bluuebunny/crossref_metadata_2025 huggingface dataset:
Sleep Duration, Mortality, and High-Risk Populations: A Nationwide Study in the United States
Authors: Kim Minjeong , Lee Hyejung , Ahn Seoyeong , Lee Whanhee
Published: January 2025

Objectives: Both insufficient and excessive sleep durations have been recognized as important risk factors for mortality. Nevertheless, the impact of sleep duration on cause-specific mortality and potential effect modifiers has not been investigated extensively. Therefore, this study aimed to assess the association between sleep duration and mortality categorized by cause of death and potential effect modifiers using data from the National Health and Nutrition Examination Survey (NHANES). Methods: We established a prospective cohort based on NHANES participants aged 50 years or older, linked to the National Death Index (NDI) in the United States between 2009 and 2018. The NDI included all-cause, cardiovascular, and respiratory deaths. Sleep duration was assessed during the NHANES examination period. A survey-weighted Cox proportional hazards model was used to evaluate the association between sleep and mortality. Results: A total of 13,947 participants with available NHANES data were included in this study. A U-shaped association between sleep duration and mortality was observed for all-cause and cardiovascular mortality, meanwhile, respiratory mortality was linked to moderately short sleep (>5 and <7 hours). For total mortality, the association with severe short sleep (5 hours or less; p<0.01) was generally stronger than the association with long sleep (>8 hours; p=0.029), with the effect of severe short sleep being significantly prominent in males (p<0.01), non-Hispanic White (0.001), high-income (0.056), and those with a body mass index ≥23.0 kg/m2 (0.001) than those in their counterparts. Conclusions: This study suggests that sleep duration is associated with the mortality risk. Our results provide evidence for a more targeted allocation of public health resources to improve sleep and health.
Multipolar multifunction terahertz tunable metasurface
Authors: Xiao Yongjiang , Liao Kun
Published: January 2025

A terahertz coded metasurface composed of VO2, polyimide, and Au is proposed. Based on line polarization multiplexing, seven functions in all are realized by designing the structure of the top VO2 resonator and the middle gold pattern. The simulation results show that when VO2 is metallic and the linearly polarized wave of f=1−2THz is vertically incident, the unit exhibits broadband absorption with an absorption rate (AR) greater than 84%. The AR in the range of 1.56–2 THz can reach more than 90%. When VO2 is insulated, the unit can achieve narrowband absorption at 1.57 THz, with an AR of nearly 100%. Meanwhile, the same coded metasurface can realize one of the five functions of beam deflection, vortex beam, deflected vortex beam, beam splitting, and superimposed vortex beam under x and y polarization modes. This work can provide certain reference for the design of multifunctional devices with metamaterial in the terahertz field.
Entangled multidirectional corrugated core lightweight mirror designs for space-based telescopes
Authors: Rahmani Mahdi , Bouafia Mohamed
Published: January 2025

This paper presents new innovative designs for lightweight mirror blanks intended for space-based telescopes, to our knowledge, utilizing new types of core structures, entangled multidirectional corrugated cores. By manipulating, entangling, and merging corrugated plates with various orientations, we developed several core designs. Using finite element modeling, we evaluated these designs and compared them with classical honeycomb core designs under axial gravity, lateral gravity, polishing pressure, and modal analysis. The entangled multidirectional corrugated core mirrors show better performances compared to classical honeycomb core mirrors. Improvements of performances up to 32.13% were achieved.
Online monitoring of a high-power CW laser optical mirror based on infrared and visible image features visualization
Authors: Luo Xinyu , Yang Peng , Li Qian , Guo Silin , Qiu Jing , Liu Guanjun
Published: January 2025

In high-power CW (continuous wave) laser systems, laser damage to optical mirrors often occurs, and it is urgent to develop timely and effective monitoring technologies to avoid laser damage or emergency stop at the early damage stage. In this paper, an online monitoring method based on the combination of infrared and visible images is proposed. The proposed method is based on the feature recognition of infrared and visible images. After setting an appropriate threshold, a decision model can be employed to enable real-time monitoring and health status evaluation of optical mirrors. Here, the thresholds for abnormal and dangerous temperatures were established at 100°C and 200°C, respectively. The results show that the temperature of the optical mirror would significantly increase after damage, with the surface temperature of the element reaching up to 250°C. At the same time, the damaged area could be captured by a visible camera and the changes in gray values were displayed in the visible image. Online monitoring of the health status of optical elements can be achieved by assessing changes in infrared image temperature, visible image spot position, and area. This monitoring method serves as an early warning method for potential optical elements damage.
Spectral shifts in partially coherent light beams passing through a crystalline human eye lens
Authors: Sahin Serkan
Published: January 2025

Our objective is to quantify the spectral changes occurring in
partially coherent light beams as they interact with the crystalline
lens of the human eye. The study reveals a significant alteration in
the wavelength of random light beams as they traverse through the
human eye. The methodology comprises three key components: the ABCD
matrix elements of the lens, the cross-spectral density matrix of the
light beam, and the spectral shifts in the beam during propagation.
Following an initial examination of how the crystalline human eye lens
responds to stochastic light, we can now analyze the interaction of
various types of light with the eye lens. The entering light is
broadband, exhibiting a range of coherence values from incoherent to
fully coherent. By employing the diffraction theory of optics
alongside ray tracing methods, we observe wavelength shifts in
partially coherent light passing through the human eye lens. The study
involves directing unpolarized random light with a cross-sectional
radius of approximately 0.3 mm numerically to the lens surface,
situated at the minimum pupil radius of around 0.5 mm. The
propagation is then analyzed over a distance of 17 mm after the
lens, representing the typical length of the vitreous humor. Numerical
plots demonstrate a wavelength shift in the incident light (with a
Gaussian profile). In summary, our findings indicate that the
correlation effects of nearly natural light on the gradient index of
the human eye lens lead to a notable spectral shift.
Broadband microwave signal generation with programmable chirp shapes via low-speed electronics-controlled phase-modulated optical loop
Authors: Lyu Weiqiang , Tian Huan , Fu Zhenwei , Zhang Lingjie , Zeng Zhen , Zhang Yaowen , Li Heping , Zhang Zhiyao , Liu Yong
Published: January 2025

Broadband microwave signals with customized chirp shapes are highly captivating in practical applications. Compared with electronic technology, photonic solutions are superior in bandwidth but suffer from flexible and rapid manipulation of chirp shape or frequency. Here, we demonstrate a concept for generating broadband microwave signals with programmable chirp shapes. Our realization is based on a recirculating phase-modulated optical loop to ultrafast manipulate the laser frequency, which breaks the limitation of the buildup time of the laser from spontaneous emission. Through heterodyne beating the frequency-agile lasers with a continuous-wave laser, microwave signals with ultrafast and programmable chirp shapes are generated. Besides, signal parameters, such as bandwidth, center frequency, and temporal duration, can be reconfigured. In the experiment, highly coherent microwave signals with various customized chirp shapes are generated, where the time resolution for programming the chirp shape is 649 ps. This flexible frequency manipulation characteristic holds promise for many applications, including LiDAR, broadband radar systems, and spectroscopy.
Semi-analytical model for electrically injected GaAs nano-ridge laser diodes monolithically integrated on silicon
Authors: Yimam Andualem Ali , Colucci Davide , Caer Charles , Yudistira Didit , De Koninck Yannick , Sar Huseyin , Baryshnikova Marina , Verheyen Peter , Van Campenhout Joris , Kunert Bernardette , Morthier Geert , Van Thourhout Dries
Published: January 2025

We present a semi-analytical model that can accurately explain the working principle behind the recently reported electrically injected In0.2Ga0.8As/GaAs monolithic nano-ridge lasers and more importantly show how the model can be used to study the effect of device parameters on the spectral behavior, the slope efficiency and the threshold gain. We show that mode beating between the fundamental mode and a higher order mode is fundamental in the operation of these lasers. Analytical expressions for codirectional mode coupling are used in developing the round-trip laser model. Results from analytical expressions are verified by comparisons with simulations and the model is supported later by measurement results.
Efficient algorithm for resource optimization in optical communication networks
Authors: Dong Yan , Peng Qi , Houichi Mehdi , Alshahrani Reem , Abeba Sana , Park Kisung
Published: January 2025

Beyond 5 G and 6 G, communication systems should be able to deliver high throughput, low latency, high dependability, and high energy efficiency services. The creation of hybrid systems that can meet and largely satisfy these needs is promised by the merging of systems based on optical communication and radio frequency (RF). Smart devices may work together to cooperatively train Machine Learning (ML) models in a distributed fashion using Federated Learning (FL), all without disclosing personal information to a central server. This paper proposes a new solution to optimize the network resources in optical-RF communication network. The main idea is to optimize user selection, transmission power and channel estimation based on multilayer perception. Then, the loss function is minimized through joint optimization of user selection and transmission power. Simulation results show that, the proposed algorithm has better performance as compared with existing algorithms.
PSLFM: a single-frame uncalibrated photometric stereoscopic light field measurement scheme based on dense convolutional neural networks
Authors: Zhang Kaiyi , Zhao Xing , Wen Ya , Li Da
Published: January 2025

In the realm of 3D measurement, photometric stereo excels in capturing high-frequency details but suffers from accumulated errors that lead to low-frequency distortions in the reconstructed surface. Conversely, light field (LF) reconstruction provides satisfactory low-frequency geometry but sacrifices spatial resolution, impacting high-frequency detail quality. To tackle these challenges, we propose a photometric stereoscopic light field measurement (PSLFM) scheme that harnesses the strengths of both methods. We have developed an integrated information acquisition system that requires only a single data acquisition and does not necessitate the light source vectors as input. This system enables uncalibrated multispectral photometric stereo reconstruction using a dense convolutional neural network (DCN). After that, the two reconstruction results are processed by frequency domain filtering, and the processed results are fused according to a certain weight, which can be adaptively determined by the algorithm according to the reconstruction error. Utilizing a light field camera as the sole acquisition device allows for natural alignment of data, mitigating registration errors. Our approach demonstrates effectiveness across both online datasets and laboratory samples, achieving an error of about 10° and lower in uncalibrated scenarios, with notable generalization. In conclusion, the proposed method facilitates single-frame measurement without calibration and exhibits strong robustness, which is expected to exert significant influence in the fields of machine vision, 3D printing and manufacturing, as well as virtual reality and augmented reality.
Multimode dynamics of a monolithically integrated, tunable, bidirectional, gain switched optical comb source
Authors: Liston Odhran , McCarthy John , O’Sullivan Diarmuid , Dernaika Mohamad , Peters Frank , Kelleher Bryan
Published: January 2025

A three-sectioned, bidirectionally coupled, tunable, optical comb source is presented. The photonic integrated circuit (PIC) consists of a gain section, a slotted mirror section and a Fabry-Perot (FP) section. Optical frequency combs (OFCs) are produced by gain switching the FP section via a high power radio frequency (RF) signal. An investigation into the effect of the RF frequency on the quality of the OFC is performed. Multimode behavior is observed with OFCs produced in multiple modes as well as the overall degradation in the quality of the combs in each mode. A minimal extension multimode rate equation model is presented that reproduces the experimental results extremely well using experimentally determined values for numerical parameters. The appearance of multimode behavior is interpreted as relating to the modified relaxation oscillation frequency of the bidirectionally coupled system.
Behavior of optical parametric amplification of space-time wave packets
Authors: Lu Kezheng , Li Zhaoyang , Leng Yuxin
Published: January 2025

The space-time wave packet (STWP) is a type of pulsed optical field, exhibiting distinctive characteristics, including the capacity to propagate without diffraction or dispersion and to have arbitrary group velocities. However, the intensity of the STWP is constrained by the low damage threshold of some indispensable optical elements like the spatial light modulator (SLM). While optical parametric amplification (OPA) has been proposed for amplifying STWPs, spatio-temporal (ST) characteristics of amplified STWPs remain significantly unexplored. In this article, we investigate the effects of OPA on STWPs and examine how key parameters influence the amplification results. Based on the numerical simulation results, we propose two methods to reduce the duration of the amplified STWP and one method to amplify the STWP with higher group velocities. These findings could facilitate the application of STWPs in strong-field optics.
10−15-level laser stabilization down to fiber thermal noise limit using self-homodyne detection
Authors: Jeon Igju , Jeong Woosong , Ahn Changmin , Kim Jungwon
Published: January 2025

We demonstrate a self-homodyne detection method to stabilize a continuous-wave 1550-nm laser to a 1-km optical fiber delay line, achieving a frequency instability of 6.3 × 10−15 at a 16-ms averaging time. This result, limited by fiber thermal noise, is achieved without the need for a vacuum system, highlighting the potential of our approach for ultra-stable laser systems in non-laboratory environments. The system utilizes only a few passive fiber optic components and a single balanced photodetector, significantly simplifying the laser stabilization process while maintaining high performance. The entire optical setup is compactly packaged in a portable metal air-tight case.
Hundred-watt-level supercontinuum generation from an erbium–ytterbium doped fiber amplifier based on the cross-phase modulation
Authors: Jiang Li , Song Rui , Li Kailong , Zhao Desheng , Hou Jing , Han Kai
Published: January 2025

The pumping mechanism based on the cross-phase modulation (XPM) effect can achieve a flat broadband supercontinuum (SC) output. In this paper, we demonstrate a novel, to the best of our knowledge, scheme for SC generation from a large mode area (LMA) erbium–ytterbium co-doped fiber (EYDF) amplifier based on this XPM effect by utilizing both the gain and dispersion characteristics of the EYDF, achieving a hundred-watt-level flat broadband SC output. The scheme consists of two pulsed lasers with a synchronized trigger signal and a LMA-EYDF amplifier. In order to enhance the XPM effect effectively, the central wavelengths of two pulsed lasers are selected as 1030 nm and 1535 nm according to the calculated group velocity curve of the passive fiber in the EYDF amplifier. The output powers of 1030 nm and 1535 nm pulses are scaled to 58 W and 131 W after the EYDF, where the dual-wavelength is first amplified and the output power is the highest level in the 1 µm/1.5 µm dual-wavelength lasers reported so far. After the dual-wavelength lasers undergo the nonlinear accumulation in the EYDF amplifier, the final SC with a spectrum spanning the 770 nm–2055 nm at −10 dB level excluding the residual pump peak is achieved and an output power of 104 W is obtained. This is the widest spectral bandwidth at −10 dB level and the highest output power in the reported SC generation from an EYDF amplifier. This work provides a common platform to generate a high-power flat broadband SC independent of fiber design, further promoting the development of LMA fiber-based SC sources.
High-speed spectral imaging via multispectral pulse illumination and temporal–spectral decoupling
Authors: Wu Jinxuan , Li Daoyu , Zhao Jiajun , Xu Hanwen , Zhang Yuzhe , Bian Liheng
Published: January 2025

Spectral imaging (SI) faces inherent trade-offs among spatial, temporal, and spectral resolutions due to limited bandwidth. Current high-speed SI systems, relying on fast modulation or specific cameras, compromise spatial resolution or suffer high complexity and cost. This work presents a low-cost, high-speed SI scheme achieving up to 240 frames per second (fps) and even μs-resolved multispectral observation. This work reveals the inherent temporal–spectral redundancy in SI videos and reports an active temporal–spectral coupling (TSC) and decoupling (TSD) strategy for high-speed SI. We established a prototype system using a snapshot SI camera and a multispectral LED array. The LEDs sequentially illuminate the scene channel by channel in one exposure for TSC acquisition. Each channel of the measurement corresponds one-to-one to an illumination moment. A transformer-based network is applied to decouple textural and spectral information from the measurement and re-couple them to reconstruct images across all channels and time instances. Experiments validated that the reported framework can successfully record μs-resolved multispectral videos.
Iterative Kramers–Kronig method for non-interferometric quantitative phase imaging: beyond the first-order Born and Rytov approximations
Authors: Shen Qian , Sun Jiasong , Zhou Shun , Fan Yao , Li Zhuoshi , Chen Qian , Trusiak Maciej , Kujawinska Malgorzata , Zuo Chao
Published: January 2025

Traditional non-interferometric quantitative phase imaging (QPI) methods often face challenges in realizing rapid and accurate imaging of large-phase samples, mainly due to slow convergence and dependence on object approximation models. In this Letter, we propose a new, to the best of our knowledge, non-interferometric QPI approach that leverages iterative Kramers–Kronig (KK) relations, named iKK-QPI, to achieve high-accuracy quantitative measurement of objects with large-phase values. In the current KK relations reconstruction framework, we impose real-part constraints on the cepstrum, breaking the restriction of weak scattering condition. With only a few iterations, iKK-QPI extends the phase range that can be reliably retrieved by non-interferometric QPI, exceeding the first-order Born and Rytov approximations. The capability of iKK-QPI is demonstrated by imaging a microlens array and COS-7 cells. We accurately reconstruct objects with large-phase ranges 6 rad (error < ± 5%), three times that of the KK relations-based method, opening up the possibility for non-interferometric QPI to measure biological and industrial samples with large-phase features.
Single-shot spontaneous Raman scattering for time-resolved one-dimensional hypersonic flow diagnostics
Authors: Bak Junhwi , Leonov Boris S. , Miles Richard B.
Published: January 2025

Spontaneous Raman scattering, also known as common old ordinary Raman scattering (COORS), is revisited to evaluate its applicability for hypersonic flow characterization. Due to its very low cross section, Raman scattering is often considered unsuitable for measuring low-pressure gas properties that are found in ground test simulations of high-altitude hypersonic flights. Utilizing a recently developed one-dimensional (1D) light scattering technique with a volume Bragg grating filter and Stokes sideband windowing, we demonstrate 1D rotational Raman measurements of temperature and neutral gas density across a bow shock in front of a blunt wedge model under Mach 6 hypersonic flow. The experiment was conducted in the Hypervelocity Expansion Tunnel at Texas A&M University. The measurements were successfully obtained during a single run of the tunnel operation, capturing the temperature and density distributions with dynamic ranges of 200–2000 K and 5×1023−4×1024/m3, respectively, over both the free-stream and post-shock regions, covering approximately 10 mm in length with a spatial resolution of <0.5mm. Time-resolved high-speed measurement capability at 100 kHz was also demonstrated, showcasing the robustness of 1D COORS for gas diagnostics.
Structuring Space-Time for Waves and Particles
Authors: Caloz Christophe , Bahrami Amir , Stevens Artuur
Published: January 2025

We present space-time metamaterials as the natural successors to time-varying metamaterials, highlighting their additional properties and potential benefits. These metamaterials offer a virtually unlimited range of new challenges based on their dynamic levels, space-time structures, and velocity regimes. They particularly provide rich opportunities for transition engineering, enabling spectral transformations to control classical and quantum state transitions.
Terminology in ecology and evolutionary biology disproportionately harms marginalized groups
Authors: Rice Mallory M. , Tumber-Dávila Shersingh Joseph , Baiz Marcella D. , Cheng Susan J. , Darragh Kathy , Estien Cesar O. , Hammond J. W. , Ignace Danielle D. , Khadempour Lily , Gaynor Kaitlyn M. , Mills Kirby L. , Smith Justine A. , Moore Alex C.
Published: January 2025

The discipline of ecology and evolutionary biology (EEB) has long grappled with issues of inclusivity and representation, particularly for individuals with systematically excluded and marginalized backgrounds or identities. For example, significant representation disparities still persist that disproportionately affect women and gender minorities; Black, Indigenous, and People of Color (BIPOC); individuals with disabilities; and people who are LGBTQIA+. Recent calls for action have urged the EEB community to directly address issues of representation, inclusion, justice, and equity. One aspect of this endeavor is to examine the use of EEB’s discipline-specific language and terminology, which may have the potential to perpetuate unjust systems and isolate marginalized groups. Through a mixed-methods survey, we examined how members of the EEB community perceive discipline-specific terminology, including how they believe it can be harmful and which terms they identified as problematic. Of the 795 survey respondents, we found that almost half agreed that there are harmful terms in EEB and that many individuals from marginalized groups responded that they have been harmed by such terminology. Most of the terms identified as harmful relate to race, ethnicity, and immigration; sex and gender; geopolitical hierarchies; and historical violence. Our findings suggest there is an urgent need for EEB to confront and critically reassess its discipline-specific terminology. By identifying harmful terms and their impacts, our study represents a crucial first step toward dismantling deeply rooted exclusionary structures in EEB. We encourage individuals, communities, and institutions to use these findings to reevaluate language used in disciplinary research, teaching and mentoring, manuscripts, and professional societies. Rectifying current harms in EEB will help promote a more just and inclusive discipline.
Role and modulation of various spinal pathways for human upper limb control in different gravity conditions
Authors: Bruel Alice , Bacha Lina , Boehly Emma , De Trogoff Constance , Represa Luca , Courtine Gregoire , Ijspeert Auke
Published: January 2025

Humans can perform movements in various physical environments and positions (corresponding to different experienced gravity), requiring the interaction of the musculoskeletal system, the neural system and the external environment. The neural system is itself comprised of several interactive components, from the brain mainly conducting motor planning, to the spinal cord (SC) implementing its own motor control centres through sensory reflexes. Nevertheless, it remains unclear whether similar movements in various environmental dynamics necessitate adapting modulation at the brain level, correcting modulation at the spinal level, or both. Here, we addressed this question by focusing on upper limb motor control in various gravity conditions (magnitudes and directions) and using neuromusculoskeletal simulation tools. We integrated supraspinal sinusoidal commands with a modular SC model controlling a musculoskeletal model to reproduce various recorded arm trajectories (kinematics and EMGs) in different contexts. We first studied the role of various spinal pathways (such as stretch reflexes) in movement smoothness and robustness against perturbation. Then, we optimised the supraspinal sinusoidal commands without and with a fixed SC model including stretch reflexes to reproduce a target trajectory in various gravity conditions. Inversely, we fixed the supraspinal commands and optimised the spinal synaptic strengths in the different environments. In the first optimisation context, the presence of SC resulted in easier optimisation of the supraspinal commands (faster convergence, better performance). The main supraspinal commands modulation was found in the flexor sinusoid’s amplitude, resp. frequency, to adapt to different gravity magnitudes, resp. directions. In the second optimisation context, the modulation of the spinal synaptic strengths also remarkably reproduced the target trajectory for the mild gravity changes. We highlighted that both strategies of modulation of the supraspinal commands or spinal stretch pathways can be used to control movements in different gravity environments. Our results thus support that the SC can assist gravity compensation.
Ensemble learning-based predictor for driver synonymous mutation with sequence representation
Authors: Bi Chuanmei , Shi Yong , Xia Junfeng , Liang Zhen , Wu Zhiqiang , Xu Kai , Cheng Na
Published: January 2025

Synonymous mutations, once considered neutral, are now understood to have significant implications for a variety of diseases, particularly cancer. It is indispensable to identify these driver synonymous mutations in human cancers, yet current methods are constrained by data limitations. In this study, we initially investigate the impact of sequence-based features, including DNA shape, physicochemical properties and one-hot encoding of nucleotides, and deep learning-derived features from pre-trained chemical molecule language models based on BERT. Subsequently, we propose EPEL, an effect predictor for synonymous mutations employing ensemble learning. EPEL combines five tree-based models and optimizes feature selection to enhance predictive accuracy. Notably, the incorporation of DNA shape features and deep learning-derived features from chemical molecule represents a pioneering effect in assessing the impact of synonymous mutations in cancer. Compared to existing state-of-the-art methods, EPEL demonstrates superior performance on the independent test dataset. Furthermore, our analysis reveals a significant correlation between effect scores and patient outcomes across various cancer types. Interestingly, while deep learning methods have shown promise in other fields, their DNA sequence representations do not significantly enhance the identification of driver synonymous mutations in this study. Overall, we anticipate that EPEL will facilitate researchers to more precisely target driver synonymous mutations. EPEL is designed with flexibility, allowing users to retrain the prediction model and generate effect scores for synonymous mutations in human cancers. A user-friendly web server for EPEL is available at http://ahmu.EPEL.bio/.
Leveraging cancer mutation data to inform the pathogenicity classification of germline missense variants
Authors: Haque Bushra , Cheerie David , Pan Amy , Curtis Meredith , Nalpathamkalam Thomas , Nguyen Jimmy , Salhab Celine , Thiruvahindrapuram Bhooma , Zhang Jade , Couse Madeline , Hartley Taila , Morrow Michelle M. , Price E. Magda , Walker Susan , Malkin David , Roth Frederick P. , Costain Gregory
Published: January 2025

Innovative and easy-to-implement strategies are needed to improve the pathogenicity assessment of rare germline missense variants. Somatic cancer driver mutations identified through large-scale tumor sequencing studies often impact genes that are also associated with rare Mendelian disorders. The use of cancer mutation data to aid in the interpretation of germline missense variants, regardless of whether the gene is associated with a hereditary cancer predisposition syndrome or a non-cancer-related developmental disorder, has not been systematically assessed. We extracted putative cancer driver missense mutations from the Cancer Hotspots database and annotated them as germline variants, including presence/absence and classification in ClinVar. We trained two supervised learning models (logistic regression and random forest) to predict variant classifications of germline missense variants in ClinVar using Cancer Hotspot data (training dataset). The performance of each model was evaluated with an independent test dataset generated in part from searching public and private genome-wide sequencing datasets from ~1.5 million individuals. Of the 2,447 cancer mutations, 691 corresponding germline variants had been previously classified in ClinVar: 426 (61.6%) as likely pathogenic/pathogenic, 261 (37.8%) as uncertain significance, and 4 (0.6%) as likely benign/benign. The odds ratio for a likely pathogenic/pathogenic classification in ClinVar was 28.3 (95% confidence interval: 24.2–33.1, p < 0.001), compared with all other germline missense variants in the same 216 genes. Both supervised learning models showed high correlation with pathogenicity assessments in the training dataset. There was high area under precision-recall curve values (0.847 and 0.829) and area under the receiver-operating characteristic curve values (0.821 and 0.774) for logistic regression and random forest models, respectively, when applied to the test dataset. With the use of cancer and germline datasets and supervised learning techniques, our study shows that cancer mutation data can be leveraged to improve the interpretation of germline missense variation potentially causing rare Mendelian disorders.
Quality of care offered by health care retail markets for medication abortion self-management: Findings from states in Nigeria and India
Authors: Shankar Mridula , Omoluabi Elizabeth , OlaOlorun Funmilola M. , Khanna Anoop , Ahmad Danish , Moreau Caroline , Bell Suzanne O.
Published: January 2025

Dispensing of misoprostol and mifepristone by pharmacies and chemist shops for self-management of medication abortion (MA) fills a crucial gap in settings where abortion care by trained health professionals is not readily available. This promising service delivery pathway, endorsed by the World Health Organization (WHO), is hindered by concerns of poor-quality care. Simulated clients collected data on MA pill dispensing practices from 92 pharmacies and chemist shops in three Nigerian states and 127 pharmacies in an Indian state that we have anonymized. Guided by the WHO’s abortion guideline, we measured process-related quality indicators such as medication use instructions, warning signs, and respectful treatment among other aspects. We aggregated indicators under three domains: technical competence, information given to clients, and client experience. Overall, 51% of facilities in the Nigerian states and 32% in the Indian state offered MA pills. Most dispensing facilities offered the misoprostol-only regimen in Nigeria (68%) and the combination regimen in the Indian state (83%). Among facilities offering MA pills, 26% in Nigeria and 78% in the Indian state provided correct instructions on route of pill administration. Accurate information on the appropriate interval between pill type in the combination regimen was low in Nigeria (27%) and the Indian state (14%). Excessive bleeding as a warning sign was discussed more frequently in the Indian (56%) versus Nigerian states (32%); other abnormal bleeding patterns were rarely mentioned. Aggregate technical competency scores were low at 18% in Nigeria and 34% in the Indian state, with highest scores for client experience at 90% and 91% respectively. Findings suggest that people using MA pills purchased from the retail market are not given accurate and adequate information for most effective self-use. If MA self-management remains outside regulatory boundaries, technical quality will remain sub-standard, imposing unnecessary costs to people, their health, and health systems.
Assessing the prevalence of insomnia and its socio-behavioral determinants among school going adolescents in Bagamati Province, Nepal
Authors: Sharma Mahesh , Bista Parvati , Khatri Bijay , Upadhyaya Dipak Prasad , Khanal Vijay Kumar , Sapkota Bhim Prasad , Tiwari Dipak Prasad , Jha Nilambar , Baral Dharanidhar , Gurung Gyanu Nepal , Acharya Dilaram
Published: January 2025

Insomnia among adolescents is a prevalent public health concern and is closely linked to suicidal tendencies, health risk behaviors, and other adverse health outcomes. This study builds on existing literature by exploring the multifaceted associations between insomnia and socio-behavioral factors, which are currently underexplored in the Nepalese context. It assesses the prevalence of insomnia and its association with socio-behavioral factors and internet addiction among adolescents in Bagmati Province, Nepal, to inform targeted public health interventions. From July to September 2022, a school-based descriptive cross-sectional study was conducted among grade 9 and 10 students (aged 13–19) using a self-administered semi-structured questionnaire. A questionnaire included the 7-item Insomnia Severity Index (ISI) for insomnia assessment and the 20-item Young’s Internet Addiction Test for evaluating internet addiction. Binary logistic regression analysis was utilized to identify factors associated with insomnia. The study identified a significant prevalence of insomnia at 24.2%. Key socio-behavioral determinants included religion [AOR 3.58; 95% CI 1.56–8.23, AOR 3.36; 95% CI 1.27–8.89], experience of a break up [AOR 1.67; 95% CI 1.10–2.55] absence of close friendships [AOR 2.62; 95% CI 1.32–5.19], exposure to bullying [AOR 1.74, 95% CI 1.12–2.70], and internet addiction [AOR 2.74; CI 1.83–4.11]. These findings highlight the complex interplay of individual and environmental factors influencing insomnia. The significant prevalence of insomnia among school-going adolescents in Bagmati Province underscores the necessity for enhancing the role of schools in health counselling that considers behavioural, social, and demographic factors. Addressing internet addiction, fostering healthy social connections, and acknowledging the impact of demographic factors like religion could enhance intervention strategies.
Toxoplasma gondii from Gabonese forest, Central Africa: First report of an African wild strain
Authors: Galal Lokman , Fritz Matthieu , Becquart Pierre , Passebosc-Faure Karine , Plault Nicolas , Boundenga Larson , Mombo Illich Manfred , Kombila Linda Bohou , Mebaley Telstar Ndong , Lenguiya Léadisaelle Hosanna , Ngoubangoye Barthélémy , N’Dilimabaka Nadine , Prugnolle Franck , Forestier Lionel , Gebremedhin Endrias Zewdu , Leroy Eric M. , Maganga Gael Darren , Mercier Aurélien
Published: January 2025

The protozoan Toxoplasma gondii is a ubiquitous and highly prevalent parasite that can theoretically infect all warm-blooded vertebrates. In humans, toxoplasmosis causes infections in both immunodeficient and immunocompetent patients, congenital toxoplasmosis, and ocular lesions. These manifestations have different degrees of severity. Clinical severity is determined by multiple factors, including the genotype of the T. gondii strain involved in the infection. T. gondii exhibits remarkable genetic diversity, which varies according to geography and ecotype (domestic or wild). Previous studies have demonstrated that wild strains of T. gondii are of particular epidemiological interest, as they have been associated with more severe forms of toxoplasmosis in different regions of the world. However, no data on wild strains of T. gondii are available from Africa. In this study, we describe for the first time a wild T. gondii strain from Africa. Wild animals from the forest environment of Gabon, Central Africa, were screened for chronic infection with T. gondii using quantitative PCR. The infecting T. gondii strains were genotyped whenever possible by the analysis of 15 microsatellite markers and by whole-genome sequencing. A new T. gondii genotype was identified in the DNA extract from a heart sample of a duiker (Cephalophus sp.) and was found to be highly divergent from previously described T. gondii populations worldwide, including those from domestic environments in Gabon. This discovery suggests the existence of a wild T. gondii population in Africa. The role of wild T. gondii strains in the incidence of severe toxoplasmosis in Africa remains unclear and requires further investigation.
Genetic variation of hemolysin co-regulated protein 1 affects the immunogenicity and pathogenicity of Burkholderia pseudomallei
Authors: Tandhavanant Sarunporn , Yimthin Thatcha , Sengyee Sineenart , Charoenwattanasatien Ratana , Lebedev Andrey A. , Lafontaine Eric R. , Hogan Robert J. , Chewapreecha Claire , West T. Eoin , Brett Paul J. , Burtnick Mary N. , Chantratita Narisara
Published: January 2025

Hemolysin co-regulated protein 1 (Hcp1) is a component of the cluster 1 Type VI secretion system (T6SS1) that plays a key role during the intracellular lifecycle of Burkholderia pseudomallei. Hcp1 is recognized as a promising target antigen for developing melioidosis diagnostics and vaccines. While the gene encoding Hcp1 is retained across B. pseudomallei strains, variants of hcp1 have recently been identified. This study aimed to examine the prevalence of hcp1 variants in clinical isolates of B. pseudomallei, assess the antigenicity of the Hcp1 variants, and the ability of strains expressing these variants to stimulate multinucleated giant cell (MNGC) formation in comparison to strains expressing wild-type Hcp1 (Hcp1wt). Sequence analysis of 1,283 primary clinical isolates of B. pseudomallei demonstrated the presence of 8 hcp1 alleles encoding three types of Hcp1 proteins, including Hcp1wt (98.05%), Hcp1variant A (1.87%) and Hcp1variant B (0.08%). Compared to strains expressing Hcp1wt, those expressing the dominant variant, Hcp1variant A, stimulated lower levels of Hcp1variant A-specific antibody responses in melioidosis patients. Interestingly, when Hcp1variant A was expressed in B. pseudomallei K96243, this strain retained the ability to stimulate MNGC formation in A549 cells. In contrast, however, similar experiments with the Hcp1variant B demonstrated a decreased ability of B. pseudomallei to stimulate MNGC formation. Collectively, these results show that B. pseudomallei strains expressing variants of Hcp1 elicit variable antibody responses in melioidosis patients and differ in their ability to promote MNGC formation in cell culture.
First detection of the S989P+V1016G+D1763Y haplotype and expansion of voltage-gated sodium channel mutations in Aedes aegypti in Taiwan in 2016–2023
Authors: Chung Han-Hsuan , Teng Hwa-Jen , Huang Chin-Gi , Tsai I-Jung , Chen Hung-Jui , Komagata Osamu , Kasai Shinji , Tsai Kun-Hsien , Chen Shiu-Ling
Published: January 2025

Background

Aedes aegypti transmits various arthropod-borne diseases such as dengue, posing a significant burden to public health in tropical and subtropical regions. Pyrethroid-based control strategies are effective in managing this vector; however, the development of insecticide resistance has hindered these efforts. Hence, long-term monitoring of insecticide resistance in mosquito populations is crucial for effective vector and disease control.

Methodology/principal findings

In this study, we identified insecticide resistance due to a voltage-gated sodium channel (vgsc) mutation in Ae. aegypti in Taiwan between 2016 and 2023. In total, 1,761 field-caught Ae. aegypti samples from Tainan, Kaohsiung, and Pingtung were genotyped. The frequencies of S989P, V1016G, T1520I, F1534C, and D1763Y amino acid variants increased over the surveillance period. A T1520I mutation was detected for the first time and has since rapidly spread throughout Taiwan. The triple-mutant haplotype PGTFY was first documented in Ae. aegypti. Moreover, the unmutated haplotype vanished in Taiwan, suggesting that the vgsc mutations were fixed in local populations of Ae. aegypti. Five resistance-associated genotypes, SVTCD/SVTCD, SGTFY/PGTFD, SVTCD/SGTFY, PGTFD/PGTFD, and SVTCD/PGTFD, exhibited an increased frequency and accounted for 76% of the total field population. We also detected the resistant genotype SVICD/PGTFD, and its frequency increased 13-fold in the field between 2016 and 2023. Moreover, we also observed that mutations differed geographically, with S989P mainly found in Kaohsiung and V1016G in Kaohsiung and Pingtung. The frequency of T1520I was noticeably higher in Kaohsiung, and D1763Y occurred mainly in Tainan.

Conclusions/significance

The emergence and expansion of mutations along with the disappearance of wild-type mosquitoes in Taiwan underscores the threat of resistance and difficulty of mosquito control in Taiwan as well as globally. This study determined the insecticide resistance status of Ae. aegypti in Taiwan, and the findings will be helpful for resistance monitoring in areas where pyrethroids are used to control Ae. aegypti.
University students’ health-related quality of life and its determinants. Results from a cross-sectional survey during the COVID-19 pandemic
Authors: Wagner Karoline , Reinhardt Zoë , Negash Sarah , Weber Lena , Wienke Andreas , Mikolajczyk Rafael , Führer Amand
Published: January 2025

Being a university student is a vulnerable period marked by transitions and uncertainties which can impair their physical and mental well-being as well as overall quality of life. The existing literature suggests that certain groups of students might be particularly affected by that. In addition, quality of life might have been further affected by the COVID-19 pandemic. Therefore, this article investigated university students’ quality of life and its determinants during the COVID-19 pandemic using an online survey among students of one German university. Quality of life was measured using SF-12’s physical (PCS) and mental dimension (MCS). We conducted stratified descriptive analyses followed by regression analyses. 875 respondents completed the questionnaire, of whom 63.0% were female and 95.7% had a German nationality and 16.0% reported having a migration background. Mean age was 23 years. Medical (17.7%) and law students (15.8%) were the biggest groups, but all other faculties of the university were also covered. Concerning respondents’ health-related quality of life, mean PCS was 51 (95%CI = (47–55)), while mean MCS was 36 (95%CI = (30–43). Students with non-German nationality (PCS: 49; MCS: 29) and students with migration background (PCS: 50; MCS: 31) showed particularly low quality of life in the mental dimension. In multivariable regression analyses, associations of the included determinants with PCS were rather weak. In contrast, there were strong associations between MCS and having a migration background with regression coefficient β = -26.1 (95%CI = (-38.5 – -13.7)) and studying Law with β = -17.7 (95%CI = (-28.2 – -7.2)). When comparing these findings with pre-pandemic studies, it seems that university students’ quality of life during the pandemic was as low as it had been before while–as in pre-pandemic studies–certain groups of students generally fared worse than others did. This suggests that universities should actively promote students’ health and should implement measures to specifically support particularly vulnerable students such as students with migration background or students of certain subjects.
GPT, ontology, and CAABAC: A tripartite personalized access control model anchored by compliance, context and attribute
Authors: Nowrozy Raza , Ahmed Khandakar , Wang Hua
Published: January 2025

As digital healthcare evolves, the security of electronic health records (EHR) becomes increasingly crucial. This study presents the GPT-Onto-CAABAC framework, integrating Generative Pretrained Transformer (GPT), medical-legal ontologies and Context-Aware Attribute-Based Access Control (CAABAC) to enhance EHR access security. Unlike traditional models, GPT-Onto-CAABAC dynamically interprets policies and adapts to changing healthcare and legal environments, offering customized access control solutions. Through empirical evaluation, this framework is shown to be effective in improving EHR security by accurately aligning access decisions with complex regulatory and situational requirements. The findings suggest its broader applicability in sectors where access control must meet stringent compliance and adaptability standards.
Expanding first-line options for depression: Protocol of a pragmatic comparative effectiveness trial of yoga vs. behavioral activation (the COMPARE study)
Authors: Sylvia Louisa G. , Busch Andrew M. , Rabideau Dustin J. , Gold Alexandra , Danhauer Suzanne C. , Schatten Heather T. , Katz Douglas , Weinstock Lauren M. , Dahne Jennifer , Schmid Sabine P. , Soetan Zainab , Tovey Roberta , Pintro Kedie , Kvaka Adrienne , Hernandez Antonietta Alvarez , Hsu Ingrid , Melendez Alba , Adkins-Hempel Melissa , Grubb Angela , Lozado Odalys , Fili Atefeh Alavi , Chau Giuliana , Uebelacker Lisa A.
Published: January 2025

Depression is a prevalent mental health condition in the United States and a significant cause of morbidity and mortality. The treatment guidelines for depression recommends either psychotherapy, such as behavioral activation (BA), or a second-generation antidepressant as a first-line treatment for adult patients with depression. However, many individuals with depression do not experience improvement from first-line treatments or choose not to engage in them due to stigma, cost, difficulty with access, and/or side effects. As such we need new treatments for depression and yoga is especially promising given recent data on its efficacy for depression. This study seeks to compare a first-line treatment for depression, or BA, versus yoga to examine whether yoga does as well as BA at improving depressive symptoms and secondary outcomes. We will also examine improvements in depressive symptoms, and secondary outcomes, by specific sub-populations to determine who might do better in which treatment (i.e., BA or yoga). Given that this is the first non-inferior, comparative effectiveness study of yoga, this paper explains the study design, the rationale for the study design, as well as lessons learned in conducting the study.