bluuebunny/crossref_metadata_2025 huggingface dataset:
Stimulated Brillouin scattering in plasmonic nanofiber containing an ensemble of metallic nanorods
Authors: Singh Mahi R , Caruso Emma
Published: October 2024

A theory of stimulated Brillouin scattering (SBS) has been developed for metallic nanohybrid fiber, which is made of an ensemble of metallic nanoparticles doped in a dielectric nanofiber. We consider that input probe light photons scatter within the nanohybrid and produce stimulated Brillouin scattered photons and acoustic phonons. The coupled-mode formalism based on Maxwell’s equations is used to obtain the SBS intensity, the SBS energy, and the SBS absorption coefficient. It is found that the SBS depends on the third-order susceptibility, which is evaluated by the density matrix method. An analytical expression of the SBS intensity, energy, and absorption coefficient is calculated in the presence of surface plasmon polaritons (SPPs) and dipole-dipole interactions (DDI) between nanoparticles in the ensemble. Next, we have compared our theory with the experimental data for a nanohybrid made of an ensemble of Au-nanorods doped in water. A good agreement between theory and experiment is found. We have also performed the numerical simulations to study the effect of SPP and DDI fields on the SBS intensity. We have predicted an enhancement in the SBS intensity due to the SPP and DDI couplings. The enhancement is due to not only the scattering mechanisms of the probe photons with acoustic phonons but also the extra scattering mechanisms from the SPP and DDI polaritons with acoustic phonons. The SBS analytical expressions can be useful for experimental scientists and engineers who can use them to plan new experiments and make new types of plasmonic devices. The enhancement effect can be used to fabricate new types of SBS nanosensors and amplifiers.
Translated object identification for efficient ghost imaging
Authors: Ruget Alice , Moodley Chané , Forbes Andrew , Leach Jonathan
Published: October 2024

Alignment of a single-pixel quantum ghost imaging setup is complex and requires extreme precision. Due to misalignment, easily created by human error in the alignment process, reconstructed images are often translated off the central imaging axis. This becomes problematic for intelligent object detection and identification in fast imaging cases, as these algorithms are unable to achieve early image identification. Here, we implemented a U-net algorithm to correctly recognize images in the early reconstruction stage regardless of any off-axis translation. The U-net was trained on a uniquely curated blurred, noised, and off-axis translated dataset. We achieved a 5× reduction in imaging speeds by early image identification in four different translation directions.
Tunable dual-band unidirectional reflectionlessness in a one-dimensional waveguide-cavity optomechanical system
Authors: Sun Xue , Zhang Ying-Qiao , Jin Xing-Ri
Published: October 2024

Tunable dual-band unidirectional reflectionless phenomena in a one-dimensional waveguide coupled with a cavity optomechanical system driven by external driving fields were investigated. The results indicated that dual-band unidirectional reflectionlessnesses can be obtained by appropriately adjusting the strengths of the external driving fields, phase shift between the two optical cavities, coupling strengths of the optical cavities to the waveguide and decay rates of the two cavities and mechanical resonators. Moreover their peaks can be tuned by changing both the effective optomechanical coupling strengths and phase shift, which can achieve unidirectional reflectionlessness by adjusting the external driving fields when the phase shift is difficult to adjust precisely. This work provides a well theoretical reference for the research and development of quantum optical devices such as optical diodes, switches, and isolators.
Spiral integrated optical phased arrays for tunable near-field-focusing emission
Authors: DeSantis Daniel M. , Torres Michael R. , Garcia Coleto Andres , Mazur Benjamin M. , Corsetti Sabrina , Notaros Milica , Notaros Jelena
Published: October 2024

Integrated optical phased arrays (OPAs) have enabled cutting-edge applications where optical beam steering can benefit from chip-scale integration. However, the majority of integrated OPA demonstrations to date have been limited to showing far-field beam forming and steering. There are, however, many emerging applications of integrated photonics where emission of focused light from a chip is desirable, such as in integrated optical tweezers for biophotonics, chip-based 3D printers, and trapped-ion quantum systems. To address this need, we have recently demonstrated the first near-field-focusing integrated OPAs; however, this preliminary demonstration was limited to emission at only one focal plane above the chip. In this paper, we show the first, to the best of our knowledge, spiral integrated OPAs, enabling emission of focusing beams with tunable variable focal heights for the first time. In the process, we develop the theory, explore the design parameters, and propose feed-structure architectures for such OPAs. Finally, we experimentally demonstrate an example spiral integrated OPA system fabricated in a standard silicon-photonics process, showing wavelength-tunable variable-focal-height focusing emission. This work introduces a first-of-its-kind integrated OPA architecture not previously explored or demonstrated in literature and, as such, enables new functionality for emerging applications of OPAs that require focusing operation.
Ultraviolet to mid-infrared optical properties of sputtered Al(Sc)N-on-SiO2 thin films and experimental demonstration of AlN integrated photonic devices in the telecom C-band
Authors: Spettel Jasmin , Andrianov Nikolai , Dubois Florian , Azeem Munir , Furci Hernán , Cassese Tommaso , Quack Niels , Villanueva Guillermo , Moridi Mohssen , Dao Thang Duy
Published: October 2024

Thin film aluminum nitride (AlN) stands out as a promising material for integrated photonics due to its wide bandgap of 6.1 eV, facilitating efficient operation across diverse spectral ranges. Its inherent electro-optic and nonlinear optical properties make it exceptionally well suited for active photonic components. Compatibility with CMOS technology further strengthens its appeal. Doping AlN with scandium (Sc) in non-centrosymmetric configurations significantly enhances its nonlinear and piezoelectric characteristics. This study explores Al(Sc)N thin films on silicon dioxide (SiO2), investigating optical properties in a broad wavelength range from 0.19 µm to 25 µm. Comprehensive material analysis of sputtered Al(Sc)N films and fabrication techniques for AlN integrated photonic devices demonstrated here highlight AlScN's potential in integrated photonic applications.
Fiber-optic radio frequency transfer with enhanced frequency stability using fiber Brillouin amplifiers
Authors: Ren Junwei , Hu Liang , Chen Jianping , Wu Guiling
Published: October 2024

The frequency stability of long-distance two-way fiber-optic radio frequency (RF) transfer is directly affected by the optical signal-to-noise ratio (OSNR) of optical amplifiers. In this paper, we have proposed a stimulated Brillouin scattering (SBS)-based optical amplification scheme with high OSNR for two-way fiber-optic RF frequency transfer over single mode fibers (SMF). At the remote and local site, the modulated carrier transferred from the opposite was amplified and then frequency upshifted by Brillouin frequency shift (BFS) for pump generation. This approach can avoid the use of additional pump lasers and phase-locked loops for wavelength stabilization of the pump. The pump was injected into the fiber link and counter-propagated with the signal to amplify the modulated carrier. A 2.2 GHz RF signal transfer with the proposed SBS-based optical amplification schemes was demonstrated over a 100 km fiber link. The experimental results illustrated that the OSNR was increased by 35 dB and 32 dB at the local site and the remote site, respectively, compared to the results obtained with erbium-doped fiber amplifiers (EDFA)-based optical amplification. Benefiting from improved OSNR, the frequency stability was increased by more than one order of magnitude below 1000 s averaging time, and the phase noise was reduced to the noise floor below 0.1 Hz offset frequency. The proposed optical signal amplification approach has a potential application for transferring atomic clocks over long-haul fiber links.
Red emission enhancement in BaYF5:Eu3+ phosphor nanoparticles by Bi3+ co-doping
Authors: Milenković Katarina , Đačanin Far Ljubica , Kuzman Sanja , Antić Željka , Ćirić Aleksandar , Dramićanin Miroslav D. , Milićević Bojana
Published: October 2024

Herein, we report the photoluminescence properties of Bi3+-sensitized BaYF5:10 mol%Eu3+ nanoparticles. The emission spectra feature Eu3+ peaks corresponding to transitions from the 5D0 excited to 7FJ (J = 1, 2, 3, 4) lower levels with two dominant emissions positioned in the orange-red (∼ 592 nm, 5D0 → 7F1) and deep-red (∼ 697 nm, 5D0 → 7F4) regions. Upon 265 nm excitation, the emission intensity increases with an increase of Bi3+ concentration up to 20 mol%. Due to the energy transfer from Bi3+ to Eu3+ ions, the integrated intensity of Eu3+ emission in the Bi3+ co-doped BaYF5:10 mol%Eu3+ is 216% stronger than in the Bi3+-free sample. Our findings demonstrated that BaYF5:Eu,Bi has potential in plant lighting technology due to strong emission in red and deep-red spectral areas.
Continous-wave and passively Q-switched laser at 1.36 µm of a Nd3+-doped phosphate fiber with a Yb3+-doped inner cladding
Authors: Wang Yafei , Sun Yan , Wang Xin , Shao Chongyun , Zhang Lei , Wang Shikai , Chen Danping , Yu Chunlei , Hu Lili
Published: October 2024

All-fiber continuous-wave (CW) and passively Q-switched lasers at 1.36 µm (4F3/2 → 4I13/2) by a Nd3+-doped double cladding phosphate fiber are demonstrated for the first time, to the best of our knowledge. To suppress the competitive 0.9 and 1.05 µm emission, the Yb3+ ions are intentionally introduced into the inner cladding of this Nd3+-doped fiber. CW laser at 1.36 µm with a signal-to-noise ratio over 50 dB is realized by using two fiber-type dielectric films as cavity mirrors. A 4.0% CW laser efficiency is obtained when the Nd3+-doped fiber length is 33 mm. The emission at 0.9 and 1.05 µm is well-suppressed, and no parasitic laser is observed. Taking a commercial semiconductor saturable absorber (SA) mirror as the SA, the compact 1.36-µm Q-switched laser is demonstrated, and the repetition rate of output pulses can be tuned from 230 to 522 kHz with a narrowest pulse duration of 152 ns. Our results may provide a promising way to realize 1.3 µm laser oscillation in Nd3+-doped fibers.
High-sensitivity pump-probe spectroscopy with a dual-comb laser and a PM-Andi supercontinuum
Authors: Gruber Christoph , Pupeikis Justinas , Camenzind Sandro L. , Willenberg Benjamin , Camargo Franco V. A. , Lang Lukas , Hamm Peter , Rampur Anupamaa , Heidt Alexander , Phillips Christopher R. , Cerullo Giulio , Keller Ursula
Published: October 2024

Amplifier-based pump-probe systems, while versatile, often suffer from
complexity and low measurement speeds, especially when probing samples
require low excitation fluences. To address these limitations, we
introduce a pump-probe system that leverages a 60-MHz single-cavity
dual-comb oscillator and an ultra-low noise supercontinuum. The setup
can operate in equivalent time sampling or in programmable optical
delay generation modes. We employ this system to study the
wavelength-dependent excited-state dynamics of the non-fullerene
electron acceptor Y6, a compound of interest in solar cell
development, with excitation fluences as low as
1 nJ/cm2, well below the onset of nonlinear exciton
annihilation effects. Our measurements reach a shot-noise limited
sensitivity in differential transmission of
3.4·10–7. The results demonstrate the
system’s potential to advance the field of ultrafast
spectroscopy.
Ptychographic Mueller matrix imaging (PMMI): principle and proof-of-concept demonstration
Authors: Gong Ming , Liu Li , Du Jinxiang , Zhuang Bailin , Liu Jiamin , Gu Honggang , Liu Shiyuan
Published: October 2024

Quantitative characterization of optical anisotropies is extremely important for wide fields and applications. The Mueller matrix, providing all the polarization-related properties of a medium, is a powerful tool for the comprehensive evaluation of optical anisotropies. Here, we propose a ptychographic Mueller matrix imaging (PMMI) technique, which features the Mueller matrix polarization modulation being introduced into the ptychography. The ptychographic reconstruction is performed for each polarization state, and the Mueller matrix can be determined from the reconstructed polarization-modulated amplitude images. A proof-of-concept of the proposed PMMI is implemented, and both simulations and experiments are conducted to demonstrate the validity of the method. Results indicate that the imaging resolution of the home-built PMMI apparatus achieves 1.550 µm at the wavelength of 633 nm, which is of the highest level for the Mueller matrix imaging to the best of our knowledge. A customized birefringent specimen is characterized, and both retardance and axis azimuth are quantitatively evaluated.
Merging bound states in the continuum-driven ultrahigh sensing figure of merit in all-dielectric metasurfaces
Authors: Li Chun , Gao Xiaomei , Deng Xinyi , Guo Jiaqi , Shen Chao , Zhang Qing
Published: October 2024

Radiation-free photonic bound states in the continuum (BIC) in metasurfaces allow ultrahigh quality (Q) factor and strongly confined mode volume, which are extremely advantageous in the development of ultrasensitive microcavity sensors. However, the conventional isolated BICs are susceptible to failure due to symmetry breaking caused by fabrication imperfection and nonzero incident angle. Here, we propose a silicon nitride-based metasurface with multiple BIC merging. The merging of accidental BIC and symmetry-protected BIC can increase the Q-factor near the Brillouin zone Γ point and thus robustly induces a figure of merit (FOM) of refractive index sensing at small incident angles two orders of magnitude higher than that in isolated BIC configuration. Specifically, the FOM in merging BIC reaches 108 at a 2° incident angle. The BIC merging can be universally achieved in square lattices with C4 symmetry, and slower decay of Q-factor and higher FOM can further occur in hexagonal lattices benefiting from higher-order topological charges. The advantage of merging BIC is also maintained when considering in-plane and out-of-plane symmetry breaking. These results offer a unique design path for high-performance metasurface sensors and can be extended to other high-Q applications such as low-threshold lasers, nonlinear frequency conversion, and low-loss waveguides.
All-optical image transmission through a dynamically perturbed multimode fiber and a ring-core fiber using diffractive deep neural networks
Authors: Zhu Jianping , Zhu Lei , Gao Ran , Wang Xishuo , Ren Jianxin , Chen Shuaidong , Jing Zexuan , Li Zhipei , Hu Shanting , Tian Qinghua , Tian Bo , Chang Huan , Guo Dong , Pan Xiaolong , Wu Zheyu , Xin Xiangjun , Liu Bo
Published: October 2024

In this study, we present an all-optical image reconstruction technique leveraging a diffractive deep neural network (D2NN) within a ring-core fiber (RCF) architecture. Orbital angular momentum (OAM) modes are employed to facilitate imaging transmission. We experimentally validate the efficacy of our approach for complex field diffractive image reconstruction through a multimode fiber (MMF) and RCF at a 1550 nm operating wavelength. The experimental results demonstrate the superior performance of the proposed method in mitigating RCF scattering-to-restoration transformation issues, significantly outperforming traditional MMF-based imaging correction techniques.
Heterogeneous polarization-integrated medium wave infrared HgCdTe focal plane array detector with pixel-wise Al gratings
Authors: Wang Weiping , Liu Shuai , Li Nan , Xu Jiuzhi , Hu Xiaoyan
Published: October 2024

Real-time polarization imaging plays a crucial role in camouflaged target detection. However, large optical crosstalk restricts the development of polarization-integrated detectors. A HgCdTe focal plane array detector heterogeneously integrated with a pixel-wise polarizer is proposed that can suppress the crosstalk by reducing the distance between gratings and photosensitive elements. The light crosstalk between adjacent polarization pixels, found to be mainly caused by the diffraction of a polarization grating pixel, was studied as a function of polarization pixel size, the alignment error between the grating pixel, and the photosensitive element and incident angle. Based on the analysis, a high depth-to-width ratio of the grating, a proper pixel size, or incorporating trench isolation can improve the extinction ratio of the integrated detector.
Nematic host and alignment layer dependence on monodomain formation in the liquid crystal blue phase
Authors: Chauhan Sumanyu , Cuypers Dieter , Wahle Markus , Lazarev Grigory , De Smet Herbert
Published: October 2024

Blue phases (BPs) of liquid crystals are highly valued in electro-optics for their fast, polarization-independent response and the advantage of not requiring alignment layers. While BP lattices do not need to be aligned to substrates, doing so can improve their electro-optic performance. Traditionally, rubbed polyimide films have been the preferred method for inducing monodomains in BPs. This study, using polarized optical microscopy, explores various BP compositions with different nematic hosts, chiral dopant concentrations, and alignment layer combinations, including polyimide, surfactants, and obliquely evaporated SiOx. The results show that while rubbed polyimide is effective for many BP compositions, it is not always the optimal choice for inducing monodomains. The research highlights that inorganic alignment methods can be more effective for BP compositions consisting of specific nematic hosts.
Tapered coreless optical fiber-based refractive index sensor for acetone concentration detection
Authors: Kadhum Yosra Hussain , Salman Ansam M. , Al-Janabi Abdulhadi
Published: October 2024

A fast-response optical fiber sensor is designed and fabricated to detect different concentrations of volatile acetone. The proposed sensor structure was fabricated by splicing a segment of tapered coreless fiber (CLF) amid two single-mode fibers (SMF). Herein, tuned tapered diameters and lengths of CLF’s cladding were immersed in various concentrations of the acetone solutions to sense the effective refractive index (RI) variations. Accordingly, the sensor’s performance with tuned diameters at different lengths of the CLF was optimized to realize the suitable size of amplified evanescent fields. The sensor responded remarkably towards acetone concentrations, with a superior sensitivity of 336.102 nm/RIU, 0.163 nm/%, and 27.531 × 10−5 nm/ppm at 5 cm length and 60 µm taper diameter of CLF. The examined sensor possesses a fast response time with a minimum detection limit of 0.244 RIU, 5.025%vol, and 2.9 ppm. Though the rapid evaporation (volatility) of the acetone compound exempted it from air pollutants, many industrial and human body processes produce acetone which needs to be detected. The examined sensor may have the potential to detect in a non-invasive approach with high accuracy and rapid diabetes in humans, lung cancer, etc.
Helico-conical vector beams for intensity and polarization 3D light shaping
Authors: Vogliardi Andrea , Bonaldo Daniele , Dal Zilio Simone , Romanato Filippo , Ruffato Gianluca
Published: October 2024

While vector beams offer an intriguing way to structure optical beams and enhance light-based technologies across many fields, their generation remains a challenging task in practical applications. Disclosing an unprecedented manipulation of light at the subwavelength scale, metaoptics have inspired smart and efficient solutions for spatially variant polarization structuring. Concurrently, the generalization of non-separability in polarization and phase manipulation extends the vectorial nature beyond standard vector vortices. In this work, we present the design and test of dual-functional metasurfaces for the compact generation of a new type of vector beam, so-called helico-conical vector beam, providing an inhomogeneous polarization pattern over customizable one-arm or two-arm 3D spirals of light. These devices pave the way to integrated optical architectures for dynamic optical manipulation and trapping in many fields, from optofluidics to quantum computing.
Dispersive Sweatt Model for Broadband Lens Design with Metasurfaces
Authors: Shih Ko-Han , Renshaw Christopher , Chen Weiyu
Published: October 2024

The Sweatt model has been extensively used to design optical systems containing diffractive optical elements (DOEs) because it captures the dispersive characteristics of DOEs. We introduce a new Dispersive Sweatt Model (DSM) that can describe meta-atom (MA) dispersion which has material and geometric contributions in addition to diffraction. It uses a wavelength-dependent scalar coefficient to modify the diffractive dispersion and describe the dispersion of a given MA basis. This provides a robust framework to design systems containing metasurface (MS) elements while including their unique dispersive properties in the design optimization. Importantly, the DSM is based on ray-optics and enables design of MS-containing systems using conventional optical design software such as Zemax and Code V. We use the DSM to demonstrate design of a hybrid refractive/MS achromatic doublet for the midwave infrared (MWIR) band. The design example includes multiple wavelengths and field-angles during optimization and demonstrates excellent agreement between the DSM and real hybrid lens performance modelled using wave-optics. We discuss the limits of the DSM and present a simple model to predict performance limits due to phase mismatch at Fresnel zone boundaries.
Explanation of Aberration of Light Based on the Theory of Absolutely Stationary Reference Frame
Authors: zhou jiajun , Zhou Qinyan
Published: October 2024

Vacuum is an absolutely static reference system. When light propagates in a vacuum, it moves in an absolutely static reference system. The propagation speed of light in a medium is a constant, which has nothing to do with the motion state of the light source, the observer or the receiver. When light propagates in a medium, it is dragged by the inertia of the medium. While light propagates in a vacuum, the vacuum is absolutely static, which cannot drag the light to move, and the speed, position, and direction of light in a vacuum are fixed. (the above viewpoint comes from reference [1],[2],[3],[4]).Based on this theory, the phenomenon of aberration of light can be explained .
So, According to this theory, it can be concluded that aberration of light is not a universal phenomenon but only exists on heavenly bodies with dense atmospheres, which are transparent and in motion. Dense atmospheres can drive light to move, causing the apparent position of heavenly bodies. On the contrary, if a heavenly body is without atmosphere, no aberrations but only parallaxes can be observed.
Low noise InGaAs/InP single-photon detector with DC to 1  GHz tunable gate frequency
Authors: Chen Jia-Lin , He De-Yong , Wang Shuang , Shi Ying-Liang , Geng Jia-Qi , Yin Zhen-Qiang , Chen Wei , Fan-Yuan Guan-Jie , Guo Guang-Can , Han Zheng-Fu
Published: October 2024

An InGaAs/InP single-photon detector (SPD) typically operates in gated mode, but the capacitive response of a single-photon avalanche diode introduces spike noise, obscuring the avalanche signal. Most avalanche signal discrimination schemes cannot completely eliminate spike noise, resulting in residual noise. Limited by residual noise, these schemes have large noise and a limited frequency tuning range. However, for applications like quantum key distribution and laser ranging, a low noise, frequency-tunable InGaAs/InP SPD is crucial for enhancing system performance. Here, we propose a (residual noise assisted) discrimination method that aligns the maximum amplitude of the avalanche signal with the peak of the residual noise. This method turns the residual noise from adversity into an advantage for signal discrimination. With this method, we achieve tunable gating frequency from DC to 1 GHz. Additionally, this method enables the discrimination of weak avalanche signals, allowing effective single-photon detection at low avalanche gain. Across the entire tuning range, at a 20% detection efficiency, the dark count rate is approximately 5.0×10−7 per gate, and the afterpulse probability is less than 1.0%, significantly lower than in previous experiments. The proposed SPD exhibits low noise and a wide tunable gating frequency range, providing a reliable foundation for various applications.
Highly sensitive plasmonic nanoridge hyperbolic metamaterial for biosensing
Authors: Yue Xinzhao , Wang Tao , Cai Yaohua , Yan Ruoqin , Wang Lu , Wang Huimin , Lv Enze , Yuan Xuyang , Zeng Jinwei , Shu Xuewen , Wang Jian
Published: October 2024

Artificially designed hyperbolic metamaterials (HMMs) with extraordinary optical anisotropy can support highly sensitive plasmonic sensing detections, showcasing significant potential for advancements in medical research and clinical diagnostics. In this study, we develop a gold nanoridge HMM and disclose the plasmonic sensing physical mechanism based on this type of HMM through theoretical and experimental studies. We determine that the high modal group velocity of plasmonic guided modes stemming from a large transverse permittivity of HMMs directly results in high sensitivity. By combining electron-beam lithography, oxygen plasma etching, and electroplating, the fabricated gold nanoridge array possesses an extremely high structural filling ratio that is difficult to obtain through conventional processes. This leads to a large transverse permittivity and enables highly confined and ultra-sensitive bulk plasmon–polariton (BPP) guided modes. By exciting these modes in the visible to near-infrared region, we achieve a record sensitivity of 53,300 nm/RIU and a figure of merit of 533. Furthermore, the developed plasmonic nanoridge HMM sensor exhibits an enhanced sensitivity of two orders of magnitude compared to that of the same type of HMM sensor in label-free biomolecule detection. Our study not only offers a promising avenue for label-free biosensing but also holds great potential to enhance early disease detection and monitoring.
scCaT: An explainable capsulating architecture for sepsis diagnosis transferring from single-cell RNA sequencing
Authors: Zheng Xubin , Meng Dian , Chen Duo , Wong Wan-Ki , To Ka-Ho , Zhu Lei , Wu JiaFei , Liang Yining , Leung Kwong-Sak , Wong Man-Hon , Cheng Lixin
Published: October 2024

Sepsis is a life-threatening condition characterized by an exaggerated immune response to pathogens, leading to organ damage and high mortality rates in the intensive care unit. Although deep learning has achieved impressive performance on prediction and classification tasks in medicine, it requires large amounts of data and lacks explainability, which hinder its application to sepsis diagnosis. We introduce a deep learning framework, called scCaT, which blends the capsulating architecture with Transformer to develop a sepsis diagnostic model using single-cell RNA sequencing data and transfers it to bulk RNA data. The capsulating architecture effectively groups genes into capsules based on biological functions, which provides explainability in encoding gene expressions. The Transformer serves as a decoder to classify sepsis patients and controls. Our model achieves high accuracy with an AUROC of 0.93 on the single-cell test set and an average AUROC of 0.98 on seven bulk RNA cohorts. Additionally, the capsules can recognize different cell types and distinguish sepsis from control samples based on their biological pathways. This study presents a novel approach for learning gene modules and transferring the model to other data types, offering potential benefits in diagnosing rare diseases with limited subjects.
Mapping the physiological changes in sleep regulation across infancy and young childhood
Authors: Webb Lachlan , Phillips Andrew J. K. , Roberts James A.
Published: October 2024

Sleep patterns in infancy and early childhood vary greatly and change rapidly during development. In adults, sleep patterns are regulated by interactions between neuronal populations in the brainstem and hypothalamus, driven by the circadian and sleep homeostatic processes. However, the neurophysiological mechanisms underlying the sleep patterns and their variations across infancy and early childhood are poorly understood. We investigated whether a well-established mathematical model for sleep regulation in adults can model infant sleep characteristics and explain the physiological basis for developmental changes. By fitting longitudinal sleep data spanning 2 to 540 days after birth, we inferred parameter trajectories across age. We found that the developmental changes in sleep patterns are consistent with a faster accumulation and faster clearance of sleep homeostatic pressure in infancy and a weaker circadian rhythm in early infancy. We also find greater sensitivity to phase-delaying effects of light in infancy and early childhood. These findings reveal fundamental mechanisms that regulate sleep in infancy and early childhood. Given the critical role of sleep in healthy neurodevelopment, this framework could be used to pinpoint pathophysiological mechanisms and identify ways to improve sleep quality in early life.
Candida albicans pathways that protect against organic peroxides and lipid peroxidation
Authors: Swenson Kara A. , Min Kyunghun , Konopka James B.
Published: October 2024

Human fungal pathogens must survive diverse reactive oxygen species (ROS) produced by host immune cells that can oxidize a range of cellular molecules including proteins, lipids, and DNA. Formation of lipid radicals can be especially damaging, as it leads to a chain reaction of lipid peroxidation that causes widespread damage to the plasma membrane. Most previous studies on antioxidant pathways in fungal pathogens have been conducted with hydrogen peroxide, so the pathways used to combat organic peroxides and lipid peroxidation are not well understood. The most well-known peroxidase in Candida albicans, catalase, can only act on hydrogen peroxide. We therefore characterized a family of four glutathione peroxidases (GPxs) that were predicted to play an important role in reducing organic peroxides. One of the GPxs, Gpx3 is also known to activate the Cap1 transcription factor that plays the major role in inducing antioxidant genes in response to ROS. Surprisingly, we found that the only measurable role of the GPxs is activation of Cap1 and did not find a significant role for GPxs in the direct detoxification of peroxides. Furthermore, a CAP1 deletion mutant strain was highly sensitive to organic peroxides and oxidized lipids, indicating an important role for antioxidant genes upregulated by Cap1 in protecting cells from organic peroxides. We identified GLR1 (Glutathione reductase), a gene upregulated by Cap1, as important for protecting cells from oxidized lipids, implicating glutathione utilizing enzymes in the protection against lipid peroxidation. Furthermore, an RNA-sequencing study in C. albicans showed upregulation of a diverse set of antioxidant genes and protein damage pathways in response to organic peroxides. Overall, our results identify novel mechanisms by which C. albicans responds to oxidative stress resistance which open new avenues for understanding how fungal pathogens resist ROS in the host.
Hybrid Machine Learning Approach to Zero-Inflated Data Improves Accuracy of Dengue Prediction
Authors: Francisco Micanaldo Ernesto , Carvajal Thaddeus M. , Watanabe Kozo
Published: October 2024

Background

Spatiotemporal dengue forecasting using machine learning (ML) can contribute to the development of prevention and control strategies for impending dengue outbreaks. However, training data for dengue incidence may be inflated with frequent zero values because of the rarity of cases, which lowers the prediction accuracy. This study aimed to understand the influence of spatiotemporal resolutions of data on the accuracy of dengue incidence prediction using ML models, to understand how the influence of spatiotemporal resolution differs between quantitative and qualitative predictions of dengue incidence, and to improve the accuracy of dengue incidence prediction with zero-inflated data.

Methodology

We predicted dengue incidence at six spatiotemporal resolutions and compared their prediction accuracy. Six ML algorithms were compared: generalized additive models, random forests, conditional inference forest, artificial neural networks, support vector machines and regression, and extreme gradient boosting. Data from 2009 to 2012 were used for training, and data from 2013 were used for model validation with quantitative and qualitative dengue variables. To address the inaccuracy in the quantitative prediction of dengue incidence due to zero-inflated data at fine spatiotemporal scales, we developed a hybrid approach in which the second-stage quantitative prediction is performed only when/where the first-stage qualitative model predicts the occurrence of dengue cases.

Principal findings

At higher resolutions, the dengue incidence data were zero-inflated, which was insufficient for quantitative pattern extraction of relationships between dengue incidence and environmental variables by ML. Qualitative models, used as binary variables, eased the effect of data distribution. Our novel hybrid approach of combining qualitative and quantitative predictions demonstrated high potential for predicting zero-inflated or rare phenomena, such as dengue.

Significance

Our research contributes valuable insights to the field of spatiotemporal dengue prediction and provides an alternative solution to enhance prediction accuracy in zero-inflated data where hurdle or zero-inflated models cannot be applied.
Music-induced emotion flow modeling by ENMI Network
Authors: Shang Yunrui , Peng Qi , Wu Zixuan , Liu Yinhua
Published: October 2024

The relation between emotions and music is substantial because music as an art can evoke emotions. Music emotion recognition (MER) studies the emotions that music brings in the effort to map musical features to the affective dimensions. This study conceptualizes the mapping of music and emotion as a multivariate time series regression problem, with the aim of capturing the emotion flow in the Arousal-Valence emotional space. The Efficient Net-Music Informer (ENMI) Network was introduced to address this phenomenon. The ENMI was used to extract Mel-spectrogram features, complementing the time series data. Moreover, the Music Informer model was adopted to train on both time series music features and Mel-spectrogram features to predict emotional sequences. In our regression task, the model achieved a root mean square error (RMSE) of 0.0440 and 0.0352 in the arousal and valence dimensions, respectively, in the DEAM dataset. A comprehensive analysis of the effects of different hyperparameters tuning was conducted. Furthermore, different sequence lengths were predicted for the regression accuracy of the ENMI Network on three different datasets, namely the DEAM dataset, the Emomusic dataset, and the augmented Emomusic dataset. Additionally, a feature ablation on the Mel-spectrogram features and an analysis of the importance of the various musical features in the regression results were performed, establishing the effectiveness of the model presented herein.
Distributional hypothesis as isomorphism between word-word co-occurrence and analogical parallelograms
Authors: Torii Takuma , Maeda Akihiro , Hidaka Shohei
Published: October 2024

Most of the modern natural language processing (NLP) techniques are based on the vector space models of language, in which each word is represented by a vector in a high dimensional space. One of the earliest successes was demonstrated by the four-term analogical reasoning task: what is to C as B is to A? The trained word vectors form “parallelograms” representing the quadruple of words in analogy. This discovery in NLP offers us insight into our understanding of human semantic representation of words via analogical reasoning. Despite successful applications of the large-scale language models, it has not been fully understood why such parallelograms emerge by learning through natural language data. As the vector space model is not optimized to form parallelograms, the key structure related to geometric shapes of word vectors is expected to be in the data, rather than the models. In the present article, we test our hypothesis that such parallelogram arrangement of word vectors readily exists in the co-occurrence statistics of language. Our approach focuses more on the data itself, and it is different from the existing theoretical approach trying to find the mechanism of parallelogram formation in the algorithms and/or vector arithmetic operations on word vectors. First, our analysis suggested that analogical reasoning is possible by decomposition of the bigram co-occurrence matrix. Second, we demonstrated the formation of a parallelepiped, a more structured geometric object than a parallelogram, by creating a small artificial corpus and its word vectors. With these results, we propose a refined form of distributional hypothesis pointing out an isomorphism between a sort of symmetry or exchangeability and word co-occurrence statistics.
Mlf mediates proteotoxic response via formation of cellular foci for protein folding and degradation in Giardia
Authors: Vinopalová Martina , Arbonová Lenka , Füssy Zoltán , Dohnálek Vít , Samad Abdul , Bílý Tomáš , Vancová Marie , Doležal Pavel
Published: October 2024

Myeloid leukemia factor 1 (Mlf1) was identified as a proto-oncoprotein that affects hematopoietic differentiation in humans. However, its cellular function remains elusive, spanning roles from cell cycle regulation to modulation of protein aggregate formation and participation in ciliogenesis. Given that structurally conserved homologs of Mlf1 can be found across the eukaryotic tree of life, we decided to characterize its cellular role underlying this phenotypic pleiotropy. Using a model of the unicellular eukaryote Giardia intestinalis, we demonstrate that its Mlf1 homolog (GiMlf) mainly localizes to two types of cytosolic foci: microtubular structures, where it interacts with Hsp40, and ubiquitin-rich, membraneless compartments, found adjacent to mitochondrion-related organelles known as mitosomes, containing the 26S proteasome regulatory subunit 4. Upon cellular stress, GiMlf either relocates to the affected compartment or disperses across the cytoplasm, subsequently accumulating into enlarged foci during the recovery phase. In vitro assays suggest that GiMlf can be recruited to membranes through its affinity for signaling phospholipids. Importantly, cytosolic foci diminish in the gimlf knockout strain, which exhibits extensive proteomic changes indicative of compromised proteostasis. Consistent with data from other cellular systems, we propose that Mlf acts in the response to proteotoxic stress by mediating the formation of function-specific foci for protein folding and degradation.
Features that matter: Evolutionary signatures can predict viral transmission routes
Authors: Wardeh Maya , Pilgrim Jack , Hui Melody , Kotsiri Aurelia , Baylis Matthew , Blagrove Marcus S. C.
Published: October 2024

Routes of virus transmission between hosts are key to understanding viral epidemiology. Different routes have large effects on viral ecology, and likelihood and rate of transmission; for example, respiratory and vector-borne viruses together encompass the majority of rapid outbreaks and high-consequence animal and plant epidemics. However, determining the specific transmission route(s) can take months to years, delaying mitigation efforts. Here, we identify the viral features and evolutionary signatures which are predictive of viral transmission routes and use them to predict potential routes for fully-sequenced viruses in silico and rapidly, for both viruses with no observed routes, as well as viruses with missing routes. This was achieved by compiling a dataset of 24,953 virus-host associations with 81 defined transmission routes, constructing a hierarchy of virus transmission encompassing those routes and 42 higher-order modes, and engineering 446 predictive features from three complementary perspectives. We integrated those data and features to train 98 independent ensembles of LightGBM classifiers. We found that all features contributed to the prediction for at least one of the routes and/or modes of transmission, demonstrating the utility of our broad multi-perspective approach. Our framework achieved ROC-AUC = 0.991, and F1-score = 0.855 across all included transmission routes and modes, and was able to achieve high levels of predictive performance for high-consequence respiratory (ROC-AUC = 0.990, and F1-score = 0.864) and vector-borne transmission (ROC-AUC = 0.997, and F1-score = 0.921). Our framework ranks the viral features in order of their contribution to prediction, per transmission route, and hence identifies the genomic evolutionary signatures associated with each route. Together with the more matured field of viral host-range prediction, our predictive framework could: provide early insights into the potential for, and pattern of viral spread; facilitate rapid response with appropriate measures; and significantly triage the time-consuming investigations to confirm the likely routes of transmission.
El papel de la clerecía regular en los conflictos y negociaciones intra e internobiliarios en la Castilla bajomedieval
Authors: Prieto Sayagués Juan Antonio
Published: October 2024

Se analiza el papel desempeñado por el clero regular en los conflictos en los que se vio inmersa la nobleza castellana durante la Baja Edad Media. Estos respondieron a varias tipologías, siendo la más frecuente la intervención de los religiosos en conflictos intrafamiliares, muchos de ellos, fruto de los repartos de herencias. También participaron en los problemas y pleitos surgidos entre dos linajes, dentro de las ciudades y en algunos conflictos que implicaban a miembros de la nobleza y a la monarquía. Destaca el gran número de religiosos de la Orden de San Jerónimo a los que la nobleza encomendó diversos encargos, principalmente como mediadores, jueces, árbitros, compromisarios y testigos, sin desdeñar el encargo de otros cometidos.
Diagnosis of chronic migraine and comorbid neurological disorders in real-life clinical practice
Authors: Golovacheva V. A. , Golovacheva A. A. , Tarshilova A. R. , Osipova V. V.
Published: October 2024

Chronic migraine (CM) is a neurological disorder whose diagnosis requires not only knowledge of its diagnostic criteria, but also the physician's ability to differentiate between various forms of primary and secondary headache (HA), as well as to recognize comorbid neurological disorders that aggravate the course of CM. Timely and correct diagnosis of CM and comorbid disorders allows to prescribe effective treatment to a patient and convert the migraine from a chronic to an episodic form. The diagnostics of CM and comorbid neurological disorders has not been sufficiently investigated in our country, which formed the basis for this study.

Objective: to evaluate the quality of diagnostics of CM and comorbid neurological disorders in real-life neurological practice.

Material and methods. The study included 200 patients with CM (63 men and 137 women, mean age 33.1±7.1 years) admitted to A.Ya. Kozhevnikov Clinic of Nervous Diseases (CND) of Sechenov University, complaining of frequent headaches. They had previously been examined and treated by neurologists in other medical institutions on an outpatient and/or inpatient basis. A clinical interview was conducted with all patients to establish a diagnosis and analyze their previous treatment, and a psychometric test was performed to assess symptoms of anxiety and depression.

Results. Only 6% of patients had been previously diagnosed with CM, the remaining 94% were incorrectly diagnosed with secondary HA. All patients had previously been prescribed additional examinations, mainly neuroimaging of the brain and ultrasound of the cerebral vessels, although there were no "red flags". None of the patients had been previously assessed for their emotional state, while almost all patients had high situational anxiety (n=190; 95%) and high personal anxiety (n = 180; 90%), there were symptoms of depression (n=190; 95%) of varying severity. Comorbid neurological disorders (medication overuse HA), insomnia, musculoskeletal pain etc.) were diagnosed in 91.5% of patients in CND and in only in 8% of patients in other medical centers.

Conclusion. In real-life clinical practice, CM and comorbid neurological disorders are inadequately diagnosed and excessive and unjustified additional examinations are prescribed.
A personalized approach to the treatment of chronic tension-type headache: quality of life of patients
Authors: Tlisova K. M. , Petelin D. S. , Voskresenskaya O. N. , Volel B. A.
Published: October 2024

Objective: to evaluate the quality of life in a personalized approach to the treatment of chronic tension-type headache (CTTH) in comparison with a standard treatment protocol.

Material and methods. The study involved 61 patients with CTTH. Patients were randomly divided into two groups. The first (main) group consisted of patients (n=30) who received a personalized approach with a psychotherapist contributing to the treatment. The comparison group consisted of patients (n=31) who were treated according to a standard protocol with counselling and observation by a neurologist. Pain intensity was assessed using the visual analogue pain scale (VAS). The SF-36 questionnaire was used to assess quality of life. Differences between the groups were analyzed by assessing individual changes in eight different domains of the SF-36 questionnaire for each patient.

Results. In the main group, parameters characterizing the physical (pain intensity) and emotional experience of the pain (mental health, social functioning, life activity; p<0.05) decreased after 6 months of treatment when a personalized approach to the treatment of CTTH was applied, compared to the control group (with a standard patient management protocol).

Conclusion. The personalized approach showed an improvement of the quality of life of patients with CTTH compared with the standard protocol, allowing us to recommend it for a wider application in clinical practice.
Therapeutic potential of naproxen in common forms of headache
Authors: Tabeeva G. R.
Published: October 2024

The most common forms of headache (HA) in clinical practice are migraine, tension-type headache (TTH), cervicocranialgia and medication overuse headache. Modern strategies for the treatment of HA include the prescription of painkillers based on their efficacy, safety, experience of use, and patient's and physician's preference. Non-steroidal anti-inflammatory drugs are a universal mean of controlling HA, associated with a high analgesic potential that has been studied in almost all forms of cephalgia. Introduction to practice, confirmed efficacy and safety of Nalgesin® forte (naproxen) in observational studies in clinical practice make it the drug of choice for the most common forms of HA, among others.