bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of carbon nano particle variant as the propellant fuel to increase specific impulses of rockets
Authors: Navalino RDA , Muda NRS , Hafizah MAE , Ruyat Y
Published: May 2024

Background This study compares propellant fuels’ specific thrust and impulse parameters using nanocarbon variant fuels from coconut shells and coal. Specific impulses and impulses are essential parameters that determine rocket performance. The specific thrust and impulses are influenced by fuel type, material composition, heat flow, and burning time parameters. The characteristics of nanocarbon as a fuel are proven to have high-value features and a long combustion time. This parameter is essential to add value to specific thrusts and impulses. Methods The method to prove the quality of solid fuel material was done experimentally. The composition of the propellant fuel variant mixed with Ammonium Perchlorate (NH4ClO4) as an oxidizer through the printing process and sample testing was carried out using scanning electron microscope (SEM), X-ray diffraction analysis (XRD), combustion time, and specific impulse tests. Results Test results with the composition of CBK2 (Coconut Shell + NH4ClO4 + Binder + Al = 15: 70: 10: 5) produced a specific impulse of 267 seconds or an increase of 37 seconds without carbon. CBB2 (Coal + NH4ClO4 + Binder + Al = 15: 70: 10: 5) produced a specific impulse of 261 seconds or an increase of 31 seconds. Conclusions The composition of nanocarbon as a solid fuel propellant has been proven to increase a rocket’s thrust and specific impulses. After all the material variants have been tested for thrust and specific impulse, the best rocket propellant is CBK2.
Review of Raynaud’s phenomenon: pathomechanisms, diagnosis and treatment
Authors: Marczyk Aleksandra , Makowska Karolina , Billewicz Marta , Lis Laura , Turek Aleksandra , Popiołek Adam , Pietrzykowska Julia , Zatorska Oksana
Published: May 2024

Introduction: Raynaud’s phenomenon (RP) is a quite common but often unrecognised vasospastic condition of the peripheral vessels. This may happen after exposure to the cold, stress, vibrations or a wide range of medical conditions. It causes episodic colour changes of the digits, firstly there is a pallor, followed by cyanosis and/or redness, usually with pain. Raynaud’s phenomenon can be primary (i.e. Raynaud’s disease) or secondary (i.e. Raynaud’s syndrome) to underlying disease. 
Aim of the study: The aim of the study was to discuss the complex and incompletely understood pathophysiology of Raynaud’s phenomenon and to evaluate treatment approaches of both ‘uncomplicated’ - mostly primary and ‘complicated’ - mostly secondary Raynaud’s phenomenon.
State of knowledge: Raynaud’s phenomenon is a common disorder with an unclear pathophysiology. Although many treatment approaches have been  reported, there is still no cure or gold standard therapy. Further investigations into treatment are required. 
Conclusions: Future research is needed to understand the complex pathogenesis of RP and to develop optimised approaches to management.
Origen de la jurisdicción contencioso administrativa
Authors: Araújo Oñate Rocío
Published: May 2024

En este artículo se presenta un breve panorama histórico de las razones que llevaron a la adopción de la Constitución de 1886 y de sus principales principios que permite reflexionar y también demostrar que la separación de poderes, sin que la Constitución establezca un sistema de pesos y contrapesos, implica la inexistencia del balance que debe existir en el ejercicio de las funciones ejecutiva, legislativa y judicial, lo cual se convirtió en la causa original de la jurisdicción contencioso administrativa en Colombia y a la vez explica la necesidad de su permanencia en nuestro sistema.
A rare cause of malignant otitis externa and skull base osteomyelitis
Authors: Harding Freya , Howlett David , Al-Hashim Muhannad
Published: May 2024

An elderly male with type 2 diabetes presented with a 2-month history of otalgia and severe headaches. He was diagnosed with malignant otitis externa (MOE) and was commenced on empirical treatment with oral ciprofloxacin. Pseudomonas is the most common cause of MOE. A baseline CT scan was undertaken that demonstrated skull base osteomyelitis (SBO) due to findings of bone erosion at the mastoid tip and an infiltrating soft tissue mass eroding the clivus. Eight weeks later, he returned with worsening and bilateral symptoms of otitis externa, hearing loss, temporomandibular pain and dysfunction. Worsening and now bilateral malignant otitis externa were confirmed with an MRI scan that also demonstrated a small fluid collection in his left temporal region. The collection was aspirated and grew scedosporium apiospermum. He was diagnosed with fungal SBO and was commenced on treatment with the antifungal voriconazole, with significant improvement in symptoms and radiological findings. Fungal osteomyelitis is more likely in immunosuppressed patients, particularly those with type 2 diabetes. Fungal aetiology should be suspected in patients with progressive symptoms, despite treatment. A microbiology diagnosis of fungal SBO or MOE can be challenging to obtain and can lead to diagnostic delay. A sampling of the external auditory canal can aid in diagnosing MOE; however, scedosporium may also be isolated as a commensal organism. Aspirations from accessible fluid collections, infratemporal fossa needle sample and bone biopsy can provide material for diagnosis. Scedosporium is a rare cause of disease in humans, however, fungal infections are increasing in humans, due to an increase in susceptible populations. Scedosporium apiospermum is a rare cause of SBO and should be considered in patients not responding to standard treatment.
The 1831 Cholera Riots in Staraia Russa
Authors: Belan Mikhail A.
Published: May 2024

Abstract: As the first detailed study of the townspeople of Staraia Russa in the two cholera riots of July 1831, this article draws on the previously unexplored records of the military investigative commission that reported on 25 November. That commission tried some 139 individuals, whose motives, actions and ultimate fate are considered along with the attitude of the authorities towards them. Merchants were punished more severely than townsmen. While the revolts were triggered by unpopular measures taken to contain the cholera, they also revealed a wider dissatisfaction with billeting and the behaviour of the urban police after the town became a centre of military colonies in 1825. Looking further back, the article concludes by suggesting that popular discontent may have reflected a deeper scepticism towards the state authorities, brewing since the time of the Napoleonic wars.
Interactional Infrastructure across Modalities: A Comparison of Repair Initiators and Continuers in British Sign Language and British English
Authors: Lutzenberger Hannah , Wael Lierin de , Omardeen Rehana , Dingemanse Mark
Published: May 2024

Abstract: Minimal expressions are at the heart of interaction: Interjections like "Huh?" and "Mhm" keep conversations flowing by establishing and reinforcing intersubjectivity among interlocutors. Crosslinguistic research has identified that similar interactional pressures can yield structurally similar words (e.g., to initiate repair across languages). While crosslinguistic comparisons that include signed languages remain uncommon, recent work has revealed similarities in discourse management strategies among signers and speakers that share much of their cultural background. This study contributes a crossmodal comparison of repair initiators and continuers in speakers of English and signers of British Sign Language (BSL). We combine qualitative and quantitative analyses of data from sixteen English speakers and sixteen BSL signers, resulting in the following: First, the interactional infrastructure drawn upon by speakers and signers overwhelmingly relies on behaviors of the head, face, and body; these are used alone or sometimes in combination with verbal elements (i.e., spoken words or manual signs), while verbal strategies alone are rare. Second, discourse management strategies are remarkably similar in form across the two languages: A held eye gaze or freeze-look is the predominant repair initiator and head nodding the main continuer. These results suggest a modality-agnostic preference for visual strategies that do not occupy the primary articulators, one that we propose is founded in recipiency; people maintain the flow of communication following principles of minimal effort and minimal interruption.
Information structure of a polarization state: the concept of metaspin
Authors: Gil J. J. , Norrman A. , Friberg A. T. , Setälä T.
Published: May 2024

A complete description of the polarization properties of a random, stationary, generally three-dimensional (3D) optical field in a point is provided by the 3×3 polarization matrix. We show that its nine degrees of freedom can be represented by nine independent and decoupled parameters with simple and significant physical meanings. These cover the three orientation angles determining the intrinsic reference frame with respect to an arbitrary one, the three principal intensities representing the strengths of the components of the electric field along the respective intrinsic reference axes, and a real-valued vector, which we term metaspin, whose three components are given by the intrinsic correlations of the field components. Consequently, any given polarization state has an associated intensity-isotropic state, called the metaspin state, whose spin vector is fully determined by the metaspin vector. We also show that the concept of metaspin provides an illustrative synthesis procedure for 3D polarization states. The results can straightforwardly be applied to any 3×3 density matrix.
Tested mirror precision alignment system using a pinhole point diffraction interferometer based on machine vision
Authors: Lu Jiasheng , Li Bing , Zhao Zhuo , Geng Leqi
Published: May 2024

In the pinhole point diffraction interferometer (PPDI), proper alignment between the reflection spot of the tested component and the pinhole is critical to obtain accurate interferograms. At present, adjusting for tilt error requires manual manipulation, and defocus error cannot be corrected. These limitations impede the instrumentation process of PPDI. To address this issue, the proposed tested mirror alignment system utilizes diffraction theory to analyze the mathematical error caused by the misalignment of the tested mirror’s reflected beam and pinhole. An alignment system based on machine vision was designed according to specific requirements. This system incorporates a CCD camera with a zoom lens, the classic PPDI with a pinhole substrate containing a lithography-made mark, and a 3-DOF stepper motor adjusting frame to mount the tested mirror. Additionally, image processing algorithms and step motor driving programs were applied to achieve precise alignment. The system implementation and experimental results indicated that the tilt errors are well-controlled, achieving the defocus error modification, making the interferogram acquisition process more convenient. From the results, this system offers desirable precision and efficiency for PPDI’s tested mirror alignment.
Image authentication with exclusive-OR operated optical vortices
Authors: Kumar Rahul , Kumar Praveen , Nishchal Naveen K. , Alfalou Ayman
Published: May 2024

Optical vortices carrying orbital angular momentum have drawn much attention because they provide high-dimensional encoding. Employing an array of optical vortices, we demonstrate an authentication verification system. For security authentication, an exclusive-OR logic operation has been implemented employing a light beam consisting of an array of vortices. A liquid crystal spatial light modulator has been used to generate orthogonal states of optical vortices. The proposed technique can provide a secure method of authentication with straightforward implementation. We have presented simulation and experimental results to verify the proposed scheme.
Non-classical correlations of light in the Jaynes-Cummings model
Authors: Maslennikov D. V. , Shishkov V. Yu. , Andrianov E. S.
Published: May 2024

The problems concerning the influence of spectral filters on the quantum properties of light have recently attracted great attention in connection with quantum cryptography and quantum data transmission. In this paper, we consider the influence of a spectral filter on the second-order coherence function of a field of a resonator mode and a two-level atom in the framework of the Jaynes-Cummings model. Since the Heisenberg equations for the operators of the field of the resonator mode and the atom can be solved exactly, it is possible to obtain exact analytical Fourier transformation of the dynamics of operators of the resonator mode and two-level atom. We demonstrate that the second-order coherence function of the resonator mode and the two-level atom is equal to zero for all possible frequencies in the spectrum of operator oscillations. We find the interbeam second-order coherence function between different frequencies of the Fourier spectrum and show that in the limit of a large number of quanta, it can take the values in the range from zero to two. Thus, non-classical correlations are formed between certain frequencies in the Fourier spectrum of emitted light. We demonstrate that in the limit of a large number of quanta in the resonator mode, when the filter sums up the frequencies near the resonator eigenfrequency, the second-order coherence function of the field of the resonator mode is not affected by the interaction with the two-level atom.
Effective algorithms for calculation of quasi-probability distributions of bright “banana” states
Authors: Nougmanov Boulat
Published: May 2024

Non-Gaussian quantum states, described by negative-valued Wigner functions, are important for both fundamental tests of quantum physics and for emerging quantum information technologies. One of the promising ways of generating a non-Gaussian state from a coherent one is the use of cubic (Kerr) optical nonlinearity, which produces the characteristic banana-like shape of the resulting quantum states. However, the Kerr effect is weak in highly transparent optical materials (dimensionless nonlinearity parameter Γ≲10−6). Therefore, a big number of the photons in the optical mode (n≳106) is necessary to generate an observable non-Gaussianity. In this case, the direct approach to calculation of the Wigner function becomes extremely computationally expensive. In this work, we develop quick algorithms for computing the Husimi and Wigner quasi-probability functions of these non-Gaussian states by means of the Kerr nonlinearity. This algorithm can be used for any realistic values of the photon numbers and the nonlinearity.
Optimal design of confocal plane equal intensity optical elements based on a genetic algorithm
Authors: Cao Yabin , Liu Jianing , Zhou Lei , Zhong Liang , Yang Huajun , Jiang Ping
Published: May 2024

In this paper, we combined spiral zone plates and gratings using a logical XOR operation, designing a new optical element called the composited modified spiral zone plate grating (CMSZPG), which can generate multiple focused vortices on the same focal plane. The parameters of the CMSZPG are optimized using a genetic algorithm, which enables the generation of equal intensity vortex beams without the complexity of manual adjustments, thereby reducing workload. The theoretical feasibility of this component has been validated through simulations and experiments. The CMSZPG can generate multiple equal intensity vortex beams, which have potential applications in light trapping and optical imaging fields.
Flexible composite film utilizing VO2 self-adaptive photothermal and infrared radiative cooling for continuous energy harvesting
Authors: Tan Liwen , Lu Xueguang , Tang Lu , Chen Kefan , Wang Jingyu , Yang Yiting , Wang Jun , Huang Wanxia
Published: May 2024

Self-adaptive photothermal (PT) and radiative cooling (RC) based on insulation-metal phase transition vanadium dioxide (VO2) are among the most promising continuous energy harvesting technologies recently. However, previous work relies on rigid substrates that cannot fit complex or non-planar surfaces. Here, we propose a flexible composite film by bonding a VO2 thin film and a polyimide (PI) substrate with polymethyl methacrylate (PMMA), which achieves efficient spectrally self-adaptive broadband absorption/emission and can convert between the daytime PT mode and nighttime RC mode. Because of the inherent absorption of VO2 and the intricate interplay within multi-layer structure, the solar absorptance of the film could to up to 0.886 in the PT mode with the incorporation of an Al2O3 anti-reflection layer. On the other hand, due to the phase change properties of VO2, this film exhibits a broadband infrared emissivity modulation from 0.32 to 0.82 and reaches a maximum RC power of approximately 244.59 W/m2 in the RC mode at night. Moreover, the film maintains the infrared spectrum switching capability and high emissivity in RC mode even after 104 bending cycles. Our work shows potential to broaden the applications of VO2 smart coatings, including tunable selective emitters, thermal management of spacecraft and smart skins.
Blue GaN-based DFB laser diode with sub-MHz linewidth
Authors: Trageser Emily , Zhang Haojun , Palmer Sonya , Morin Theodore , Guo Joel , Zhang Jiaao , Geske Evan , Wang Heming , Boes Andreas , Nakamura Shuji , Bowers John E. , DenBaars Steven P.
Published: May 2024

Distributed feedback laser diodes (DFBs) serve as simple, compact, narrow-band light sources supporting a wide range of photonic applications. Typical linewidths are on the order of sub-MHz for free-running III-V DFBs at infrared wavelengths, but linewidths of short-wavelength GaN-based DFBs are considerably worse or unreported. Here, we present a free-running InGaN DFB operating at 443 nm with an intrinsic linewidth of 685 kHz at a continuous wave output power of 40 mW. This performance is achieved using a first-order embedded hydrogen silsesquioxane (HSQ) surface grating. The frequency noise is measured using a cross-correlated self-heterodyne frequency discriminator, and two estimations of integrated linewidth are evaluated using 1/π integration and β-separation line integration methods.
Electro-optically tunable optical delay on a lithium niobate photonic chip
Authors: Zhang Ji-Zhe , Chen Jia-Lin , Fan Jia-Wen , Wang Jia-Qi , Yang Yuan-Hao , Xu Xin-Biao , Liu Bi-Heng , Chen Wei , Guo Guang-Can , Zou Chang-Ling
Published: May 2024

An approach for continuous tuning of on-chip optical delay with a microring resonator is proposed and demonstrated. By introducing an electro-optically tunable waveguide coupler, the bus waveguide to the resonance coupling can be effectively tuned from the under-coupling regime to the over-coupling regime. The optical delay is experimentally characterized by measuring the relative phase shift between lasers and shows a large dynamic range of delay from −600 to 600 ps and an efficient tuning of delay from −430 to −180 ps and from 40 to 240 ps by only a 5 V voltage.
Continuous-wave quasi-single-mode random lasing in CH3NH3PbBr3 perovskite films on patterned sapphire substrates
Authors: Weng Guoen , Su Zhan , Ye Shoujie , Sun Xinyue , Cao Fuyi , Wang Cong , Jiang Dongxin , Hu Xiaobo , Tao Jiahua , Akiyama Hidefumi , Chu Junhao , Chen Shaoqiang
Published: May 2024

We report intriguing continuous-wave quasi-single-mode random lasing in methylammonium lead bromide (CH3NH3PbBr3) perovskite films synthesized on a patterned sapphire substrate (PSS) under excitation of a 532-nm laser diode. The random laser emission evolves from a typical multi-mode to a quasi-single-mode with increasing pump fluences. The full width at half-maximum of the lasing peak is as narrow as 0.06 nm at ∼547.8 nm, corresponding to a high Q-factor of ∼9000. Such excellent random lasing performance is plausibly ascribed to the exciton resonance in optical absorption at 532 nm and the enhanced optical resonance due to the increased likelihood for randomly scattered light to re-enter the optical loops formed among the perovskite grains by multi-reflection at the perovskite/PSS interfaces. This work demonstrates the promise of single-mode perovskite random lasers by introducing the exciton resonance effect and ingeniously designed periodic nano/micro optical structure.
Wideband finely tunable, ultralow-phase noise microwave generation in a Brillouin cavity
Authors: Zhang Zhexin , Xu Yin , Luo Xiaojie , Wang Jiaxuan , Bao Hualong
Published: May 2024

A novel, to the best of our knowledge, approach to generate frequency-tunable microwave sources with low-phase-noise based on a Brillouin laser frequency comb is proposed and experimentally demonstrated. The Brillouin laser frequency comb is generated by combining stimulated Brillouin scattering, frequency shifting optical injection locking, modulation sideband optical injection locking (MSOIL), and four-wave mixing effects. By beating the generated comb lines, the microwave is generated with an extremely low-level phase noise of –120 dBc/Hz at a 10-kHz offset. The frequency of the microwave signal can be finely tuned in steps of a Brillouin cavity mode spacing (i.e., 2 MHz) and coarsely adjusted to integer times the applied RF signal frequency in the MSOIL unit. Remarkably, the phase noise of the microwave source can be kept at almost the same low level during the whole tuning process over the frequency range of 30-75 GHz. The proposed tunable low-phase-noise microwave generation approach has great potential applications in communications, radars, and metrology.
Tunable high energy pulse generation in the range of 2.9–3.6 μm enabled by an actively Q switched Er3+/Dy3+ codoped fluoride fiber oscillator
Authors: Zhao Xiangyu , Luo Hongyu , Li Jianfeng , Liu Yong
Published: May 2024

We demonstrate, for the first time, an actively Q switched red-diode-clad-pumped Er3+/Dy3+ codoped fluoride fiber oscillator. Its wavelength can be continuously tuned over the range of 2.906–3.604 μm (698 nm), representing the widest tuning span of pulsed fluoride fiber oscillators in the mid-infrared. In addition, the achieved pulse energy at each wavelength of >2.95 μm is also higher than that of a previously reported pulsed fluoride fiber oscillator at the corresponding wavelength, to the best of our knowledge. By tuning the wavelength to 3.204 μm, the highest pulse energy of 82 μJ has been gotten with a pulse width of 520 ns at a repetition rate of 500 Hz.
Low complexity equalization in coherent optical communication based on Fermat number transform
Authors: Liu Zheli , Chen Chen , Chen Junda , Li Yuqi , Tang Ming
Published: May 2024

In order to reduce the power consumption of the receivers in coherent optical communication system during digital signal processing (DSP), a low complexity equalization scheme in DSP flow of a 400Gb/s-DP-16QAM system has been proposed. This scheme is based on Fermat number transform (FNT), which sequentially performs static equalization (SE) and dynamic equalization (DE) in the transform domain. For different distances, the proposed scheme finds the optimal solution under the condition that transform length and data bitwidth are mutually restricted under different transmission distances, while achieving low complexity and optimal performance. The experimental results show that the adopted TrDE scheme has better computational complexity than traditional frequency domain equalization (FDE) and time domain equalization (TDE) nearly without any performance loss. In the 80km, 160km, and 240km scenarios, the number of multiplier is reduced by more than 72%, and the advantage becomes more obvious as the transmission capacity increases.
Three-dimensional polarization-dependent full-wavelength beam splitter written by femtosecond laser in LiNbO3 crystal
Authors: Lv Jinman , Li Ge , Yu Mingyang , Ma Yujie , Chen Feng
Published: May 2024

We report on the fabrication of Y-branched waveguide beam splitters with cladding structures in LiNbO3 crystal by direct femtosecond laser writing. The femtosecond laser writes tracks near the surface of the crystal, constructing a square structure based on the Type II geometry. The waveguides beam splitters support propagation of full-wavelength light from the visible to mid-infrared, which was experimentally and numerically investigated. In addition, it has been found that the guidance is only along the vertical (i.e., TM) polarization, which is due to the different refractive indices in the longitudinal and transverse directions. The femtosecond-laser writing here also represents an alternative for fabricating complex integrated light guiding in crystals.
Mode-bases gain difference for Different phase profiles in Few-mode Erbium-doped Fiber Amplifiers
Authors: Zhang Jie , Gao She , Tu Jiajing , Li Wei , Du Cheng , Liu Weiping , Li Zhaohui
Published: May 2024

In few-mode erbium-doped fiber, which is key sections in space division multiplexing (SDM) communication system, linearly polarized (LP) and orbital angular momentum (OAM) mode as two groups of mode-bases with different phase profile can be transformed into each other for the fiber’s weakly guiding condition. In principle, the LPand OAM modes have different mode spatial intensity distribution and a gain difference for FM -EDF amplifier. How to analyze and characterize the differential mode-bases gain (DMBG) is important but still an issue. Here, we build for the first time a local analysis model composed of discrete elements of the FM-EDF cross-section in mode spatial intensity distribution azimuthal variations areas. Using the model during the two mode-bases, the description of local gain difference details and the analysis of local particle number distribution is realized, and the overall gain difference is obtained. By building the amplifier system based on mode phase profile controlling, the gain of two mode-bases is characterized experimentally. The measured DMBG is about 0.8dB in the second-order mode, which is consistent with the simulation result. This DMBG can be used to improve the performance of SDM communication system by switching the mode-bases with controlling the mode phase profile.
Electric tuning of plasmonic resonances in ultrathin gold nanoribbon arrays
Authors: Wang Zhenxin , Krasavin Alexey V. , Pan Chenxinyu , Zheng Junsheng , Li Zhiyong , Guo Xin , Zayats Anatoly V. , Tong Limin , Wang Pan
Published: May 2024

Ultrathin plasmonic nanostructures offer an unparalleled opportunity for the study of light–matter interactions at the nanoscale and realization of compact nanophotonic devices. In this study, we introduce an ultrathin gold nanoribbon array and demonstrate an electric approach to actively tuning its plasmonic resonance, which leveraging the extreme light confinement capability in the ultrathin plasmonic nanostructure and a robust nanoscale electro-optical effect in indium tin oxide. Optimizing the design (to a total thickness as small as 12 nm for a 2-nm-thick gold nanoribbon array), we numerically demonstrate a spectral shift in the plasmonic resonance up to 36 nm along with an approximately 16% change in the transmission at a gate voltage below 1.7 V at the wavelength of 1.47 μm. This work presents progress towards electric tuning of plasmonic resonances in ultrathin metallic nanostructures for various applications including surface-enhanced spectroscopy, spontaneous emission enhancement, and optical modulation.
Mathematical modeling of the evolution of resistance and aggressiveness of high-grade serous ovarian cancer from patient CA-125 time series
Authors: Jitmana Kanyarat , Griffiths Jason I. , Fereday Sian , DeFazio Anna , Bowtell David ,   for Australian Ovarian Cancer Study, Adler Frederick R.
Published: May 2024

A time-series analysis of serum Cancer Antigen 125 (CA-125) levels was performed in 791 patients with high-grade serous ovarian cancer (HGSOC) from the Australian Ovarian Cancer Study to evaluate the development of chemoresistance and response to therapy. To investigate chemoresistance and better predict the treatment effectiveness, we examined two traits: resistance (defined as the rate of CA-125 change when patients were treated with therapy) and aggressiveness (defined as the rate of CA-125 change when patients were not treated). We found that as the number of treatment lines increases, the data-based resistance increases (a decreased rate of CA-125 decay). We use mathematical models of two distinct cancer cell types, treatment-sensitive cells and treatment-resistant cells, to estimate the values and evolution of the two traits in individual patients. By fitting to individual patient HGSOC data, our models successfully capture the dynamics of the CA-125 level. The parameters estimated from the mathematical models show that patients with inferred low growth rates of treatment-sensitive cells and treatment-resistant cells (low model-estimated aggressiveness) and a high death rate of treatment-resistant cells (low model-estimated resistance) have longer survival time after completing their second-line of therapy. These findings show that mathematical models can characterize the degree of resistance and aggressiveness in individual patients, which improves our understanding of chemoresistance development and could predict treatment effectiveness in HGSOC patients.
Pairtools: From sequencing data to chromosome contacts
Authors:   Open2C, Abdennur Nezar , Fudenberg Geoffrey , Flyamer Ilya M. , Galitsyna Aleksandra A. , Goloborodko Anton , Imakaev Maxim , Venev Sergey V.
Published: May 2024

The field of 3D genome organization produces large amounts of sequencing data from Hi-C and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive and heterogeneous 3C+ data require high-performance and flexible processing of sequenced reads into contact pairs. To meet these challenges, we present pairtools–a flexible suite of tools for contact extraction from sequencing data. Pairtools provides modular command-line interface (CLI) tools that can be flexibly chained into data processing pipelines. The core operations provided by pairtools are parsing of.sam alignments into Hi-C pairs, sorting and removal of PCR duplicates. In addition, pairtools provides auxiliary tools for building feature-rich 3C+ pipelines, including contact pair manipulation, filtration, and quality control. Benchmarking pairtools against popular 3C+ data pipelines shows advantages of pairtools for high-performance and flexible 3C+ analysis. Finally, pairtools provides protocol-specific tools for restriction-based protocols, haplotype-resolved contacts, and single-cell Hi-C. The combination of CLI tools and tight integration with Python data analysis libraries makes pairtools a versatile foundation for a broad range of 3C+ pipelines.
Comparison of the intrageneric neutralization scope of monospecific, bispecific/monogeneric and polyspecific/monogeneric antisera raised in horses immunized with sub-Saharan African snake venoms
Authors: Sánchez Andrés , Durán Gina , Segura Álvaro , Herrera María , Vargas Mariángela , Villalta Mauren , Arguedas Mauricio , Moscoso Edwin , Umaña Deibid , Gómez Aarón , Gutiérrez José María , León Guillermo
Published: May 2024

Background

Snakebite envenomation inflicts a high burden of mortality and morbidity in sub-Saharan Africa. Antivenoms are the mainstay in the therapy of envenomation, and there is an urgent need to develop antivenoms of broad neutralizing efficacy for this region. The venoms used as immunogens to manufacture snake antivenoms are normally selected considering their medical importance and availability. Additionally, their ability to induce antibody responses with high neutralizing capability should be considered, an issue that involves the immunization scheme and the animal species being immunized.

Methodology/Principal findings

Using the lethality neutralization assay in mice, we compared the intrageneric neutralization scope of antisera generated by immunization of horses with monospecific, bispecific/monogeneric, and polyspecific/monogeneric immunogens formulated with venoms of Bitis spp., Echis spp., Dendroaspis spp., spitting Naja spp. or non-spitting Naja spp. It was found that the antisera raised by all the immunogens were able to neutralize the homologous venoms and, with a single exception, the heterologous congeneric venoms (considering spitting and non-spitting Naja separately). In general, the polyspecific antisera of Bitis spp, Echis spp, and Dendroaspis spp gave the best neutralization profile against venoms of these genera. For spitting Naja venoms, there were no significant differences in the neutralizing ability between monospecific, bispecific and polyspecific antisera. A similar result was obtained in the case of non-spitting Naja venoms, except that polyspecific antiserum was more effective against the venoms of N. melanoleuca and N. nivea as compared to the monospecific antiserum.

Conclusions/Significance

The use of polyspecific immunogens is the best alternative to produce monogeneric antivenoms with wide neutralizing coverage against venoms of sub-Saharan African snakes of the Bitis, Echis, Naja (non-spitting) and Dendroaspis genera. On the other hand, a monospecific immunogen composed of venom of Naja nigricollis is suitable to produce a monogeneric antivenom with wide neutralizing coverage against venoms of spitting Naja spp. These findings can be used in the design of antivenoms of wide neutralizing scope for sub-Saharan Africa.
Initial data analysis for longitudinal studies to build a solid foundation for reproducible analysis
Authors: Lusa Lara , Proust-Lima Cécile , Schmidt Carsten O. , Lee Katherine J. , le Cessie Saskia , Baillie Mark , Lawrence Frank , Huebner Marianne ,   on behalf of TG3 of the STRATOS Initiative
Published: May 2024

Initial data analysis (IDA) is the part of the data pipeline that takes place between the end of data retrieval and the beginning of data analysis that addresses the research question. Systematic IDA and clear reporting of the IDA findings is an important step towards reproducible research. A general framework of IDA for observational studies includes data cleaning, data screening, and possible updates of pre-planned statistical analyses. Longitudinal studies, where participants are observed repeatedly over time, pose additional challenges, as they have special features that should be taken into account in the IDA steps before addressing the research question. We propose a systematic approach in longitudinal studies to examine data properties prior to conducting planned statistical analyses. In this paper we focus on the data screening element of IDA, assuming that the research aims are accompanied by an analysis plan, meta-data are well documented, and data cleaning has already been performed. IDA data screening comprises five types of explorations, covering the analysis of participation profiles over time, evaluation of missing data, presentation of univariate and multivariate descriptions, and the depiction of longitudinal aspects. Executing the IDA plan will result in an IDA report to inform data analysts about data properties and possible implications for the analysis plan—another element of the IDA framework. Our framework is illustrated focusing on hand grip strength outcome data from a data collection across several waves in a complex survey. We provide reproducible R code on a public repository, presenting a detailed data screening plan for the investigation of the average rate of age-associated decline of grip strength. With our checklist and reproducible R code we provide data analysts a framework to work with longitudinal data in an informed way, enhancing the reproducibility and validity of their work.
Incidence and predictors of mortality among road traffic accident victims admitted to hospitals at Hawassa city, Ethiopia
Authors: Afacho Amanuel Ayele , Belayneh Teshale , Markos Terefe , Geleta Dereje
Published: May 2024

Background

Globally, road traffic accidents are the eighth-leading cause of death for all age groups. The estimated number of road traffic deaths in low income countries was more than three times as high as in high-income countries. Africa had the highest rate of fatalities attributed to road traffic accidents. Ethiopia has the highest number of road traffic fatalities among Sub-Saharan African countries. The main objective of this study was to determine the incidence and predictors of mortality among road traffic victims admitted to hospitals in Hawassa City.

Methods

A facility-based retrospective cohort study was conducted using secondary data from hospital records. A total of 398 road traffic accident victims admitted to selected hospitals in Hawassa city from January 2019 to December 2021 participated in the study. Data were analyzed using STATA version 14.1. The Cox regression model was used to determine the predictors of mortality. A hazard ratio with a 95% confidence interval and a cut-off value of P<0.05 was used to declare the risk and statistical significance, respectively.

Result

The incidence rate of mortality for road traffic accident victims was 7.34 per 10,000 person-hours. The predictors of mortality were the value of GCS at admission <8 (aHR = 5.86; 95% CI: 2.00–17.19), GCS at admission 9–12 (aHR = 3.27; 95% CI: 1.28–8.40), the value of SBP at admission ≤89mmHg (aHR = 4.41; 95% CI: 2.22–8.77), admission to the ICU (aHR = 3.89; 95% CI: 1.83–8.28) and complications (aHR = 5.48; 95% CI: 2.74–10.01).

Conclusion

The incidence of mortality among road traffic victims admitted to hospitals in Hawassa city was high. Thus, thorough follow-up and intensive management should be given to victims with critical health conditions.
The every woman study™ low- and middle-income countries edition protocol: A multi-country observational study to assess opportunities and challenges to improving survival and quality of life for women with ovarian cancer
Authors: Reid Frances , Adams Tracey , Adel Rafe Sadnan , Andrade Carlos E. , Bajwa Anmol , Bambury Ian G. , Benhima Nada , Bolatbekova Raikhan , Leon David Cantu-De , Charlton Phaedra , Chirinos Carlos Chávez , Cohen Robin , Eiken Mary , Estrada Erick Estuardo , Kaidarova Dilyara , Lau Iren , MacKay Clara , Makondi Precious Takondwa , Mukhopadhyay Asima , Mustapha Aisha , Noll Florencia , Origa Martin , Pariyar Jitendra , Pervin Shahana , Phan Ngoc T. H. , Refky Basel , Shaffi Afrin F. , Strömsholm Eva-Maria , Woo Yin Ling , Yoon Sook-Yee , Zakirova Nargiza , Chidebe Runcie C. W. , Funston Garth , Soerjomataram Isabelle
Published: May 2024

Background

Ovarian cancer is a challenging disease to diagnose and treat effectively with five-year survival rates below 50%. Previous patient experience research in high-income countries highlighted common challenges and opportunities to improve survival and quality of life for women affected by ovarian cancer. However, no comparable data exist for low-and middle-income countries, where 70% of women with the disease live. This study aims to address this evidence gap.

Methods

This is an observational multi-country study set in low- and middle-income countries. We aim to recruit over 2000 women diagnosed with ovarian cancer across multiple hospitals in 24 countries in Asia, Africa and South America. Country sample sizes have been calculated (n = 70–96 participants /country), taking account of varying national five-year disease prevalence rates. Women within five years of their diagnosis, who are in contact with participating hospitals, are invited to take part in the study. A questionnaire has been adapted from a tool previously used in high-income countries. It comprises 57 multiple choice and two open-ended questions designed to collect information on demographics, women’s knowledge of ovarian cancer, route to diagnosis, access to treatments, surgery and genetic testing, support needs, the impact of the disease on women and their families, and their priorities for action. The questionnaire has been designed in English, translated into local languages and tested according to local ethics requirements. Questionnaires will be administered by a trained member of the clinical team.

Conclusion

This study will inform further research, advocacy, and action in low- and middle-income countries based on tailored approaches to the national, regional and global challenges and opportunities. In addition, participating countries can choose to repeat the study to track progress and the protocol can be adapted for other countries and other diseases.
Comparative proteomics analysis of biofilms and planktonic cells of Enterococcus faecalis and Staphylococcus lugdunensis with contrasting biofilm-forming ability
Authors: Cho Jung-Ah , Jeon Sangsoo , Kwon Youngmin , Roh Yoo Jin , Lee Chang-Hun , Kim Sung Jae
Published: May 2024

Biofilms make it difficult to eradicate bacterial infections through antibiotic treatments and lead to numerous complications. Previously, two periprosthetic infection-related pathogens, Enterococcus faecalis and Staphylococcus lugdunensis were reported to have relatively contrasting biofilm-forming abilities. In this study, we examined the proteomics of the two microorganisms’ biofilms using LC-MS/MS. The results showed that each microbe exhibited an overall different profile for differential gene expressions between biofilm and planktonic cells as well as between each other. Of a total of 929 proteins identified in the biofilms of E. faecalis, 870 proteins were shared in biofilm and planktonic cells, and 59 proteins were found only in the biofilm. In S. lugdunensis, a total of 1125 proteins were identified, of which 1072 proteins were found in common in the biofilm and planktonic cells, and 53 proteins were present only in the biofilms. The functional analysis for the proteins identified only in the biofilms using UniProt keywords demonstrated that they were mostly assigned to membrane, transmembrane, and transmembrane helix in both microorganisms, while hydrolase and transferase were found only in E. faecalis. Protein-protein interaction analysis using STRING-db indicated that the resulting networks did not have significantly more interactions than expected. GO term analysis exhibited that the highest number of proteins were assigned to cellular process, catalytic activity, and cellular anatomical entity. KEGG pathway analysis revealed that microbial metabolism in diverse environments was notable for both microorganisms. Taken together, proteomics data discovered in this study present a unique set of biofilm-embedded proteins of each microorganism, providing useful information for diagnostic purposes and the establishment of appropriately tailored treatment strategies. Furthermore, this study has significance in discovering the target candidate molecules to control the biofilm-associated infections of E. faecalis and S. lugdunensis.
Spatial analysis of digital economy and its driving factors: A case study of the Yangtze River Delta City Cluster in China
Authors: Zhong Haidong , Wang Bifeng , Zhang Shaozhong
Published: May 2024

The digital economy (DE) has become a major breakthrough in promoting industrial upgrading and an important engine for high-quality economic growth. However, most studies have neglected the important driving effect of regional economic and social (RES) development on DE. In this paper, we discuss the mechanism of RES development promoting the development of DE, and establish a demand-driven regional DE development model to express the general idea. With the help of spatial analysis toolbox in ArcGIS software, the spatial development characteristics of DE in the Yangtze River Delta City Cluster (YRDCC) is explored. We find the imbalance of spatial development is very significant in YRDCC, no matter at the provincial level or city level. Quantitative analysis reveals that less than 1% likelihood that the imbalanced or clustered pattern of DE development in YRDCC could be the result of random chance. Geographically weighted regression (GWR) analysis with publicly available dataset of YRDCC indicates RES development significantly promotes the development of DE.
Spatio-temporal pattern and the evolution of the distributional dynamics of county-level agricultural economic resilience in China
Authors: Li Chengmin , Yu Guoxin , Deng Haoyu , Liu Jian , Li Dongmei
Published: May 2024

Because the complexity of the external environment has put great pressure on the agricultural economy, making it vulnerable, it is necessary to promote a system of resilience in the agricultural economy so that Chinese agriculture can continue to persevere in the face of serious external uncertainties. Therefore, this paper investigates the spatio-temporal pattern and evolution of the distributional dynamics of China’s county-level agricultural economic resilience based on 2000–2020 data covering 2,545 counties. The results are as follows: first, from 2000 to 2020, the mean value of China’s county-level agricultural economic resilience showed an obvious upward trend, which indicates that China’s agricultural economy gradually increased its ability to resist risks and continued to develop in a favourable manner. Specifically, the county-level agricultural economic resilience index of the northeast region grew the most significantly, while the index of county units in the western region was relatively low. Second, the centre of gravity of the spatial distribution of China’s agricultural economic resilience gradually migrated to the northwest, showing a dominant direction from northeast to southwest and a tendency to develop from southeast to northwest. Third, the spatial differences in China’s agricultural economic resilience generally showed an upward trend, while county-level differences were the main source of the overall differences, followed by inter-provincial differences, inter-municipal differences and inter-regional differences. Additionally, the contribution of county-level differences to the overall differences fluctuated within the range of 54%-58%. Fourth, there is a possibility of localized convergence in China’s agricultural economic resilience, which is continuous in spatial effects and has obvious positively correlated spatial effects at different times and in different county spaces.
Perceived exertion can be lower when exercising in field versus indoors
Authors: Olsson Karin Sofia Elisabeth , Ceci Ruggero , Wahlgren Lina , Rosdahl Hans , Schantz Peter
Published: May 2024

Purpose

Studies indicate that the rated perceived exertion (RPE) during physical exercise can be lower in field environments than indoors. The environmental conditions of those studies are explored. Furthermore, we study if the same phenomenon is valid when cycling indoors versus in cycle commuting environments with high levels of stimuli from both traffic and suburban-urban elements.

Methods

Twenty commuter cyclists underwent measurements of heart rate (HR) and oxygen uptake (V˙O2) and RPE assessments for breathing and legs, respectively, while cycling in both laboratory and field conditions. A validated mobile metabolic system was used in the field to measure V˙O2. Three submaximal cycle ergometer workloads in the laboratory were used to establish linear regression equations between RPE and % of HR reserve (%HRR) and %V˙O2max, separately. Based on these equations, RPE from the laboratory was predicted and compared with RPE levels at the participants’ individual cycle commutes at equal intensities. The same approach was used to predict field intensities and for comparisons with corresponding measured intensities at equal RPE levels.

Results

The predicted RPE levels based on the laboratory cycling were significantly higher than the RPE levels in cycle commuting at equal intensities (67% of HRR; 65% of V˙O2max). For breathing, the mean RPE levels were; 14.0–14.2 in the laboratory and 12.6 in the field. The corresponding levels for legs were; 14.0–14.2 and 11.5. The range of predicted field intensities in terms of %HRR and %V˙O2max was 46–56%, which corresponded to median differences of 19–30% compared to the measured intensities in field at equal RPE.

Conclusion

The cycle commuters perceived a lower exertion during their cycle commutes compared to ergometer cycling in a laboratory at equal exercise intensities. This may be due to a higher degree of external stimuli in field, although influences from other possible causes cannot be ruled out.