bluuebunny/crossref_metadata_2025 huggingface dataset:
From electron tomography of dislocations to field dislocation mechanics: application to olivine
Authors: Weidner Timmo , Taupin Vincent , Demouchy Sylvie , Gouriet Karine , Guitton Antoine , Cordier Patrick , Mussi Alexandre
Published: November 2023

We propose a new procedure to extract information from electron tomography and use them as an input in a field dislocation mechanics. Dislocation electron tomography is an experimental technique that provides three-dimensional (3D) information on dislocation lines and Burgers vectors within a thin foil. The characterized 3D dislocation lines are used to construct the spatial distribution of the equivalent Nye dislocation density tensor. The model dislocation lattice incompatibility equation and stress balance equation are solved with a spectral code based on fast Fourier transform algorithms. As an output of the model, one obtains the 3D distribution of mechanical fields, such as strains, rotations, stresses, resolved shear stresses (RSSs) and energy, inside the material. To assess the potential of the method, we consider two regions from a previously compressed olivine sample. Our results reveal significant local variations in local stress fields and RSSs in various slip systems, which can impact the strong plastic anisotropy of olivine and the activation of different dislocation slip systems. It also evidences the built-up of kinematic hardening down to the nanometre scale.
Charge collection efficiency of commercially available parallel-plate ionisation chambers in ultra-high dose-per-pulse electron beams
Authors: Bourgouin Alexandra , Paz-Martín Jose , Gedik Yunus Can , Frei Franziska , Peier Peter , Rossomme Séverine , Schönfeld Andreas A , Schüller Andreas , Rodriguez Faustino Gomez , Kapsch Ralf-Peter
Published: November 2023

Objective. This investigation aims to experimentally determine the charge collection efficiency (CCE) of six commercially available parallel-plate ionisation chamber (PPIC) models in ultra-high dose-per-pulse (UHDPP) electron beams. Approach. The CCE of 22 PPICs has been measured in UHDPP electron beams at the National Metrology Institution of Germany (PTB). The CCE was determined for a dose per pulse (DPP) range between 0.1 and 6.4 Gy (pulse duration of 2.5 μs). The results obtained with the different PPICs were compared to evaluate the reproducibility, intra- and inter-model variation, and the performance of a CCE empirical model. Main results. The intra-model variation was, on average, 4.0%, which is more than three times the total combined relative standard uncertainty and was found to be greater at higher DPP (up to 20%). The inter-model variation for the PPIC with 2 mm electrode spacing, which was found to be, on average, 10%, was also significant compared to the relative uncertainty and the intra-model variation. The observed CCE variation could not be explained only by the expected deviation of the electrode spacing from the nominal value within the manufacturing tolerance. It should also be noted that a substantial polarity effect, between 0.914(5) and 1.201(3), was observed, and significant intra- and inter-model variation was observed on this effect. Significance. For research and pre-clinical study, the commercially available PPIC with a well-known CCE (directly measured for the specific chamber) and with a small electrode spacing could be used for relative and absolute dosimetry with a lower-limit uncertainty of 1.6% (k = 1) in the best case. However, to use a PPIC as a secondary standard in UHDPP electron beams for clinical purposes would require new model development to reduce the ion recombination, the polarity effect, and the total standard uncertainty on the dose measurement.
Voltage-controlled magnetic solitons motion in an anisotropic ferromagnetic nanowire
Authors: Zhao Yi-Miao , Jin Xin-Wei , Yang Zhan-Ying
Published: November 2023

The precise manipulation of magnetic solitons remains a challenge and is considered a crucial process in magnetic storage. In this paper, we investigate the control of velocity and spatial manipulation of magnetic solitons using the voltage-controlled magnetic anisotropy effect. A long-wave model, known as the generalized derivative nonlinear Schrödinger (GDNLS) equation, is developed to describe the dynamics of magnetic solitons in an anisotropic ferromagnetic nanowire. By constructing the Lax pair for the GDNLS equation, we obtain the exact solutions including magnetic dark solitons, anti-dark solitons, and periodic solutions. Moreover, we propose two approaches to manipulate magnetic solitons: direct voltage application and inhomogeneous insulation layer design. Numerically results show the direct modulation of soliton velocity by a constant voltage, while time-varying voltage induces periodic oscillations. Investigation of Gaussian-type defects reveals soliton being trapped beyond a critical defect depth. These results provide a theoretical basis for future applications in magnetic soliton-based memory devices.
On the magnetic bistability of small iron clusters used in scanning tunneling microscopy tip preparation
Authors: Yu Jisoo , Urdaniz Corina , Namgoong Young , Wolf Christoph
Published: November 2023

The combination of electron spin resonance with scanning tunneling microscopy has resulted in a unique surface probe with sub-nm spatial and neV energy resolution. The preparation of a stable magnetic microtip is of central importance, yet, at the same time remains one of the hardest tasks. In this work, we rationalize why creating such microtips by picking up a few iron atoms often results in magnetically stable probes with two distinct magnetic states. By using density functional theory, we show that randomly formed clusters of five iron atoms can exhibit this behavior with magnetic anisotropy barriers of up to 73 meV. We explore the dependence of the magnetic behavior of such clusters on the geometrical arrangement and find a strong correlation between magnetic and geometric anisotropy—the less regular the cluster the higher its magnetic anisotropy barrier. Finally, our work rationalizes the experimental strategy of obtaining stable magnetic microtips.
Quantum hypothesis testing via robust quantum control
Authors: Xu Han , Wang Benran , Yuan Haidong , Wang Xin
Published: November 2023

Quantum hypothesis testing plays a pivotal role in quantum technologies, making decisions or drawing conclusions about quantum systems based on observed data. Recently, quantum control techniques have been successfully applied to quantum hypothesis testing, enabling the reduction of error probabilities in the task of distinguishing magnetic fields in presence of environmental noise. In real-world physical systems, such control is prone to various channels of inaccuracies. Therefore improving the robustness of quantum control in the context of quantum hypothesis testing is crucial. In this work, we utilize optimal control methods to compare scenarios with and without accounting for the effects of signal frequency inaccuracies. For parallel dephasing and spontaneous emission, the optimal control inherently demonstrates a certain level of robustness, while in the case of transverse dephasing with an imperfect signal, it may result in a higher error probability compared to the uncontrolled scheme. To overcome these limitations, we introduce a robust control approach optimized for a range of signal noise, demonstrating superior robustness beyond the predefined tolerance window. On average, both the optimal control and robust control show improvements over the uncontrolled schemes for various dephasing or decay rates, with the robust control yielding the lowest error probability.
Holographic Einstein rings of an AdS black hole in massive gravity
Authors: Hu Xin-Yun , Israr Aslam M. , Saleem Rabia , Zeng Xiao-Xiong
Published: November 2023

In the context of holography, the Einstein ring of an AdS black hole (BH) in massive
gravity (MG) is depicted. An oscillating Gaussian source on one side of the AdS boundary
propagates in bulk, and we impose a response function to explain it. Using a wave optics imaging
system, we obtain the optical appearance of the Einstein ring. Our research reveals that the ring
can change into a luminosity-deformed ring or light spots depending on the variation of parameters
and observational positions. When observers are positioned at the north pole, the holographic
profiles always appear as a ring with concentric stripe surroundings, and a bright ring appears at
the location of the photon sphere of the BH. To investigate the distinct features of the MG AdS BH
from previous studies, we discussed the relation between the temperature T and the event horizon
 ue
, which shows the decaying behavior with the increasing values of the event horizon
 ue
, when the graviton parameter m is fixed. These in turn influence the behavior of the
response function and the Einstein ring. For example, the amplitude of the lensed response
function |〈O〉| increases with the increasing values of the graviton parameter m,
for the fixed value of the horizon ue
. On the other hand, the amplitude of the lensed
response function |〈O〉| decreases with the increasing values of the horizon
 ue
, for the fixed value of graviton parameter m. These differences are also reflected in
the Einstein ring, where the intensities and the locations of the Einstein ring significantly vary
according to the numerical values of the involved parameters. These findings are also observed in
the brightness profiles and the best fit comparison between the results obtained by wave optics
and geometric optics for different values of graviton parameter m. In this perspective, our
study contributes to a better understanding of the analytical studies of holographic theory, which
can be used to evaluate different types of BHs for a fixed wave source and optical system.
Confronting global 21-cm signal with ℤ3symmetric dark matter models
Authors: Paul Debarun , Dey Antara , Dutta Banik Amit , Pal Supratik
Published: November 2023

While the ℤ3symmetric dark matter models have shown tremendous prospects in addressing a number of (astro-)particle physics problems, they can leave interesting imprints on cosmological observations as well. We consider two such promising models: semi-annihilating dark matter (SADM) and Co-SIMP 2 → 3 interaction, and investigate their effects on the global 21-cm signal. SADM alone cannot address the EDGES dip but can perform better with the aid of an excess radio background, whereas Co-SIMP can naturally explain the EDGES absorption feature by virtue of an intrinsic cooling effect without invoking any such excess radiation. Hence, the latter model turns out to be a rare model within the domain of CDM, that uses leptophilic interaction to achieve the EDGES dip. Further, keeping in mind the ongoing debate between EDGES and SARAS 3 on the global 21-cm signal, we demonstrate that our chosen models can still remain viable in this context, even if the EDGES data requires reassessment in future. We then extend our investigation to possible reflections on the Dark Ages, followed by a consistency check with the CMB and BAO observations via Planck 2018(+BAO) datasets. This work thus presents a compelling case of exploring these interesting particle physics models in the light of different cosmological observations.
Cosmology with a supersymmetric local B - L model
Authors: Jeong Kwang Sik , Park Wan-il
Published: November 2023

We propose a minimal gauged U(1)
B-L
extension of the minimal supersymmetric Standard
Model (MSSM) which resolves the cosmological moduli problem via thermal inflation, and realizes
late-time Affleck-Dine leptogensis so as to generate the right amount of baryon asymmetry at the
end of thermal inflation. The present relic density of dark matter can be explained by
sneutrinos, MSSM neutralinos, axinos, or axions. Cosmic strings from U(1)
B-L
breaking are
very thick, and so the expected stochastic gravitational wave background from cosmic string loops
has a spectrum different from the one in the conventional Abelian-Higgs model, as would be
distinguishable at least at LISA and DECIGO. The characteristic spectrum is due to a flat
potential, and may be regarded as a hint of supersymmetry. Combined with the resolution of moduli
problem, the expected signal of gravitational waves constrains the U(1)
B-L
breaking scale to
be 𝒪(1012–13) GeV. Interestingly, our model provides a natural possibility
for explaining the observed ultra-high-energy cosmic rays thanks to the fact that the core width
of strings in our scenario is very large, allowing a large enhancement of particle emissions from
the cusps of string loops. Condensation of LHu
flat-direction inside of string cores arises
inevitably and can also be the main source of the ultra-high-energy cosmic rays accompanied by
ultra-high-energy lightest supersymmetric particles.
Improving the capacity of quantum dense coding via non-Hermitian operation
Authors: Leng Yang , Chen Fei
Published: November 2023

We propose a novel method to enhance the capacity of quantum dense coding under amplitude damping noise using non-Hermitian operations. With the assistance of non-Hermitian operations, we show that the capacity of quantum dense coding can always be larger than 1 for any two-qubit states. In particular, the non-Hermitian operation can improve quantum dense coding more efficiently in the case of strong decoherence strength than those with small decoherence strength. Our results shed new light on the protection of quantum dense coding in a quantum environment.
The single crystal diamond-based diagnostic suite of the JET tokamak for 14 MeV neutron counting and spectroscopy measurements in DT plasmas
Authors: Rigamonti D. , Dal Molin A. , Muraro A. , Rebai M. , Giacomelli L. , Gorini G. , Nocente M. , Perelli Cippo E. , Conroy S. , Ericsson G. , Eriksson J. , Kiptily V. , Ghani Z. , Štancar Ž. , Tardocchi M. ,   JET Contributors
Published: November 2023

The Joint European Torus (JET) has recently conducted its second deuterium–tritium (DT) experimental campaign DTE2, providing unique opportunity for studying both physics and engineering aspects of nuclear fusion plasmas. This also allowed the exploitation of new diagnostics and technologies that were not available during the first JET DT campaign held in 1997. Among these new instruments, the enhancement projects of the JET nuclear diagnostics lead to the development and installation of synthetic single crystal diamond detectors along different collimated line of sights. This paper describes the single crystal diamond-based diagnostic suite of the JET tokamak and the enhanced 14 MeV neutron diagnostic capabilities in terms of neutron yield and high resolution neutron spectroscopy. The diamond characterization measurements and the calibration procedure at JET are shown, together with performance of the diamond based neutron spectrometer as 14 MeV neutron yield monitor which allows the separation of 2.5 MeV and 14 MeV neutrons in trace tritium plasmas. The first high-resolution 14 MeV neutron spectroscopy measurements in neutral beam injection-heated DT plasmas are presented, allowing thermal and non-thermal neutron component separation. Prospects for the diagnose of DT burning plasmas such as ITER and SPARC will be presented.
Beyond dollars and cents: why socio-political factors matter in energy system modeling
Authors: Dioha Michael O , Montgomery Mikenna , Almada Rolando , Dato Prudence , Abrahams Leslie
Published: November 2023

Traditional energy system modeling (ESM) has predominantly focused on techno-economic factors such as costs and efficiency. However, this narrow perspective fails to capture the intricate interplay between energy systems and socio-political dynamics that significantly influence their real-world impact. This piece underlines the importance of incorporating socio-political factors into ESM and highlights the need for a more comprehensive approach. We identify several reasons why socio-political factors are often overlooked in ESM, including technical bias, complexity, data standardization challenges, time and resource constraints, and societal biases. These factors must be addressed to improve the relevancy of ESM, reduce social injustice, and promote innovation in the design of future energy systems. Incorporating socio-political factors into ESM offers several benefits. To achieve these benefits, the paper suggests a shift towards a more comprehensive and value-driven approach and offers several options for improving ESM including: (I) recognizing that socio-political factors are just as important as techno-economic factors (II) improving the structure of the modeling process (III) developing new and innovative metrics for socio-political factors (IV) linking different types of models (V) emphasizing the need for interdisciplinarity in ESM. By prioritizing the aspects of the energy system that concern people to the same degree we prioritize cost, we can derive value-driven insights to assist in creating a more sustainable future for all.
Ship recycling—estimating future stocks and readiness for green steel transformation
Authors: Bleischwitz Raimund , Höller Jannik , Kriegl Michael
Published: November 2023

This article addresses ship recycling. Often criticized for dire health and safety conditions at breaking destinations in the Global South, our article considers ship recycling as a potential future source for secondary steel in green transformations. It represents an analysis of forthcoming changes in the regulatory framework, an initial assessment of steel stocks based on publicly available data, and a local case study. Here, the article assesses the capability of Bremen, a city in Northern Germany, to gain a relevant future market share. Our results indicate (a) the regulatory framework is dynamic due to the entry into force of the Hong Kong Convention in 2025 und the current revision of the EU Ship Recycling Regulation; (b) the future market is significant, roughly equivalent to the entire current US car fleet in terms of steel stocks; (c) the ability to act locally depends on a variety of critical factors, including political will, entrepreneurial capital, and space requirements. The article concludes with an outlook on the importance of such a development for the transition towards ‘net zero steel’ and provides a perspective on future research needs.
Fluctuation of the phase boundary in the six-vertex model with domain wall boundary conditions: a Monte Carlo study
Authors: Lyberg Ivar , Korepin Vladimir , Viti Jacopo
Published: November 2023

We consider the six-vertex model with domain wall boundary conditions in a square lattice of dimensionN × N. Our main interest is the study of the fluctuations of the extremal lattice path about the arctic curves. We address the problem through Monte Carlo simulations. AtΔ=0, the fluctuations of the extremal path along any line parallel to the square diagonal were rigorously proven to follow the Tracy-Widom distribution. We provide strong numerical evidence that this is true also for other values of the anisotropy parameter Δ (0⩽Δ<1). We argue that the typical width of the fluctuations of the extremal path about the arctic curves scales asN1/3and provide a numerical estimate for the parameters of the scaling random variable.
Comprehensive assessment of solid waste management of a highly urbanized city in Metro Manila, Philippines during the COVID-19 pandemic
Authors: Osorio E , Bularan L , Tanchuling M , Ty S , Inocencio B , Lu P , Requejo B , Caraan L
Published: November 2023

This study aims to gather primary and secondary data on the municipal SWM system of an urban area in Metro Manila during the pandemic to design targeted and effective measures to improve SWM practices and reduce plastic pollution. The study results show that the city’s waste generation rate is at 0.93 kg/cap/day, while the disposal rate is at 0.66 kg/cap/day. Most of the wastes in both generation and disposal are biodegradables, mainly consisting of food wastes. Among the plastic wastes, lightweight plastic bags were the most abundant in terms of weight. From total plastics waste generation, about 7% of them entered the water system; 5% retained on land and the remaining are burnt or in storm drains. An important recommendation from this baseline study is the effective segregation of biodegradable, recyclable, residual, and special wastes.
Effect of rare earth Ce addition on inclusions in offshore engineering steel containing arsenic
Authors: Yu Yinhong , Feng Xiaoming , Luo Diqiang , Zhang Zhenming , Lai Chaobin
Published: November 2023

The present study investigates the impact of rare earth Ce addition and holding time on inclusions in offshore engineering steel containing arsenic. The analysis was conducted using scanning electron microscopy and energy spectrum (SEM-EDS), automatic statistics of inclusions, and thermodynamic analysis. The results indicate that prior to the addition of rare earth Ce, the typical inclusions in the steel were Al2O3, MnS and Al2O3-MnS, with an average size of approximately 2.51 μm and an irregular or stripe morphology. Upon the addition of rare earth Ce, the inclusions in the steel were transformed into Ce-S(-O), Ce-As(-O) and Ce-S-As(-O), with a smaller average size and a spherical or ellipsoidal morphology. The smallest average size of inclusions in the steel was observed when rare earth Ce was added and held for 5 min; this size was 33% smaller than that prior to the addition of Ce. The thermodynamic calculation revealed that the Ce-S(-O) inclusion is formed in molten steel, while the Ce-As(-O) inclusion is formed during the solidification stage. As element replaced parts of the S and O elements in the Ce-S(-O) inclusion and formed the Ce-S-As(-O) complex inclusion, characterized by a double-layered structure.
A comprehensive modeling for the CO2 electroreduction to CO
Authors: Agliuzza Matteo , Pirri Candido Fabrizio , Sacco Adriano
Published: November 2023

In the research for the decarbonization processes, electrochemistry is among the most studied routes for the conversion of carbon dioxide in added-value products, thanks to the up-scalability and the mild conditions of work of the technology. In this framework, modeling the electrochemical reactor is a powerful tool to predict and optimize important features of the electroreduction. In this study, we propose a comprehensive modeling for the whole electrochemical reactor, which has been validated through the experiments with good agreement. In particular, the performance of the cell is studied as a function of the voltage applied, for different sizes of the reactor. Furthermore, the model has been used to study the chemical conditions at the cathode surface, as well as electrochemical conditions at different applied biases and flow rates of the electrolyte.
2023 roadmap on ammonia as a carbon-free fuel
Authors: David William I F , Agnew Gerry D , Bañares-Alcántara René , Barth James , Bøgild Hansen John , Bréquigny Pierre , de Joannon Mara , Fürstenberg Stott Sofia , Fürstenberg Stott Conor , Guati-Rojo Andrea , Hatzell Marta , MacFarlane Douglas R , Makepeace Joshua W , Mastorakos Epaminondas , Mauss Fabian , Medford Andrew , Mounaïm-Rousselle Christine , Nowicki Duncan A , Picciani Mark A , Postma Rolf S , Rouwenhorst Kevin H R , Sabia Pino , Salmon Nicholas , Simonov Alexandr N , Smith Collin , Torrente-Murciano Laura , Valera-Medina Agustin
Published: November 2023

The 15 short chapters that form this 2023 ammonia-for-energy roadmap provide a comprehensive assessment of the current worldwide ammonia landscape and the future opportunities and associated challenges facing the use of ammonia, not only in the part that it can play in terms of the future displacement of fossil-fuel reserves towards massive, long-term, carbon-free energy storage and heat and power provision, but also in its broader holistic impacts that touch all three components of the future global food-water-energy nexus.
Impact of the
Ce 4f
states in the electronic structure of the intermediate-valence superconductor CeIr3
Authors: Fujimori Shin-ichi , Kawasaki Ikuto , Takeda Yukiharu , Yamagami Hiroshi , Sasabe Norimasa , Sato Yoshiki J , Nakamura Ai , Shimizu Yusei , Maurya Arvind , Homma Yoshiya , Li Dexin , Honda Fuminori , Aoki Dai
Published: November 2023

The electronic structure of the f-based superconductor

C
e
I

r
3

was studied by photoelectron spectroscopy. The energy distribution of the

C
e

 
4
f

states were revealed by the

C
e

 
3
d
−
4
f

resonant photoelectron spectroscopy. The

C
e

 
4
f

states were mostly distributed in the vicinity of the Fermi energy, suggesting the itinerant character of the

C
e

 
4
f

states. The contribution of the

C
e

 
4
f

states to the density of states (DOS) at the Fermi energy was estimated to be nearly half of that of the

I
r

 
5
d

states, implying that the

C
e

 
4
f

states have a considerable contribution to the DOS at the Fermi energy. The

C
e

 
3
d

core-level and

C
e

 
3
d

x-ray absorption spectra were analyzed based on a single-impurity Anderson model. The number of the

C
e

 
4
f

states in the ground state was estimated to be

0.8
−
0.9

, which is much larger than the values obtained in the previous studies (i.e.

0
−
0.4

).
Heart rate detection of ballistocardiogram based on improved DAE and template matching method
Authors: Mou Zonglei , Han Lei , Chen Yu
Published: November 2023

Ballistocardiogram (BCG) is a non-invasive physiological signal detection method that can be used for non-contact detection of resting heart rate (RHR) and has been widely used in human health monitoring. However, the BCG signal is vulnerable to noise, making it challenging to accurately measure heart rate. In this paper, we propose a noise reduction model for the BCG signal based on Gramian Angular Field (GAF) and an improved Denoising Autoencoder (DAE), referred to as the GDAE model, to accurately detect heart rate in noise-contaminated signals. First, the Gramian Angular Field transform is used to convert the one-dimensional BCG signal into two-dimensional image information, highlighting the difference between the signal centroid information and noise information; after that, the transformed image is denoised by the Denoising Autoencoder to obtain a denoised BCG signal. After noise reduction, the heart rate of the subject is calculated using the adaptive template matching method. The test proves that under the strong noise interference, the proposed method improves the recall by 6.87% and the accuracy by 6.02% compared with the traditional method, indicating a better detection effect. Furthermore, the comparison test shows that the GDAE model has a significant noise reduction effect on the BCG signal, which improves the practicality of the BCG method for heart rate detection.
Development and Validation of Facial Line Distress Scale for Forehead Lines: FINE-FL
Authors: Kang Eunjee , Kang Danbee , Kim Sooyeon , Choi Kyeongrok , Lee Wooshun , Cho Juhee
Published: November 2023

Background

Forehead lines (FL) are one of the main signs of aging. Traditional tools to measure FL have limited ability to evaluate the multidimensional impact of these lines on appearance, confidence, and psychological and social relationships.

Objectives

We developed and validated the Facial Line Distress Scale–Forehead Lines (FINE-FL) to evaluate the severity and psychosocial distress associated with FL.

Methods

We conducted a cross-sectional survey for FINE-FL psychometric validation at a tertiary hospital and 2 local clinics in Korea. First, a preliminary item pool for the FINE-FL was developed through a qualitative interview based on literature reviews and expert consultations. Second, cognitive interviews and a pilot test were conducted to evaluate comprehension, ease of response, acceptability of terminology, phrasing, and response options. FINE-FL consisted of 26 items. In this study, exploratory factor analysis was conducted to identify the underlying factor structure of the FINE-FL, and internal consistency and test-retest reliability were also examined.

Results

We found 21 items in 4 domains. The model fit was good. Coefficient αs ranged from 0.89 to 0.95 for subdomains and 0.96 for the total. The FINE-FL was moderately correlated with the appearance appraisal score. On the test-retest, the range of the intraclass correlation coefficient was 0.65 to 0.79.

Conclusions

FINE-FL is a reliable, valid, and comprehensive patient-reported outcome measure for assessing FL severity and distress. This will be helpful in determining a patient's eligibility for inclusion in a study and measuring primary or secondary effectiveness endpoints for forehead line treatment.
pyScoMotif: discovery of similar 3D structural motifs across proteins
Authors: Cia Gabriel , Kwasigroch Jean , Stamatopoulos Basile , Rooman Marianne , Pucci Fabrizio
Published: November 2023

Motivation

The fast and accurate detection of similar geometrical arrangements of protein residues, known as 3D structural motifs, is highly relevant for many applications such as binding region and catalytic site detection, drug discovery and structure conservation analyses. With the recent publication of new protein structure prediction methods, the number of available protein structures is exploding, which makes efficient and easy-to-use tools for identifying 3D structural motifs essential.

Results

We present an open-source Python package that enables the search for both exact and mutated motifs with position-specific residue substitutions. The tool is efficient, flexible, accurate, and suitable to run both on computer clusters and personal laptops. Two successful applications of pyScoMotif for catalytic site identification are showcased.

Availability and implementation

The pyScoMotif package can be installed from the PyPI repository and is also available at https://github.com/3BioCompBio/pyScoMotif. It is free to use for non-commercial purposes.
Exercise enhances placental labyrinth trophoblast development by activation of PGC-1α and FNDC5/irisin
Authors: Chae Song Ah , Du Min , Zhu Mei-Jun , Son Jun Seok
Published: November 2023

Placental chorion/labyrinth trophoblasts are energy demanding which is met by the mitochondrial oxidative phosphorylation. Exercise enhances placental development and mitochondrial biogenesis, but the underlying mechanisms remain poorly understood. To address, female C57BL/6 J mice were randomly assigned into two groups: a control group and an exercise (EX) group. All animals were acclimated to treadmill exercise for 1 week before mating, but only the EX group was subjected to daily exercise during pregnancy from embryonic day (E) 1.5 to E16.5. Placenta were collected at E18.5 for biochemical and histochemical analyses, and primary trophoblast cells were isolated from the E18.5 placenta for further analyses. The data showed that exercise during pregnancy promoted the expression of syncytiotrophoblast cell markers, indicating trophoblast cell differentiation, which was closely associated with elevated mitochondrial biogenesis and oxidative metabolism in the E18.5 placenta. In addition, exercise during pregnancy activated peroxisome proliferator-activated receptor γ coactivator-1 α (PGC-1α), which was associated with upregulated placental α-ketoglutarate and the expression of isocitrate dehydrogenases and ten-eleven translocations, facilitating DNA demethylation of the Pgc1a promoter. Furthermore, exercise upregulated fibronectin type III domain containing 5 expression and the secretion of its cleaved form, irisin, which is known to activate PGC-1α. These data suggest that exercise-induced activation of PGC-1α, via epigenetic modifications, is responsible for promoting mitochondrial energy metabolism and chorion/labyrinth trophoblast development.
Multiscale adaptive management of social–ecological systems
Authors: Garmestani Ahjond , Allen Craig R , Angeler David G , Gunderson Lance , Ruhl J B
Published: November 2023

Adaptive management is an approach for stewardship of social–ecological systems in circumstances with high uncertainty and high controllability. Although they are largely overlooked in adaptive management (and social–ecological system management), it is important to account for spatial and temporal scales to mediate within- and cross-scale effects of management actions, because cross-scale interactions increase uncertainty and can lead to undesirable consequences. The iterative nature of an adaptive approach can be expanded to multiple scales to accommodate different stakeholder priorities and multiple ecosystem attributes. In this Forum, we introduce multiscale adaptive management of social–ecological systems, which merges adaptive management with panarchy (a multiscale model of social–ecological systems) and demonstrate the importance of this approach with case studies from the Great Plains of North America and the Platte River Basin, in the United States. Adaptive management combined with a focus on the panarchy model of social–ecological systems can help to improve the management of social–ecological systems.
Elevated mortality among the second-generation (children of migrants) in Europe: what is going wrong? A review
Authors: Wallace Matthew , Hiam Lucinda , Aldridge Robert
Published: November 2023

Introduction

The ‘second-generation’ (i.e. the children of migrants) represent one of the fastest growing subpopulations of the child and young adult populations in Europe today. The research so far appears to indicate that their mortality risk is elevated relative to people with non-migrant backgrounds.

Sources of data

Peer-reviewed publications.

Areas of agreement

Second-generation status is a clear marker of elevated mortality risk in Europe in early life (including stillbirth, perinatal, neonatal and infant mortality) and adulthood, particularly if the parent(s) were born outside of Europe. Socioeconomic inequality plays an important, albeit rarely defining, role in these elevated risks.

Areas of controversy

It remains unclear what causes-of-death are driving these elevated mortality risks. The exact influence of (non-socioeconomic) explanatory factors (e.g. health care, racism & discrimination, and factors related to integration) on the elevated mortality risks of the second-generation also remains unclear.

Growing points

The second-generation will continue to grow and diversify in Europe; we must intervene to address these inequalities now.

Areas timely for developing research

Place more emphasis on the complexity of migration background, specific causes-of-death, and understanding the roles of explanatory factors beyond socioeconomic background.
Optimization of patient-specific stereo-EEG recording sensitivity
Authors: Dessert Grace E , Thio Brandon J , Grill Warren M
Published: November 2023

Stereo-EEG is a minimally invasive technique used to localize the origin of epileptic activity (the epileptogenic zone) in patients with drug-resistant epilepsy. However, current stereo-EEG trajectory planning methods are agnostic to the spatial recording sensitivity of implanted electrodes. In this study, we used image-based patient-specific computational models to design optimized stereo-EEG electrode configurations. Patient-specific optimized electrode configurations exhibited substantially higher recording sensitivity than clinically implanted configurations, and this may lead to a more accurate delineation of the epileptogenic zone. The optimized configurations also achieved equally good or better recording sensitivity with fewer electrodes compared with clinically implanted configurations, and this may reduce the risk for complications, including intracranial haemorrhage. This approach improves localization of the epileptogenic zone by transforming the clinical use of stereo-EEG from a discrete ad hoc sampling to an intelligent mapping of the regions of interest.
Treating erythroplasia of Queyrat with photodynamic therapy following circumcision and dermabrasion
Authors: Yao Shulan , Lin Zheng , Li Yan , Lu Bin
Published: November 2023

We describe a case of a patient with erythroplasia of Queyrat located on the whole glans and end of the prepuce that was successfully treated with three courses of photodynamic therapy after the completion of circumcision and dermabrasion. Skin lesions disappeared after receiving this combination of treatments and have not recurred during the past 6 months of follow-up.
Differential diagnosis of red scalp: the importance of trichoscopy
Authors: Waśkiel-Burnat Anna , Czuwara Joanna , Blicharz Leszek , Olszewska Małgorzata , Rudnicka Lidia
Published: November 2023

Red scalp is a common complaint that may constitute a diagnostic and therapeutic challenge in daily clinical practice. Among the numerous diseases to cause diffuse scalp erythema are psoriasis, seborrhoeic dermatitis, contact dermatitis, diffuse lichen planopilaris, dermatomyositis and scalp rosacea. Accurate diagnosis is crucial for optimal treatment outcomes. Histology most frequently discriminates the underlying condition, but it requires scalp biopsy. In many cases, the combination of clinical examination and trichoscopy is sufficient for establishing the correct diagnosis. The main trichoscopic features of psoriasis are silver–white scaling, regularly distributed dotted (glomerular) vessels or twisted red loops, and punctate haemorrhages. Yellowish–white scaling and thin arborizing vessels are typical features of seborrhoeic dermatitis. Contact dermatitis is characterized by the presence of yellow exudate and polymorphic vessels, while perifollicular scaling and erythema with the lack of follicular openings are typical findings in lichen planopilaris. In scalp dermatomyositis, tortuous and arborizing vessels with interfollicular and perifollicular pigmentation may be detected. The most characteristic features of scalp rosacea are perifollicular scaling and polygonal/arborizing vessels. This review also summarizes histological features and therapeutic options for these conditions.
Olanzapine-induced progressive facial oedema mimicking Morbihan disease
Authors: Herlihy Maeve , Duff Eimaer , Sadlier Muriel
Published: November 2023

We present the case of a 55-year-old man with a 20-year history of olanzapine-induced progressive solid facial oedema mimicking Morbihan disease. Olanzapine was not initially considered as the cause of his facial oedema as he had been on treatment for years prior to disease onset. This case reminds us to do a thorough drug review to rule out an iatrogenic cause before making a diagnosis of Morbihan disease.
Therapeutic Phages as Modulators of the Immune Response: Practical Implications
Authors: Górski Andrzej , Międzybrodzki Ryszard , Jończyk-Matysiak Ewa , Kniotek Monika , Letkiewicz Sławomir
Published: November 2023

While the medical community awaits formal proof of the efficacy of phage therapy, as is required by evidence-based medicine, existing data suggest that phages could also be applied based on their non-antibacterial action, especially phage-mediated immunomodulation. Promising avenues have been revealed by findings indicating that phages may mediate diverse actions in the immune system, while the list of phages able to dampen the aberrant immunity associated with a variety of disorders continuously grows. Here we summarize what is known in this field and possible options for the future. While available data are still scarce and preliminary, it appears that “phage repurposing” is worthy of more research, which could reveal new perspectives on applying phage therapy in contemporary medicine.
Therapeutic Phage Monitoring: A Review
Authors: Bosco Kiran , Lynch Stephanie , Sandaradura Indy , Khatami Ameneh
Published: November 2023

With the global rise in antimicrobial resistance, there has been a renewed interest in the application of therapeutic phages to treat bacterial infections. Therapeutic phage monitoring (TPM) is proposed as an essential element of phage therapy (PT) protocols to generate data and fill knowledge gaps regarding the in vivo efficacy of therapeutic phages, patients’ immune responses to PT, and the wider ecological effects of PT. By monitoring phage concentrations in blood and tissues, together with immune responses and possible ecological changes during PT, TPM may enable the optimization of dosing and the implementation of precision medicine approaches. Furthermore, TPM can validate diagnostic surrogates of efficacy, direct research efforts, and establish quality assurance indicators for therapeutic phage products. Thus, TPM holds great potential for enhancing our understanding of the multidirectional phage–bacteria–host interactions and advancing “best practice” PT, ultimately improving patient care.
Advanced Manufacturing, Formulation and Microencapsulation of Therapeutic Phages
Authors: Malik Danish J , Goncalves-Ribeiro Henrique , GoldSchmitt Dirk , Collin Joe , Belkhiri Aouatif , Fernandes Diogo , Weichert Henry , Kirpichnikova Anya
Published: November 2023

Manufacturing and formulation of stable, high purity, and high dose bacteriophage drug products (DPs) suitable for clinical usage would benefit from improved process monitoring and control of critical process parameters that affect product quality attributes. Chemistry, Manufacturing, and Controls (CMC) for both upstream (USP) and downstream processes (DSP) need mapping of critical process parameters (CPP) and linking these to critical quality attributes (CQA) to ensure quality and consistency of phage drug substance (DS) and DPs development. Single-use technologies are increasingly becoming the go-to manufacturing option with benefits both for phage bioprocess development at the engineering run research stage and for final manufacture of the phage DS. Future phage DPs under clinical development will benefit from implementation of process analytical technologies (PAT) for better process monitoring and control. These are increasingly being used to improve process robustness (to reduce batch-to-batch variability) and productivity (yielding high phage titers). Precise delivery of stable phage DPs that are suitably formulated as liquids, gels, solid-oral dosage forms, and so forth, could significantly enhance efficacy of phage therapy outcomes. Pre-clinical development of phage DPs must include at an early stage of development, considerations for their formulation including their characterization of physiochemical properties (size, charge, etc.), buffer pH and osmolality, compatibility with regulatory approved excipients, storage stability (packaging, temperature, humidity, etc.), ease of application, patient compliance, ease of manufacturability using scalable manufacturing unit operations, cost, and regulatory requirements.
Collecting Multi-country Retrospective Antimicrobial Consumption and Use Data: Challenges and Experience
Authors: Prifti Kristi , Chi Kyu-young Kevin , Eraly Emmanuel , Joh Hea Sun , Sujan Mohammad Julhas , Poudyal Nimesh , Marks Florian , Holm Marianne
Published: November 2023

Excessive or inappropriate antimicrobial use contributes to antimicrobial resistance, emphasizing the need to monitor and document the types and quantities of antibiotics used. Thus, data on antimicrobial consumption (AMC) and antimicrobial usage (AMU) are key in informing and promoting judicious use. Our study, conducted during 2019–2023, as part of the CAPTURA project, aimed to understand the state of data availability and quality for AMC and AMU monitoring in Asia. In this article, we describe the challenges and opportunities faced and provide examples of AMU and AMC analysis. World Health Organization (WHO) and country-tailored methodologies and tools were applied to collect retrospective data from 2016 to 2019 in Bangladesh, Bhutan, Laos, Nepal, Pakistan, Papua New Guinea, Sri Lanka, and Timor-Leste. The primary indicator for national AMC was total level of consumption, expressed as total defined daily doses (DDD) per 1000 inhabitants per day for the year or period of data collected. For facility AMC and AMU, the primary indicator was total DDD per admissions per day for the year or period of data collected. Although many countries faced infrastructural challenges in data collection and storage, we managed to collect and analyze AMC data from 6 countries and AMU data from 5. The primary indicators, and additional findings, were visualized to facilitate dissemination and promote the development of action plans. Looking ahead, it is crucial that future initiatives empower each country to establish surveillance infrastructures tailored to their unique contexts, ensuring sustainable progress in the fight against antimicrobial resistance.
Enhancing Auditory Brainstem Response Classification Based On Vision Transformer
Authors: Abubakir Ahmed Hunar , Majidpour Jafar , Hussein Ahmed Mohammed , Kais Jameel Samer , Majidpour Amir
Published: November 2023

A method for testing the health of ear’s peripheral auditory nerve and its connection to the brainstem is called an auditory brainstem response (ABR). Manual quantification of ABR tests by an audiologist is not only costly but also time-consuming and susceptible to errors. Recently in machine learning have prompted a resurgence of research into ABR classification. This study presents an automated ABR recognition model. The initial step in our design process involves collecting a dataset by extracting ABR test images from sample test reports. Subsequently, we employ an elastic distortion approach to generate new images from the originals, effectively expanding the dataset while preserving the fundamental structure and morphology of the original ABR content. Finally, the Vision Transformer method was exploited to train and develop our model. In the testing phase, the incorporation of both the newly generated and original images yields an impressive accuracy rate of 97.83%. This result is noteworthy when benchmarked against the latest research in the field, underscoring the substantial performance enhancement achieved through the utilization of generated data.
Pharmacological Therapies for the Management of Fistulizing Crohn’s Disease: A Systematic Review and Meta-Analysis
Authors: Vuyyuru Sudheer K , Solitano Virginia , Narula Neeraj , Lee Matthew J , MacDonald John K , McCurdy Jeffrey D , Singh Siddharth , Ma Christopher , Jairath Vipul
Published: November 2023

Background

Fistulas are a debilitating complication of Crohn’s disease [CD]. We conducted a systematic review to assess the efficacy of medical therapies for fistulizing CD.

Methods

MEDLINE, Embase, and CENTRAL were searched on May 26, 2022, for randomized controlled trials [RCTs] of pharmacological therapy in adults with fistulizing CD. The primary outcome was induction and maintenance of fistula response. Pooled risk ratios [RRs] and 95% confidence intervals [CIs] were calculated. GRADE was used to assess the certainty of evidence.

Results

Thirty-eight RCTs were included. Nineteen trials [50%] exclusively involved perianal fistula. The remaining studies included some participants with non-perianal fistula. Pooled RRs for anti-tumour necrosis factor [TNF] agents were not statistically significant for induction [RR 1.36, 95% CI 0.97–1.91] or maintenance of fistula response [RR 1.48, 95% CI 0.97–2.27]. However, in a sensitivity analysis of studies with fistula response as the primary outcome, anti-TNFs were superior to placebo for induction [RR 1.94, 95% CI 1.10–3.41] and maintenance [RR 1.88, 95% CI 1.23–2.88] of fistula response. Oral small molecules [RR 2.56, 95% CI 1.18–5.53] and mesenchymal stem cell [MSC] therapy [RR 1.26, 95% CI 1.01–1.57] were effective for induction of fistula response. Ustekinumab was associated with maintenance of fistula response [RR 1.80, 95% CI 1.04–3.11]. Vedolizumab was not superior to placebo. The certainty of evidence ranged from very low to moderate.

Conclusion

Very low- to moderate-certainty evidence suggests that anti-TNF therapy, oral small molecules, ustekinumab, and MSCs are effective for perianal fistulizing CD. Dedicated fistula studies evaluating biologics and small molecules are needed.