bluuebunny/crossref_metadata_2025 huggingface dataset:
High key rate continuous-variable quantum key distribution using telecom optical components
Authors: Wang Tao , Huang Peng , Li Lang , Zhou Yingming , Zeng Guihua
Published: January 2024

Quantum key distribution (QKD) is one quantum technology that can provide secure encryption keys for data transmission. The secret key rate (SKR) is a core performance indicator in QKD, which directly determines the transmission rate of enciphered data. Here, for the first time, we demonstrate a high-key-rate Gaussian-modulated continuous-variable QKD (CV-QKD) using telecom optical components. The framework of CV-QKD over these components is constructed. Specifically, the high-rate low-noise Gaussian modulation of coherent states is realized by a classical optical IQ modulator. High-baud low-intensity quantum signals are received by an integrated coherent receiver under the shot-noise limit. A series of digital signal processing algorithms are proposed to achieve accurate signal recovery and key distillation. The system can yield a high asymptotic SKR of 10.37 Mbps within 20 km standard telecom fiber, and the secure distance can exceed 100 km. This result confirms the feasibility of CV-QKD with state-of-the-art performance using telecom optical components. Besides, due to the ease of integrating these discrete components, it provides a high-performance and miniaturized QKD solution for the metropolitan quantum network.
Enhancing variational quantum state diagonalization using reinforcement learning techniques
Authors: Kundu Akash , Bedełek Przemysław , Ostaszewski Mateusz , Danaci Onur , Patel Yash J , Dunjko Vedran , Miszczak Jarosław A
Published: January 2024

The variational quantum algorithms are crucial for the application of NISQ computers. Such algorithms require short quantum circuits, which are more amenable to implementation on near-term hardware, and many such methods have been developed. One of particular interest is the so-called variational quantum state diagonalization method, which constitutes an important algorithmic subroutine and can be used directly to work with data encoded in quantum states. In particular, it can be applied to discern the features of quantum states, such as entanglement properties of a system, or in quantum machine learning algorithms. In this work, we tackle the problem of designing a very shallow quantum circuit, required in the quantum state diagonalization task, by utilizing reinforcement learning (RL). We use a novel encoding method for the RL-state, a dense reward function, and an ε-greedy policy to achieve this. We demonstrate that the circuits proposed by the RL methods are shallower than the standard variational quantum state diagonalization algorithm and thus can be used in situations where hardware capabilities limit the depth of quantum circuits. The methods we propose in the paper can be readily adapted to address a wide range of variational quantum algorithms.
Non-stabilizerness and entanglement from cat-state injection
Authors: Peres Filipa C R , Wagner Rafael , Galvão Ernesto F
Published: January 2024

Recently, cat states have been used to heuristically improve the runtime of a classical simulator of quantum circuits based on the diagrammatic ZX-calculus. Here we investigate the use of cat-state injection within the quantum circuit model. We explore a family of cat states,

c
a
t

m
∗

, and describe circuit gadgets using them to concurrently inject non-stabilizerness (also known as magic) and entanglement into any quantum circuit. We provide numerical evidence that cat-state injection does not lead to speed-up in classical simulation. On the other hand, we show that our gadgets can be used to widen the scope of compelling applications of cat states. Specifically, we show how to leverage them to achieve savings in the number of injected qubits, and also to induce scrambling dynamics in otherwise non-entangling Clifford circuits in a controlled manner.
A collective perception model for neighbor selection in groups based on visual attention mechanisms
Authors: Li Kang , Li Liang , Groß Roderich , Zhao Shiyu
Published: January 2024

The mechanisms by which individuals visually perceive and select others within a group to interact with are of fundamental importance to various collective motion behaviors. However, they remain poorly understood theoretically, partially due to the challenges of modeling neurological perception systems. Here, the classic zoom-lens visual attention model is introduced into collective perception, leading to an attention-based model with only a single parameter. Numerical experiments reveal that the proposed model offers a unified mechanism for collective perception, as reflected in three aspects. First, this model describes both conspecific (e.g. flocking) and heterospecific (e.g. predator-prey) collective behaviors. Second, this model unifies the well-known topological and visibility models in the context of neighbor selection in conspecific groups. Third, in the context of prey selection in heterospecific groups, the model can simultaneously replicate the well-known confusion and oddity effects. These findings demonstrate the fundamental role of visual attention underlying a diverse array of collective motion behaviors.
Penetration of particles through vertical cracks
Authors: Orabi M
Published: January 2024

In a previous study, a new deposition model was developed to account for deposition of aerosol particles on the inner walls of small containers. In this article, the model applicability is extended by including deposition on horizontal surfaces, both upward-facing and downward-facing. After that, the model is applied to study a vital new issue, which is the penetration of aerosols to the indoors through vertical wall cracks. Previous studies, both theoretically and experimentally, never addressed penetration through vertical cracks. This study therefore aims to show the difference between penetration through vertical cracks and horizontal ones by applying the fourth-power model, which is very successful in describing deposition in small volumes. The penetration model formulated in this study takes into account, not only the thickness and depth of the crack, as usually happens in most penetration models, but all the three dimensions of the crack; thickness, depth and width. The obtained results are in a good agreement with the experimental data. This demonstrates the success of the extended fourth-power model in describing deposition inside cracks. Moreover, the results show a clear difference between vertical and horizontal cracks for the penetration of aerosols with diameter larger than

∼
1

μ
m
.

An application of the developed deposition and penetration models is presented, where a method for calculating the radioactive aerosols indoor concentrations is explained.
Magnetic flutter effect on validated edge turbulence simulations
Authors: Zhang Kaiyu , Zholobenko Wladimir , Stegmeir Andreas , Eder Konrad , Jenko Frank
Published: January 2024

Small magnetic fluctuations (

B
1

/

B
0

∼

10

−
4

) are intrinsically present in a magnetic confinement plasma due to turbulent currents. While the perpendicular transport of particles and heat is typically dominated by fluctuations of the electric field, the parallel stream of plasma is affected by fluttering magnetic field lines. In particular through electrons, this indirectly impacts the turbulence dynamics. Even in low beta conditions, we find that E × B turbulent transport can be reduced by more than a factor 2 when magnetic flutter is included in our validated edge turbulence simulations of L-mode ASDEX Upgrade. The primary reason for this is the stabilization of drift-Alfvén-waves, which reduces the phase shifts of density and temperature fluctuations with respect to potential fluctuations. This stabilization can be qualitatively explained by linear analytical theory and appreciably reinforced by the flutter nonlinearity. As a secondary effect, the steeper temperature gradients and thus higher η

i
increase the impact of the ion-temperature-gradient mode on overall turbulent transport. With increasing beta, the stabilizing effect on E × B turbulence increases, balancing the destabilization by induction, until direct electromagnetic perpendicular transport is triggered. We conclude that including flutter is crucial for predictive edge turbulence simulations.
An analytical model of how the negative triangularity cuts off the access to the second stable region in tokamak plasmas
Authors: Zhang Y. , Guo Z.B. , Ma R.R. , Xu M.
Published: January 2024

We present an analytical model to evaluate the triangularity-shaping effects in accessing the second stable region for the ideal ballooning mode. Our results indicate that if the triangularity is sufficiently negative, the path from the first to the second stable region will be closed. The reason is that negative triangularity can weaken the stabilizing effect of the ‘magnetic well’, and even convert the ‘magnetic well’ into a ‘magnetic hill’, which will destabilize the ballooning mode. We also show that the synergistic effects of elongation, inverse aspect ratio, and safety factor can reopen the path to the second stable region. Through a variational approach, we derive an analytical expression of the critical negative triangularity for closing the access to the second stable region. Furthermore, our analysis reveals that in the second ballooning stable regime, the negative triangularity tends to inhibit the emergence of quasi marginally stable discrete Alfvén eigenmodes. These findings provide a quantitative understanding of how the negative triangularity configuration impacts the confinement of tokamak plasmas.
Feasibility of using 3D CZT drift strip detectors for small Compton camera space missions
Authors: Owe S.R.H. , Kuvvetli I. , Zoglauer A. , Budtz-Jørgensen C.
Published: January 2024

This feasibility study explores the possibility of using 3D CZT drift strip detectors
developed by DTU Space in a small Compton camera payload, with the primary objective of technology
demonstration. We have defined a scalable mass model for the payload, comprising eight 3D CZT
drift strip detectors surrounded by CsI scintillator detectors for active shielding. The payload's
angular resolution, effective area, and efficiency are evaluated through simulations of far-field
monochromatic point sources. The instrument's sensitivity is assessed in a low Earth orbit
background environment for

nuclear line and continuum emission sources.
With a 3σ point source
sensitivity in the order of 10-4 [ph/cm2/s], it is evident that such an instrument only
allows for limited scientific goals. In-orbit simulations of bright sources are conducted,
resulting in reasonable observation times for the Crab Nebula at a 5σ significance
level. Furthermore, in-orbit simulations of a selection of bright gamma-ray bursts indicate the
potential for observing bright transient events. The study underscores the potential of using 3D
CZT drift strip detectors in Compton camera configurations but also highlights the need for a
larger effective area to improve sensitivity. However, for a technology demonstration aimed at
increasing the Technology Readiness Level of the 3D CZT drift strip detector, a small Compton
camera configuration like the one presented in this study could be a viable solution.
Optimizing and characterizing the Timepix2 hybrid pixel detector: enhancing
performance and precision for scientific and industrial applications
Authors: Hladik D. , Jakubek J. , Sykorova K. , Cerna T. , Doubravova D. , Urban M. , Polansky S.
Published: January 2024

The introduction of the new hybrid pixel detector Timepix2, as a successor to the well-known Timepix detector, has presented new opportunities for optimizing and characterizing this novel device. In this paper, we study the Timepix2 detector optimization and analyze its behavior, which enables better parameter setting for specific applications, resulting in enhanced device performance. Our newly developed equalization process, in conjunction with the device optimization, has led to significant improvements in the detector's accuracy and performance, facilitating more precise data collection and analysis. These advancements pave the way for the broader utilization of Timepix2 in numerous applications, such as space weather monitoring, X-ray diffraction, etc. Overall, our study provides valuable insights into the optimization and characterization of Timepix2, highlighting its potential as a powerful tool in various scientific, industrial and space applications.
Characterization of organic glass scintillator bars and their potential for a hybrid neutron/gamma ray imaging system for proton radiotherapy range verification
Authors: Turko J. , Beyer R. , Junghans A.R. , Meric I. , Mueller S.E. , Pausch G. , Ratliff H.N. , Römer K. , Schellhammer S.M. , Setterdahl L.M. , Urlass S. , Wagner A. , Kögler T. ,   the NOVO collaboration
Published: January 2024

For accurate and simultaneous imaging of fast neutrons (FNs)
and prompt gamma rays (PGs) produced during proton therapy, the
selection of a highly performant detector material is crucial. In
this work, a promising candidate material known as organic glass
scintillator (OGS) is characterized for this task. To this end, a
precisely-timed source of neutrons and Bremsstrahlung radiation
produced by the nELBE facility was used to study the light
output and neutron/gamma ray pulse shape discrimination (PSD)
properties of a 1 × 1 × 20 cm3 OGS bar with
double-sided readout. Furthermore, the energy, timing, and
depth-of-interaction (DOI) resolutions of 1 × 1 × 10 cm3 and 1 × 1 × 20 cm3 OGS and EJ-200 bars were
characterized with radioactive sources. For electron-equivalent
energies above 0.5 MeVee, OGS was found to have excellent PSD
capabilities (figure-of-merit above 1.27), energy resolution (below
12%), coincident time resolution (below 500 ps), and DOI
resolution (below 10 mm). This work establishes the data analysis
methods required for hybrid FN/PG imaging using OGS, and
demonstrates the materials' excellent performance for this
application.
Evaluation of antimicrobial photodynamic action of a pluronic and pectin based film loaded with methylene blue against methicillin resistant Staphylococcus aureus
Authors: Chakraborty Sourabrata , Shukla Shivangi , Rastogi Mahima , Mund Sai Sarbani , Chowdhury Anupam , Mukherjee Chandrachur , Sahu Khageswar , Majumder Shovan Kumar
Published: January 2024

Antimicrobial wound dressings play a crucial role in treatment of wound infections. However, existing commercial options fall short due to antibiotic resistance and the limited spectrum of activity of newly emerging antimicrobials against bacteria that are frequently encountered in wound infections. Antimicrobial photodynamic therapy (aPDT) is very promising alternative therapeutic approach against antibiotic resistant microbes such as methicillin resistant Staphylococcus aureus (MRSA). However, delivery of the photosensitizer (PS) homogeneously to the wound site is a challenge. Though polymeric wound dressings based on synthetic and biopolymers are being explored for aPDT, there is paucity of data regarding their in vivo efficacy. Moreover, there are no studies on use of PS loaded, pluoronic (PL) and pectin (PC) based films for aPDT. We report development of a polymeric film for potential use in aPDT. The film was prepared using PL and PC via solvent casting approach and impregnated with methylene blue (MB) for photodynamic inactivation of MRSA in vitro and in vivo. Atomic force microscopic imaging of the films yielded vivid pictures of surface topography, with rough surfaces, pores, and furrows. The PL:PC ratio (2:3) was optimized that would result in an intact film but exhibit rapid release of MB in time scale suitable for aPDT. The film showed good antibacterial activity against planktonic suspension, biofilm of MRSA upon exposure to red light. Investigations on MRSA infected excisional wounds of mice reveal that topical application of MB loaded film for 30 min followed by red light exposure for 5 min (fluence; ∼30 J cm−2) or 10 min (fluence; ∼60 J cm−2) reduces ∼80% or ∼92% of bioburden, respectively. Importantly, the film elicits no significant cytotoxicity against keratinocytes and human adipose derived mesenchymal stem cells. Taken together, our data demonstrate that PS-loaded PL-PC based films are a promising new tool for treatment of MRSA infected wounds.
Quantifying Bell nonlocality of a pure two-qudit state via its entanglement
Authors: Loubenets Elena R , Kuznetsov Sergey , Hanotel Louis
Published: January 2024

For the maximal violation of all Bell inequalities by an arbitrary pure two-qudit state of any dimension, we derive a new lower bound expressed via the concurrence of this pure state. This new lower bound and the upper bound on the maximal Bell violation, found in Loubenets and Namkung (2022 J. Phys. A: Math. Theor.
55 285301) and also expressed via the concurrence, analytically quantify Bell nonlocality of a pure two-qudit state via its entanglement, in particular, prove explicitly that entanglement of a pure two-qudit state is necessary and sufficient for its Bell nonlocality. By re-visiting the pure two-qubit case, we also find and rigorously prove the new results on correlation properties of an arbitrary pure two-qubit state.
Polymorphic states investigations in thermal conductivity of 1-fluoroadamantane
Authors: Szewczyk Daria , Krivchikov Alexander I , Jeżowski Andrzej
Published: January 2024

The temperature dependencies of the thermal conductivity coefficient, κ(T), in 1-fluoroadamantane were investigated for two different orientationally-disordered states. In the first one, κ(T) exhibits a crystalline character with a typical maximum and two anomalous regions marked at higher temperatures. Here, the low-temperature power-law dependence is reduced due to a relatively large contribution of dislocations and defects in the polycrystalline sample. Above 196 K, there is an anomalous plateau in thermal conductivity resulting from the presence of an intermediate centrosymmetric state. Further, a significant increase in κ occurs above 234 K, resulting from a phase transition to a high-temperature disordered cubic phase. Subsequent cooling of the sample leads to an irreversible transition towards a disordered state resulting in a κ(T) dependence corresponding to an amorphous material behavior. The primary anomaly at 196 K disappears, while the second one associated with the phase transition at 227 K shifts towards lower temperatures. The irreversibility of this transformation is also verified by scanning microscopy images. Thermal conductivity in both phases has an additional contribution of an Arrhenius type in their temperature dependences.
Predicting willingness to pay and implement different rooftop strategies to characterize social perception of climate change mitigation and adaptation
Authors: Untereiner Erin , Toboso-Chavero Susana , Fariñas Ana Vázquez , Madrid-Lopez Cristina , Villalba Gara , Durany Xavier Gabarrell
Published: January 2024

With the latest IPCC report, dramatic global climate action must be taken immediately to limit global warming to 1.5 °C, or face more frequent and extreme weather events with catastrophic implications. Cities must invest in climate resilience development; however, government policies are only effective if they are supported by the society in which they serve. As such, this study aims to characterize the social perception of climate resilience development, in particular the implementation of sustainable urban rooftop strategies, to support policy makers and enable individual action. This was accomplished through the analysis of 1,100 answered surveys in Cerdanyola del Vallès (Spain), to assess one’s willingness to pay (WTP) and willingness to implement (WTI) rooftop strategies according to: 1. socio-demographical characteristics; 2. social perceptions and beliefs; and 3. surrounding land use and land cover, and vulnerabilities identified through temperature and normalized difference vegetation index (NDVI) maps. The results of this study found age played a significant role in predictability, with 18–39-year-olds being the most willing to pay and implement the various rooftop scenarios. However, our results uncovered societal inequality as those 85+ were the second group most interested in rooftop agriculture but the most financially restricted. Belief in the viability of rooftop strategies increased respondents WTP and WTI while having access to ones’ rooftop increased willingness to partake in rooftop food cultivation and enhance rooftop greenery. A new finding presented by this study is the quantifiable impact that urban greenery plays on increasing survey respondents WTP and WTI.
Impact of nano crack and loading direction on the tensile features of FeCr alloy: a molecular dynamics analysis
Authors: Gowthaman S , Jagadeesha T
Published: January 2024

The existence of cracks and variations in loading direction has invoked greater modifications in the material properties. In this work, the tensile features of cracked and non-cracked FeCr polycrystals have been analyzed under numerous temperatures (300 K, 500 K, 700 K, and 900 K) and loading directions (parallel and normal to the crack cross-sectional directions) through molecular dynamics and it is originated that temperature has raised a higher impact on the tensile features trailed by the existence of crack and loading directions, owing to the formation of larger kinetic energy (KE) amidst the atoms. The existence of crack offers a moderate impression on the tensile behavior followed by the loading direction, due to its dominant impact on the tensile behavior through greater stress concentrations. Additionally, it is stated that the greater temperature along with the existence of crack and loading along normal to the crack cross section offers greater reductions in the tensile features of FeCr polycrystal, owed to the interactive effect of larger KE and discontinuity among atoms. Furthermore, the shear strain and displacement contour map and materials feature also confirm a similar occurrence which leads to altering its material behavior.
A novel approach of jet polishing for interior surface of small-grooved components using three developed setups
Authors: Gu Qinming , Zhang Zhenyu , Zhou Hongxiu , Yu Jiaxin , Wang Dong , Feng Junyuan , Shi Chunjing , Yang Jianjun , Qi Junfeng
Published: January 2024

Highlights

A novel approach of multi-phase jet polishing is proposed using a developed polisher, consisting of solid, liquid and gas phases.

An abrasive air jet polishing is suggested through a customized polisher, including solid and gas phases.

After jet polishing, surface roughness Sa decreases from pristine 8.596 to 0.701 and 0.336 μm, and Sa reduces 92% and 96%, respectively.

Defect volume of unit area achieved by optimized parameters lessens 1/12 that of non-optimized ones.
Study on the preparation and mechanical and fatigue properties of alkali excited recycled concrete
Authors: Su Qing
Published: January 2024

This study aims to explore the preparation process of alkali excited recycled concrete, and evaluate its performance in terms of mechanical and fatigue properties, so as to provide theoretical and practical support for the application of sustainable development and environmental protection building materials. Laboratory test and performance evaluation were used to prepare alkali-stimulated recycled concrete specimens with different proportions by adjusting fly ash, alkali activator and water solid ratio in recycled concrete. Then, the mechanical properties of the specimen were tested, including the influence of the cementing material on its compressive strength and the influence of the aggregate quality on its compressive strength. Finally, the fatigue life test is used to analyze the fatigue performance of alkali stimulated recycled concrete, and the influence of different ages and different stress levels on fatigue damage performance of alkali stimulated recycled concrete specimens is studied. The experimental results show that the mechanical properties of recycled concrete can be significantly improved by using alkali excited recycled concrete preparation technology. It is found that under the same stress ratio, with the increase of age, the corresponding fatigue life will increase, the flexural tensile strength will increase, and the fatigue resistance will improve. At the same age, the fatigue life of specimens decreases with the increase of stress ratio, and the flexural tensile strength and fatigue resistance remain unchanged. This study proves the effectiveness of alkali excited recycled concrete preparation technology in improving the mechanical properties and fatigue properties of recycled concrete. Alkali stimulated recycled concrete is not only conducive to resource reuse, reduce the impact of waste on the environment, but also provides a new choice for the sustainable development of building materials. However, further research and application are needed to promote the widespread application of alkali excited recycled concrete in engineering practice.
Mud-Net: multi-domain deep unrolling network for simultaneous sparse-view and metal artifact reduction in computed tomography
Authors: Shi Baoshun , Jiang Ke , Zhang Shaolei , Lian Qiusheng , Qin Yanwei , Zhao Yunsong
Published: January 2024

Sparse-view computed tomography (SVCT) is regarded as a promising technique to accelerate data acquisition and reduce radiation dose. However, in the presence of metallic implants, SVCT inevitably makes the reconstructed CT images suffer from severe metal artifacts and streaking artifacts due to the lack of sufficient projection data. Previous stand-alone SVCT and metal artifact reduction (MAR) methods to solve the problem of simultaneously sparse-view and metal artifact reduction (SVMAR) are plagued by insufficient correction accuracy. To overcome this limitation, we propose a multi-domain deep unrolling network, called Mud-Net, for SVMAR. Specifically, we establish a joint sinogram, image, artifact, and coding domains deep unrolling reconstruction model to recover high-quality CT images from the under-sampled sinograms corrupted by metallic implants. To train this multi-domain network effectively, we embed multi-domain knowledge into the network training process. Comprehensive experiments demonstrate that our method is superior to both existing MAR methods in the full-view MAR task and previous SVCT methods in the SVMAR task.
Life cycle environmental benchmarks for Flemish dwellings
Authors: Mouton Lise , Ramon Delphine , Trigaux Damien , Allacker Karen , Crawford Robert H
Published: January 2024

To reduce the environmental effects caused by building construction and operation, life cycle assessment (LCA) is increasingly applied. In recent years, national building regulations have implemented LCA requirements to support building life cycle impact reduction. A key element in these regulations are environmental benchmarks which allow designers to compare their building designs with reference values. This study aims to develop bottom-up life cycle environmental benchmarks that represent the range of environmental impact results achieved with conventional construction in Flanders, Belgium. For this purpose, the study investigates the potential of using a database of building energy performance calculations. Specifically, this study considers 39 residential buildings identified as representative of the Flemish energy performance of buildings database of 2015–2016, applying modifications to establish scenarios that are still relevant in 2025. The buildings are assessed with the Belgian LCA tool TOTEM to calculate an aggregated environmental score based on the European product environmental footprint (PEF) weighting approach and including 12 main impact categories. In addition to the aggregated score, the climate change (CC) indicator is analysed individually. In view of the benchmarks, variations were applied to the 39 original buildings in terms of heating system and materialisation. The variation in heating system included changing gas boilers to electric heat pumps to comply with upcoming (2025) Flemish building regulations. The variations in building materials included three sets of conventional Flemish building element compositions that were applied to generate a wider spread of impact results as a basis for benchmarks. Benchmark values were derived through a statistical analysis of the 117 modelled variants: a best-practice value (10th percentile), reference value (median) and limit value (90th percentile). For the environmental score, the benchmark values are 86, 107 and 141 millipoints per square meter of gross heated floor area (GHFA) (mPt m−2GHFA), respectively; and for CC, the benchmark values are 844, 1015 and 1284 kg CO2-eq m−2 GHFA. Finally, the study discusses the representativeness, implications and limitations of the final benchmarks and benchmark approach.
Temporal public perceptions and experiences during water service disruptions: the case of Jackson, Mississippi
Authors: Safarpour Haniye , Spearing Lauryn A
Published: January 2024

Failures in urban water systems are becoming a common occurrence in the US due to disasters, aging infrastructure, and financial constraints, among other concerns. For example, Jackson, Mississippi has experienced reoccurring water outages, burdening community members as they must seek alternative water sources. Prior research has primarily focused on technical, institutional, and public health aspects of water crises, with limited attention to community perspectives. Understanding such social aspects can shed light on, for example, community priorities, levels of trust, mental health concerns, and communication gaps. Here, we document the temporal experiences and perceptions of community members during the Jackson Water Crises. To do so, we qualitatively analyzed news media data and employed topic modeling techniques on social media data from two years, capturing two service disruption events. Our results reveal the cascading impacts of water outages on end-users, including financial, social, and technical issues. For example, over time, results indicate that trust in the government and water providers in Jackson eroded, which may hinder public support. Our results show that social media can be a useful tool for utilities to understand public perceptions in real-time. Recommendations proposed here can inform future responses to water crises in Jackson and other communities, ensuring end-users’ perspectives are incorporated.
GB12-09, a bispecific antibody targeting IL4Rα and IL31Rα for atopic dermatitis therapy
Authors: Deng Feiyan , Qiu Yuxin , Zhang Xiangling , Guo Nining , Hu Junhong , Yang Wenjie , Shang Wei , Liu Bicheng , Qin Suofu
Published: January 2024

Atopic dermatitis (AD) is a chronic inflammatory skin condition characterized by dysregulated immune responses. The key mediators of AD pathogenesis are T helper 2 (TH2) cells and TH2 cytokines. Targeting interleukin 4 (IL4), IL13 or IL31 has become a pivotal focus in both research and clinical treatments for AD. However, the need remains pressing for the development of a more effective and safer therapy, as the current approaches often yield low response rates and adverse effects. In response to this challenge, we have engineered a immunoglobulin G—single-chain fragment variable (scFv) format bispecific antibody (Ab) designed to concurrently target IL4R and IL31R. Our innovative design involved sequence optimization of VL-VH and the introduction of disulfide bond (VH44-VL100) within the IL31Rα Ab scFv region to stabilize the scFv structure. Our bispecific Ab efficiently inhibited the IL4/IL13/IL31 signaling pathways in vitro and reduced serum immunoglobulin E and IL31 levels in vivo. Consequently, this intervention led to improved inflammation profiles and notable amelioration of AD symptoms. This research highlighted a novel approach to AD therapy by employing bispecific Ab targeting IL4Rα and IL31Rα with potent efficacy.
Fruit softening: evidence for rhamnogalacturonan lyase action in vivo in ripe fruit cell walls
Authors: Al-Hinai Thurayya Z S , Mackay C Logan , Fry Stephen C
Published: January 2024

Background and Aims

The softening of ripening fruit involves partial depolymerization of cell-wall pectin by three types of reaction: enzymic hydrolysis, enzymic elimination (lyase-catalysed) and non-enzymic oxidative scission. Two known lyase activities are pectate lyase and rhamnogalacturonan lyase (RGL), potentially causing mid-chain cleavage of homogalacturonan and rhamnogalacturonan-I (RG-I) domains of pectin respectively. However, the important biological question of whether RGL exhibits action in vivo had not been tested.

Methods

We developed a method for specifically and sensitively detecting in-vivo RGL products, based on Driselase digestion of cell walls and detection of a characteristic unsaturated ‘fingerprint’ product (tetrasaccharide) of RGL action.

Key Results

In model experiments, potato RG-I that had been partially cleaved in vitro by commercial RGL was digested by Driselase, releasing an unsaturated tetrasaccharide (‘ΔUA-Rha-GalA-Rha’), taken as diagnostic of RGL action. This highly acidic fingerprint compound was separated from monosaccharides (galacturonate, galactose, rhamnose, etc.) by electrophoresis at pH 2, then separated from ΔUA-GalA (the fingerprint of pectate lyase action) by thin-layer chromatography. The ‘ΔUA-Rha-GalA-Rha’ was confirmed as 4-deoxy-β-l-threo-hex-4-enopyranuronosyl-(1→2)-l-rhamnosyl-(1→4)-d-galacturonosyl-(1→2)-l-rhamnose by mass spectrometry and acid hydrolysis. Driselase digestion of cell walls from diverse ripe fruits [date, sea buckthorn, cranberry, yew (arils), mango, plum, blackberry, apple, pear and strawberry] yielded the same fingerprint compound, demonstrating that RGL had been acting in vivo in these fruits prior to harvest. The ‘fingerprint’ : (galacturonate + rhamnose) ratio in digests from ripe dates was approximately 1 : 72 (mol/mol), indicating that ~1.4 % of the backbone Rha→GalA bonds in endogenous RG-I had been cleaved by in-vivo RGL action.

Conclusions

The results provide the first demonstration that RGL, previously known from studies of fruit gene expression, proteomic studies and in-vitro enzyme activity, exhibits enzyme action in the walls of soft fruits and may thus be proposed to contribute to fruit softening.
Associations between Informant-Reported Cognitive Complaint and Longitudinal Cognitive Decline in Subjective Cognitive Decline A 7-Year Longitudinal Study
Authors: Liu Yuanyuan , Su Ning , Li Wei , Hong Bo , Yan Feng , Wang Jinghua , Li Xia , Chen Jianhua , Xiao Shifu , Yue Ling
Published: January 2024

Objective

This study aimed to determine the predictive values of informant-reported memory decline (IMD) among subjective cognitive decline (SCD) older adults from a 7-year community-based cohort study.

Method

Ninety SCD participants were included. Demographic data and neuropsychological test scores at both baseline and 7-year follow-up were collected. Differences between SCD with IMD (+IMD) and SCD without IMD (−IMD) were compared. Logistic regression models were used to determine whether baseline IMD could predict diagnostic outcomes at 7-year follow-up.

Results

Forty-one percent of SCD adults had IMD. At baseline, the +IMD group showed more depressive symptoms (p = 0.016) than the −IMD group. Furthermore, the Beijing-version Montreal Cognitive Assessment (MoCA), Digit Span Test-Forward, Visual Matching and Reasoning, and Wechsler Adult Intelligence Scale-RC Picture Completion (WAIS-PC) scores in the +IMD group were significantly lower than those in the −IMD group. Fifty-four percent of +IMD participants converted to mild cognitive impairment (MCI) or dementia at follow-up, and 22.6% of the −IMD participants converted to MCI. Follow-up Mini-Mental State Examination, MoCA, and Verbal Fluency Test scores of the +IMD group were significantly lower than those in the −IMD group. The +IMD group was more likely to progress to cognitive impairment at 7-year follow-up (OR = 3.361, p = 0.028).

Conclusions

SCD participants with +IMD may have poorer cognition and are more likely to convert to cognitive impairment over time. Our long-term follow-up study confirmed the importance of informants’ perceptions of SCD, which can help clinicians identify individuals at risk of cognitive decline.
DeepRank-GNN-esm: a graph neural network for scoring protein–protein models using protein language model
Authors: Xu Xiaotong , Bonvin Alexandre M J J
Published: January 2024

Motivation

Protein–Protein interactions (PPIs) play critical roles in numerous cellular processes. By modelling the 3D structures of the correspond protein complexes valuable insights can be obtained, providing, e.g. starting points for drug and protein design. One challenge in the modelling process is however the identification of near-native models from the large pool of generated models. To this end we have previously developed DeepRank-GNN, a graph neural network that integrates structural and sequence information to enable effective pattern learning at PPI interfaces. Its main features are related to the Position Specific Scoring Matrices (PSSMs), which are computationally expensive to generate, significantly limits the algorithm's usability.

Results

We introduce here DeepRank-GNN-esm that includes as additional features protein language model embeddings from the ESM-2 model. We show that the ESM-2 embeddings can actually replace the PSSM features at no cost in-, or even better performance on two PPI-related tasks: scoring docking poses and detecting crystal artifacts. This new DeepRank version bypasses thus the need of generating PSSM, greatly improving the usability of the software and opening new application opportunities for systems for which PSSM profiles cannot be obtained or are irrelevant (e.g. antibody-antigen complexes).

Availability and implementation

DeepRank-GNN-esm is freely available from https://github.com/DeepRank/DeepRank-GNN-esm.
SciDataFlow: a tool for improving the flow of data through science
Authors: Buffalo Vince
Published: January 2024

Motivation

Managing data and code in open scientific research is complicated by two key problems: large datasets often cannot be stored alongside code in repository platforms like GitHub, and iterative analysis can lead to unnoticed changes to data, increasing the risk that analyses are based on older versions of data.

Results

SciDataFlow is a fast, concurrent command-line tool paired with a simple Data Manifest specification that streamlines tracking data changes, uploading data to remote repositories, and pulling in all data necessary to reproduce a computational analysis.

Availability and implementation

SciDataFlow is available at https://github.com/vsbuffalo/scidataflow.
CircSI-SSL: circRNA-binding site identification based on self-supervised learning
Authors: Cao Chao , Wang Chunyu , Yang Shuhong , Zou Quan
Published: January 2024

Motivation

In recent years, circular RNAs (circRNAs), the particular form of RNA with a closed-loop structure, have attracted widespread attention due to their physiological significance (they can directly bind proteins), leading to the development of numerous protein site identification algorithms. Unfortunately, these studies are supervised and require the vast majority of labeled samples in training to produce superior performance. But the acquisition of sample labels requires a large number of biological experiments and is difficult to obtain.

Results

To resolve this matter that a great deal of tags need to be trained in the circRNA-binding site prediction task, a self-supervised learning binding site identification algorithm named CircSI-SSL is proposed in this article. According to the survey, this is unprecedented in the research field. Specifically, CircSI-SSL initially combines multiple feature coding schemes and employs RNA_Transformer for cross-view sequence prediction (self-supervised task) to learn mutual information from the multi-view data, and then fine-tuning with only a few sample labels. Comprehensive experiments on six widely used circRNA datasets indicate that our CircSI-SSL algorithm achieves excellent performance in comparison to previous algorithms, even in the extreme case where the ratio of training data to test data is 1:9. In addition, the transplantation experiment of six linRNA datasets without network modification and hyperparameter adjustment shows that CircSI-SSL has good scalability. In summary, the prediction algorithm based on self-supervised learning proposed in this article is expected to replace previous supervised algorithms and has more extensive application value.

Availability and implementation

The source code and data are available at https://github.com/cc646201081/CircSI-SSL.
FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data
Authors: Koutrouli Mikaela , Nastou Katerina , Piera Líndez Pau , Bouwmeester Robbin , Rasmussen Simon , Martens Lennart , Jensen Lars Juhl
Published: January 2024

Motivation

Protein networks are commonly used for understanding how proteins interact. However, they are typically biased by data availability, favoring well-studied proteins with more interactions. To uncover functions of understudied proteins, we must use data that are not affected by this literature bias, such as single-cell RNA-seq and proteomics. Due to data sparseness and redundancy, functional association analysis becomes complex.

Results

To address this, we have developed FAVA (Functional Associations using Variational Autoencoders), which compresses high-dimensional data into a low-dimensional space. FAVA infers networks from high-dimensional omics data with much higher accuracy than existing methods, across a diverse collection of real as well as simulated datasets. FAVA can process large datasets with over 0.5 million conditions and has predicted 4210 interactions between 1039 understudied proteins. Our findings showcase FAVA's capability to offer novel perspectives on protein interactions. FAVA functions within the scverse ecosystem, employing AnnData as its input source.

Availability and implementation

Source code, documentation, and tutorials for FAVA are accessible on GitHub at https://github.com/mikelkou/fava. FAVA can also be installed and used via pip/PyPI  as well as via the scverse ecosystem https://github.com/scverse/ecosystem-packages/tree/main/packages/favapy.
The role of epicardial fat radiomic profiles for atrial fibrillation identification and recurrence risk with coronary CT angiography
Authors: Wu Jingping , Li Yuwei , Wu Dan , Schoepf Uwe-Joseph , Zhao Pengfei , Goller Markus , Li Junhuan , Tian Jinwen , Shen Mingzhi , Cao Kunlin , Yang Li , Zhang Fan
Published: January 2024

Objectives

Fat radiomic profile (FRP) was a promising imaging biomarker for identifying increased cardiac risk. We hypothesize FRP can be extended to fat regions around pulmonary veins (PV), left atrium (LA), and left atrial appendage (LAA) to investigate their usefulness in identifying atrial fibrillation (AF) and the risk of AF recurrence.

Methods

We analysed 300 individuals and grouped patients according to the occurrence and types of AF. We used receiver operating characteristic and survival curves analyses to evaluate the value of imaging biomarkers, including fat attenuation index (FAI) and FRP, in distinguishing AF from sinus rhythm and predicting post-ablation recurrence.

Results

FRPs from AF-relevant fat regions showed significant performance in distinguishing AF and non-AF with higher AUC values than FAI (peri-PV: FRP = 0.961 vs FAI = 0.579, peri-LA: FRP = 0.923 vs FAI = 0.575, peri-LAA: FRP = 0.900 vs FAI = 0.665). FRPs from peri-PV, peri-LA, and peri-LAA were able to differentiate persistent and paroxysmal AF with AUC values of 0.804, 0.819, and 0.694. FRP from these regions improved AF recurrence prediction with an AUC of 0.929, 0.732, and 0.794. Patients with FRP cut-off values of ≥0.16, 0.38, and 0.26 had a 7.22-, 5.15-, and 4.25-fold higher risk of post-procedure recurrence, respectively.

Conclusions

FRP demonstrated potential in identifying AF, distinguishing AF types, and predicting AF recurrence risk after ablation. FRP from peri-PV fat depot exhibited a strong correlation with AF. Therefore, evaluating epicardial fat using FRP was a promising approach to enhance AF clinical management.

Advances in knowledge

The role of epicardial adipose tissue (EAT) in AF had been confirmed, we focussed on the relationship between EAT around pulmonary arteries and LAA in AF which was still unknown. Meanwhile, we used the FRP to excavate more information of EAT in AF.
Utility of three-dimensional proton density-weighted sequence MRI in knee for the assessment of Anterolateral complex in Anterior cruciate ligament injury
Authors: Guruprasad Ankith , Sinha Upasna , Kumar Sudeep , Kumar Avinash , Ahmad Shamshad , Kumar Prem , Agrawal Prabhat
Published: January 2024

Objectives

To assess the proportion and pattern of injury of the anterolateral ligament (ALL) and the Kaplan fibre (KF) complex in knees with anterior cruciate ligament (ACL) injuries on MRI using three-dimensional (3D) proton density (PD) sequences.

Methods

A total of 88 patients having ACL injury were included in this cross-sectional study. 3D PD sequences were used to assess injury of ALL and the KF complex and were graded on a scale of 0 to 3. MR images were evaluated by two radiologists. Interobserver agreement was determined using Cohen Kappa.

Results

Femoral, meniscal, and tibial portions of ALL were visualized in 90.9%, 92%, and 94.3% of the study subjects, respectively. Proximal and distal KF were visualized in 92% and 93.2% of patients, respectively. Injury to ALL and KF was seen in 63.6% and 17% of the patients, respectively. Excellent interobserver agreement was noted for the identification and grading of ALL and KF complex injuries.

Conclusions

Oblique reformatted 3DPD MRI reliably detect ALC; however, ALL injury is better characterized than KF injury using this sequence.

Advances in knowledge

Given the potential role of anterolateral complex (ALC) in maintaining the rotational stability of the knee, ALC assessment using the 3D PD sequences and their oblique reformatted images should be incorporated as routine review area of the knee MRI, particularly in the setting of ACL tear.
A case of low-grade endometrial stromal sarcoma presented as an intramyometrial mass mimicking uterine leiomyoma on MRI
Authors: Tamada Soichiro , Edo Hiromi , Sakima Taishi , Tanaka Ryo , Shikata Kohei , Nishitani Soko , Miyamoto Morikazu , Takano Masashi , Kuboshima Keisuke , Miyai Kosuke , Ogata Sho , Shinmoto Hiroshi
Published: January 2024

A low-grade endometrial stromal sarcoma (ESS) has a pattern of presenting as an intramyometrial mass and is often misdiagnosed as cellular leiomyoma or degenerative uterine leiomyoma. A low-grade ESS is a malignant tumour that requires total hysterectomy with bilateral salpingo-oophorectomy; while a leiomyoma is a benign tumour and could be acceptable for enucleation. As the treatment strategies differ between a low-grade ESS and leiomyoma, radiologists should be familiar with the characteristic MRI findings of a low-grade ESS. A 51-year-old woman with abnormal uterine bleeding had been observed for 2 years at a previous hospital for a uterine leiomyoma based on MRI findings. A contrast-enhanced MRI demonstrated an intramyometrial mass composed of three components with the hypointense rim on T2-weighted images (T2WI): the first component was a homogeneous solid structure with mild hyperintensity on T2WI with a low apparent diffusion coefficient value; the second component was cystic; the third component was a structure of low signal intensity on T2WI similar to the muscle. Although a degenerative uterine leiomyoma was a differential diagnosis, these MRI findings were suggestive of a low-grade ESS. A total abdominal hysterectomy, bilateral salpingo-oophorectomy, pelvic lymphadenectomy, and partial omentectomy were performed. The pathological diagnosis was a low-grade ESS. In a low-grade ESS, there are three major patterns of MRI findings: one of these patterns is the less popular but clinically important intramyometrial mass pattern, which can be misdiagnosed as a leiomyoma, and this case conformed to this pattern.