bluuebunny/crossref_metadata_2025 huggingface dataset:
Compact Silicon Micro-Ring Resonators with Optimized Low-loss Bends
Authors: Hsia Chih-Chieh , Tseng Shuo-Yen
Published: December 2024

Compact micro-ring resonators with optimized inner circumferences using Bezier curves for low bending losses are proposed. For a resonator with 2µm outer radius, Q of 19532, FWHM of 0.078nm, and FSR of 57nm are obtained.
Using the Temperature Degree of Freedom to Prevent Overfitting in Infrared Spectroscopic Ellipsometry
Authors: Yin Shenwei , Feng Demeng , Cho Jin-Woo , Kumar Tanuj , Wan Chenghao , Mei Hongyan , Kats Mikhail A.
Published: December 2024

We performed high-precision measurements of the mid-infrared (5–25 µm) optical properties of fused-silica glass, from room temperature to 600 °C, using variable-angle spectroscopic ellipsometry. We developed a technique that limits overfitting of ellipsometric data using the additional information available via the temperature-dependent measurements.
Towards Polarization-encoded QKD with room-temperature telecom single-photon source over 32.5 km fiber
Authors: Xingjian Zhang , Haoran Zhang , Weibo Gao , Ling Alexander
Published: December 2024

We report a polarization-encoded BB84 experiment using O-band single photons from a GaN emitter, over a 32.5km fiber spool. A Quantum Bit Error Rate (QBER) of 6.4% and a secure key rate of 47.3 bps are obtained.
Inflatable Foley Catheter based Speculum-Free Probe Design for Cervix Imaging
Authors: Kumar Sandeep , Bhushan Pratyush , Hussain Mohammed Aamir , Pal Uttam M. , Anantharaju Arpitha
Published: December 2024

The work proposes a configuration of Foley catheter around the GynoSight transvaginal imaging probe for speculum-free imaging of cervical tissues.
Development of Stokes Mueller based polarimeter for tissue characterization
Authors: Makkithaya Kausalya Neelavara , Melanthota Sindhoora Kaniyala , Zhuo Guan-Yu , Mazumder Nirmal
Published: December 2024

Tissue characterization is vital for diagnosing and treating diseases. Measuring tissues’ optical properties aids in identifying abnormalities and tracking disease progression. Polarimetry offers detailed insights into the polarization state of light transmitted through tissue samples.
Optimization of Length of Two-Mode FBG Sensors
Authors: Kumar Ajay , Sharma Anurag
Published: December 2024

Two-mode (LP01 and LP11) fiber Bragg gratings have been proposed for simultaneous measurement of temperature and refractive index. We have optimized the length of the FBGs to prevent the excitation of unwanted LP02 mode.
3D phase profile for biological particle characterization using digital holographic microscopy
Authors: Kadhim Ahmed C. , Azzahrani Ahmad S. , Taha Bakr A.
Published: December 2024

A hybrid digital holographic microscope is used to record a hologram of biological cells with fluorescent and phase information. The resultant hologram is processed for phase recovery using the deep learning algorithm to extract 3D phase distribution.
Sensitivity Of Time-Resolved Diffuse Reflectance To Optical Coefficients In Bilayered Tissues
Authors: Rajasekhar Suraj , Vishwanath Karthik
Published: December 2024

Theoretical sensitivity of diffuse reflectance from a bilayer turbid tissue model using time-domain diffusion theory are estimated across varying source-detector separations. We establish limits for recovery of absorption and scattering properties of each layer.
High-Speed, Single-Shot Measurement of the Intensity and Phase of Optical Waveforms
Authors: Kane Daniel J.
Published: December 2024

A hybrid optical and electric linear pulse measurement system capable of the measurement of the intensity and phase of sub-picosecond optical waveforms is presented. Multishot verification and single-shot acquisition at 1 MHz is demonstrated.
Carrier Dynamics and Transport Properties of Ge using Optical–Pump Terahertz–Probe Spectroscopy
Authors: Haldar Amit , Li Jingwen , Yang Chia-Jung , Saha Kush , Pal Shovon
Published: December 2024

We investigate the evolution of THz conductivity in Ge via optical pump THz-probe spectroscopy. The transient photo-conductivity deviates from the Drude to Drude- Lorentz/Smith models depending on the 1s–2p transition and backscattering process.
Distortions in the Angular Distribution of Nonlinear Thomson Scattering as a Focal Diagnostic
Authors: Sun Y. , Barr K. , Jones A. , Sá N. B. , Ware M. , Peatross J.
Published: December 2024

We present measurements of nonlinear Thomson scattering out the side of an intense laser focus, showing how subtle defects in laser field including spatial chirp imprint on the angular distribution of the scattered light.
Transverse Mode Control in Few Mode Fiber using Transmission Matrix Engineering
Authors: Jian Wu Shuin , Banerji Anindya , Bromberg Yaron , Ling Alexander
Published: December 2024

We use mechanical perturbations controlled by a computational optimization algorithm to selectively guide a single mode of light in a few mode fiber that supports multiple transverse modes.
Assessing chromatic discrimination in individuals varying in iris color and ethnic origin
Authors: Paramei Galina V. , Nwanedo Nnaemeka , Owen Robin , Zlatkova Margarita , Senna Irene
Published: December 2024

This study aimed to investigate how variation in iris color, along with ethnic origin, affects color vision. For color vision deficiency screening, the Ishihara, D-15, and D-15d tests were employed. Chromatic discrimination was assessed in normal trichromats using the Cambridge Colour Test (CCT). Three groups were tested: light-eyed White (N = 30), hazel-eyed White (N = 30), and brown-eyed Black (N = 29). Black observers revealed significantly higher CCT measures—protan and tritan thresholds (Trivector) and Ellipse measures (major axis, axis ratio, and angle); no significant differences were found between the two White observer groups. We attribute Black observers’ subtle tritan-type impairment to prereceptoral factors, in particular, the higher optical density of the macular pigment, which filters out short-wavelength light, affecting S-cone-mediated chromatic discrimination, and, also, is likely to reduce retinal illuminance. The elevated protan thresholds are discussed in relation to the receptoral level; considered are possible causes of genetically determined L-cone characteristics in observers of African descent.
Direct phase sensing via an end-to-end model under high-order aberrations
Authors: Liu Dongming , Liu Hui , Jin Zhenyu
Published: December 2024

We propose an end-to-end model that estimates the exit pupil wavefront directly from phase diversity images using deep learning. The aim is to restore the exit pupil wavefront through zonal reconstruction to obtain more high-order modal aberrations, thereby improving the reconstruction quality of degraded images. Our simulated experimental results show that zonal reconstruction significantly outperforms modal reconstruction in restoring high-order aberrations. The ResNet50 model, which outputs Zernike modes of [3,28] orders, is limited by the order of reconstruction, and high-order aberrations lead to errors in these Zernike modes. Zonal reconstruction without mode restrictions, however, can obtain more high-order modal aberrations and achieve higher fitting accuracy across all aberrations. By comparing the reconstruction results of degraded images, as well as analyzing the normalized power spectrum curves and intensity profiles, we further validate the accuracy of the wavefront restoration by zonal reconstruction. The reconstructed images are richer in high spatial frequency details and provide more accurate reconstruction results.
Computational Coded Imaging Systems Using Trained/Untrained Neural Networks
Authors: Nakamura Tomoya
Published: December 2024

Computational coded imaging systems employ image-reconstruction algorithms to decode captured images. In this talk, I introduce lensless and super-resolution imaging systems utilizing trained/untrained neural networks for image reconstruction processing.
Full Polarization Characterization of a Broadband High-harmonic Source
Authors: Oldal L. Gulyás , Gilicze B. , Bartyik T. , Kiss D. , Frassetto F. , Zeni G. , Poletto L. , Csizmadia T. , Major B.
Published: December 2024

We present full characterization and demonstrate impurities in the polarization state of a high-harmonic source using a double-stage extreme-ultraviolet polarimeter and an in-situ method based on photoelectron momentum distributions recorded by a Reaction Microscope.
Kerr squeezing across a full Nyquist window with a 1 GHz frequency comb
Authors: Herman Daniel I. , Kreider Molly Kate , Walsh Mathieu , Lind Alexander J. , Lordi Noah , Tsao Eugene J. , Heyrich Matthew , Combes Joshua , Genest Jérôme , Diddams Scott A.
Published: December 2024

We demonstrate a simple setup for amplitude-squeezed frequency comb generation in polarization-maintaining highly nonlinear fiber. Without optical amplification, injection of <20 pJ pulses results in >3.0 dB of squeezing.
Compact 88Sr Optical Lattice Clock System with Metasurface Optics for Laser Cooling
Authors: Luo Zheng , Ferdinand Andrew R. , Jammi Sindhu , Newman Zachary L. , Spektor Grisha , Koksal Okan , Patel Parth , Sheredy Dan , Lunden William , Rakholia Akash , Boyd Martin , Agrawal Amit , Zhu Wenqi , Briles Travis C. , Papp Scott B.
Published: December 2024

We demonstrate a scalable, integrated photonics infrastructure for compact optical clocks. In this alignment-free MOT 88Sr atoms are cooled to 3 µK and loaded into an optical lattice, ready for ultranarrow clock transition interrogation.
Realization of a low loss thin-film lithium niobate edge coupler based on a staircase structure
Authors: Wang Mengke , Yao Hao , Deng Jiayao , Sun Yuzhe , Hu Zhefeng , Chen Kaixin
Published: December 2024

Thin film lithium niobate (TFLN) has been proven to be a promising platform to realize high-performance integrated photonic devices. However, due to the large mode field mismatch between fibers and TFLN waveguides, low-loss edge couplers are necessary for practical TFLN devices. In this paper, we experimentally demonstrated a low-loss TFLN edge coupler based on our previously proposed staircase structure. The edge coupler has a minimum feature size of 3.0 μm and exhibits a high tolerance to lithographic overlay misalignment, ensuring its feasibility for fabrication using a contact aligner. Special etching mask patterns and etching processes were developed to efficiently fabricate the desired staircase structure. Test results show that a fiber-to-chip coupling loss of 1.5 dB/facet for TE polarized light is achieved at 1560 nm wavelength, and the polarization-dependent loss (PDL) is lower than 0.5 dB. To the best of our knowledge, it is the first low-loss TFLN edge coupler fabricated with a contact aligner, which paves the way for low-cost fabrication of practical TFLN devices.
Research on the influence of aperture process defects on the measurement precision and accuracy of autocollimator and compensation methods
Authors: Li Renpu , Yan Juan , Cui Jiwen , Guo Junqi , Kulikov Andrei , Konyakhin Igor , Nikitin Mikhail , Guo Yongrui , Wen Dandan
Published: December 2024

As a benchmark apparatus for small-angle precision measurements, enhancing the measurement accuracy of autocollimators has always been a focal point of industry attention. However, there are currently no reports on the investigation of the impact that internal aperture processing quality has on measurement precision and accuracy. This paper integrates the general Hough transform image recognition and localization algorithm to analyze the mechanisms inducing measurement uncertainty and error in autocollimators caused by defects in the optical stop aperture. A method utilizing femtosecond laser (FSL) processing of the crosshair aperture is proposed to compensate for the traditional optical stop aperture roughness. Compared to conventional machining, this method reduces the autocollimator measurement uncertainty by 31.6% and 48.1% in the yaw and pitch angle directions, respectively, and decreases the measurement root mean square (RMS) error by 35.9% and 41.8%, respectively.
Volumetric imaging of H2O transportation in laminar jets issuing from polygonal nozzles by masked and regularized tomographic absorption spectroscopy
Authors: Shi Dingfeng , Jiao Tengfei , Cheong Kin-Pang , Chen Wei , Liu Yushuai , Song Yong , Liu Yan , Ren Wei
Published: December 2024

We report high-spatial-resolution 3D tomographic imaging of H2O transportation in laminar jets issued from polygonal (triangular, square, and pentagonal) nozzles using laser absorption spectroscopy. An experimental platform containing a single laser source setup and motorized stages was built for 3D sampling. Numerical analysis was conducted to identify the suitable optical scheme and reconstruction algorithm. Our results show that the algebraic reconstruction technique with the masking operation and total variance regularization outperforms the other approaches in accuracy and artifact suppression. With proper initial incident angles, the volume fraction of H2O in the triangular, square, and pentagonal jet flows can be effectively reconstructed using three, four, and five projection angles, respectively, in good agreement with CFD simulations. By evaluating the H2O diffusions, these measurements show the triangular one prevails in mixing enhancement. This study provides a new method for the visualization and quantification of species mixing in complex flows.
Quasi-ray tracing realization using a Bessel beam for optical alignment
Authors: Chen Zhaowei , Parks Robert E. , Dhawan Bhawna , Gurunarayanan Surya Prakash , Kim Daewook
Published: December 2024

In this study, we explore the behavior of Bessel beams as they propagate through a misaligned apertured optical system in practice. Based on experimental observations, we propose what we believe to be a novel hypothesis that a Bessel beam propagating through an optical system behaves identically to a paraxial ray under certain conditions. We then derive analytical formulas for the propagation of Bessel beams in Cartesian coordinates and the Huygens-Fresnel principle. Additionally, another simulation employing Gaussian decomposition was conducted, and we compared both simulations with experimental results, demonstrating a high correlation. Our findings indicate that Bessel beams can be interpreted as meridional rays when passing through misaligned spherical surface systems, allowing us to achieve quasi-ray tracing in practice. We further discuss the significance of utilizing this property of Bessel beams for precise optical alignment, highlighting its potential to enhance the accuracy and efficiency of optical systems.
Calibration of backscattering coefficients with coherent heterodyne lidar utilizing molecular scattering
Authors: Kalmankoski Kim , Shang Xiaoxia , Komppula Mika , Toivonen Juha
Published: December 2024

Coherent heterodyne lidars are typically used for windspeed and attenuated backscattering measurements. The lack of molecular backscattering detection capability has limited the calibrated backscattering measurements until recent advances in coherent lidar technology. In this work, the simultaneous detection of aerosol and molecular backscattering is demonstrated with coherent heterodyne lidar, and the results are compared with a state-of-the-art Raman lidar PollyXT as a reference in a long-range for the first time. The molecular scattering is measured up to 3 km altitude and the extinction of laser power is calculated based on the attenuation. The essential corrections for the molecular scattering data are described and discussed. The backscattering coefficients are calculated with simple high spectral resolution lidar algorithms and the low altitude overlap is calibrated with on-site ceilometer data. A successful high spectral resolution measurement within coherent heterodyne lidar enables the self-calibration of the measured data and removes guessing of the backscatter to extinction ratio and initial values for the typical inversion algorithms. The self-calibration also enables basic aerosol classification based on the measured backscatter to extinction ratios.
Enhancing the sub-bandgap photo-response of silicon by inert element co-hyperdoping
Authors: Zhu Jun-Jie , Zhao Ji-Hong , Dong Meng-Di , Liu Xiao-Hang , Chen Zhan-Guo , Chen Qi-Dai , Sun Hong-Bo
Published: December 2024

The introduction of intermediate bands by hyperdoping is an efficient way to realize infrared light absorption of silicon. In this Letter, inert element (helium and argon for specific)-doped black silicon is obtained by helium ion-implantation followed by femtosecond pulse laser irradiation in an argon atmosphere based on near-intrinsic silicon substrates. Within the 200 nm of the silicon surface, the concentrations of helium and argon are both above the order of 1019 cm-3. The defect states related to impurities and structural defects contribute to the absorption in sub-bandgap (1100–2500 nm). Vertically structured devices based on the inert element-doped black silicon exhibit the responsivity of 350 mA/W for 1550 nm and 165 mA/W for 1310 nm at 12 V operating bias, respectively, proving its potential application in infrared detection.
Enhanced birefringence of a Ta2O5 thin film obliquely deposited on a polymer grating
Authors: Jen Yi-Jun , Wang Ming-Yuan , Zhan Bo-Wei , Lin Meng-Jie
Published: December 2024

In this study, Ta2O5 was obliquely deposited on a polymer grating, resulting in a nanostructured thin film (NTF) with pronounced anisotropic optical properties. We measured and compared the principal indices and principal axes orientations of NTFs grown on both a grating and a smooth glass substrate. By adjusting the deposition angle, we observed a significant variation in the columnar angle and principal indices of the NTF on the grating, compared to the NTF on a smooth surface. Furthermore, the phase retardation and corresponding birefringence of the NTFs on the gratings were notably larger than those on a smooth substrate, highlighting the enhanced optical performance achieved through this method.
Second harmonic generation via double topological disclination states
Authors: Luo Lanxin , Dai Xiaoyu , Hu Weipeng , Xiang Yuanjiang
Published: December 2024

The topological disclination state (TDS) in topological insulators (TIs) has strong localization, and its impact on nonlinear effects has garnered significant attention. Second harmonic generations (SHGs) have been proven to be generated individually in topological corner states and topological edge states. However, the SHGs in TDSs have not been discussed so far. Here, a scheme for satisfying the SHG condition through the coupling of double TDS has been proposed, and the high conversion efficiency and strong robustness with disorder have been proven due to the doubly resonant TDS. Our method provides a new perspective for exploring the nonlinear effects of topological states caused by topological defects.
Enhanced stability of microwave absorption in island-bridge structured organohydrogels
Authors: Zeng Yanan , Gong Xiaofeng , Fang Xiang , Luo Jie , Wu Zhuang , Yang Yuntao , Zou Wenxing , Chu Zengyong , Zou Yanhong
Published: December 2024

Stretchable microwave absorbers (SMAs) are vital for flexible electronics. Traditional SMAs display unstable tensile properties resulting from inconsistencies between the constrained conductive layer and the flexible dielectric layer. This study introduces an organohydrogel-based stretchable microwave absorber (OSMA) that incorporates an organohydrogel within an island-bridge structure. Leveraging standing wave and field concentration effects, along with strain dissipation, the OMSA achieves 90% absorption in the 5–18 GHz range and maintains stable broadband absorption under a 30% uniaxial stretch, exhibiting tunable absorption and angular performance under transverse electric/magnetic (TE/TM) polarization. This approach offers a versatile, customizable, and cost-effective solution for SMAs.
Five-mode erbium-doped waveguide amplifiers with low differential modal gain
Authors: Gao Lizhan , Zhang Meiling , Shi Jiahui , Li Changlong , Bao Jingxin , Gou Ruilin , Wang Fei
Published: December 2024

In this work, a five-mode erbium-doped waveguide amplifier with low differential modal gain (DMG) is first proposed. A novel, to the best of our knowledge, gain equalization scheme for synergistic reconfiguration of refractive index and concentration doping is adopted to equalize the modal gains based on the dual-layer ring core structure. NaYF4:5%Gd3+,20%Yb3+,2%Er3+@NaYF4 nanoparticles are synthesized by annealing treatment to improve the emission spectral properties and the concentration doped in a host core material. Leveraging the genetic algorithm and the minimization algorithm, the distributions of refractive index and layered doping are optimized. The high-precision alignment technology is presented to fabricate the devices. The crosstalk, near-field light spots, and loss and gain performances of the device are characterized. With only backward pumping of LP01 at a power of 150 mW, an average gain of 9.68 dB at 1550 nm with a DMG of 0.76 dB for five signal modes without distortion is achieved. This achievement establishes the foundation for enhancements in system data transmission capacity and integration scale.
Axons compensate for biophysical constraints of variable size to uniformize their action potentials
Authors: Brunner János , Arszovszki Antónia , Tarcsay Gergely , Szabadics János
Published: December 2024

Active conductances tune the kinetics of axonal action potentials (APs) to support specialized functions of neuron types. However, the temporal characteristics of voltage signals strongly depend on the size of neuronal structures, as capacitive and resistive effects slow down voltage discharges in the membranes of small elements. Axonal action potentials are particularly sensitive to these inherent biophysical effects because of the large diameter variabilities within individual axons, potentially implying bouton size-dependent synaptic effects. However, using direct patch-clamp recordings and voltage imaging in small hippocampal axons in acute slices from rat brains, we demonstrate that AP shapes remain uniform within the same axons, even across an order of magnitude difference in caliber. Our results show that smaller axonal structures have more Kv1 potassium channels that locally re-accelerate AP repolarization and contribute to size-independent APs, while they do not preclude the plasticity of AP shapes. Thus, size-independent axonal APs ensure consistent digital signals for each synapse within axons of same types.
The thalamus encodes and updates context representations during hierarchical cognitive control
Authors: Chen Xitong , Leach Stephanie C. , Hollis Juniper , Cellier Dillan , Hwang Kai
Published: December 2024

Cognitive flexibility relies on hierarchically structured task representations that organize task contexts, relevant environmental features, and subordinate decisions. Despite ongoing interest in the human thalamus, its role in cognitive control has been understudied. This study explored thalamic representation and thalamocortical interactions that contribute to hierarchical cognitive control in humans. We found that several thalamic nuclei, including the anterior, mediodorsal, ventrolateral, and pulvinar nuclei, exhibited stronger evoked responses when subjects switch between task contexts. Decoding analysis revealed that thalamic activity encodes task contexts within the hierarchical task representations. To determine how thalamocortical interactions contribute to task representations, we developed a thalamocortical functional interaction model to predict task-related cortical representation. This data-driven model outperformed comparison models, particularly in predicting activity patterns in cortical regions that encode context representations. Collectively, our findings highlight the significant contribution of thalamic activity and thalamocortical interactions for contextually guided hierarchical cognitive control.
Stable developmental patterns of gene expression without morphogen gradients
Authors: Majka Maciej , Becker Nils B. , ten Wolde Pieter Rein , Zagorski Marcin , Sokolowski Thomas R.
Published: December 2024

Gene expression patterns in developing organisms are established by groups of cross-regulating target genes that are driven by morphogen gradients. As development progresses, morphogen activity is reduced, leaving the emergent pattern without stabilizing positional cues and at risk of rapid deterioration due to the inherently noisy biochemical processes at the cellular level. But remarkably, gene expression patterns remain spatially stable and reproducible over long developmental time spans in many biological systems. Here we combine spatial-stochastic simulations with an enhanced sampling method (Non-Stationary Forward Flux Sampling) and a recently developed stability theory to address how spatiotemporal integrity of a gene expression pattern is maintained in developing tissue lacking morphogen gradients. Using a minimal embryo model consisting of spatially coupled biochemical reactor volumes, we study a prototypical stripe pattern in which weak cross-repression between nearest neighbor expression domains alternates with strong repression between next-nearest neighbor domains, inspired by the gap gene system in the Drosophila embryo. We find that tuning of the weak repressive interactions to an optimal level can prolong stability of the expression patterns by orders of magnitude, enabling stable patterns over developmentally relevant times in the absence of morphogen gradients. The optimal parameter regime found in simulations of the embryo model closely agrees with the predictions of our coarse-grained stability theory. To elucidate the origin of stability, we analyze a reduced phase space defined by two measures of pattern asymmetry. We find that in the optimal regime, intact patterns are protected via restoring forces that counteract random perturbations and give rise to a metastable basin. Together, our results demonstrate that metastable attractors can emerge as a property of stochastic gene expression patterns even without system-wide positional cues, provided that the gene regulatory interactions shaping the pattern are optimally tuned.
Homeodynamic feedback inhibition control in whole-brain simulations
Authors: Stasinski Jan , Taher Halgurd , Meier Jil Mona , Schirner Michael , Perdikis Dionysios , Ritter Petra
Published: December 2024

Simulations of large-scale brain dynamics are often impacted by overexcitation resulting from heavy-tailed structural network distributions, leading to biologically implausible simulation results. We implement a homeodynamic plasticity mechanism, known from other modeling work, in the widely used Jansen-Rit neural mass model for The Virtual Brain (TVB) simulation framework. We aim at heterogeneously adjusting the inhibitory coupling weights to reach desired dynamic regimes in each brain region. We show that, by using this dynamic approach, we can control the target activity level to obtain biologically plausible brain simulations, including post-synaptic potentials and blood-oxygen-level-dependent functional magnetic resonance imaging (fMRI) activity. We demonstrate that the derived dynamic Feedback Inhibitory Control (dFIC) can be used to enable increased variability of model dynamics. We derive the conditions under which the simulated brain activity converges to a predefined target level analytically and via simulations. We highlight the benefits of dFIC in the context of fitting the TVB model to static and dynamic measures of fMRI empirical data, accounting for global synchronization across the whole brain. The proposed novel method helps computational neuroscientists, especially TVB users, to easily “tune” brain models to desired dynamical regimes depending on the specific requirements of each study. The presented method is a steppingstone towards increased biological realism in brain network models and a valuable tool to better understand their underlying behavior.
Mathematical basis and toolchain for hierarchical optimization of biochemical networks
Authors: Viswan Nisha Ann , Tribut Alexandre , Gasparyan Manvel , Radulescu Ovidiu , Bhalla Upinder S.
Published: December 2024

Biological signalling systems are complex, and efforts to build mechanistic models must confront a huge parameter space, indirect and sparse data, and frequently encounter multiscale and multiphysics phenomena. We present HOSS, a framework for Hierarchical Optimization of Systems Simulations, to address such problems. HOSS operates by breaking down extensive systems models into individual pathway blocks organized in a nested hierarchy. At the first level, dependencies are solely on signalling inputs, and subsequent levels rely only on the preceding ones. We demonstrate that each independent pathway in every level can be efficiently optimized. Once optimized, its parameters are held constant while the pathway serves as input for succeeding levels. We develop an algorithmic approach to identify the necessary nested hierarchies for the application of HOSS in any given biochemical network. Furthermore, we devise two parallelizable variants that generate numerous model instances using stochastic scrambling of parameters during initial and intermediate stages of optimization. Our results indicate that these variants produce superior models and offer an estimate of solution degeneracy. Additionally, we showcase the effectiveness of the optimization methods for both abstracted, event-based simulations and ODE-based models.
Theta oscillations optimize a speed-precision trade-off in phase coding neurons
Authors: Amil Adrián F. , Albesa-González Albert , Verschure Paul F. M. J.
Published: December 2024

Theta-band oscillations (3–8 Hz) in the mammalian hippocampus organize the temporal structure of cortical inputs, resulting in a phase code that enables rhythmic input sampling for episodic memory formation and spatial navigation. However, it remains unclear what evolutionary pressures might have driven the selection of theta over higher-frequency bands that could potentially provide increased input sampling resolution. Here, we address this question by introducing a theoretical framework that combines the efficient coding and neural oscillatory sampling hypotheses, focusing on the information rate (bits/s) of phase coding neurons. We demonstrate that physiologically realistic noise levels create a trade-off between the speed of input sampling, determined by oscillation frequency, and encoding precision in rodent hippocampal neurons. This speed-precision trade-off results in a maximum information rate of ∼1–2 bits/s within the theta frequency band, thus confining the optimal oscillation frequency to the low end of the spectrum. We also show that this framework accounts for key hippocampal features, such as the preservation of the theta band along the dorsoventral axis despite physiological gradients, and the modulation of theta frequency and amplitude by running speed. Extending the analysis beyond the hippocampus, we propose that theta oscillations could also support efficient stimulus encoding in the visual cortex and olfactory bulb. More broadly, our framework lays the foundation for studying how system features, such as noise, constrain the optimal sampling frequencies in both biological and artificial brains.
The landscape and level of alcohol policy enforcement in Tanzania
Authors: Madundo Kim , Hudda Aliza , Seekles Maaike L. , Mmbaga Blandina , Obasi Angela
Published: December 2024

Harmful use of alcohol causes more deaths in Sub-Saharan Africa than in any other region. In Tanzania, where alcohol use disorders rates are twice the overall African average, harmful alcohol consumption is a public health concern. Given the lack of a contemporary overview of the alcohol policy landscape, we conducted a mixed-methods review of key alcohol-related policies, implementers, and initiatives in Tanzania. We conducted a desk-based review of policy-related documents, and in-depth interviews with eight key informants guided by the 10-composite-indicator framework of a tool for measuring alcohol policy implementation developed by World Health Organization. Representatives were from health-service delivery, community-based organizations, governmental organizations, research, and policymakers whose work is related to alcohol in Tanzania. Data was collected in June and October 2022, and finalized in March 2023. Findings were analyzed using Microsoft Word v2021. Themes were identified, collected, combined, and tabulated. Differences were then resolved by first and second authors. Our findings revealed no single comprehensive national alcohol policy. Pending finalization of a draft policy, various documents and actors govern alcohol production, distribution, licensing, and consumption. Little intersectoral linkage between entities contributes to poor enforcement of these regulations. Regulation is stronger in urban areas, and restrictions more effective on industrial alcohol. However, the majority of consumed alcohol in Tanzania is informally-produced, especially in rural settings. Socio-cultural context plays a key role in alcohol production and consumption, contributing to early-age exposure to alcohol. Alcohol is a growing source of revenue for the Tanzanian government and, therefore, imposing further restrictions is a low priority. There are important policy gaps in various sectors pertaining to alcohol regulation. Our results strongly suggest the need for a comprehensive approach to developing an overarching alcohol policy, with involvement of key stakeholders, stronger enforcement, and increased awareness, resources, and collaborations.
Cost-effectiveness of the Healthy Options group psychosocial intervention for perinatal women living with HIV and depression in Tanzania
Authors: Saronga Happiness Pius , Kaaya Sylvia , Fawzi Mary C. Smith
Published: December 2024

Healthy Options is a psychosocial support group intervention facilitated by community-based health workers (CBHWs) to reduce symptoms of depression in perinatal women living with HIV in Tanzania. The objective of this study was to determine incremental cost-effectiveness of Healthy Options intervention in comparison to enhanced usual care for depression (EUDC) intervention. This study is a cost-effectiveness analysis of Healthy Options intervention. The primary outcome for the Healthy Options intervention was level of depressive symptoms. We estimated disability adjusted life years (DALYs) by considering life years lived with disability and years of life lost due to premature mortality resulting from depression. This study applied ingredients approach to cost all resources used in the intervention. We estimated total cost, unit cost, and incremental cost-effectiveness ratio (ICER) from a health care provider perspective. We used 3-year time horizon, univariate sensitivity analysis, and adjusted costs to 2017 value. Healthy Options intervention demonstrated effectiveness in reducing depressive symptoms among pregnant women with HIV in Tanzania. Total cost of Healthy Options was $319,729. Cost per woman treated was $883. ICER at 6 weeks postpartum is $89,699 per mean decrease in depression score and $310,030 per mean decrease in depression score at 9 months. ICER per DALY averted is $24,754 at 6 months and $4,169 at 9 months. Benefits of Healthy Options are sustained through 9 months postpartum. Healthy Options is nevertheless not cost-effective because ICER is above cost-effectiveness threshold. However, since mental health care is scarce in Tanzania, working with CBHWs is likely to offer effective intervention for maternal depression among women with HIV and it can be a less costly alternative to formal mental health professionals.
Three years of insecticide resistance evolution and associated mechanisms in Aedes aegypti populations of Ouagadougou, Burkina Faso
Authors: Yaméogo Félix , Sombié Aboubacar , Oté Manabu , Saiki Erisha , Sakurai Tatsuya , Wangrawa Dimitri W. , McCall Philip J. , Weetman David , Kanuka Hirotaka , Badolo Athanase
Published: December 2024

Background

Resistance to insecticides is spreading among populations of Aedes aegypti, the primary vector of important human arboviruses. The escalating insecticide resistance poses a significant threat to dengue vector control, with an expanding number of countries affected by the disease.

To gain a deeper insight into the evolution of insecticide resistance, it is essential to have longitudinal surveillance results, which are currently lacking, particularly from African Ae. aegypti populations.

Here we report on three-years of surveillance of Ae. aegypti susceptibility to insecticide resistance phenotypes and associated kdr mutations in Burkina Faso, a country with regular dengue outbreaks.

Methods

Ae. aegypti susceptibility to insecticides and the V410L, V1016I, and F1534C kdr target site mutations linked to pyrethroid insecticide resistance were monitored in Ouagadougou from 2016 to 2018. Larvae were collected from artificial containers at two sites and reared to adulthood in an insectary. Bioassays were conducted on female adults, along with a laboratory-susceptible strain, following standard WHO protocols. Allele-specific PCR genotyping assays were utilized to identify the V410L, V1016I, and F1534C kdr pyrethroid target site mutations.

Results

Bioassays revealed a high level of resistance to permethrin and deltamethrin that progressively increased over the three-year period in both localities. The 1534C mutation was nearly fixed throughout the three years at each locality, and while the closely-related 410L and 1016I mutations did not vary between localities, their frequency notably increased from 2016 to 2018. Interestingly, Ae. aegypti populations in both areas remained susceptible to bendiocarb, fenitrothion, and malathion. Modelling the mortality data further confirmed the escalating resistance trend over the years and emphasized the significant role played by the three kdr mutations in conferring resistance to pyrethroids.

Conclusion

Mortality rates indicate that Ae. aegypti populations from Ouagadougou are becoming increasingly resistant to pyrethroid insecticides, likely due to an increase in the frequencies of the 410L and 1016I kdr mutations. Organophosphate insecticides are likely to be better alternative options for control.
Combating climate-induced health threats through Co-Constitutive Risk (CCR) Messaging: A One Health Communication approach
Authors: Landrum Asheley R. , Stecuła Dominik A. , Motta Matthew
Published: December 2024

Climate-facilitated spread of mosquito-borne pathogens to new environments elevates the importance of policies that limit greenhouse gas emissions as well as the development and uptake of new pharmaceutical interventions. Whereas past research attempts to bolster support for both through either climate or health risk communication, fewer attempt to combine the risks borne by climate change and infectious disease with a single messaging intervention, i.e., co-constitutive risk messaging (CCR), a strategy of an integrative approach we call One Health Communication. In a pre-registered experiment embedded in a nationally representative survey (N = 2,200), we test whether CCR messaging impacts support for pharmaceutical interventions to minimize dengue fever health risks and/or policy efforts to mitigate climate change. We find that CCR messages are generally effective at increasing support for pharmaceutical interventions aimed at ameliorating the health risks posed by dengue fever. Moreover, we find suggestive evidence that people who hold more collectivistic worldviews are especially receptive to messages that emphasize the public (vs. the personal) health risks of dengue fever. In post hoc exploratory analyses, we show that CCR messages affect public support for climate change mitigation policies among those who express doubts about human-caused climate change. We conclude by discussing the usefulness of CCR messaging and One Health Communication approaches more broadly in various strategic communication contexts and considering additional avenues for future research.
An experimental target-based platform in yeast for screening Plasmodium vivax deoxyhypusine synthase inhibitors
Authors: Fernandes Silva Suélen , Hollunder Klippel Angélica , Sigurdardóttir Sunniva , Mahdizadeh Sayyed Jalil , Tiukova Ievgeniia , Bourgard Catarina , Salazar-Alvarez Luis Carlos , do Amaral Prado Heloísa Monteiro , de Araujo Renan Vinicius , Costa Fabio Trindade Maranhão , Bilsland Elizabeth , King Ross D. , Brauer Massirer Katlin , Eriksson Leif A. , Bengtson Mário Henrique , Zanelli Cleslei Fernando , Sunnerhagen Per
Published: December 2024

The enzyme deoxyhypusine synthase (DHS) catalyzes the first step in the post-translational modification of the eukaryotic translation factor 5A (eIF5A). This is the only protein known to contain the amino acid hypusine, which results from this modification. Both eIF5A and DHS are essential for cell viability in eukaryotes, and inhibiting DHS is a promising strategy to develop new therapeutic alternatives. DHS proteins from many are sufficiently different from their human orthologs for selective targeting against infectious diseases; however, no DHS inhibitor selective for parasite orthologs has previously been reported.

Here, we established a yeast surrogate genetics platform to identify inhibitors of DHS from Plasmodium vivax, one of the major causative agents of malaria. We constructed genetically modified Saccharomyces cerevisiae strains expressing DHS genes from Homo sapiens (HsDHS) or P. vivax (PvDHS) in place of the endogenous DHS gene from S. cerevisiae. Compared with a HsDHS complemented strain with a different genetic background that we previously generated, this new strain background was ~60-fold more sensitive to an inhibitor of human DHS.

Initially, a virtual screen using the ChEMBL-NTD database was performed. Candidate ligands were tested in growth assays using the newly generated yeast strains expressing heterologous DHS genes. Among these, two showed promise by preferentially reducing the growth of the PvDHS-expressing strain. Further, in a robotized assay, we screened 400 compounds from the Pathogen Box library using the same S. cerevisiae strains, and one compound preferentially reduced the growth of the PvDHS-expressing yeast strain. Western blot revealed that these compounds significantly reduced eIF5A hypusination in yeast. The compounds showed antiplasmodial activity in the asexual erythrocyte stage; EC50 in high nM to low μM range, and low cytotoxicity.

Our study demonstrates that this yeast-based platform is suitable for identifying and verifying candidate small molecule DHS inhibitors, selective for the parasite over the human ortholog.
Cellular and molecular characterization of peripheral glia in the lung and other organs
Authors: Hall Shaina , Liu Shixuan , Liang Irene , Schulz Shawn , Ezran Camille , Tan Mingqian , Kuo Christin S.
Published: December 2024

Peripheral glia are important regulators of diverse physiologic functions yet their molecular distinctions and locations in almost all visceral organs are not well-understood. We performed a systematic analysis of peripheral glia, focusing on the lung and leveraging single cell RNA sequencing (scRNA-seq) analysis to characterize their cellular and molecular features. Using in vivo lineage studies, we characterized the anatomic, cellular, and molecular features of the Sox10+ glial lineage of the mouse lung. Using high-resolution imaging, we quantified the distribution and cellular morphologies of myelinating, non-myelinating, satellite, and terminal glial cells with their intricate extensions along peripheral nerves, including terminals at specialized neurosensory structures within the lung. Spatial analysis of selectively expressed myelinating (periaxin/Prx, claudin 19/Cldn) or non-myelinating (sodium channel/Scn7a) glial cell genes identified by scRNA-seq analysis revealed molecularly distinct populations surrounding myelinated nerve fibers in the lung. To extend this analysis to primates and other organs, we extracted rare peripheral glial cells in whole organism scRNA-seq atlases of mouse lemur and human. Our cross-species data analysis and integration of scRNA-seq data of ~700 peripheral glial cells from mouse, mouse lemur, and human glial cells identified conserved gene expression of molecularly distinct peripheral glial cell populations. This foundational knowledge facilitates subsequent functional studies targeting molecularly distinct subsets of peripheral glia and integrating them into organ-specific disorders of autonomic dysregulation. In addition, our cross-species analysis identifying conserved gene expression patterns and glial networks in extrapulmonary organs provides a valuable resource for studying the functional role of peripheral glia in multiorgan human diseases.
A qualitative study of lived experience and life courses following dam release flooding in Northern Ghanaian communities: Implications for damage and loss assessment
Authors: Asamoah Moses , Dzodzomenyo Mawuli , Gyimah Faustina Twumwaa , Li Chengxiu , Agyemang Linda , Wright Jim
Published: December 2024

Background

Dams provide water for industrial, agricultural, and domestic use, particularly in arid regions. However, controlled dam releases due to heavy rainfall may affect downstream communities’ livelihoods and life courses such long-term impacts may be omitted from damage and loss assessments. This study aims to assess the lived experiences and long-term consequences of dam release flooding for downstream populations, comparing these with the typical scope of a damage and loss assessment (DaLA).

Methods

This research was conducted in two flood-prone districts in the White Volta basin, Ghana, subject to dam spillage. Four Focus Group Discussions (FGDs) with community opinion headers, household heads, chiefs, local politicians, and institutional staff were conducted and analysed, alongside semi-structured interviews with twelve opinion leaders and disaster-related institutions.

Results

Flood-affected communities struggled to attract partners for marriage due to stigmatisation from flooding impacts. Women outside flooded areas rejected male members’ marriage proposals, while communities offered young girls for marriage to wealthy men for greater financial security. Out-migration of female members to seek better livelihoods frequently led to divorce, subsequently affecting children’s education and well-being. Participants reported long-term trauma from flood-related contact with dangerous wildlife, travel disruption, disease risk, livelihood loss, and accidents. Such life course events and long-term trauma would be omitted from a DaLA exercise.

Conclusion

Beyond its immediate impacts, flooding undermines family relationships and marriage, impairing children’s education and traumatises affected communities. We recommend livelihood diversification programmes, psychological support and family counselling to address these long-term impacts, with expansion of DaLA’s scope to underpin such support.