bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of soil fraction, carbon storage capacity, and rate of carbon uptake from three coastal ecosystems: Mangroves, seagrass, and mudflats in Benoa Bay, Indonesia
Authors: DHARMAYASA I GUSTI NGURAH PUTU , SUGIANA I PUTU , PUTRI PUTU YUDI ADITYA , BOONYASANA KWANRUETAI
Published: August 2024

Abstract. Dharmayasa IGNP, Sugiana IP, Putri PYA, Boonyasana K. 2024. Assessment of soil fraction, carbon storage capacity, and rate of carbon uptake from three coastal ecosystems: Mangroves, seagrass, and mudflats in Benoa Bay, Indonesia. Biodiversitas 25: 2541-2549. Coastal habitats, known as blue carbon ecosystems, are highly productive at absorbing and storing carbon. Most carbon is stored as soil organic carbon, and its quantity can vary depending on various factors, including the presence of plants such as mangroves and seagrass, and environmental conditions, including soil fraction. This study quantifies soil carbon stored and its burial rate in three primary coastal ecosystems: mangroves, seagrasses, and mudflats. The ashing method (loss on ignition) is used to quantify carbon content, which is then converted into soil carbon storage and burial rate. Gravimetry and the settling time method are used to determine the soil fraction. We also measure the soil and water properties directly during the sampling time. This study revealed significant soil carbon stock and burial rate variations across different ecosystems. The order of ecosystems with the most extensive carbon stock and burial rate is as follows: mangrove (69-145 tC ha-1 and 1.6-3.4 tCha-1yr-1)>seagrass (63-75 tC ha-1 and 1.5-1.7 tCha-1yr-1)>mudflat (49-61 tC ha-1 and 1.2-1.4 tCha-1yr-1). Mangroves with natural growth have a higher carbon storage capacity than rehabilitated ones. Soil carbon content is highly correlated with the soil and water pH, Dissolved Oxygen (DO), water content, bulk density, and soil type. The findings demonstrate that carbon absorption capability varies among coastal habitats, with vegetated environments exhibiting higher carbon storage levels. Converting land, particularly mudflats, into seagrass beds or mangrove forests may maximize the efficiency of coastal ecosystems as carbon sinks. However, it should be noted that these findings are only estimates, and the precise measurement numbers may differ due to seasonal circumstances or reclamation activities, which might cause oscillations in sedimentation rates. These variations, in turn, could affect the levels of carbon stored and the speed at which it is buried.
Land management and factors influencing agroforestry adoption on potato farmlands in the Dieng Plateau, Indonesia
Authors: PUJIWINARKO ARI , SOEPROBOWATI TRI RETNANINGSIH , KISMARTINI KISMARTINI
Published: August 2024

Abstract. Pujiwinarko A, Soeprobowati TR, Kismartini. 2024. Land management and factors influencing agroforestry adoption on potato farmlands in the Dieng Plateau, Indonesia. Biodiversitas 25: 2623-2641. The Dieng area in Indonesia has long experienced agricultural land degradation, and intensive potato monoculture farming is one of the leading causes. Vegetative-based programs such as agroforestry have been implemented, but the level of adoption still needs to improve. This research aims to evaluate land management systems and analyze practices and the factors influencing agroforestry adoption of potato farming land in Dieng. We surveyed 260 potato farmers and interviewed 12 Key Informant Interviews (KII). Data were analyzed using binary logistic regression, descriptive statistics, and narrative approaches. Our research found changes in how potato farmers manage land regarding planting frequency and mulch use. The combination of potatoes and MPTS (Multi-Purpose Tree Species) is the plant composition most commonly found in agroforestry practices. Carrots (Daucus carota L.) are the vegetables that farmers most often plant when rotating potato crops. Mountain pine (Casuarina junghuhniana Miq.) and Carica (Carica pubescens (A.DC.) Lenne & K.Koch) are the species of trees and MPTS most commonly found in the fields of potato farmers who adopt agroforestry. Farmers maintain MPTS and trees on their land due to their suitability with main food crops and economic considerations. Several factors, including the species of energy source, use of mulch, frequency of potato planting, perception of disasters, farmer interest, prices, markets, the experience of vegetative activities, and government policy, significantly influence agroforestry adoption. Considering local agricultural systems, including the presence of principal crops and their management on the land, socio-economic and farmers' perspectives are essential to further increase agroforestry adoption in Dieng.
Effect of refugia plant (Zinnia sp.) population on the presence of stem borer (Scirpophaga innotata Walker) and natural enemies in rice
Authors: OLSIVIANA OLSIVIANA , YASSI AMIR , MELINA MELINA
Published: August 2024

Abstract. Olsiviana, Yassi A, Melina. 2024. Effect of refugia plant (Zinnia sp.) population on the presence of stem borer (Scirpophaga innotata Walker) and natural enemies in rice. Biodiversitas 25: 2652-2660. This study supports biological control by preserving natural enemies in rice cultivation through habitat modification. The research aimed to analyze the effects of different population levels of refugia (Zinnia sp.) on pest attack rates, the presence and diversity of natural enemies of rice stem borer (Scirpophaga innotata Walker 1863), and rice (Oryza sativa L.) production. The study was designed using a Randomized Group Design (RGD) with four population treatment levels: control (no Zinnia sp.), sparse population (32 polybags of Zinnia sp.), medium population (96 polybags of Zinnia sp.), and dense population (160 polybags of Zinnia sp.). The results showed that the dense population (160 polybags of Zinnia sp.) produced the lowest stem borer infestation rate in the eighth week of observation (1.67%). Pests in all treatments belonged to four orders: Lepidoptera, Hemiptera, Coleoptera, and Diptera, with Hemiptera being the most prevalent. Natural enemies of rice pests belonged to three orders: Coleoptera, Hymenoptera, and Orthoptera. The dense population treatment (160 polybags of Zinnia sp.) yielded the highest values for diversity index (H') at 2.1785, species richness index (R) at 2.1837, and evenness index (E) at 0.9915. This treatment also achieved the highest average rice production at 8.64 tons/ha. Meanwhile, the highest dominance value (C) of 0.2489 was found in the control treatment. Thus, this study supports the idea that increasing the population of Zinnia sp. as a refugia plant can increase the diversity of natural enemies, reduce rice stem borer infestation, and increase rice plant production.
Assessment of the current condition and ontogenetic structure of the populations of Leontice incerta Pall. (Berberidaceae) in the Kyzyl-Kum Desert, Uzbekistan
Authors: BOBOKANDOV NODIRJON , NOMOZOVA ZEBUNISSO , TASHPULATOV YIGITALI , ISOMOV ELDOR , AKHMEDOV AKBAR
Published: August 2024

Abstract. Bobokandov N, Nomozova Z, Tashpulatov Y, Isomov E, Akhmedov A. 2024. Assessment of the current condition and ontogenetic structure of the populations of Leontice incerta Pall. (Berberidaceae) in the Kyzyl-Kum Desert, Uzbekistan. Biodiversitas 25: 2757-2764. The desert ecosystems of central Asia, including Uzbekistan, have a rich biodiversity and unique plant communities. High human pressure and long drought periods due to climate change have caused habitat destruction in these areas and a parallel crisis in vegetation cover. This study aimed to estimate the current population of Leontice incerta Pall., primarily distributed in the Kyzyl-Kum Desert, Uzbekistan. This focal species grew under climatic changes and human pressure in the Kyzyl-Kum Desert. The study identified five populations of L. incerta in the Kyzyl-Kum Desert. All 5 populations were estimated and measured by delta-omega and the population spectrum was determined. In the plant community, there are mostly dominated by Asteraceae (6 species), followed by Fabaceae (5 species), Amaranthaceae (4 species), Lamiaceae (4 species), Apiaceae (3 species), and other families. The plant communities consist of 49 species, including 1 species of tree, 6 species of shrubs, 6 species of semi-shrubs, 26 species of perennial herbs, and 10 species of annual herbs. The ontogenetic structure was incomplete, that is, it did not include all age groups due to biological features and harsh conditions. At all sites, the population density was low with most populations classified as young ontogenetic structures. The results will make it possible to understand estimating the current state of L. incerta. It indicated this species might, soon, become rare in the wild, therefore conservation and protection areas for this focal species are necessary.
Short Communication: Habitat preferences of epiphytic orchids and potential pollinators in Sumber Pawon Forest, Kediri District, East Java, Indonesia
Authors: PUTRA STEVANUS R. T. , TRISNAWATI INDAH
Published: August 2024

Abstract. Putra SRT, Trisnawati I. 2024. Short Communication: Habitat preferences of epiphytic orchids and potential pollinators in Sumber Pawon Forest, Kediri District, East Java, Indonesia. Biodiversitas 25: 2780-2787. Sumber Pawon Forest, a unique and biodiverse ecosystem in Kediri, Indonesia, is home to approximately 30,000 orchids (family Orchidaceae), which can grow terrestrial or as epiphytes. A diversity of different taxa has been recorded as orchid pollinators. The distribution of epiphytic orchids in this forest is determined by habitat preferences including vertical distribution zone and host tree's characteristics. This research, conducted in the captivating Sumber Pawon Forest, aims to determine habitat preferences influencing the abundance of epiphytic orchids and provide a review of potential epiphytic orchid pollinators. The data were collected by systematic sampling method. Analysis of epiphytic orchids' habitat preferences was done using the ordination method. The study found 3 epiphytic orchids and 5 species of host trees, revealing new insights into their distribution. Epiphytic orchids include Cymbidium sp., Dendrobium crumenatum, and Rhynchostylis retusa. The host trees include Alstonia scholaris, Artocarpus elasticus, Bischofia javanica, Ficus elastica, and Samanea saman. Epiphytic orchids were mainly found in zone 4 rather than in zone 5. The characteristics of host trees, which are preferentially selected by epiphytic orchids, include tree height (ranging from 28.65 to 33.65 m), large DBH (ranging from 165.61 to 175.80 m), and closed canopy cover (ranging from 51 to 75%). One of the pollinator taxa (named Hymenoptera) was found to pollinate epiphytic orchid species, adding to our understanding of their ecological interactions.
Crenças e atitudes linguísticas: um estudo de caso em comentários do Facebook
Authors: Pereira Anesio Marcilio dos Santos , Paim Marcela Moura
Published: August 2024

São nas redes sociais que hoje podemos observar várias propagações da noção de erro, que vão desde comentários até publicações jocosas, visto que são nesses lugares de interação virtual que muitos indivíduos se aproveitam para corrigir a escrita de outros usuários e levar adiante a homogeneidade da língua. Nesse sentido, este trabalho tem como objetivo analisar e descrever as crenças e atitudes linguísticas manifestadas através de comentários de internautas da rede social Facebook. Este trabalho justifica-se pela necessidade de analisar e refletir como as crenças de alguns internautas influenciam a sua atitude linguística frente à variação linguística encontrada na escrita de outros usuários na rede em questão. A pesquisa é de natureza explicativa e abordagem qualitativa, tendo como corpus imagens com publicações e comentários coletados de algumas páginas do Facebook. Conclui-se que, diante das variações linguísticas expressas no Facebook, há grande incidência do preconceito linguístico advindo de atitudes negativas de indivíduos que inferiorizam, estigmatizam e desprestigiam a variante utilizada por outros indivíduos.
Libras e a organização escolar: o papel da gestão para difusão da cultura surda
Authors: Moraes Luana , Dalgalo Vanderlize
Published: August 2024

O estudo busca problematizar como a gestão escolar pode contribuir para a difusão da Libras e da cultura surda. Para tanto, percorre os seguintes objetivos: a) definir gestão escolar, b) esclarecer a relação existente entre a gestão escolar e a Libras e c) elucidar como essa relação tece sentidos com a luta do movimento surdo. A produção tem cunho qualitativo, pautada em pesquisa bibliográfica e se apoia em referenciais teóricos que abarcam tanto a gestão educacional e escolar (DOURADO, 2003; LIBÂNEO, 2009; LUCK, 2010), quanto a discussão em torno da Libras (QUADROS, 2020; STREIECHEN, 2017, 2020; STROBEL, 2014), além de legislações centrais para o debate, tais como a Constituição Federal de 1988 e a LDB n°9394/96, dentre outras. Depreende que, se embasada em uma perspectiva que contemple as pautas do movimento surdo, a gestão escolar passa a assumir um papel de facilitadora no alcance de seus ideais, já que articuladora da organização escolar.
Gêneros acadêmicos no ensino médio: uma análise de atividades de produção textual a partir da Base Nacional Comum Curricular (BNCC)
Authors: Sousa Santos Maria Eduarda , Ramos de Melo Bárbara Olímpio
Published: August 2024

Os gêneros acadêmicos (GAs) são essenciais para uma participação efetiva em práticas comunicativas universitárias. Considerando isso, a Base Nacional Comum Curricular (BNCC) trata sobre como tais gêneros podem ser abordados ainda na Educação Básica. Desse modo, este artigo tem como objetivo geral investigar atividades de produção textual de livros didáticos do ensino médio voltadas para gêneros acadêmicos, com auxílio das propostas da BNCC. Para tal fim, fundamentamos esta pesquisa em estudos sobre gêneros textuais (SWALES, 1990; BAWARSHI; REIFF, 2013; BEZERRA, 2022); letramentos acadêmicos (LEA; STREET, 1998; BEZERRA, 2012; SILVA; BASSETTO, 2014), bem como os postulados conceituais contidos na BNCC (BRASIL, 2018). A partir de uma metodologia bibliográfica, descritiva e documental, examinamos as atividades de produção textual da coleção de livros didáticos Português Contemporâneo: Diálogo, Reflexão e Uso, no qual identificamos os GAs lá presentes, descrevemos a abordagem dada a eles e analisamos se ela condiz com as indicações BNCC. Os resultados indicam que, apesar de algumas lacunas, a coleção atende às propostas da Base visto que promove o conhecimento e a elaboração de GAs diversos - como o seminário, o verbete, o projeto de pesquisa, entre outros – e ainda viabiliza a familiarização inicial com seus suportes e métodos de investigação. Portanto, acreditamos que pesquisas voltadas para práticas basilares da aprendizagem de GAs oferecem oportunidades para compreender os conhecimentos prévios dos alunos e assim promover seu letramento acadêmico.
O booktube: um instrumento para o letramento literário e a formação de leitores
Authors: Ferreira Coêlho Tahís Evelin , Batalha de Siqueira Renda Vera Lúcia
Published: August 2024

O presente trabalho apresenta como tema o letramento literário e a formação de leitores no Ensino Médio, focalizando a relação entre o booktube e a leitura, sobretudo no que tange ao potencial desse como uma ferramenta para o desenvolvimento do letramento literário de educandos desse segmento escolar. Os problemas que motivaram este estudo foram a falta de gosto e prazer pela leitura literária de muitos estudantes do Ensino Médio; a abordagem, por vezes infrutífera, do ensino tradicional de literatura, que se pauta primordialmente na historiografia literária e na leitura canônica; e a necessidade de se incorporar o digital às práticas de leitura escolares. Este estudo objetiva oferecer subsídios, na forma de uma proposta didática, a fim de que o professor de Língua Portuguesa e/ou Literatura possa utilizar o booktube como uma ferramenta para o letramento literário e a formação de leitores no Ensino Médio. Teoricamente, a pesquisa baseou-se na concepção bakhtiniana de linguagem e gênero discursivo (BAKHTIN, 2011) e nos conceitos de letramento e multiletramentos (GRUPO NOVA LONDRES, 2021). Metodologicamente, este trabalho trata de uma pesquisa de caráter qualitativo do tipo bibliográfico com proposta de resolução de um problema. Como resultado, apresenta-se uma proposta didática sobre a obra Assassinato no Expresso do Oriente, de Agatha Christie. Conclui-se que o booktube pode ser um instrumento valioso para o desenvolvimento do letramento literário, além de contribuir significativamente para a formação de leitores.
Automorphism Group of the Holomorph of a Cyclic Group
Authors: Sato Kazuki
Published: August 2024

Abstract: We show that the holomorph of a cyclic group of order n is isomorphic to its own automorphism group when n is twice of a power of an odd prime.
Dual-window polarization filtering characteristics of rectangular photonic crystal fibers
Authors: Gao Zhijun , Ge Huan , Si Guangyuan , Ying Yu
Published: August 2024

This paper presents a photonic crystal fiber (PCF) polarization filter with a square array arrangement of gold film fillings, allowing for filtering at dual wavelengths. The paper analyzes the dispersion characteristics and loss properties of this structure and optimizes the structural parameters through adjustments to achieve the best performance. At 1310 nm, the confinement losses of x and y polarization fundamental modes are 903.54 dB/cm and 30.51 dB/cm, respectively; at 1640 nm, the confinement losses of y and x polarization fundamental modes are 479.02 dB/cm and 88.72 dB/cm, respectively. The corresponding filtering bandwidths are 390 and 350 nm, while the full width half maximum (FWHM) is 59.56 nm, indicating excellent selectivity and resolution of the filter. The performance metrics, such as confinement loss, extinction ratios, and bandwidth, are compared in the paper with those reported for other filters. Additionally, the study also analyzed the filter’s performance under varying manufacturing tolerances of gold film thickness and air hole diameter by 5%, revealing that the filter’s performance remains stable and feasible even in the presence of errors.
Probing diffusive media through speckle differencing
Authors: Balaji Muralidhar Madabhushi , Ahsanullah Danyal , Rangarajan Prasanna
Published: August 2024

Temporally varying speckle patterns, produced by light-matter interaction encode valuable information about inhomogeneities embedded within a scattering medium. These speckle fluctuations arise either from the tuning of the emission frequency of a laser illuminating a static scattering medium or from the microscopic motion of scatterers within a dynamically scattering medium. In this work, we detect embedded inhomogeneities by probing static and dynamic scattering media with coherent light and leveraging the statistical distribution of temporal speckle differences. In addition, we utilize the insights from the speckle differencing paradigm, to present the first experimental results of detecting inhomogeneities embedded within a scattering medium using bio-inspired neuromorphic sensors. The proposed neuromorphic approach simplifies the optical and electronic design, and significantly reduces data throughput by capturing only the differential information in the form of 1-bit spikes.
SODL-IR-FISTA: sparse online dictionary learning with iterative reduction FISTA for cone-beam X-ray luminescence computed tomography
Authors: Cao Xin , Tang Wenlong , Gao Huimin , Wang Yifan , Chen Yi , Gao Chengyi , Zhao Fengjun , Su Linzhi
Published: August 2024

Cone beam X-ray luminescence computed tomography (CB-XLCT) is an emerging imaging technique with potential for early 3D tumor detection. However, the reconstruction challenge due to low light absorption and high scattering in tissues makes it a difficult inverse problem. In this study, the online dictionary learning (ODL) method, combined with iterative reduction FISTA (IR-FISTA), has been utilized to achieve high-quality reconstruction. Our method integrates IR-FISTA for efficient and accurate sparse coding, followed by an online stochastic approximation for dictionary updates, effectively capturing the sparse features inherent to the problem. Additionally, a re-sparse step is introduced to enhance the sparsity of the solution, making it better suited for CB-XLCT reconstruction. Numerical simulations and in vivo experiments were conducted to assess the performance of the method. The SODL-IR-FISTA achieved the smallest location error of 0.325 mm in in vivo experiments, which is 58% and 45% of the IVTCG-L1 (0.562 mm) and OMP-L0 (0.721 mm), respectively. Additionally, it has the highest DICE similarity coefficient, which is 0.748. The results demonstrate that our approach outperforms traditional methods in terms of localization precision, shape restoration, robustness, and practicality in live subjects.
Illumination-adjustable photoacoustic and harmonic ultrasound for tracking magnetically driven microrobots
Authors: Wang Chongyun , Lam Wah Shing , Huang Hanjin , Zhao Han , Zhang Chunqi , Sun Dong
Published: August 2024

The development of microrobots for biomedical applications has enabled tasks such as targeted drug delivery, minimally invasive surgeries, and precise diagnostics. However, effective in vivo navigation and control remain challenging due to their small size and complex body environment. Photoacoustic (PA) and ultrasound (US) imaging techniques, which offer high contrast, high resolution, and deep tissue penetration, are integrated to enhance microrobot visualization and tracking. Traditional imaging systems have a narrow effective illumination area, suffer from severe reflection artifacts, and are affected by strong electromagnetic fields. To address this, we present an illumination-adjustable PA and harmonic US imaging system with a customized pushrod mechanism for real-time focus adjustment. Experiments demonstrate high-resolution imaging and accurate microrobot positioning, showcasing the potential for biomedical applications, especially in minimally invasive procedures.
Ex vivo optical coherence tomography combined with near infrared targeted fluorescence: towards in-vivo esophageal cancer detection
Authors: Vaselli Margherita , Gabriels Ruben Y. , Schmidt Iris , Sterkenburg Andrea J. , Kats-Ugurlu Gursah , Nagengast Wouter B. , de Boer Johannes F.
Published: August 2024

Early detection of (pre)malignant esophageal lesions is critical to improve esophageal cancer morbidity and mortality rates. In patients with advanced esophageal adenocarcinoma (EAC) who undergo neoadjuvant chemoradiation therapy, the efficacy of therapy could be optimized and unnecessary surgery prevented by the reliable assessment of residual tumors after therapy. Optical coherence tomography (OCT) provides structural images at a (sub)-cellular level and has the potential to visualize morphological changes in tissue. However, OCT lacks molecular imaging contrast, a feature that enables the study of biological processes at a cellular level and can enhance esophageal cancer diagnostic accuracy. We combined OCT with near-infrared fluorescence molecular imaging using fluorescently labelled antibodies (immuno-OCT). The main goal of this proof of principle study is to investigate the feasibility of immuno-OCT for esophageal cancer imaging. We aim to assess whether the sensitivity of our immuno-OCT device is sufficient to detect the tracer uptake using an imaging dose (∼100 times smaller than a dose with therapeutic effects) of a targeted fluorescent agent. The feasibility of immuno-OCT was demonstrated ex-vivo on dysplastic lesions resected from Barrett’s patients and on esophageal specimens resected from patients with advanced EAC, who were respectively topically and intravenously administrated with the tracer bevacizumab-800CW. The detection sensitivity of our system (0.3 nM) is sufficient to detect increased tracer uptake with micrometer resolution using an imaging dose of labelled antibodies. Moreover, the absence of layered structures that are typical of normal esophageal tissue observed in OCT images of dysplastic/malignant esophageal lesions may further aid their detection. Based on our preliminary results, immuno-OCT could improve the detection of dysplastic esophageal lesions.
Lossless contention ultraviolet MAC protocol based on dynamic bandwidth allocation
Authors: Wang Leitao , Xu Zhiyong , Wang Jingyuan , Zhao Jiyong , Wang Yimin , Li Jianhua
Published: August 2024

Ultraviolet (UV) optical communication can eliminate aiming, tracking, and pointing systems in conventional free-space optical (FSO) communications, rendering it more suitable for small and micro platforms. Currently, efficient medium access control (MAC) layer protocols for UV optical communication are lacking. To further improve the channel utilization of UV networks, an ultraviolet lossless contention MAC protocol with dynamic bandwidth allocation (UVLLC-DBA) based on optical power superposition was proposed. Simultaneously, the protocol employed token buckets to allocate bandwidth for different services, thereby enabling differentiated services. The simulation results show that the proposed protocol can achieve dynamic bandwidth allocation and has nearly 100% channel utilization and acceptable delay, providing a reference for the development of a UV MAC protocol.
Machine-learning-based impairment-aware dynamic RMSCA in multi-core elastic optical networks
Authors: Ravipudi Jaya Lakshmi , Brandt-Pearce Maïté
Published: August 2024

This paper presents a routing, modulation, spectrum, and core assignment (RMSCA) algorithm for space-division-multiplexing-based elastic optical networks (SDM-EONs) comprising multi-core links. A network state-dependent route and core selection method is proposed using a deep neural network (DNN) classifier. The DNN is trained using a metaheuristic optimization algorithm to predict lightpath suitability, considering the quality of transmission and resource availability. Physical layer impairments, including inter-core crosstalk, amplified spontaneous emission, and Kerr fiber nonlinearities, are considered, and a random forest (RF)-based link noise estimator is proposed. A feature importance selection analysis is provided for all the features considered for the DNN classifier and the RF link noise estimator. The proposed machine-learning-enabled RMSCA approach is evaluated on three network topologies, USNET, NSFNET, and COST-239 with 7-core and 12-core fiber links. It is shown to be superior in terms of blocking probability, bandwidth blocking probability, and acceptable computational speed compared to the standard and published benchmarks at different traffic loads.
Fast and slow waves in a chain of superconducting split-ring resonators with staggered coupling strengths
Authors: Chang Yu-Han , Abdelghany R. A. , Peng Wei Lun , Wu Cen-Shawn , Kuo Watson
Published: August 2024

The transmission and reflection spectra of a linear chain comprising superconducting split-ring resonators operating at 6 GHz, with staggered coupling strength are investigated. The collective mode and the associated transmission and reflection on resonances can be fully analyzed by employing finite-element simulations focused on the unit cell structure and an effective hopping model. Robust coupling energies, equivalent to approximately 4% of the resonant frequency, enable significant transmission through the collective modes. Furthermore, the resonance modes exhibit substantial quality factors, leading to distinct superluminal and retarding propagation effects for reflected and transmitted microwaves, respectively. The chain configuration allows for 200 ns in either advance or delay for a 1 µs microwave pulse at the resonance frequency. These findings shed light on the unique behavior of superconducting split-ring resonator arrays and their potential applications in microwave signal manipulation.
Research on optical interferometric imaging with flexible control using optical fibers and PIC chip
Authors: Wang Zihao , Cai Xin , Jiang Ping , Shi Guangming , He Jincheng , Gao Dahua , Sun Yanling , Liao Jiali , Jin Li , Feng Junbo
Published: August 2024

We propose a prototype called a flexible integrated resolution and efficient light-imaging-expanded synthetic system (FIREFLIES). This paper describes the design, manufacturing, and experimental demonstration of the proposed system. FIREFLIES enables interferometric imaging at approximately 1550 nm using a variable baseline sampling technique, in which the baseline-collected light field forms interference fringes that are captured by an on-chip photodetector. This innovation extends the limited sampling distance imposed by the processing size restrictions of traditional photonic integrated circuit (PIC) links. Furthermore, we introduce a unique method for achieving super-resolution sampling by flexibly controlling the baseline. An experimental platform is constructed to test the FIREFLIES against a one-dimensional grating target. The experimental curves closely align with the theoretical predictions, confirming the efficacy of the system in super-resolution sampling and imaging performance.
Fourier Raman light field microscopy based on surface-enhanced Raman scattering
Authors: Wang Jingfan , Chen Ming , Zhao Xing , Wang Yan , Li Da
Published: August 2024

Raman scattering, as a vibrational spectrum that carries material information, has no photobleaching that enables long-duration imaging. Raman spectra have very narrow emission peaks, and multiplex Raman imaging can be achieved by using different Raman scattering peak signals. These advantages make Raman imaging widely used in biology, cytology, and medicine, which has a wider range of application scenarios. However, obtaining a three-dimensional (3D) Raman image requires scanning for tens of minutes to several hours at present. Therefore, a fast non-scanning 3D Raman imaging method is greatly needed. In this article, we propose a Fourier Raman light field microscopy based on surface-enhanced Raman scattering (sers-FRLFM). Using flower-like gap-enhanced Raman nanoparticles (F-GERNs) to enhance Raman scattering signals, a Fourier-configured light field microscope (LFM) is capable of recording complete four-dimensional Raman field information in a single frame, facilitating the 3D reconstruction of the Raman image without generating reconstruction artifacts at the native object plan. Moreover, F-GERNs can mark specific locations and have the potential to become a new tracing method to achieve specific imaging. This imaging method has great potential in the 3D real-time Raman imaging of cells, microorganisms, and tissues with the lateral resolution of 2.40 µm and an axial resolution of 4.02 µm.
Salmonella Typhimurium exploits host polyamines for assembly of the type 3 secretion machinery
Authors: Miki Tsuyoshi , Uemura Takeshi , Kinoshita Miki , Ami Yuta , Ito Masahiro , Okada Nobuhiko , Furuchi Takemitsu , Kurihara Shin , Haneda Takeshi , Minamino Tohru , Kim Yun-Gi
Published: August 2024

Bacterial pathogens utilize the factors of their hosts to infect them, but which factors they exploit remain poorly defined. Here, we show that a pathogenic Salmonella enterica serovar Typhimurium (STm) exploits host polyamines for the functional expression of virulence factors. An STm mutant strain lacking principal genes required for polyamine synthesis and transport exhibited impaired infectivity in mice. A polyamine uptake-impaired strain of STm was unable to inject effectors of the type 3 secretion system into host cells due to a failure of needle assembly. STm infection stimulated host polyamine production by increasing arginase expression. The decline in polyamine levels caused by difluoromethylornithine, which inhibits host polyamine production, attenuated STm colonization, whereas polyamine supplementation augmented STm pathogenesis. Our work reveals that host polyamines are a key factor promoting STm infection, and therefore a promising therapeutic target for bacterial infection.
A transfer learning approach to identify Plasmodium in microscopic images
Authors: Ramos Jonathan da Silva , Vieira Ivo Henrique Provensi , Rocha Wan Song , Esquerdo Rosimar Pires , Watanabe Carolina Yukari Veludo , Zanchi Fernando Berton
Published: August 2024

Plasmodium parasites cause Malaria disease, which remains a significant threat to global health, affecting 200 million people and causing 400,000 deaths yearly. Plasmodium falciparum and Plasmodium vivax remain the two main malaria species affecting humans. Identifying the malaria disease in blood smears requires years of expertise, even for highly trained specialists. Literature studies have been coping with the automatic identification and classification of malaria. However, several points must be addressed and investigated so these automatic methods can be used clinically in a Computer-aided Diagnosis (CAD) scenario. In this work, we assess the transfer learning approach by using well-known pre-trained deep learning architectures. We considered a database with 6222 Region of Interest (ROI), of which 6002 are from the Broad Bioimage Benchmark Collection (BBBC), and 220 were acquired locally by us at Fundação Oswaldo Cruz (FIOCRUZ) in Porto Velho Velho, Rondônia—Brazil, which is part of the legal Amazon. We exhaustively cross-validated the dataset using 100 distinct partitions with 80% train and 20% test for each considering circular ROIs (rough segmentation). Our experimental results show that DenseNet201 has a potential to identify Plasmodium parasites in ROIs (infected or uninfected) of microscopic images, achieving 99.41% AUC with a fast processing time. We further validated our results, showing that DenseNet201 was significantly better (99% confidence interval) than the other networks considered in the experiment. Our results support claiming that transfer learning with texture features potentially differentiates subjects with malaria, spotting those with Plasmodium even in Leukocytes images, which is a challenge. In Future work, we intend scale our approach by adding more data and developing a friendly user interface for CAD use. We aim at aiding the worldwide population and our local natives living nearby the legal Amazon’s rivers.
Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes
Authors: Commichaux Seth , Luan Tu , Muralidharan Harihara Subrahmaniam , Pop Mihai
Published: August 2024

For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and to taxonomically profile microbial communities. However, the 16S rRNA gene has been criticized for being too conserved to differentiate between distinct species. We argue that the inability to differentiate between species is not a unique feature of the 16S rRNA gene. Rather, we observe the gradual loss of species-level resolution for other nearly-universal prokaryotic marker genes as the number of gene sequences increases in reference databases. This trend was strongly correlated with how represented a taxonomic group was in the database and indicates that, at the gene-level, the boundaries between many species might be fuzzy. Through our study, we argue that any approach that relies on a single marker to distinguish bacterial taxa is fraught even if some markers appear to be discriminative in current databases.
Mild and moderate COVID-19 during Alpha, Delta and Omicron pandemic waves in urban Maputo, Mozambique, December 2020-March 2022: A population-based surveillance study
Authors: Ingelbeen Brecht , Cumbane Victória , Mandlate Ferão , Barbé Barbara , Nhachungue Sheila Mercedes , Cavele Nilzio , Manhica Cremildo , Cubai Catildo , Nguenha Neusa Maimuna Carlos , Lacroix Audrey , Mariën Joachim , de Weggheleire Anja , van Kleef Esther , Selhorst Philippe , van der Sande Marianne A. B. , Peeters Martine , Widdowson Marc-Alain , Ismael Nalia , Macicame Ivalda
Published: August 2024

In sub-Saharan Africa, reported COVID-19 numbers have been lower than anticipated, even when considering populations’ younger age. The extent to which risk factors, established in industrialised countries, impact the risk of infection and of disease in populations in sub-Saharan Africa, remains unclear. We estimated the incidence of mild and moderate COVID-19 in urban Mozambique and analysed factors associated with infection and disease in a population-based surveillance study. During December 2020-March 2022, 1,561 households (6,049 participants, median 21 years, 54.8% female, 7.3% disclosed HIV positive) of Polana Caniço, Maputo, Mozambique, were visited biweekly to report respiratory symptoms, anosmia, or ageusia, and self-administer a nasal swab for SARS-CoV-2 testing. Every three months, dried blood spots of a subset of participants (1,412) were collected for detection of antibodies against SARS-CoV-2 spike glycoprotein and nucleocapsid protein. Per 1000 person-years, 364.5 (95%CI 352.8–376.1) respiratory illness episodes were reported, of which 72.2 (95%CI 60.6–83.9) were COVID-19. SARS-CoV-2 seroprevalence rose from 4.8% (95%CI 1.1–8.6%) in December 2020 to 34.7% (95%CI 20.2–49.3%) in June 2021, when 3.0% were vaccinated. Increasing age, chronic lung disease, hypertension, and overweight increased risk of COVID-19. Older age increased the risk of SARS-CoV-2 seroconversion. We observed no association between socio-economic status, behaviour and COVID-19 or SARS-CoV-2 seroconversion. Active surveillance in an urban population confirmed frequent COVID-19 underreporting, yet indicated that the large majority of cases were mild and non-febrile. In contrast to reports from industrialised countries, social deprivation did not increase the risk of infection nor disease.
Factors associated with the spatiotemporal distribution of dog rabies in Tunisia
Authors: Kalthoum Sana , Mzoughi Samia , Gharbi Raja , Lachtar Monia , Bel Haj Mohamed Bassem , Hajlaoui Haikel , Khalfaoui Wiem , Dhaouadi Anissa , Ben Sliman Imed , Ben Salah Chafik , Kessa Haykel , Benkirane Hend , Fekih Ahmed Jawher , Barrak Kahoula , Sayari Hajer , Bahloul Chokri , Porphyre Thibaud
Published: August 2024

Despite continuous efforts of veterinary services to control rabies in dogs since 1982, rabies remains a cause of death in Tunisia, with more than five reported human cases in 2022. As little is known on the determinants of transmission of rabies in dogs, better understand which factors contribute to its spatial heterogeneity in Tunisia is critical for developing bespoke mitigation activities. In this context, we developed Bayesian Poisson mixed-effect spatio-temporal model upon all cases of rabid dogs reported in each delegation during the period from 2019 to 2021. The best fitting model highlighted the association between the risk of rabies and the mean average monthly temperature, the density of markets and the density of dogs in delegations. Interestingly, no relationship was found between intensity of vaccination in dogs and the risk of rabies. Our results provided insights into the spatio-temporal dynamics of dog rabies transmission and highlighted specific geographic locations where the risk of infection was high despite correction for associated explanatory variables. Such an improved understanding represent key information to design bespoke, cost-efficient, rabies prevention and control strategies to support veterinary services activities and policymaking.
Human granulocytotropic anaplasmosis—A systematic review and analysis of the literature
Authors: Schudel Sophie , Gygax Larissa , Kositz Christian , Kuenzli Esther , Neumayr Andreas
Published: August 2024

Human granulocytotropic anaplasmosis (HGA) is a zoonotic tick-borne bacterial infection caused by Anaplasma phagocytophilum. While most cases are reported from North America, HGA has been recognized as an emerging disease in several regions of the world in recent decades. Most available data comes from case reports, case series and retrospective studies, while prospective studies and clinical trials are largely lacking. To obtain a clearer picture of the currently known epidemiologic distribution, clinical and paraclinical presentation, diagnostic aspects, complications, therapeutic aspects, and outcomes of HGA, we systematically reviewed the literature and analyzed and summarized the data.

Cases of HGA are reported from all continents except from Antarctica. HGA primarily presents as an unspecific febrile illness (88.5% of the cases) often accompanied by thrombocytopenia (71.8% of the cases), abnormal liver injury tests (66.7% of the cases), and leukopenia (49.8% of the cases). Although we found complications reported in a total of 40.5% of the reviewed cases and severe and even life-threatening complications are not infrequent (e.g. acute renal failure 9.8%, multi organ failure 7.5%, ARDS 6.3%, a.o.), sequelae are rare (2.1% of the cases) and lethality is low (3.0% of the cases). Treatment with doxycycline shows a rapid response, with the fever subsiding in the majority of patients within one day of starting treatment. Unlike in human monocytotropic ehrlichiosis (HME), reports of opportunistic infections complicating HGA are rare. HGA during pregnancy does not appear to be associated with unfavorable outcomes. In addition, our analysis provides some evidence that HGA may differ in clinical aspects and laboratory characteristics in different regions of the world. Overall, the data analyzed indicates a non-negligible bias in reporting/publication, so a certain degree of caution is required when generalizing the data.
The hidden costs of inflation: A critical analysis of industrial development and environmental consequences
Authors: Zheng Dan , Addas Abdullah , Waseem Liaqat Ali , Asad Naqvi Syed Ali , Ahmad Muneeb , Sharif Kashif
Published: August 2024

The study draws attention to the associations between monetary and economic elements and their potential environmental impacts. The study uses time series data from 1960 to 2022 to examine the connection between CO2 emissions, industrial growth, GNE, and inflation in China. The researchers utilized the well-known econometric technique of nonlinear autoregressive distributed lag (NARDL) to examine nonlinear correlations between these variables. The results reveal that GDP, inflation, and economic development influence long-term CO2 emissions. The strong positive correlation between gross national expenditures and economic activity increases CO2 emissions. In the short run, CO2 emissions are positively and statistically significantly affected by inflation. While inflation temporarily affects CO2 emissions, this effect dissipates with time. Industrial activity increases CO2 emissions, and China’s fast industrialization has damaged the environment. The energy-intensive fertiliser manufacturing process and fossil fuels increase CO2 emissions. The research shows how government officials and academics may collaborate to create tailored measures to alleviate the environmental impacts of economic activity.
Genome-wide association study of the loci and candidate genes associated with agronomic traits in Amomum villosum Lour
Authors: Li Wenxiu , Luo Ping , Shi Yunfeng , Zhang Hualin , Yan Qing , Ye Yana , Yao Yanli , He Junjun
Published: August 2024

Amomum villosum Lour. (A. villosum) is a valuable herbaceous plant that produces the famous traditional Chinese medicine Amori Fructus. Identifying molecular markers associated with the growth of A. villosum can facilitate molecular marker-assisted breeding of the plant. This study employed 75 A. villosum accessions as the test material and utilized 71 pairs of polymorphic simple sequence repeat (SSR) molecular markers to genotype the population. The study analyzed the association between SSR markers and phenotypic traits through the linkage imbalance and population structure analysis. Candidate genes associated with the molecular markers were also identified. The results showed that the phenotypic diversity index range of the 12 agronomic traits was 4.081–4.312 and conformed to a normal distribution. Moreover, 293 allelic variations were detected in the 75 accessions, with an average of 5.32 amplified alleles per loci, ranging from 3 to 8. The maximum number of amplified alleles for AVL12 was 8. The population structure and cluster analysis indicated that the accessions could be divided into two subgroups. Using the mixed linear model (MLM) model of population structure (Q)+kinship matrix (K) for association analysis, three SSR molecular markers significantly associated with the agronomic traits were detected. Fluorescence quantification was used to analyze the expression levels of six candidate genes, and it was found that three of the genes were differentially expressed in phenotypically different accessions. This study is the first to use SSR markers for genome-wide association study (GWAS) mapping and identification of the associated agronomic traits in A. villosum. The results of this study provide a basis for identifying genetic markers for growth traits for marker-assisted breeding in A. villosum.
Within-plant genetic drift to control virus adaptation to host resistance genes
Authors: Tamisier Lucie , Fabre Frédéric , Szadkowski Marion , Chateau Lola , Nemouchi Ghislaine , Girardot Grégory , Millot Pauline , Palloix Alain , Moury Benoît
Published: August 2024

Manipulating evolutionary forces imposed by hosts on pathogens like genetic drift and selection could avoid the emergence of virulent pathogens. For instance, increasing genetic drift could decrease the risk of pathogen adaptation through the random fixation of deleterious mutations or the elimination of favorable ones in the pathogen population. However, no experimental proof of this approach is available for a plant-pathogen system. We studied the impact of pepper (Capsicum annuum) lines carrying the same major resistance gene but contrasted genetic backgrounds on the evolution of Potato virus Y (PVY). The pepper lines were chosen for the contrasted levels of genetic drift (inversely related to Ne, the effective population size) they exert on PVY populations, as well as for their contrasted resistance efficiency (inversely related to the initial replicative fitness, Wi, of PVY in these lines). Experimental evolution was performed by serially passaging 64 PVY populations every month on six contrasted pepper lines during seven months. These PVY populations exhibited highly divergent evolutionary trajectories, ranging from viral extinctions to replicative fitness gains. The sequencing of the PVY VPg cistron, where adaptive mutations are likely to occur, allowed linking these replicative fitness gains to parallel adaptive nonsynonymous mutations. Evolutionary trajectories were well explained by the genetic drift imposed by the host. More specifically, Ne, Wi and their synergistic interaction played a major role in the fate of PVY populations. When Ne was low (i.e. strong genetic drift), the final PVY replicative fitness remained close to the initial replicative fitness, whereas when Ne was high (i.e. low genetic drift), the final PVY replicative fitness was high independently of the replicative fitness of the initially inoculated virus. We show that combining a high resistance efficiency (low Wi) and a strong genetic drift (low Ne) is the best solution to increase resistance durability, that is, to avoid virus adaptation on the long term.