bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigating the role of dispersion corrections and anharmonic effects on the phase transition in SrZrS3: A systematic analysis from AIMD free energy calculations
Authors: Jaykhedkar Namrata , Bystrický Roman , Sýkora Milan , Bučko Tomáš
Published: January 2024

A thermally driven needle-like (NL) to distorted perovskite (DP) phase transition in SrZrS3 was investigated by means of ab initio free energy calculations accelerated by machine learning. As a first step, a systematic screening of the methods to include long-range interactions in semilocal density functional theory Perdew–Burke–Ernzerhof calculations was performed. Out of the ten correction schemes tested, the Tkatchenko–Scheffler method with iterative Hirshfeld partitioning method was found to yield the best match between calculated and experimental lattice geometries, while predicting the correct order of stability of NL and DP phases at zero temperature. This method was then used in free energy calculations, performed using several approaches, so as to determine the effect of various anharmonicity contributions, such as the anisotropic thermal lattice expansion or the thermally induced internal structure changes, on the phase transition temperature (TNP→DP). Accounting for the full anharmonicity by combining the NPT molecular dynamics data with thermodynamic integration with harmonic reference provided our best estimate of TNL→DP = 867 K. Although this result is ∼150 K lower than the experimental value, it still provides an improvement by nearly 300 K compared to the previous theoretical report by Koocher et al. [Inorg. Chem. 62, 11134–11141 (2023)].
Impossibility theorems for feature attribution
Authors: Bilodeau Blair , Jaques Natasha , Koh Pang Wei , Kim Been
Published: January 2024

Despite a sea of interpretability methods that can produce plausible explanations, the field has also empirically seen many failure cases of such methods. In light of these results, it remains unclear for practitioners how to use these methods and choose between them in a principled way. In this paper, we show that for moderately rich model classes (easily satisfied by neural networks), any feature attribution method that is complete and linear—for example, Integrated Gradients and Shapley Additive Explanations (SHAP)—can provably fail to improve on random guessing for inferring model behavior. Our results apply to common end-tasks such as characterizing local model behavior, identifying spurious features, and algorithmic recourse. One takeaway from our work is the importance of concretely defining end-tasks: Once such an end-task is defined, a simple and direct approach of repeated model evaluations can outperform many other complex feature attribution methods.
Development of prediction models to identify hotspots of schistosomiasis in endemic regions to guide mass drug administration
Authors: Singer Benjamin J. , Coulibaly Jean T. , Park Hailey J. , Andrews Jason R. , Bogoch Isaac I. , Lo Nathan C.
Published: January 2024

Schistosomiasis is a neglected tropical disease affecting over 150 million people. Hotspots of
Schistosoma
transmission—communities where infection prevalence does not decline adequately with mass drug administration—present a key challenge in eliminating schistosomiasis. Current approaches to identify hotspots require evaluation 2–5 y after a baseline survey and subsequent mass drug administration. Here, we develop statistical models to predict hotspots at baseline prior to treatment comparing three common hotspot definitions, using epidemiologic, survey-based, and remote sensing data. In a reanalysis of randomized trials in 589 communities in five endemic countries, a regression model predicts whether
Schistosoma mansoni
infection prevalence will exceed the WHO threshold of 10% in year 5 (“prevalence hotspot”) with 86% sensitivity, 74% specificity, and 93% negative predictive value (NPV; assuming 30% hotspot prevalence), and a regression model for
Schistosoma haematobium
achieves 90% sensitivity, 90% specificity, and 96% NPV. A random forest model predicts whether
S. mansoni
moderate and heavy infection prevalence will exceed a public health goal of 1% in year 5 (“intensity hotspot”) with 92% sensitivity, 79% specificity, and 96% NPV, and a boosted trees model for
S. haematobium
achieves 77% sensitivity, 95% specificity, and 91% NPV. Baseline prevalence is a top predictor in all models. Prediction is less accurate in countries not represented in training data and for a third hotspot definition based on relative prevalence reduction over time (“persistent hotspot”). These models may be a tool to prioritize high-risk communities for more frequent surveillance or intervention against schistosomiasis, but prediction of hotspots remains a challenge.
Fission-independent compartmentalization of mitochondria during budding yeast cell division
Authors: Yoshii Saori R. , Barral Yves
Published: January 2024

Lateral diffusion barriers compartmentalize membranes to generate polarity or asymmetrically partition membrane-associated macromolecules. Budding yeasts assemble such barriers in the endoplasmic reticulum (ER) and the outer nuclear envelope at the bud neck to retain aging factors in the mother cell and generate naïve and rejuvenated daughter cells. However, little is known about whether other organelles are similarly compartmentalized. Here, we show that the membranes of mitochondria are laterally compartmentalized at the bud neck and near the cell poles. The barriers in the inner mitochondrial membrane are constitutive, whereas those in the outer membrane form in response to stresses. The strength of mitochondrial diffusion barriers is regulated positively by spatial cues from the septin axis and negatively by retrograde (RTG) signaling. These data indicate that mitochondria are compartmentalized in a fission-independent manner. We propose that these diffusion barriers promote mitochondrial polarity and contribute to mitochondrial quality control.
IL-23 to see: Gut DCs shine bright in inductive sites
Authors: Ulmert Isabel , Lahl Katharina
Published: January 2024

The cytokine IL-23 plays important roles in intestinal barrier protection and integrity, but is also linked to chronic inflammation. In this issue of JEM, Ohara et al. (https://doi.org/10.1084/jem.20230923) provide clarity on the much-debated question of which cells produce IL-23.
A bearing fault diagnosis method with improved symplectic geometry mode decomposition and feature selection
Authors: Chen Shengfan , Zheng Xiaoxia
Published: January 2024

A rolling bearing fault diagnosis method based on improved symplectic geometry mode decomposition (SGMD) and feature selection was proposed to solve the problem of low fault identification due to the influence of noise on early bearing fault features. First, the SGMD SGMD is improved to enhance its robustness in decomposing signals with noise, then the time domain, frequency domain, and time-frequency features of each symplectic geometric component are extracted as feature vectors. Second, a comprehensive feature selection strategy is proposed to select the optimal subset of features that are conducive to fault classification. Finally, considering the problem of low classification accuracy of a single machine learning model, the AdaBoost-WSO-SVM model is constructed for fault classification using the AdaBoost algorithm of integrated learning. Experimental decomposition of complex signals with noise indicates that the improved SGMD is more effective compared to traditional SGMD. Subsequently, multiple experiments were conducted using the bearing datasets from Case Western Reserve University (CWRU) and Jiangnan University (JNU). The experimental results reveal that, after comprehensive feature selection and ensemble learning pattern recognition experiments on the CWRU dataset, the average accuracy of fault diagnosis can reach 99.67%. On the JNU dataset, the proposed fault diagnosis method achieves an average accuracy of 95.03%. This suggests that, compared to other feature selection methods and classification models, the proposed approach in this paper exhibits higher accuracy and generalization capabilities.
Defining ferroelectric characteristics with reversible piezoresponse: PUND switching spectroscopy PFM characterization
Authors: Alikin Denis , Safina Violetta , Abramov Alexander , Slautin Boris , Shur Vladimir , Pavlenko Anatoly , Kholkin Andrei
Published: January 2024

Detecting ferroelectricity at micro- and nanoscales is crucial for advanced nanomaterials and materials with complicated topography. Switching spectroscopy piezoresponse force microscopy (SSPFM), which involves measuring piezoelectric hysteresis loops via a scanning probe microscopy tip, is a widely accepted approach to characterize polarization reversal at the local scale and confirm ferroelectricity. However, the local hysteresis loops acquired through this method often exhibit unpredictable shapes, a phenomenon often attributed to the influence of parasitic factors such as electrostatic forces and current flow. Our research has uncovered that the deviation in hysteresis loop shapes can be caused by spontaneous backswitching occurring after polarization reversal. Moreover, we’ve determined that the extent of this effect can be exacerbated when employing inappropriate SSPFM waveform parameters, including duration, frequency, and AC voltage amplitude. Notably, the conventional ‘pulse-mode’ SSPFM method has been found to intensify spontaneous backswitching. In response to these challenges, we have redesigned SSPFM approach by introducing the positive up-negative down (PUND) method within the ‘step-mode’ SSPFM. This modification allows for effective probing of local piezoelectric hysteresis loops in ferroelectrics with reversible piezoresponse while removing undesirable electrostatic contribution. This advancement extends the applicability of the technique to a diverse range of ferroelectrics, including semiconductor ferroelectrics and relaxors, promising a more reliable and accurate characterization of their properties.
Integration of epitaxial LiNbO3 thin films with silicon technology
Authors: Bartasyte Ausrine , Oliveri Stefania , Boujnah Sondes , Margueron Samuel , Bachelet Romain , Saint-Girons Guillaume , Albertini David , Gautier Brice , Boulet Pascal , Nuta Ioana , Blanquet Elisabeth , Astié Vincent , Decams Jean-Manuel
Published: January 2024

Development of bulk acoustic wave filters with ultra-wide pass bands and operating at high frequencies for 5th and 6th generation telecommunication applications and micro-scale actuators, energy harvesters and sensors requires lead-free piezoelectric thin films with high electromechanical coupling and compatible with Si technology. In this paper, the epitaxial growth of 36°Y-X and 30°X-Y LiNbO3 films by direct liquid injection chemical vapour deposition on Si substrates by using epitaxial SrTiO3 layers, grown by molecular beam epitaxy, has been demonstrated. The stability of the interfaces and chemical interactions between SrTiO3, LiNbO3 and Si were studied experimentally and by thermodynamical calculations. The experimental conditions for pure 36°Y-X orientation growth have been optimized. The piezoelectricity of epitaxial 36°Y-X LiNbO3/SrTiO3/Si films was confirmed by means of piezoelectric force microscopy measurements and the ferroelectric domain inversion was attained at 85 kV.cm−1 as expected for the nearly stoichiometric LiNbO3. According to the theoretical calculations, 36°Y-X LiNbO3 films on Si could offer an electromechanical coupling of 24.4% for thickness extension excitation of bulk acoustic waves and a comparable figure of merit of actuators and vibrational energy harvesters to that of standard PbZr1−x
Ti
x
O3 films.
Quantitative pulsatility measurements using 3D dynamic ultrasound localization microscopy
Authors: Bourquin Chloé , Porée Jonathan , Rauby Brice , Perrot Vincent , Ghigo Nin , Belgharbi Hatim , Bélanger Samuel , Ramos-Palacios Gerardo , Cortes Nelson , Ladret Hugo , Ikan Lamyae , Casanova Christian , Lesage Frédéric , Provost Jean
Published: January 2024

A rise in blood flow velocity variations (i.e. pulsatility) in the brain, caused by the stiffening of upstream arteries, is associated with cognitive impairment and neurodegenerative diseases. The study of this phenomenon requires brain-wide pulsatility measurements, with large penetration depth and high spatiotemporal resolution. The development of dynamic ultrasound localization microscopy (DULM), based on ULM, has enabled pulsatility measurements in the rodent brain in 2D. However, 2D imaging accesses only one slice of the brain and measures only 2D-projected and hence biased velocities . Herein, we present 3D DULM: using a single ultrasound scanner at high frame rate (1000–2000 Hz), this method can produce dynamic maps of microbubbles flowing in the bloodstream and extract quantitative pulsatility measurements in the cat brain with craniotomy and in the mouse brain through the skull, showing a wide range of flow hemodynamics in both large and small vessels. We highlighted a decrease in pulsatility along the vascular tree in the cat brain, which could be mapped with ultrasound down to a few tens of micrometers for the first time. We also performed an intra-animal validation of the method by showing consistent measurements between the two sides of the Willis circle in the mouse brain. Our study provides the first step towards a new biomarker that would allow the detection of dynamic abnormalities in microvessels in the brain, which could be linked to early signs of neurodegenerative diseases.
Motion artifact correction in cardiac CT using cross-phase temporospatial information and synergistic attention gate and spatial transformer sub-networks
Authors: Gong Hao , Ahmed Zaki , Chang Shaojie , Koons Emily K , Thorne Jamison E , Rajiah Prabhakar , Foley Thomas A , Fletcher Joel G , McCollough Cynthia H , Leng Shuai
Published: January 2024

Objectives. To improve quality of coronary CT angiography (CCTA) images using a generalizable motion-correction algorithm. Approach. A neural network with attention gate and spatial transformer (ATOM) was developed to correct coronary motion. Phantom and patient CCTA images (39 males, 32 females, age range 19–92, scan date 02/2020 to 10/2021) retrospectively collected from dual-source CT were used to create training, development, and testing sets corresponding to 140- and 75 ms temporal resolution, with 75 ms images as labels. To test generalizability, ATOM was deployed for locally adaptive motion-correction in both 140- and 75 ms patient images. Objective metrics were used to assess motion-corrupted and corrected phantom and patient images, including structural-similarity-index (SSIM), dice-similarity-coefficient (DSC), peak-signal-noise-ratio (PSNR), and normalized root-mean-square-error (NRMSE). In objective quality assessment, ATOM was compared with several baseline networks, including U-net, U-net plus attention gate, U-net plus spatial transformer, VDSR, and ResNet. Two cardiac radiologists independently interpreted motion-corrupted and -corrected images at 75 and 140 ms in a blinded fashion and ranked diagnostic image quality (worst to best: 1–4, no ties). Main results. ATOM improved quality metrics (p < 0.05) before/after correction: in phantom, SSIM 0.87/0.95, DSC 0.85/0.93, PSNR 19.4/22.5, NRMSE 0.38/0.27; in patient images, SSIM 0.82/0.88, DSC 0.88/0.90, PSNR 30.0/32.0, NRMSE 0.16/0.12. ATOM provided more consistent improvement of objective image quality, compared to the presented baseline networks. The motion-corrected images received better ranks than un-corrected at the same temporal resolution (p < 0.05): 140 ms images 1.65/2.25, and 75 ms images 3.1/3.2. The motion-corrected 75 ms images received the best rank in 65% of testing cases. A fair-to-good inter-reader agreement was observed (Kappa score 0.58). Significance. ATOM reduces motion artifacts, improving visualization of coronary arteries. This algorithm can be used to virtually improve temporal resolution in both single- and dual-source CT.
Ultralong-lasting plasma-activated water: production and control mechanisms
Authors: Ran Congfu , Zhou Xiongfeng , Wang Zhiyong , Liu Kun , Ostrikov Kostya (Ken)
Published: January 2024

Despite the rapidly growing interest stemming from the broad-spectrum, high inactivation capacity, and environmental friendliness of the plasma-activated water (PAW), practical applications are limited because of the PAW’s short lifetime. While low-temperature storage can extend the lifetime, but the freezing and thawing processes are energy- and labor-intense and are generally not suitable for large-scale applications such as environmental and biomedical disinfection. This work addresses this issue by developing the ultra-long-life PAW at room temperature. The innovative approach is based on using DC needle-water discharges, wherein the gaseous products are blown out and absorbed separately by a gas flow. By simply adjusting the voltage and gas flow rates, two distinctive types of PAW with acidic hydrogen peroxide and nitrite as the main products are produced and separated in the discharge chamber and gas bubbling chamber. Intentional mixing of these two PAWs causes a chain chemical reaction dominated by peroxynitrite (ONOOH). This reaction can generate a variety of short-lived reactive species, thereby achieving the ultralong-lasting PAW with very stable bactericidal ability. This study further demonstrates the ability to effectively control the reaction products in both chambers and provides insights into the secondary activation mechanism of short-lived reactive species stimulated by ONOOH.
Deformation control method for active shape morphing lattice structure using topology optimization approach
Authors: Xu Bo , Gu Xiaojun , Wang Jun , Zhang Yahui , Zhu Jihong , Zhang Weihong
Published: January 2024

This study introduces an active shape-morphing lattice structure along with a method for controlling its deformation. A shape memory alloys (SMA) based smart lattice unit cell is proposed, this smart lattice unit cell is capable of accomplishing three distinct types of basic deformations by activating various SMA actuators through heating. By assembling these smart lattice unit cells, an entire structure can be constructed, which can undergo various modes of deformation through the activation of different actuators. To assess the deformation effects, a 3D printed active shape morphing lattice structure model is employed. Furthermore, a deformation control method for active shape morphing lattice structure using topology optimization approach is established. The optimization model takes into account both energy consumption and structural deformation errors. To illustrate the application of this approach, a numerical example involving an airfoil structure with bending deformation is presented. The desired deformation is attained with minimal energy consumption and only a 1% margin of error in deformation.
Free-surface proximity induced bistability and semi-semicoherency in precipitation systems
Authors: Raghavendra R M , Subramaniam Anandh , Iyer Ganesh
Published: January 2024

In systems without a ‘high misfit’ and in the early stage of growth, the precipitates tend to remain coherent with the parent matrix. On further growth beyond a critical size (r*), the precipitates undergo a coherent to semi-coherent transition by formation of interfacial misfit dislocation loops to minimize the total strain energy of the system. The variation of r* with domain size has been studied and the concept of re-entrant interface transition to the coherent state was demonstrated in finite crystals. Dislocations can exist in a state of mechanical equilibrium; but are thermodynamically metastable. In the proximity of ‘interfaces’ dislocations experience a configurational force. The current work pertains to study the stability of an interfacial misfit dislocation loop in the proximity of a free-surface; wherein we evaluate configurational effects in a semi-infinite body. The Cu-2 wt%γFe alloy is used as a model system in this study. In this work we: (i) demonstrate the stabilization of the coherent state (divergence of r*), induced by the proximity of the free-surface; (ii) discover the existence of bistability in materials at the microstructural scale, resulting from the destabilization of the equatorial position of the dislocation loop and arising from symmetry breaking in climb of the interfacial loop due to the vicinity of a free-surface. (iii) identify regimes of ‘equi-bistablity’ and regions with asymmetry in energy wells, (iv) establish the existence of a ‘semi’-semicoherent state. Here, one specific system has been chosen to illustrate the effects; however, we expect the conclusions to have a broader applicability.
Ciliary neurotrophic factor mediated growth of retinal ganglion cell axons on PGS/PCL scaffolds
Authors: Behtaj Sanaz , Karamali Fereshteh , Najafian Samaneh , Masaeli Elahe , Rybachuk Maksym
Published: January 2024

Ciliary neurotrophic factor (CNTF) promotes survival and/or differentiation of a variety of neuronal cells including retinal ganglion cells (RGCs). Delivery of CNTF requires a suitable medium capable of mediating diffusion and premature release of CNTF within the target tissue. Polymeric tissue-engineered scaffolds have been readily used as substrates for cell transplantation, expansion, and differentiation and, as carriers of cell growth factors. Their functions to CNTF release for RGC proliferation have remained so far unexplored, especially to CNTF affinity to the scaffold and subsequent RGC fate. Electrospun poly(glycerol sebacate)/poly(ϵ-caprolactone) (PGS/PCL) biopolymer scaffolds have recently shown promising results in terms of supporting regeneration of RGC neurites. This work explores covalent immobilization of CNTF on PGS/PCL scaffold and the way immobilised CNTF mediates growth of RGC axons on the scaffold. An ex-vivo three-dimensional model of rodent optic nerve on PGS/PCL revealed that RGC explants cultured in CNTF mediated environment increased their neurite extensions after 20 d of cell culture employing neurite outgrowth measurements. The CNTF secretion on PGS/PCL scaffold was found bio-mimicking natural extracellular matrix of the cell target tissue and, consequently, has shown a potential to improve the overall efficacy of the RGC regeneration process.
Inorganic nanocarriers for siRNA delivery for cancer treatments
Authors: Kandasamy Ganeshlenin , Maity Dipak
Published: January 2024

RNA interference is one of the emerging methodologies utilized in the treatment of a wide variety of diseases including cancer. This method specifically uses therapeutic RNAs (TpRNAs) like small interfering RNAs (siRNAs) to regulate/silence the cancer-linked genes, thereby minimizing the distinct activities of the cancer cells while aiding in their apoptosis. But, many complications arise during the transport/delivery of these TpRNAs that include poor systemic circulation, instability/degradation inside the body environment, no targeting capacity and also low cellular internalization. These difficulties can be overcome by using nanocarriers to deliver the TpRNAs inside the cancer cells. The following are the various categories of nanocarriers—viral vectors (e.g. lentivirus and adenovirus) and non-viral nanocarriers (self-assembling nanocarriers and inorganic nanocarriers). Viral vectors suffer from disadvantages like high immunogenicity compared to the non-viral nanocarriers. Among non-viral nanocarriers, inorganic nanocarriers gained significant attention as their inherent properties (like magnetic properties) can aid in the effective cellular delivery of the TpRNAs. Most of the prior reports have discussed about the delivery of TpRNAs through self-assembling nanocarriers; however very few have reviewed about their delivery using the inorganic nanoparticles. Therefore, in this review, we have mainly focussed on the delivery of TpRNAs—i.e. siRNA, especially programmed death ligand-1 (PD-L1), survivin, B-cell lymphoma-2 (Bcl-2), vascular endothelial growth factor and other siRNAs using the inorganic nanoparticles—mainly magnetic, metal and silica nanoparticles. Moreover, we have also discussed about the combined delivery of these TpRNAs along with chemotherapeutic drugs (mainly doxorubicin) and in vitro and in vivo therapeutic effectiveness.
Fabrication of bioactive glass/phosphorylated chitosan composite scaffold and its effects on MC3T3-E1 cells
Authors: Wenxiu Liu , Guojiang Han , Liying Qin , Wenli Dong , Baoqin Han , Liming Jin , Yan Yang
Published: January 2024

This study aimed to synthesize bioactive glass (BG) and phosphorylated chitosan (PCS), and fabricate a BG/PCS composite scaffold. The physical properties (mechanical strength, swelling degree, and degradation rate) of the BG/PCS scaffold were tested. The in vitro mineralization properties of composite scaffolds in simulated body fluid were investigated. MC3T3-E1 cell responses with the BG/PCS scaffold were investigated using live/dead cell staining, actin staining, alkaline phosphatase (ALP) activity, and Alizarin red staining. Our results showed that the scaffold had an inner porous structure, good swelling properties, and good degradation rate. After immersion in SBF, the scaffolds demonstrated high properties in inducing mineralization. Leaching solutions of the composite scaffolds exhibited good cytocompatibility. MC3T3-E1 cells adhered, spread, and proliferated on the scaffold. The BG/PCS composite scaffold showed osteo-inductive activity by increasing ALP activity and calcium deposition. Our results indicated that the BG/PCS scaffold had potential applications as a bone-defect repair biomaterial.
Mesoporous silica nanoparticles accommodating electrospun nanofibers as implantable local drug delivery system processed by cold atmospheric plasma and spin coating approaches
Authors: Erdoğan Nursu , Şen Karaman Didem , Yıldız Özlem , Özdemir Gizem Dilara , Ercan Utku Kürşat
Published: January 2024

Nanofibers (NF) and nanoparticles are attractive for drug delivery to improve the drug bioavailability and administration. Easy manipulation of NF as macroscopic bulk material give rise to potential usages as implantable local drug delivery systems (LLDS) to overcome the failures of systemic drug delivery systems such as unmet personalized needs, side effects, suboptimal dosage. In this study, poly(ethylene glycol) polyethyleneimine (mPEG:PEI) copolymer blended poly ϵ-caprolactone NFs, NFblend accommodating mesoporous silica nanoparticles (MSN) as the implantable LLDS was achieved by employing spin coating and cold atmospheric plasma (CAP) as the post-process for accommodation on NFblend. The macroporous morphology, mechanical properties, wettability, and in vitro cytocompatibility of NFblend ensured their potential as an implantable LLDS and superior features compared to neat NF. The electron microscopy images affirmed of NFblend random fiber (average diameter 832 ± 321 nm) alignments and accessible macropores before and after MSN@Cur accommodation. The blending of polymers improved the elongation of NF and the tensile strength which is attributed as beneficial for implantable LLDS. CAP treatment could significantly improve the wettability of NF observed by the contact angle changes from ∼126° to ∼50° which is critical for the accommodation of curcumin-loaded MSN (MSN@Cur) and in vitro cytocompatibility of NF. The combined CAP and spin coating as the post-processes was employed for accommodating MSN@Cur on NFblend without interfering with the electrospinning process. The post-processing aided fine-tuning of curcumin dosing (∼3 µg to ∼15 µg) per dose unit and sustained zero-order drug release profile could be achieved. Introducing of MSN@Cur to cells via LLDS promoted the cell proliferation compared to MSN@Cur suspension treatments and assigned as the elimination of adverse effects by nanocarriers by the dosage form integration. All in all, NFblend-MSN@Cur was shown to have high potential to be employed as an implantable LLDS. To the best of our knowledge, this is the first study in which mPEG:PEI copolymer blend NF are united with CAP and spin coating for accommodating nano-drug carriers, which allows for NF both tissue engineering and drug delivery applications.
Future fire-PM2.5 mortality varies depending on climate and socioeconomic changes
Authors: Park Chae Yeon , Takahashi Kiyoshi , Fujimori Shinichiro , Phung Vera Ling Hui , Li Fang , Takakura Jun’ya , Hasegawa Tomoko , Jansakoo Thanapat
Published: January 2024

Fire emits hazardous air pollutants, the most dominant of which is fine particulate matter of diameter ⩽2.5 μm (PM2.5). PM2.5 is a great concern due to its adverse effects on public health. Previous studies have examined the health burden from fire-related PM2.5 for the historical period; however, future global mortality associated with fire-PM2.5, particularly under the coexisting impacts of climate and socioeconomic changes, is yet to be projected. Here, we estimated the mortality associated to fire-PM2.5 (fire-PM2.5 mortality) for the present period (2010s) and then projected the mortality for the 2050s and 2090s under 10 scenarios created by combining two Representative Concentration Pathways (RCP2.6 or 6.0) with five Shared Socioeconomic Pathways (SSP1–5). We used the Li-Park fire model in combination with a chemical transport model and health risk assessment to calculate fire-PM2.5 mortality. For the present period, the estimated fire-PM2.5 mortality was 135 180 (105 403–163 738), which is 1.7 deaths per 100 000 population globally. When countries were grouped by income, the fire-PM2.5 mortality rate was the highest in the high-income country group and lowest in the lowest-income country group. For the 2050s and 2090s, the fire-PM2.5 mortality rate was projected to decrease under most scenarios because of decreases in fire emissions and baseline mortality rate. However, a scenario of high population growth and low technical development (SSP3) together with severe global warming (RCP6.0) would lead to an increase in the fire-PM2.5 mortality rate in the 2090s, particularly in the highest-income countries, due to increased fire under drier and warmer weather conditions. Stratification of countries by gross domestic product indicated the need for adaptation efforts in the highest-income countries to avoid future increases of mortality associated with fire-PM2.5.
Thermally activated escape rate and dynamics of a particle under a harmonic potential
Authors: Abebe Yoseph , Birhanu Tibebe , Bassie Yigermal
Published: January 2024

In this paper, we study the dynamics of particles along a semiconductor layer by imposing a confinement potential assisted by both thermal noise strength D and trap potential ϕ. By applying a nonhomogeneous cold temperature alongside the uniform background temperature, the system is driven towards a phase transition. When a weak signal is pass across a semiconductor layer, the thermally activated particles become easily hop from one lattice site to another lattice site. We perform a numerical simulation of the trajectory of a particle under a harmonic potential represents a bistable and tristable effective potential as a function of thermal noise. As a result, at an optimal level of noise, the particle synchronizes with a weak periodic signal.
Elliptical vibration chiseling: a novel process for texturing ultra-high-aspect-ratio microstructures on the metallic surface
Authors: Li Zhiwei , Zhang Jianfu , Zheng Zhongpeng , Feng Pingfa , Yu Dingwen , Wang Jianjian
Published: January 2024

Highlights

Elliptical vibration chiseling is proposed based on a game-changing process principle for the high-efficient texturing of ultrahigh-aspect-ratio surface microstructures.

Uniformed microstructures with an aspect ratio of 2–12 in the spacing scale of 1–10 μm have been successfully fabricated using elliptical vibration chiseling.

The developed process model of elliptical vibration chiseling has been verified by the measured results of the microstructures’ geometric parameters.

An inclined elliptical trajectory of tool vibration is more suitable for elliptical vibration chiseling than the standard elliptical trajectory.

The deterministic process effects on the surface generation of microstructure in elliptical vibration chiseling have been demonstrated.
Role of structural asymmetry on the delivery of all-optical logical binary half adder in an asymmetric triple core photonic crystal fiber
Authors: Uthayakumar T , Nallamuthu N , Madhu A , Srinatha N
Published: January 2024

This article explores the influence of structural asymmetry on the delivery of all-optical logical binary half adder function through triple-core photonic crystal fiber. For the proposed aim, the study considers different configurations of symmetric as well as asymmetric triple-core photonic crystal fiber involving optical guiding cores arranged in a planar and triangular fashion. The role of geometrical asymmetry is investigated by considering an asymmetric triple core photonic crystal fiber with a minor variation in one of the guiding core radii. Through the extinction ratio calculations, with suitable input signal combinations and control signal power, the half adder operation is demonstrated via logic outputs. The obtained results show the significant role of geometrical asymmetry indicated by the variation in the extinction ratios for the individual configurations. However, the half adder operation is found to be robust even in the presence of considerable geometrical asymmetry, with a significant figure of merit. Apart from this, a minor shift in the control signal phase is also observed between symmetric and asymmetric configurations for delivering logic gates based on the half adder function.
Design and control of LSTM-ANN controllers for an efficient energy management system in a smart grid based on hybrid renewable energy sources
Authors: Wesley Bhukya John , Babu G Suresh , Kumar P Satish
Published: January 2024

Many isolated locations, including hilly areas, remote sites, and military camps, lack feasible access to the main power grid. In these conditions, locally established Microgrids can provide the necessary power supply. However, to meet the demands of these isolated areas, numerous individual Microgrids are required. Although some of these Microgrids might be integratable, geographical constraints may preclude full integration. Under these circumstances, the establishment of a smart grid—integrating multiple Microgrids with a battery management system—can potentially solve many power supply issues. A smart grid control system paired with a centralized battery management system is proposed in this paper. The system considers the use of multiple renewable energy sources at various locations for stable and reliable power generation. The proposed method incorporates a long short-term memory (LSTM)-based artificial neural network (ANN) to ensure a stable, high-quality power supply at different load buses. Additionally, this work introduces an artificial intelligence-based operating system designed to maintain energy management under various conditions. To enhance voltage quality, a 7-level aligned multilevel inverter is incorporated into the system. As compared with PI and Fuzzy controllers, the proposed method with LSTM-ANN controller is improved the power quality under sudden changes in the system which are also presented in results, Voltage variation of PI, Fuzzy, and LSTM-ANN is 370V,180V,and 70V . The effectiveness of the proposed energy management system (EMS) is verified by using a hardware-in the-loop approach with OPAL-RT modules, yielding realistic results.
Three distinct metabolic phases of polychlorinated biphenyls/biphenyl degrader Acidovorax sp. KKS102 in nutrient broth
Authors: Sakai Keiichiro , Kishida Kouhei , Matsumoto Satoshi , Nagata Yuji , Tsuda Masataka , Ohtsubo Yoshiyuki
Published: January 2024

Acidovorax sp. KKS102 is a beta-proteobacterium capable of degrading polychlorinated biphenyls (PCBs). In this study, we examined its growth in liquid nutrient broth supplemented with different carbon sources. KKS102 had at least 3 distinct metabolic phases designated as metabolic phases 1-3, with phase 2 having 2 sub-phases. For example, succinate, fumarate, and glutamate, known to repress the PCB/biphenyl catabolic operon in KKS102, were utilized in phase 1, while acetate, arabinose, and glycerol in phase 2, and glucose and mannose in phase 3. We also showed that the BphQ response regulator mediating catabolite control in KKS102, whose expression level increased moderately through the growth, plays important roles in carbon metabolism in phases 2 and 3. Our study elucidates the hierarchical growth of KKS102 in nutrient-rich media. This insight is crucial for studies exploiting microbial biodegradation capabilities and advancing studies for catabolite regulation mechanisms.
Wild bumblebees use both absolute and relative evaluation when foraging
Authors: Hemingway Claire T , Pimplikar Smruti , Muth Felicity
Published: January 2024

Foraging theory assumes that animals assess value based on objective payoffs; however, animals often evaluate rewards comparatively, forming expectations based on recent experience. This form of evaluation may be particularly relevant for nectar foragers such as bumblebees, where individuals can visit thousands of flowers daily that vary in nectar quality. While many animals, including bees, demonstrate reference-based evaluation in experimental contexts, it is unclear whether this occurs in the wild. Here, we asked how daily experience with wildflower nectar influenced wild bumblebees’ reward evaluation. We measured the daily nectar concentration of bee-visited wildflowers (Penstemon spp.), before presenting foragers with conspecific flowers filled with a range of artificial nectar concentrations. We recorded bees’ acceptance of artificial nectar, the probability of subsequent visits to flowers on the same plant, and residence time. While bees had a minimum threshold of nectar acceptability that was unaffected by experience, when there was higher-concentration environmental nectar, they were less likely to accept lower-quality rewards on manipulated plants. Bees also visited more flowers and stayed longer on plants with higher-concentration nectar. This study shows evidence for both absolute and reference-based evaluation in wild bees and points towards differences between bees’ behavior in lab- and wild-foraging contexts.
MulinforCPI: enhancing precision of compound–protein interaction prediction through novel perspectives on multi-level information integration
Authors: Nguyen Ngoc-Quang , Park Sejeong , Gim Mogan , Kang Jaewoo
Published: January 2024

Forecasting the interaction between compounds and proteins is crucial for discovering new drugs. However, previous sequence-based studies have not utilized three-dimensional (3D) information on compounds and proteins, such as atom coordinates and distance matrices, to predict binding affinity. Furthermore, numerous widely adopted computational techniques have relied on sequences of amino acid characters for protein representations. This approach may constrain the model’s ability to capture meaningful biochemical features, impeding a more comprehensive understanding of the underlying proteins. Here, we propose a two-step deep learning strategy named MulinforCPI that incorporates transfer learning techniques with multi-level resolution features to overcome these limitations. Our approach leverages 3D information from both proteins and compounds and acquires a profound understanding of the atomic-level features of proteins. Besides, our research highlights the divide between first-principle and data-driven methods, offering new research prospects for compound–protein interaction tasks. We applied the proposed method to six datasets: Davis, Metz, KIBA, CASF-2016, DUD-E and BindingDB, to evaluate the effectiveness of our approach.
Structural coverage of the human interactome
Authors: Kosoglu Kayra , Aydin Zeynep , Tuncbag Nurcan , Gursoy Attila , Keskin Ozlem
Published: January 2024

Complex biological processes in cells are embedded in the interactome, representing the complete set of protein–protein interactions. Mapping and analyzing the protein structures are essential to fully comprehending these processes’ molecular details. Therefore, knowing the structural coverage of the interactome is important to show the current limitations. Structural modeling of protein–protein interactions requires accurate protein structures. In this study, we mapped all experimental structures to the reference human proteome. Later, we found the enrichment in structural coverage when complementary methods such as homology modeling and deep learning (AlphaFold) were included. We then collected the interactions from the literature and databases to form the reference human interactome, resulting in 117 897 non-redundant interactions. When we analyzed the structural coverage of the interactome, we found that the number of experimentally determined protein complex structures is scarce, corresponding to 3.95% of all binary interactions. We also analyzed known and modeled structures to potentially construct the structural interactome with a docking method. Our analysis showed that 12.97% of the interactions from HuRI and 73.62% and 32.94% from the filtered versions of STRING and HIPPIE could potentially be modeled with high structural coverage or accuracy, respectively. Overall, this paper provides an overview of the current state of structural coverage of the human proteome and interactome.
Subset scanning for multi-trait analysis using GWAS summary statistics
Authors: Cao Rui , Olawsky Evan , McFowland Edward , Marcotte Erin , Spector Logan , Yang Tianzhong
Published: January 2024

Motivation

Multi-trait analysis has been shown to have greater statistical power than single-trait analysis. Most of the existing multi-trait analysis methods only work with a limited number of traits and usually prioritize high statistical power over identifying relevant traits, which heavily rely on domain knowledge.

Results

To handle diseases and traits with obscure etiology, we developed TraitScan, a powerful and fast algorithm that identifies potential pleiotropic traits from a moderate or large number of traits (e.g. dozens to thousands) and tests the association between one genetic variant and the selected traits. TraitScan can handle either individual-level or summary-level GWAS data. We evaluated TraitScan using extensive simulations and found that it outperformed existing methods in terms of both testing power and trait selection when sparsity was low or modest. We then applied it to search for traits associated with Ewing Sarcoma, a rare bone tumor with peak onset in adolescence, among 754 traits in UK Biobank. Our analysis revealed a few promising traits worthy of further investigation, highlighting the use of TraitScan for more effective multi-trait analysis as biobanks emerge. We also extended TraitScan to search and test association with a polygenic risk score and genetically imputed gene expression.

Availability and implementation

Our algorithm is implemented in an R package “TraitScan” available at https://github.com/RuiCao34/TraitScan.
Rapid emergence of recalcitrant dermatophytosis caused by a cluster of multidrug-resistant Trichophyton indotineae in China
Authors: Xie Wenting , Kong Xue , Zheng Hailin , Mei Huan , Ge Naicen , Hu Suquan , Wang Qiong , Huang Yuying , She Xiaodong , Liu Weida , Liang Guanzhao , Li Xiaofang
Published: January 2024

We describe 14 cases of native refractory dermatophytes caused by Trichophyton indotineae diagnosed at a hospital in China since 2021, primarily diagnosed in the past 1 year and from the same province. Trichophyton indotineae isolates were resistant to multiple antifungals and harboured Phe397Leu or Leu393Ser substitutions in the squalene epoxidase enzyme. Short-term rapid emergence of multidrug-resistant T. indotineae in China poses increasing threats to public safety and warrants continued public health surveillance.
Long-term outcomes after appendicectomy as experimental treatment for patients with therapy-refractory ulcerative colitis
Authors: Reijntjes Maud A , Heuthorst Lianne , Stellingwerf Merle E , D’Haens Geert R , Bemelman Wilhelmus A , Buskens Christianne J
Published: January 2024

This study assessed 25 patients with severe ulcerative colitis undergoing appendicectomy. During a median postoperative follow-up of 7.5 years, the median duration of clinical response, as observed in 15 patients, was 80 months; the median duration of endoscopic improvement, as observed in 12 of patients, was 46 months.
Time trends and geographical variation in major lower limb amputation related to peripheral arterial disease in England
Authors: Maheswaran Ravi , Tong Thaison , Michaels Jonathan , Brindley Paul , Walters Stephen , Nawaz Shah
Published: January 2024

Background

Above and below knee amputation (AKA, BKA) are treatments of last resort for peripheral arterial disease (PAD). The aim was to examine amputation rates, AKA:BKA ratios, previous revascularization and minor amputation, lengths of stay in hospital, mortality following amputation, and regional variation in people with and without diabetes in England.

Methods

The study used population-based ecological and cohort study designs, 31 672 census areas, hospital admissions from 2006 to 2018 and Poisson, logistic and Cox regression.

Results

There were 47 249 major lower limb amputations (50.7% AKA; 48% had diabetes), giving an annual PAD-related amputation rate of 11 per 100 000 in the population aged 25+ years. Amputation rates were higher in men and substantially higher in people with diabetes. The AKA:BKA ratio was 0.63 in patients with diabetes (n = 22 702) and 1.62 in patients without diabetes (n = 24 547). Of patients having AKA, 25.3% died within 90 days of amputation compared with 11.9% for BKA. Median survival following amputation ranged from only 1.68 years following AKA in patients with diabetes to 5.72 years following BKA in patients without diabetes. Amputation rates decreased over time mainly in the population with diabetes. Short-term mortality and lengths of stay in hospital also decreased over time, while the percentage with previous revascularization generally increased. Amputation rates and AKA:BKA ratios were highest in the North. Adjustment for age, sex and deprivation did not substantially alter geographical patterns. Adjusted 90-day mortality was generally higher in the North and the Midlands but also high in London. There were also regional variations in adjusted duration from admission to amputation, duration from amputation to discharge or death in hospital, previous revascularization and previous minor amputation.

Conclusions

There were large variations in amputation rates and survival following amputation in relation to diabetes status and amputation level, and regional variations which remained after adjustment for deprivation.
Living with a rare disease: a patient perspective of life with trimethylaminuria
Authors: Quigley Claire , Loftus Clodagh , Clowry Julianne , Irvine Alan D
Published: January 2024

A 45-year-old woman provides her perspective on living with a rare disorder, trimethylaminuria, also known as ‘fish odour syndrome’. She describes the negative quality-of-life impact this diagnosis has had on her life, and feeling misunderstood and isolated with this diagnosis.