ‘important but not critical’ were ranked in order of their importance. Consensus was defined a priori, and all rounds were conducted anonymously.

Results

In total, 47 participants from 14 countries completed round 1, with 42 (89%) retained by round 3 when consensus was determined. Round 4 was completed by 36 (77%) participants. Participants completing all four rounds predominantly included healthcare professionals (n = 28/36; 78%) and patient support group representatives (n = 7/36; 19%). In round 1, 21 diagnostic features were rated. Participants suggested an additional 10 features, which were subsequently added to the round 2 survey. After three rounds, consensus was achieved for five diagnostic features: whiteness, itch, changes in anatomy, burying of the clitoral area and improvement in response to topical steroids. There were also 12 features rated as ‘important but not critical’ and participants subsequently ranked them in the fourth round.

Conclusions

Experts agreed on 5 critical diagnostic features for vulval LS in adults and an additional 12 features that may also be important. Future research should assess these clinical features for diagnostic validity through a multicentre diagnostic test accuracy study.
The effects of dialysate calcium prescription on mortality outcomes in incident patients on hemodialysis
Authors: ter Meulen Karlien J , Carioni Paola , Bellocchio Francesco , van der Sande Frank M , Bouman Heleen J , Stuard Stefano , Neri Luca , Kooman Jeroen P
Published: October 2024

Background

The appropriate prescription of dialysate calcium concentration for hemodialysis is debated. We investigated the association between dialysate calcium and all-cause, cardiovascular mortality and sudden cardiac death.

Methods

In this historical cohort study, we included adult incident hemodialysis patients who initiated dialysis between 1 January 2010 and 30 June 2017 who survived for at least 6 months (grace period). We evaluated the association between dialysate calcium 1.25 or 1.50 mmol/l and outcomes in the 2 years after the grace period, using multivariable Cox regression models. Moreover, we examined the association between the serum dialysate to calcium gradient and outcomes.

Results

We included 12 897 patients with dialysate calcium 1.25 mmol/l and 26 989 patients with dialysate calcium 1.50 mmol/l. The median age was 65 years, and 61% were male. The unadjusted risk of all-cause mortality was higher for dialysate calcium 1.50 mmol/l [hazard ratio (HR) 1.07, 95% confidence intervals (CI) 1.01–1.12]. However, in the fully adjusted model, no significant differences were noted (HR 1.05, 95% CI 0.99–1.12). Similar results were observed for the risk of cardiovascular mortality (HR 1.03, 95% CI 0.94–1.13). Adjusted risk of sudden cardiac death was lower for dialysate calcium 1.50 mmol/l (HR 0.81, 95% CI 0.67–0.97). Significant and positive associations with all outcomes were observed with larger serum-to-dialysate calcium gradients, primarily mediated by the serum calcium level.

Conclusions

In contrast to the unadjusted analysis that showed a higher risk for dialysate calcium of 1.50 mmol/l, after adjusting for confounders, there were no significant differences in the risk of all-cause and cardiovascular mortality between dialysate calcium concentrations of 1.50 and 1.25 mmol/l. After adjustment, a lower risk of sudden cardiac death was observed in patients with dialysate calcium 1.50 mmol/l. A higher serum-to-dialysate calcium gradient is associated with an increased risk for adverse outcomes.
Disentangling Anemia in Frailty: Exploring the Role of Inflammation
Authors: Herpich Catrin , Göger Lea , Faust Lea , Kalymon Magdalena , Ott Christiane , Walter Sophia , Lehmkuhl Elke , Grune Tilman , Moskiou Varvara , Müller-Werdan Ursula , Norman Kristina
Published: October 2024

Background

In older patients, frailty and anemia frequently coexist. However, only few studies have been conducted in older patients with multimorbidity and several overlapping causes of anemia, such as inflammation, inadequate nutrition, or certain pathologies. This analysis aims to decipher potential factors associated with anemia in older hospital patients with frailty.

Methods

Patients (n = 208, age: 62–98 years) were categorized as prefrail (n = 68) and frail (n = 140) using the Fried frailty phenotype. We quantified serum concentrations of markers of iron metabolism (iron, ferritin, transferrin, soluble transferrin receptor, and hepcidin), inflammation (interleukin [IL]-6 and IL-10 C-reactive protein), and hematology (hemoglobin). Principal component analysis was conducted to evaluate biomarker patterns and associations with frailty were assessed with logistic regression analysis.

Results

Anemia prevalence was higher in patients with frailty (84.3% vs 70.6%, p = .021). Three principal components (PC1–3) were identified. PC1 was characterized by high factor loadings representing inflammation and factor scores differed between patients with prefrailty and frailty (−0.04 (interquartile range [IQR]: 1.45) vs −0.51 (IQR: 0.87), p < .001]. PC2 represents macrocytic anemia and thus vitamin B12 or folate deficiency, whereas PC3 indicates hematological pathologies. Only PC1 was associated with frailty status when controlled for age, sex, number of drugs, and comorbidities (OR: 2.018, 95% CI: 1.316; 3.094, p = .001). PC2 and PC3 were not associated with frailty.

Conclusions

Our results suggest that anemia in patients with frailty is driven by inflammation rather than being disease-related or solely the result of micronutrient deficiencies.
Biopharmaceutical pipeline funded by venture capital firms, 2014 to 2024
Authors: Kang So-Yeon , Liu Mingqian , Ballreich Jeromie , Gupta Ravi , Anderson Gerard
Published: October 2024

Venture capital (VC) firms fund biopharmaceutical research and development (R&D) while incurring substantial financial risk. VC firms seek to invest in clinical areas with the greatest potential for financial return. Using a combination of data for clinical trials and VC investment deals between January 2014 and March 2024, we found that approximately 75% of VC investments were allocated to clinical trials studying small-molecule drugs compared to biologics or gene therapies, without substantial changes over the study period. Most of VC firms’ investment in biopharmaceutical R&D was concentrated in phase 1 and phase 2 clinical trials. This trend has increased in recent years, with phase 1 trials accounting for nearly half of total deals and capital investments in 2023. VC investments were concentrated in several therapeutic areas, including cancer.
Understanding the factors that impact federal rulemaking: a survey of former EPA regulators
Authors: Topazian Rachel J , McGinty Emma E , Hearne Shelley A
Published: October 2024

While federal rulemaking is an essential part of American governance, it is not well understood by researchers and advocates. We surveyed 115 former regulators at the Environmental Protection Agency to understand their views on the kinds of information they valued most and their communication preferences (June-August 2023). Respondents highly valued information about the scope of a problem (96%), legal analysis (97%), technology assessments (96%), and impacts of a proposed rule (99%). Regulators had difficulty accessing several kinds of information: 16% of respondents viewed racial equity information as easy to access and 30% thought financial information was easy to access. Respondents valued communications that provided data (99% viewed as effective), made compelling arguments (97%) or technical recommendations (93%), and storytelling (88%). Respondents indicated that the content of comment letters was important: 94% viewed letters containing data as important and 90% valued technical recommendations. Only 22% thought that repetition of the same comments across letters was important. Our findings reveal opportunities for researchers and advocates to help fill information gaps and identify communication strategies that might resonate with federal regulators.